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Schneider A, Bergsch J, Lipps G. The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically. Nucleic Acids Res 2023; 51:5087-5105. [PMID: 37099378 PMCID: PMC10250227 DOI: 10.1093/nar/gkad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/27/2023] Open
Abstract
The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the large regulatory subunits of archaeoeukaryotic heterodimeric primases in one protein chain. The recombinant protein primes on templates containing a triplet with a central thymidine, thus displaying a pronounced sequence specificity typically observed with bacterial type primases only. The N. equitans primase (NEQ395) is a highly active primase enzyme synthesizing short RNA primers. Termination occurs preferentially at about nine nucleotides, as determined by HPLC analysis and confirmed with mass spectrometry. Possibly, the compact monomeric primase NEQ395 represents the minimal archaeoeukaryotic primase and could serve as a functional and structural model of the heterodimeric archaeoeukaryotic primases, whose study is hindered by engagement in protein assemblies and rather low activity.
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Affiliation(s)
- Andy Schneider
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Jan Bergsch
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
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2
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Zhao Z, Xie X, Liu W, Huang J, Tan J, Yu H, Zong W, Tang J, Zhao Y, Xue Y, Chu Z, Chen L, Liu YG. STI PCR: An efficient method for amplification and de novo synthesis of long DNA sequences. Mol Plant 2022; 15:620-629. [PMID: 34968732 DOI: 10.1016/j.molp.2021.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/06/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Despite continuous improvements, it is difficult to efficiently amplify large sequences from complex templates using current PCR methods. Here, we developed a suppression thermo-interlaced (STI) PCR method for the efficient and specific amplification of long DNA sequences from genomes and synthetic DNA pools. This method uses site-specific primers containing a common 5' tag to generate a stem-loop structure, thereby repressing the amplification of smaller non-specific products through PCR suppression (PS). However, large target products are less affected by PS and show enhanced amplification when the competitive amplification of non-specific products is suppressed. Furthermore, this method uses nested thermo-interlaced cycling with varied temperatures to optimize strand extension of long sequences with an uneven GC distribution. The combination of these two factors in STI PCR produces a multiplier effect, markedly increasing specificity and amplification capacity. We also developed a webtool, calGC, for analyzing the GC distribution of target DNA sequences and selecting suitable thermo-cycling programs for STI PCR. Using this method, we stably amplified very long genomic fragments (up to 38 kb) from plants and human and greatly increased the length of de novo DNA synthesis, which has many applications such as cloning, expression, and targeted genomic sequencing. Our method greatly extends PCR capacity and has great potential for use in biological fields.
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Affiliation(s)
- Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Weizhi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jingjing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Haixin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jintao Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yanchang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhizhan Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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3
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Sedky NK, Arafa RK. Undergraduate laboratory series that employs a complete polymerase chain reaction-restriction fragment length polymorphism experiment for determination of a single nucleotide polymorphism in CYP2R1 gene. Biochem Mol Biol Educ 2022; 50:193-200. [PMID: 35084793 DOI: 10.1002/bmb.21604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Nowadays, novel Biochemistry lab techniques are being introduced at a very fast pace in scientific research. This requires development of new labs for undergraduate Biochemistry courses to equip the students with up-to-date techniques. However, the time limit of Biochemistry labs for undergraduate students represents a major obstacle. This article presents a clear set of laboratory exercises designed to introduce students to the use of polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) as a means of detection of genetic variants. Three consecutive lab experiments have been designed for the undergraduate students to serve this purpose. The first session was performed in a computer lab (dry lab) where students were taught how to obtain a specific gene sequence, identify an exact single nucleotide polymorphism location, choose the target sequence for amplification, design specific primers for this particular sequence and choose the most suitable restriction enzyme from web tools. The second and third lab sessions were performed as wet labs where in the second lab session, students optimized PCR conditions and performed a successful PCR. The PCR products were kept for use in the third lab session where they utilized the selected restriction enzyme and carried out gel electrophoresis to determine the exact genotype.
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Affiliation(s)
- Nada K Sedky
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, Egypt
- Drug Design and Discovery Laboratory, University of Science and Technology, Zewail City of Science and Technology, Cairo, Egypt
| | - Reem K Arafa
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, Egypt
- Drug Design and Discovery Laboratory, University of Science and Technology, Zewail City of Science and Technology, Cairo, Egypt
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4
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Yu Y, Li R, Ma Z, Han M, Zhang S, Zhang M, Qiu Y. Development and evaluation of a novel loop mediated isothermal amplification coupled with TaqMan probe assay for detection of genetically modified organism with NOS terminator. Food Chem 2021; 356:129684. [PMID: 33812194 DOI: 10.1016/j.foodchem.2021.129684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 03/06/2021] [Accepted: 03/19/2021] [Indexed: 01/14/2023]
Abstract
In this study, we aim to develop a novel loop mediated isothermal amplification (LAMP) coupled with TaqMan (LAMP-TaqMan) method for quick qualitative detection of genetically modified organism (GMOs). We designed four LAMP primers and one TaqMan probe for the LAMP-TaqMan detection method to detect the nopaline synthase gene (NOS) terminator in GMOs. This assay enabled the amplification of DNA within ~20 min at a constant temperature of 65 °C. This assay detected as few as five copies of target sequences, which had a high specificity similar to the TaqMan qPCR method. Furthermore, the LAMP-TaqMan detection method was successfully used to amplify and detect DNA from food samples of the major crops (soybean, maize, rice, etc.). In summary, a novel LAMP-TaqMan assay has been developed, which has the similar sensitivity but takes less time than the TaqMan qPCR method. This method offers a novel approach for rapid detection of GMOs in foods.
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Affiliation(s)
- Yanbo Yu
- College of Life Science, Northeast Agricultural University, Changjiang Road 600, Harbin 150030, China
| | - Rui Li
- College of Life Science, Northeast Agricultural University, Changjiang Road 600, Harbin 150030, China
| | - Zonghua Ma
- College of Life Science, Northeast Agricultural University, Changjiang Road 600, Harbin 150030, China
| | - Meihong Han
- College of Animal Science, Yangtze University, Nanhuan Road 1, Jingzhou 434020, China
| | - Sen Zhang
- College of Animal Science, Yangtze University, Nanhuan Road 1, Jingzhou 434020, China
| | - Minghui Zhang
- College of Life Science, Northeast Agricultural University, Changjiang Road 600, Harbin 150030, China; College of Animal Science, Yangtze University, Nanhuan Road 1, Jingzhou 434020, China.
| | - Youwen Qiu
- College of Life Science, Northeast Agricultural University, Changjiang Road 600, Harbin 150030, China.
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5
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Kim JM, Jung S, Jeon EJ, Kim BK, No JY, Kim MJ, Kim H, Song CS, Kim SK. Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection. ACS Appl Mater Interfaces 2021; 13:30295-30305. [PMID: 34165969 DOI: 10.1021/acsami.1c03434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.
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Affiliation(s)
- Jung Min Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eui Ju Jeon
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bong Kyun Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin Yong No
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Myung Jong Kim
- Functional Composite Materials Research Center, KIST, Jeonbuk 55324, Republic of Korea
| | - Heesuk Kim
- Photo-Electronic Hybrids Research Center, KIST, Seoul 02792, Republic of Korea
- Division of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Republic of Korea
| | - Chang Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Biomedical Research Institute, 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
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6
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Abstract
RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).
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Affiliation(s)
- Fatima Alghoul
- Université de Strasbourg-Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg-Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Strasbourg, France
| | - Franck Martin
- Université de Strasbourg-Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Strasbourg, France.
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7
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Tomek KJ, Volkel K, Indermaur EW, Tuck JM, Keung AJ. Promiscuous molecules for smarter file operations in DNA-based data storage. Nat Commun 2021; 12:3518. [PMID: 34112775 PMCID: PMC8192770 DOI: 10.1038/s41467-021-23669-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022] Open
Abstract
DNA holds significant promise as a data storage medium due to its density, longevity, and resource and energy conservation. These advantages arise from the inherent biomolecular structure of DNA which differentiates it from conventional storage media. The unique molecular architecture of DNA storage also prompts important discussions on how data should be organized, accessed, and manipulated and what practical functionalities may be possible. Here we leverage thermodynamic tuning of biomolecular interactions to implement useful data access and organizational features. Specific sets of environmental conditions including distinct DNA concentrations and temperatures were screened for their ability to switchably access either all DNA strands encoding full image files from a GB-sized background database or subsets of those strands encoding low resolution, File Preview, versions. We demonstrate File Preview with four JPEG images and provide an argument for the substantial and practical economic benefit of this generalizable strategy to organize data.
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Affiliation(s)
- Kyle J Tomek
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kevin Volkel
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Elaine W Indermaur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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8
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Covey SD. An adaptable dry lab for SYBR based RT-qPCR primer design to reinforce concepts in molecular biology and nucleic acids. Biochem Mol Biol Educ 2021; 49:262-270. [PMID: 32897640 DOI: 10.1002/bmb.21446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The real time PCR (qPCR) method provides a powerful method to assess levels of particular species of DNA. When combined with reverse transcription (RT-qPCR) it is the predominate technique to measure expression of gene transcripts. While this approach is very powerful, particular care must be taken in the design of the primers to facilitate specific and sensitive detection. Herein describes the framework for an undergraduate assignment which aims to teach primer design for SYBR based RT-qPCR. Beyond gaining direct experience with primer design, students will gain familiarity with important bioinformatic resources as well as a deeper theoretical understanding of the RT-qPCR approach and potential limitations. Moreover, as students' progress through the assignment they re-encounter many important concepts in molecular biology, gene expression, and nucleic acids, creating an opportunity for spiral learning. As this exercise only requires access to free web-based resources and does not require a laboratory it can be used in most science education settings. Despite not being a wet lab, this is a highly authentic research experience as this design process is commonplace in a molecular biology laboratory. Furthermore, the assignment is highly adaptable for different learning outcomes, time frames, and student background and ability. This article seeks to highlight connections and expanded learning outcomes for those already teaching such material, as well as a step-by-step guide for those new to teaching such content.
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Affiliation(s)
- Scott D Covey
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Murayama K, Okita H, Kuriki T, Asanuma H. Nonenzymatic polymerase-like template-directed synthesis of acyclic L-threoninol nucleic acid. Nat Commun 2021; 12:804. [PMID: 33547322 PMCID: PMC7864931 DOI: 10.1038/s41467-021-21128-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/04/2021] [Indexed: 02/08/2023] Open
Abstract
Evolution of xeno nucleic acid (XNA) world essentially requires template-directed synthesis of XNA polymers. In this study, we demonstrate template-directed synthesis of an acyclic XNA, acyclic L-threoninol nucleic acid (L-aTNA), via chemical ligation mediated by N-cyanoimidazole. The ligation of an L-aTNA fragment on an L-aTNA template is significantly faster and occurs in considerably higher yield than DNA ligation. Both L-aTNA ligation on a DNA template and DNA ligation on an L-aTNA template are also observed. High efficiency ligation of trimer L-aTNA fragments to a template-bound primer is achieved. Furthermore, a pseudo primer extension reaction is demonstrated using a pool of random L-aTNA trimers as substrates. To the best of our knowledge, this is the first example of polymerase-like primer extension of XNA with all four nucleobases, generating phosphodiester bonding without any special modification. This technique paves the way for a genetic system of the L-aTNA world.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Hikari Okita
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Takumi Kuriki
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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10
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Dudley DM, Newman CM, Weiler AM, Ramuta MD, Shortreed CG, Heffron AS, Accola MA, Rehrauer WM, Friedrich TC, O’Connor DH. Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples. PLoS One 2020; 15:e0244882. [PMID: 33382861 PMCID: PMC7775089 DOI: 10.1371/journal.pone.0244882] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Frequent surveillance of individuals attending work or school is currently unavailable to most people but will likely be necessary to reduce the ~50% of transmission that occurs when individuals are nonsymptomatic. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed primary samples with a limit of detection (LOD) of ~625 copies/μl, approximately 100-fold lower sensitivity than qRT-PCR. While less sensitive than extraction-based molecular methods, RT-LAMP without RNA extraction is fast and inexpensive. Here we also demonstrate that adding a lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 surveillance programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.
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Affiliation(s)
- Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Andrea M. Weiler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mitchell D. Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cecilia G. Shortreed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anna S. Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - William M. Rehrauer
- University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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11
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Zhang Z, Yao J, Huang X, Zhang L, Wang T, Weng Z, Xie G. Multiplex real-time PCR using double-strand primers and probes for the detection of nucleic acids. Anal Methods 2020; 12:5392-5396. [PMID: 33111715 DOI: 10.1039/d0ay01661f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Multiplex PCR encounters difficulties in primer designing with all the primer pairs working at the same annealing temperature. In this study, we have developed a double-strand primer-mediated multiple strand displacement reaction for the detection of SARS-COV-2 ORF, N and E genes (as examples). The double primer is composed of a 5'-modified fluorophore strand, which does not impact polymerase extension and a 3'-modified quencher strand, which cannot impact elongation. At the annealing temperature, the fluorophore strand combined with the template, extended and resulted in fluorescence signal release. Results showed that the double-strand primer relatively exhibits a wide annealing temperature range and good compatibility between three pairs of primers and probes. These merits allow the simple and multiplex real-time fluorescence quantification of nucleic acids. The detection limit was 400 copies/mL, and the detection time was approximately 2 h. In addition to its extreme specificity and simplicity, this method has a wide range of applications such as multiple PCR and SNP detection.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
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Wang Y, Noor-A-Rahim M, Zhang J, Gunawan E, Guan YL, Poh CL. Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:2176-2182. [PMID: 31514147 DOI: 10.1109/tcbb.2019.2940177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA has become an attractive medium for long-term data archiving due to its extremely high storage density and longevity. Short single-stranded DNAs, called oligonucleotides (oligos), have been designed and synthesized to store digital data. Previous works designed the oligos with a pair of primer binding sites (PBSs) (each with a length of around 200) attached at the two ends of each basic readable data block. The addition of PBSs decreases the data density significantly because in the current DNA synthesis, the maximum length of a synthesized oligo in good quality is around 200. Furthermore, the maximum homopolymer run allowed by the existing experiments has been reported to be three nucleotides. In this work, to increase the data density, we have devised and tested an oligo design for DNA-based storage with the basic readable data block appended by a single PBS at one end only, while allowing the maximum homopolymer run to be increased to 4. We also present an oligo assembly algorithm that can reconstruct oligos with a single PBS from the error-prone raw readouts obtained from the sequencing process. We have conducted a wet lab experiment to validate the proposed design, where we tested with 398KB of data stored into 10,750 oligos. The experimental results show that it is possible to recover over 99 percent of the oligo sequences without error, which proves that one PBS is sufficient for implementing a DNA-based data storage system with maximum homopolymer run relaxed to 4. The use of single PBS leads to a significant data density gain from 14.3 to 140.2 percent over the existing short-strand DNA data storage schemes by reserving more nucleotides for storing information bits.
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13
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Yu S, Nimse SB, Kim J, Song KS, Kim T. Development of a Lateral Flow Strip Membrane Assay for Rapid and Sensitive Detection of the SARS-CoV-2. Anal Chem 2020; 92:14139-14144. [PMID: 32967427 PMCID: PMC7539551 DOI: 10.1021/acs.analchem.0c03202] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023]
Abstract
The infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has threatened public health worldwide. The easy human-to-human transmission of this virus has rapidly evolved into a global pandemic. Therefore, to control the community spread of the virus, it is crucial to identify the infected individuals, including asymptomatic people. Hence, a specific and rapid assay is crucial for the early diagnosis and active monitoring of individuals potentially exposed to SARS-CoV-2 for controlling the COVID-19 outbreak. In this study, we have developed the novel lateral flow strip membrane (LFSM) assay that allows the simultaneous detection of RdRp, ORF3a, and N genes using the PCR product obtained by using the single-tube reverse transcription polymerase chain reaction (RT-PCR). The LFSM assay allows detection of SARS-CoV-2 in 30 min at 25 °C after the RT-PCR with the detection limit of 10 copies/test for each gene. The clinical performance of the LFSM assay for the detection of SARS-Cov-2 was evaluated using 162 clinical samples previously detected by using the commercial assay. The percent positive agreement, percent negative agreement, and overall percent agreement of the LFSM assay with the commercial assay were 100% (94.2-100%), 99.0% (94.6-100%), and 99.4% (96.6-100%), respectively. Therefore, the results of the LFSM assay showed significantly high concordance with the commercial assay for the detection of SARS-CoV-2 in clinical specimens. Therefore, we conclude that the developed LFSM assay can be used alone or complementary to the RT-PCR or other methods for the diagnosis and monitoring of the patients to curb community transmission and the pandemic.
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Affiliation(s)
- Sangheon Yu
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Junghoon Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Keum-Soo Song
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Taisun Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
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14
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Touroutine D, Tanis JE. A Rapid, SuperSelective Method for Detection of Single Nucleotide Variants in Caenorhabditis elegans. Genetics 2020; 216:343-352. [PMID: 32817008 PMCID: PMC7536863 DOI: 10.1534/genetics.120.303553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/09/2020] [Indexed: 12/30/2022] Open
Abstract
With the widespread use of single nucleotide variants generated through mutagenesis screens and genome editing technologies, there is pressing need for an efficient and low-cost strategy to genotype single nucleotide substitutions. We have developed a rapid and inexpensive method for detection of point mutants through optimization of SuperSelective (SS) primers for end-point PCR in Caenorhabditis elegans Each SS primer consists of a 5' "anchor" that hybridizes to the template, followed by a noncomplementary "bridge," and a "foot" corresponding to the target allele. The foot sequence is short, such that a single mismatch at the terminal 3' nucleotide destabilizes primer binding and prevents extension, enabling discrimination of different alleles. We explored how length and sequence composition of each SS primer segment affected selectivity and efficiency in various genetic contexts in order to develop simple rules for primer design that allow for differentiation between alleles over a broad range of annealing temperatures. Manipulating bridge length affected amplification efficiency, while modifying the foot sequence altered discriminatory power. Changing the anchor position enabled SS primers to be used for genotyping in regions with sequences that are challenging for standard primer design. After defining primer design parameters, we demonstrated the utility of SS primers for genotyping crude C. elegans lysates, suggesting that this approach could also be used for SNP mapping and screening of CRISPR mutants. Further, since SS primers reliably detect point mutations, this method has potential for broad application in all genetic systems.
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Affiliation(s)
- Denis Touroutine
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
| | - Jessica E Tanis
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716
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15
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Boonham N, Tomlinson J, Ostoja-Starzewska S, McDonald RA. A pond-side test for Guinea worm: Development of a loop-mediated isothermal amplification (LAMP) assay for detection of Dracunculus medinensis. Exp Parasitol 2020; 217:107960. [PMID: 32755552 PMCID: PMC7526612 DOI: 10.1016/j.exppara.2020.107960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/18/2022]
Abstract
Guinea worm Dracunculus medinensis causes debilitating disease in people and is subject to an ongoing global eradication programme. Research and controls are constrained by a lack of diagnostic tools. We developed a specific and sensitive LAMP method for detecting D. medinensis larval DNA in copepod vectors. We were able to detect a single larva in a background of field-collected copepods. This method could form the basis of a “pond-side test” for detecting potential sources of Guinea worm infection in the environment, in copepods, including in the guts of fish as potential transport hosts, enabling research, surveillance and targeting of control measures. The key constraint on the utility of this assay as a field diagnostic, is a lack of knowledge of variation in the temporal and spatial distribution of D. medinensis larvae in copepods in water bodies in the affected areas and how best to sample copepods to obtain a reliable diagnostic sample. These fundamental knowledge gaps could readily be addressed with field collections of samples across areas experiencing a range of worm infection frequencies, coupled with field and laboratory analyses using LAMP and PCR. LAMP tests were developed for Dracunculus medinensis and D. insignis and were shown to be specific and sensitive. A LAMP test was developed to amplify DNA from copepods to use as an internal amplification control during testing. Samples of copepods taken from ponds could be tested using the LAMP tests and Dracunculus medinensis could be detected. Results are achieved in less than 30 min using just the Genie III instrument and no other laboratory equipment is necessary.
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Affiliation(s)
- Neil Boonham
- Newcastle University, Kings Rd, Newcastle Upon Tyne, NE1 7RU, UK.
| | | | | | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, TR10 9FE, UK
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16
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Duzdevich D, Carr CE, Szostak JW. Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res 2020; 48:e70. [PMID: 32427335 PMCID: PMC7337528 DOI: 10.1093/nar/gkaa400] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
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Affiliation(s)
- Daniel Duzdevich
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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17
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Ivanov AV, Safenkova IV, Drenova NV, Zherdev AV, Dzantiev BB. Development of lateral flow assay combined with recombinase polymerase amplification for highly sensitive detection of Dickeya solani. Mol Cell Probes 2020; 53:101622. [PMID: 32569728 DOI: 10.1016/j.mcp.2020.101622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023]
Abstract
Dickeya solani, one of the most significant bacterial pathogens, infects potato plants, resulting in severe economic damage. In this study, a lateral flow assay (LFA) combined with isothermal DNA amplification was developed for rapid, specific, and sensitive diagnosis of the potato blackleg disease caused by D. solani. Recombinase polymerase amplification (RPA) was chosen for this purpose. Five primer pairs specific to different regions of the D. solani genome were designed and screened. A primer pair providing correct recognition of the target sequence was aligned with the SOL-C region specific to D. solani and flanked by fluorescein (forward primer) and biotin (reverse primer). Lateral flow test strips were constructed to detect DNA amplicons. The RPA-LFA demonstrated a detection limit equal to 14,000 D. solani colony-forming units per gram of potato tuber. This assay provided sensitivity corresponding to the polymerase chain reaction (PCR) but was implemented at a fixed temperature (39 °C) over 30 min. No unspecific reactions with Pectobacterium, Clavibacter, and other Dickeya species were observed. Detection of latent infection of D. solani in the potato tubers by the developed RPA-LFA was verified by PCR. The obtained results confirmed that RPA-LFA has great potential for highly sensitive detection of latent infection.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Natalia V Drenova
- All-Russian Plant Quarantine Centre, Pogranichnaya Street, 32, Bykovo-2, Moscow Region, 140150, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow, 119071, Russia.
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18
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Zhang S, Cai Y, Zhang J, Liu X, He L, Cheng L, Hua K, Hui W, Zhu J, Wan Y, Cui Y. Tetra-primer ARMS-PCR combined with GoldMag lateral flow assay for genotyping: simultaneous visual detection of both alleles. Nanoscale 2020; 12:10098-10105. [PMID: 32350488 DOI: 10.1039/d0nr00360c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rapid and simple detection of single nucleotide polymorphism (SNP) is vital for individualized diagnosis and eventual treatment in the current clinical setting. In this study, we developed a tetra-primer ARMS-PCR combined lateral flow assay (T-ARMS-PCR-LFA) method for simultaneous visual detection of two alleles. By using four primers labeled with digoxin, biotin and Cy5 separately in one PCR reaction, the amplified allele-specific products could be captured by streptavidin and the anti-Cy5 antibody on two separated test lines of a LFA strip, which allows the presentation of both alleles within the single LFA strip. Both DNA and whole blood can be used as templates in this genotyping method in which the whole detection process is completed within 75 minutes. The performance assay of T-ARMS-PCR-LFA demonstrates the accuracy, specificity and sensitivity of this method. One hundred human whole blood samples were used for MTHFR C677T genotyping in T-ARMS-PCR-LFA. The concordance rate of the results detected was up to 100% when compared with that of the sequencing results. Collectively, this newly developed method is highly applicable for SNP screening in clinical practices.
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Affiliation(s)
- Sinong Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
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19
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Pinzon-Reyes E, Alvarez WA, Rondon-Villarreal P, Hernandez HG. Softepigen: Primers Design Web-Based Tool for MS-HRM Technique. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:354-357. [PMID: 30176603 DOI: 10.1109/tcbb.2018.2867600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Polymerase Chain Reaction (PCR) based techniques for DNA methylation techniques includes the MS-HRM technique. Methylation Sensitive High-Resolution Melting (MS-HRM) primer-design requires a set of necessary recommendations for such DNA methylation assessment. However, there were not any available software that allows an automatic design of this kind primers. We present Softepigen, the first complete MS-HRM primer design software. Softepigen allows to search for primers in a genomic region following Wojdacz's recommendations and targets primer binding regions with high linguistic complexity sequences that increase the specificity of the converted sequence of the human genome. We performed in-silico PCR analysis through BiSearch ePCR tool to validate the specificity of the of the primers designed using Softepigen. Softepigen for MS-HRM performance in our genomic regions of interest show satisfactory specificity measurements, and we implemented it for freely available use in the web-based interface at www.soft-epigen.com.
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20
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Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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21
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Kaygusuz D, Vural S, Aytekin AÖ, Lucas SJ, Elitas M. DaimonDNA: A portable, low-cost loop-mediated isothermal amplification platform for naked-eye detection of genetically modified organisms in resource-limited settings. Biosens Bioelectron 2019; 141:111409. [PMID: 31207569 DOI: 10.1016/j.bios.2019.111409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/13/2019] [Accepted: 06/02/2019] [Indexed: 01/08/2023]
Abstract
The steady increase in commercialization of genetically modified organisms (GMOs) demands low-cost, rapid and portable GMO-detection methods that are technically and economically sustainable. Traditional nucleic acid detection platforms are still expensive, immobile and generate complex read-outs to be analyzed by experienced personal. Herein, we report the development of a portable, rapid and user-friendly GMO-detection biosensor, DaimonDNA. The system specifically amplifies the target DNA using loop-mediated isothermal amplification (LAMP) and provides real-time, naked-eye detection with Hydroxynaphthol blue reagent in less than 30 min. The construction of the platform relies on 3D printing and off-the-shelf electronic components that makes it extremely low-cost (<25 Euro), light weight (108 g), mobile (6 × 6 × 3 cm) and suitable for field deployment. We present the detection of the soybean lectin gene as a species control, and P35S as a transgene element found in many GMO varieties. We confirmed specificity of the DaimonDNA biosensor using" RoundUp Ready (RRS)" and MON89788 soybean genomic DNA with P35S and lectin primer sets. We characterized sensitivity of our system using 76.92, 769.2 and 7692 copies of RRS soybean genomic DNA in a non-GMO background. We benchmarked the DNA amplification and detection efficiency of our system against a thermocycling machine by quantifying the images obtained from gel electrophoresis and showed that our system is comparable to most other reported isothermal amplification techniques. This system can also be used for widespread point-of-care or field-based testing that is infrequently performed due to the lack of rapid, inexpensive, user-friendly and portable methods.
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Affiliation(s)
- Doğukan Kaygusuz
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Sümeyra Vural
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Ali Özhan Aytekin
- Yeditepe University, Faculty of Engineering, Department of Genetics and Bioengineering, Kayisdagi Cad., 34755, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Center, 34956, Istanbul, Turkey
| | - Meltem Elitas
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey; Sabanci University Nanotechnology Research and Application Center, 34956, Istanbul, Turkey.
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22
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Aldasoro M, Garin I, Vallejo N, Baroja U, Arrizabalaga-Escudero A, Goiti U, Aihartza J. Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination. PLoS One 2019; 14:e0220081. [PMID: 31339936 PMCID: PMC6656351 DOI: 10.1371/journal.pone.0220081] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/07/2019] [Indexed: 01/01/2023] Open
Abstract
Knowledge on the trophic interactions among predators and their prey is important in order to understand ecology and behaviour of animals. Traditionally studies on the diet composition of insectivorous bats have been based on the morphological identification of prey remains, but the accuracy of the results has been hampered due to methodological limitations. Lately, the DNA metabarcoding and High Throughput Sequencing (HTS) techniques have changed the scene since they allows prey identification to the species level, ultimately giving more precision to the results. Nevertheless, the use of one single primer set to amplify faecal DNA produces biases in the assessed dietary composition. Three horseshoe bats overlap extensively in their distribution range in Europe: Rhinolophus euryale, R. hipposideros and R. ferrumequinum. In order to achieve the deepest insight on their prey list we combined two different primers. Results showed that the used primers were complementary at the order and species levels, only 22 out of 135 prey species being amplified by both. The most frequent prey of R. hipposideros belonged to Diptera and Lepidoptera, to Lepidoptera in R. euryale, and Lepidoptera, Diptera and Coleoptera in R. ferrumequinum. The three bats show significant resource partitioning, since their trophic niche overlap is not higher than 34%. Our results confirm the importance of combining complementary primers to describe the diet of generalist insectivorous bats with amplicon metabarcoding techniques. Overall, each primer set showed a subset of the prey composition, with a small portion of the total prey being identified by both of them. Therefore, each primer presented a different picture of the niche overlap among the three horseshoe bats due to their taxonomic affinity.
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Affiliation(s)
- Miren Aldasoro
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Unai Baroja
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Aitor Arrizabalaga-Escudero
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, The Basque Country
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23
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Yoon SB, Park YH, Choi SA, Yang HJ, Jeong PS, Cha JJ, Lee S, Lee SH, Lee JH, Sim BW, Koo BS, Park SJ, Lee Y, Kim YH, Hong JJ, Kim JS, Jin YB, Huh JW, Lee SR, Song BS, Kim SU. Real-time PCR quantification of spliced X-box binding protein 1 (XBP1) using a universal primer method. PLoS One 2019; 14:e0219978. [PMID: 31329612 PMCID: PMC6645673 DOI: 10.1371/journal.pone.0219978] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/05/2019] [Indexed: 12/21/2022] Open
Abstract
X-box binding protein 1 (XBP1) mRNA processing plays a crucial role in the unfolded protein response (UPR), which is activated in response to endoplasmic reticulum (ER) stress. Upon accumulation of the UPR-converted XBP1 mRNA splicing from an unspliced (u) XBP1 (inactive) isoform to the spliced (s) XBP1 (active) isoform, inositol-requiring enzyme 1 α (IRE1α) removes a 26-nucleotide intron from uXBP1 mRNA. Recent studies have reported the assessment of ER stress by examining the ratio of sXBP1 to uXBP1 mRNA (s/uXBP1 ratio) via densitometric analysis of PCR bands relative to increased levels of sXBP1 to uXBP1 using a housekeeping gene for normalization. However, this measurement is visualized by gel electrophoresis, making it very difficult to quantify differences between the two XBP1 bands and complicating data interpretation. Moreover, most commonly used housekeeping genes display an unacceptably high variable expression pattern of the s/uXBP1 ratio under different experimental conditions, such as various phases of development and different cell types, limiting their use as internal controls. For a more quantitative determination of XBP1 splicing activity, we measured the expression levels of total XBP1 (tXBP1: common region of s/uXBP1) and sXBP1 via real-time PCR using specific primer sets. We also designed universal real-time PCR primer sets capable of amplifying a portion of each u/s/tXBP1 mRNA that is highly conserved in eukaryotes, including humans, monkeys, cows, pigs, and mice. Therefore, we provide a more convenient and easily approachable quantitative real-time PCR method that can be used in various research fields to assess ER stress.
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Affiliation(s)
- Seung-Bin Yoon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeollabuk-do, Republic of Korea
| | - Young-Ho Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Seon-A Choi
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Hae-Jun Yang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Pil-Soo Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jae-Jin Cha
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Sanghoon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Seung Hwan Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jong-Hee Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Bo-Woong Sim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeollabuk-do, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Bong-Seok Song
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (BSS); (SUK)
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (BSS); (SUK)
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Whiley DM, Mhango L, Jennison AV, Nimmo G, Lahra MM. Direct Detection of penA Gene Associated with Ceftriaxone-Resistant Neisseria gonorrhoeae FC428 Strain by Using PCR. Emerg Infect Dis 2019; 24:1573-1575. [PMID: 30016236 PMCID: PMC6056102 DOI: 10.3201/eid2408.180295] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone was first observed in Japan in 2015, and in 2017, it was documented in Denmark, Canada, and Australia. Here, we describe a PCR for direct detection of the penA gene associated with this strain that can be used to enhance surveillance activities.
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Armson B, Walsh C, Morant N, Fowler V, Knowles NJ, Clark D. The development of two field-ready reverse transcription loop-mediated isothermal amplification assays for the rapid detection of Seneca Valley virus 1. Transbound Emerg Dis 2019; 66:497-504. [PMID: 30372584 PMCID: PMC6434928 DOI: 10.1111/tbed.13051] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 09/11/2018] [Accepted: 10/19/2018] [Indexed: 12/25/2022]
Abstract
Seneca Valley virus 1 (SVV-1) has been associated with vesicular disease in swine, with clinical signs indistinguishable from those of other notifiable vesicular diseases such as foot-and-mouth disease. Rapid and accurate detection of SVV-1 is central to confirm the disease causing agent, and to initiate the implementation of control processes. The development of rapid, cost-effective diagnostic assays that can be used at the point of sample collection has been identified as a gap in preparedness for the control of SVV-1. This study describes the development and bench validation of two reverse transcription loop-mediated amplification (RT-LAMP) assays targeting the 5'-untranslated region (5'-UTR) and the VP3-1 region for the detection of SVV-1 that may be performed at the point of sample collection. Both assays were able to demonstrate amplification of all neat samples diluted 1/100 in negative pig epithelium tissue suspension within 8 min, when RNA was extracted prior to the RT-LAMP assay, and no amplification was observed for the other viruses tested. Simple sample preparation methods using lyophilized reagents were investigated, to negate the requirement for RNA extraction. Only a small delay in the time to amplification was observed for these lyophilized reagents, with a time from sample receipt to amplification achieved within 12 min. Although diagnostic validation is recommended, these RT-LAMP assays are highly sensitive and specific, with the potential to be a useful tool in the rapid diagnosis of SVV-1 in the field.
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Affiliation(s)
- Bryony Armson
- The Pirbright InstitutePirbrightSurreyUK
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- GeneSys Biotech LimitedCamberleySurreyUK
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Ghosh DK, Kokane SB, Kokane AD, Warghane AJ, Motghare MR, Bhose S, Sharma AK, Reddy MK. Development of a recombinase polymerase based isothermal amplification combined with lateral flow assay (HLB-RPA-LFA) for rapid detection of "Candidatus Liberibacter asiaticus". PLoS One 2018; 13:e0208530. [PMID: 30540789 PMCID: PMC6291142 DOI: 10.1371/journal.pone.0208530] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 11/18/2018] [Indexed: 02/01/2023] Open
Abstract
Huanglongbing (HLB) or citrus greening is highly destructive disease that is affecting the citrus industry worldwide and it has killed millions of citrus plants globally. HLB is caused by the phloem limited, Gram negative, non-culturable, alpha-proteobacterium, 'Candidatus Liberibacter asiaticus'. Currently, polymerase chain reaction (PCR) and real time PCR have been the gold standard techniques used for detection of 'Ca. L. asiaticus'. These diagnostic methods are expensive, require well equipped laboratories, not user-friendly and not suitable for on-site detection of the pathogen. In this study, a sensitive, reliable, quick and low cost recombinase polymerase based isothermal amplification combined with lateral flow assay (HLB-RPA-LFA) technique has been developed as a diagnostic tool for detection of 'Ca. L. asiaticus'. The assay was standardized by designing the specific primer pair and probe based on the conserved 16S rRNA gene of 'Ca. L. asiaticus'. The assay was optimized for temperature and reaction time by using purified DNA and crude plant extracts and the best HLB-RPA-LFA was achieved at the isothermal temperature of 38°C for 20 to 30 min. The efficacy and sensitivity of the assay was carried out by using field grown, HLB-infected, HLB-doubtful and healthy citrus cultivars including mandarin, sweet orange cv. mosambi, and acid lime. The HLB-RPA-LFA did not show cross-reactivity with other citrus pathogens and is simple, cost-effective, rapid, user-friendly and sensitive. Thus, the HLB-RPA-LFA method has great potential to provide an improved diagnostic tool for detection of 'Ca. L. asiaticus' for the farmers, nurserymen, disease surveyors, mobile plant pathology laboratories, bud-wood certification and quarantine programs.
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Affiliation(s)
- Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Sunil B. Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Amol D. Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Ashish J. Warghane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Manali R. Motghare
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Sumit Bhose
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - M. Krishna Reddy
- Plant Virology Laboratory, ICAR-Indian Institute of Horticulture, Bengaluru, Karnataka, India
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Gao W, Tian J, Huang K, Yang Z, Xu W, Luo Y. Ultrafast, universal and visual screening of dual genetically modified elements based on dual super PCR and a lateral flow biosensor. Food Chem 2018; 279:246-251. [PMID: 30611487 DOI: 10.1016/j.foodchem.2018.12.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/13/2018] [Accepted: 12/01/2018] [Indexed: 12/13/2022]
Abstract
In this study, a cascade screening system has been developed combining Dual Super Polymerase Chain Reaction (DSPCR) with the universal Lateral Flow Biosensor (LFB) for the ultrafast, universal and visual screening of dual GM elements, taking P-35s × T-nos for example. In the design of DSPCR for universal screening, gene-specific forward primers were labelled with biotin and gene-specific reverse primers were tagged with Cy5 and digoxin, respectively. In 2.5-min, DSPCR effectively amplified the dual target fragments through our prototype facility. Then, through specific antigen-antibody binding, a universal lateral flow biosensor exported visually dual-amplified results simultaneously without cross contamination. After optimization, the detection limit allowed 0.05% GM maize, corresponding to nine copies in maize. The entire detection process could be achieved in 10 min without any large-scale instrumentation. This method may be useful for the ultrafast, universal and visual screening of dual GM elements (P-35s × T-nos) in GM crop lines and is expected to be of great promise for rapid GMO screening and point-of-care tests.
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Affiliation(s)
- Wei Gao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingjing Tian
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China
| | - Zhansen Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China.
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China.
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Chheda P, Chanekar M, Salunkhe Y, Dama T, Pais A, Pande S, Bendre R, Shah N. A Study of Triplet-Primed PCR for Identification of CAG Repeat Expansion in the HTT Gene in a Cohort of 503 Indian Cases with Huntington's Disease Symptoms. Mol Diagn Ther 2018; 22:353-359. [PMID: 29619771 DOI: 10.1007/s40291-018-0327-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder with an average age at onset of 40 years. It is a polyglutamine (polyQ) disorder that is caused by an increase in the number of CAG repeats in the huntingtin (HTT) gene. Genetic tests that accurately determine the number of CAG repeats are performed for confirmation of diagnosis, predictive testing of persons at genetic risk for inheriting HD, and prenatal testing. The aim of our study was to evaluate efficacy of triplet-primed polymerase chain reaction (TP-PCR) for routine diagnosis of HD in suspected cases from India. METHODS We evaluated a combination of CAG flanking PCR and triplet-primed PCR for estimation of CAG repeats in 503 cases with clinical suspicion of HD. RESULTS There were 250 cases (49.7%) that showed the presence of expanded alleles, with 241 (47.9%) being fully penetrant alleles and nine (1.8%) in the reduced penetrance category. There were seven juvenile cases with an age of onset of < 20 years, with the longest allele comprising 106 CAG repeats found in an 8-year-old male patient. The results demonstrated an inverse (R = - 0.67) relationship between CAG length and age at clinical onset. CONCLUSION Our study on pan-Indian cases is one of the largest studies reported so far in India and focuses on the most accurate and comprehensive molecular diagnostic evaluation of HD.
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Affiliation(s)
- Pratiksha Chheda
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India.
| | - Milind Chanekar
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India
| | - Yogita Salunkhe
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India
| | - Tavisha Dama
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India
| | - Anurita Pais
- Genetics Department, Metropolis Healthcare Ltd, Mumbai, 400 070, India
| | - Shailesh Pande
- Genetics Department, Metropolis Healthcare Ltd, Mumbai, 400 070, India
| | - Rajesh Bendre
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India
| | - Nilesh Shah
- Department of Molecular Pathology, Metropolis Healthcare Ltd, Commercial Building A, Unit No. 409 to 416, 4th Floor, Kohinoor City, Near Kohinoor Mall, Kirol Road, Kurla-W, Mumbai, 400 070, India
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Huang L, Wang DB, Singh N, Yang F, Gu N, Zhang XE. A dual-signal amplification platform for sensitive fluorescence biosensing of leukemia-derived exosomes. Nanoscale 2018; 10:20289-20295. [PMID: 30371719 DOI: 10.1039/c8nr07720g] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Exosomes as nanosized biomarkers hold great potential for the diagnosis of cancer. However, the low concentration of cancer-derived exosomes present in biofluids makes early diagnosis strenuous. Here, we developed a fluorescent biosensing platform, namely a dual signal amplification, for the ultrasensitive detection of leukemia cell-derived exosomes. The protocol consists of three steps: first, leukemia-derived exosomes containing CD63 and nucleolin were captured by anti-CD63 antibody modified magnetic bead conjugates (MB-CD63); then, a DNA primer comprising a nucleolin-recognition aptamer (AS1411) was applied to bind the exosomes which further initiated a rolling circle amplification (RCA) reaction to generate many repeat sequences for hybridization with gold nanoparticle (GNP)-DNA-fluorescent dye (FAM) conjugates (GNP-DNA-FAM); finally, nicking endonuclease (Nb·BbvCI) assisted target recycling was introduced. As a result, FAM was released from GNP-DNA-FAM conjugates, transformed from the quenching state to the emission state and thus fluorescence signals continuously accumulated. With this dual signal amplification platform, as low as 1 × 102 particles per μL exosomes could be detected. Furthermore, we have successfully applied this method for the detection of exosomes in spiked serum samples, indicating a promising tool for clinical application.
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Affiliation(s)
- Lin Huang
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China.
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Abstract
Proximity ligation assay (PLA), also referred to as Duolink® PLA technology, permits detection of protein-protein interactions in situ (at distances <40 nm) at endogenous protein levels. It exploits specific antibodies identifying (either directly or indirectly) the two proteins of interest and utilizes specific DNA primers covalently linked to the antibodies. A hybridization step followed by DNA amplification with fluorescent probes permit visualization of spots of proximity by fluorescence microscopy. Since the development of PLA in 2002, it has been increasingly used to detect the interaction between two proteins with high sensitivity and specificity. It is a simple and sensitive technique to study protein-protein interaction in cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Muhammad S Alam
- Laboratory of Immune Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Thomsen MCF, Hasman H, Westh H, Kaya H, Lund O. RUCS: rapid identification of PCR primers for unique core sequences. Bioinformatics 2018; 33:3917-3921. [PMID: 28968748 PMCID: PMC5860091 DOI: 10.1093/bioinformatics/btx526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/29/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. Results Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. Availability and implementation Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. Contact mcft@cbs.dtu.dk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin Christen Frølund Thomsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
- To whom correspondence should be addressed.
| | - Henrik Hasman
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
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Abstract
DNA Pol θ-mediated end joining (TMEJ) is a microhomology-based pathway for repairing double-strand breaks in eukaryotes. TMEJ is also a pathway for nonspecific integration of foreign DNAs into host genomes. DNA Pol θ shares structural homology with the high-fidelity replicases, and its polymerase domain (Polθ) has been shown to extend ssDNA without an apparent template. Using oligonucleotides with distinct sequences, we find that with Mg2+ and physiological salt concentrations, human Polθ has no terminal transferase activity and requires a minimum of 2 bp and optimally 4 bp between a template/primer pair for DNA synthesis. Polθ can tolerate a mismatched base pair at the primer end but loses >90% activity when the mismatch is 2 bp upstream from the active site. Polθ is severely inhibited when the template strand has a 3' overhang within 3-4 bp from the active site. In line with its TMEJ function, Polθ has limited strand-displacement activity, and the efficiency and extent of primer extension are similar with or without a downstream duplex.
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Affiliation(s)
- Peng He
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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Hendling M, Pabinger S, Peters K, Wolff N, Conzemius R, Barišić I. Oli2go: an automated multiplex oligonucleotide design tool. Nucleic Acids Res 2018; 46:W252-W256. [PMID: 29718464 PMCID: PMC6030895 DOI: 10.1093/nar/gky319] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/04/2018] [Accepted: 04/17/2018] [Indexed: 01/11/2023] Open
Abstract
The success of widely used oligonucleotide-based experiments, ranging from PCR to microarray, strongly depends on an accurate design. The design process involves a number of steps, which use specific parameters to produce high quality oligonucleotides. Oli2go is an efficient, user friendly, fully automated multiplex oligonucleotide design tool, which performs primer and different hybridization probe designs as well as specificity and cross dimer checks in a single run. The main improvement to existing oligonucleotide design web-tools is that oli2go combines multiple steps in an all-in-one solution, where other web applications only accomplish parts of the whole design workflow. Especially, the oli2go specificity check is not only performed against a single species (e.g. mouse), but against bacteria, viruses, fungi, invertebrates, plants, protozoa, archaea and sequences from whole genome shotgun sequence projects and environmental samples, at once. This allows the design of highly specific oligonucleotides in multiplex applications, which is further assured by performing dimer checks not only on the primers themselves, but in an all-against-all fashion. The software is freely accessible to all users at http://oli2go.ait.ac.at/.
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Affiliation(s)
- Michaela Hendling
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Stephan Pabinger
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Konrad Peters
- University of Vienna, Faculty of Informatics, Währinger Straße 29, 1090 Vienna, Austria
| | - Noa Wolff
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Rick Conzemius
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
| | - Ivan Barišić
- AIT Austrian Institute of Technology, Center for Health, and Bioresources, Molecular Diagnostics, Muthgasse 11, 1190 Vienna, Austria
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Chahin N, Uribe LA, Debela AM, Thorimbert S, Hasenknopf B, Ortiz M, Katakis I, O'Sullivan CK. Electrochemical primer extension based on polyoxometalate electroactive labels for multiplexed detection of single nucleotide polymorphisms. Biosens Bioelectron 2018; 117:201-206. [PMID: 29906767 DOI: 10.1016/j.bios.2018.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Polyoxymetalates (POMs) ([SiW11O39{Sn(CH2)2CO)}]4- and [P2W17O61{Sn(CH2)2CO)}]6-) were used to modify dideoxynucleotides (ddNTPs) through amide bond formation, and applied to the multiplexed detection of single nucleotide polymorphisms (SNPs) in an electrochemical primer extension reaction. Each gold electrode of an array was functionalised with a short single stranded thiolated DNA probe, specifically designed to extend with the POM-ddNTP at the SNP site to be interrogated. The system was applied to the simultaneous detection of 4 SNPs within a single stranded 103-mer model target generated using asymmetric PCR, highlighting the potential of POM-ddNTPs for targeted, multiplexed SNP detection. The four DNA bases were successfully labelled with both ([SiW11O39{Sn(CH2)2CO)}]4- and [P2W17O61{Sn(CH2)2CO)}]6-), and [SiW11O39{Sn(CH2)2CO)}]4- demonstrated to be the more suitable due to its single oxidation peak, which provides an unequivocal signal. The POM-ddNTP enzymatically incorporated to the DNA anchored to the surface was visualised by AFM using gold coated mica. The developed assay has been demonstrated to be highly reproducible, simple to carry out and with very low non-specific background signals. Future work will focus on applying the developed platform to the detection of SNPs associated with rifampicin resistance in real samples from patients suffering from tuberculosis.
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Affiliation(s)
- Nassif Chahin
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Laura A Uribe
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ahmed M Debela
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Serge Thorimbert
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Bernold Hasenknopf
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Mayreli Ortiz
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ioannis Katakis
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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Zhou Z, Wei Q, Yang Y, Li M, Gu JD. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Appl Microbiol Biotechnol 2018; 102:5859-5871. [PMID: 29802476 DOI: 10.1007/s00253-018-9078-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 01/21/2023]
Abstract
Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH4+ and NO2- biochemically to form N2 gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Qiaoyan Wei
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, People's Republic of China.
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Molin WT, Wright AA, VanGessel MJ, McCloskey WB, Jugulam M, Hoagland RE. Survey of the genomic landscape surrounding the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant Amaranthus palmeri from geographically distant populations in the USA. Pest Manag Sci 2018; 74:1109-1117. [PMID: 28686355 DOI: 10.1002/ps.4659] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Glyphosate resistance in Amaranthus palmeri, one of the most prevalent herbicide-resistant weeds in the USA, is attributable to amplification and increased expression of the gene encoding the target site of glyphosate, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). The EPSPS gene and the surrounding 287 kilobases (kb) of amplified sequence are unique to glyphosate-resistant plants and termed the EPSPS cassette. It has only been sequenced in one A. palmeri population from Mississippi. This research compares EPSPS cassettes in seven resistant and five sensitive populations from geographically distant locations within the USA, including Mississippi, Arizona, Kansas, Maryland, Delaware and Georgia. RESULTS Polymerase chain reaction (PCR) products from 40 primer pairs specific to the cassette were similar in size and sequence in resistant populations. Several primer pairs failed to generate PCR products in sensitive populations. Regions of the cassette sequenced in the resistant populations were found to be nearly identical to those from Mississippi. Gene expression analysis showed that both EPSPS and another gene in the cassette, a reverse transcriptase, were elevated in all resistant populations tested relative to the sensitive populations. CONCLUSION EPSPS cassettes from distant resistant populations were nearly homologous. Considering the complexity of the cassette, and the degree of similarity among some cassette sequences, the results are consistent with the hypothesis that glyphosate resistance probably evolved once and then rapidly spread across the USA. © 2017 Society of Chemical Industry.
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Affiliation(s)
- William T Molin
- Crop Production Systems Research Unit, United States Department of Agriculture, Stoneville, MS, USA
| | - Alice A Wright
- Crop Production Systems Research Unit, United States Department of Agriculture, Stoneville, MS, USA
| | - Mark J VanGessel
- Research and Education Center, University of Delaware, Georgetown, DE, USA
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Robert E Hoagland
- Crop Production Systems Research Unit, United States Department of Agriculture, Stoneville, MS, USA
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Salbe C, Trevisiol C, Ferruzzi E, Mancuso T, Nascimbeni R, Di Fabio F, Salerni B, Dittadi R. Molecular Detection of Codon 12 K-RAS Mutations in Circulating DNA from Serum of Colorectal Cancer Patients. Int J Biol Markers 2018; 15:300-7. [PMID: 11192825 DOI: 10.1177/172460080001500404] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Point mutations of the K-RAS gene at codon 12 are found in about 40% of cases with colorectal cancer. The diagnostic implications of the detection of these mutations and their clinical utility are still unclear. The aim of this study was to test both the feasibility of the detection of the mutated K-RAS gene in serum and its potential role in colorectal cancer detection and monitoring. Codon 12 K-RAS mutations were examined in DNA extracted from the serum of 35 patients with colorectal cancer and were compared with the K-RAS status in the corresponding primary tumor. Molecular detection was performed by the mutant-enriched PCR (ME-PCR) assay, a sensitive method capable of distinguishing a small quantity of mutated DNA in the presence of abundant wild-type DNA. The occurrence of mutations was compared with clinicopathological parameters as well as CEA and CA19.9 serum levels. We found codon 12 K-RAS mutations in the tissue of 13/35 (37%) patients. Serum mutations were detected in 5/13 (38.5%) patients with mutated K-RAS in the tissue. 26/35 (74%) patients showed an identical K-RAS pattern in tissue and serum. No codon 12 K-RAS alterations were found in serum samples of 22 patients with benign gastrointestinal diseases. Elevated serum CEA levels were detected in 16 patients, four of whom also presented serum RAS mutations. Our results confirm that K-RAS mutations can be found in circulating DNA extracted from serum samples of patients with colorectal cancer and show that there is a correspondence between serum and tissue K-RAS patterns.
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Affiliation(s)
- C Salbe
- Center for Biological Markers of Malignancy, Regional Hospital ULSS 12, Venice, Italy.
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38
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Kang ST, Hsieh YS, Feng CT, Chen YT, Yang PE, Chen WM. miPrimer: an empirical-based qPCR primer design method for small noncoding microRNA. RNA 2018; 24:304-312. [PMID: 29208706 PMCID: PMC5824350 DOI: 10.1261/rna.061150.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/29/2017] [Indexed: 05/05/2023]
Abstract
MicroRNAs (miRNAs) are 18-25 nucleotides (nt) of highly conserved, noncoding RNAs involved in gene regulation. Because of miRNAs' short length, the design of miRNA primers for PCR amplification remains a significant challenge. Adding to the challenge are miRNAs similar in sequence and miRNA family members that often only differ in sequences by 1 nt. Here, we describe a novel empirical-based method, miPrimer, which greatly reduces primer dimerization and increases primer specificity by factoring various intrinsic primer properties and employing four primer design strategies. The resulting primer pairs displayed an acceptable qPCR efficiency of between 90% and 110%. When tested on miRNA families, miPrimer-designed primers are capable of discriminating among members of miRNA families, as validated by qPCR assays using Quark Biosciences' platform. Of the 120 miRNA primer pairs tested, 95.6% and 93.3% were successful in amplifying specifically non-family and family miRNA members, respectively, after only one design trial. In summary, miPrimer provides a cost-effective and valuable tool for designing miRNA primers.
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Affiliation(s)
| | | | | | - Yu-Ting Chen
- Quark Biosciences, Zhubei, Hsinchu, 30261, Taiwan
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Coutinho-Camillo CM, Miracca EC, dos Santos ML, Salaorni S, Sarkis AS, Nagai MA. Identification of Differentially Expressed Genes in Prostatic Epithelium in Relation to Androgen Receptor CAG Repeat Length. Int J Biol Markers 2018; 21:96-105. [PMID: 16847812 DOI: 10.1177/172460080602100205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The CAG repeat within exon 1 of the androgen receptor (AR) has been associated with the development of prostate cancer. The shorter number of glutamine residues in the protein has been associated with a higher transcriptional activity of the AR and increased relative risk for prostate cancer. In an attempt to identify differentially expressed genes in prostate cancer in relation to AR CAG repeat length variation, in this study we used total mRNA from normal and tumor tissues from 2 prostate cancer patients with AR alleles containing 19 and 26 CAG repeats to perform differential-display RT-PCR analysis. We were able to identify 48 different transcripts that showed homology to several known genes associated with different biological pathways. Among the differentially expressed genes, ATRX and SFRP1 were further validated by quantitative RT-PCR. The transcripts of both ATRX and SFRP1 genes proved to be down-regulated in most of the prostate tumors analyzed by quantitative RT-PCR. Hypermethylation of the promoter region of the SFRP1 gene was found in 17.5% (7/40) of the cases analyzed and was associated with the loss of SFRP1 expression (p=0.014). The differentially expressed genes identified in this study are implicated in several cellular pathways that, when up- or down-regulated, might play a role in the tumorigenic process of the prostate.
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Affiliation(s)
- C M Coutinho-Camillo
- Laboratório de Genética Molecular do Câncer, Disciplina de Oncologia, Departamento de Radiologia, FMUSP, São Paulo, Brazil
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Abstract
Horizontal gene transfer by mobile genetic elements plays an important role in the evolution of bacteria, allowing them to rapidly acquire new traits, including antibiotic resistance. Mobile genetic elements such as conjugative and mobilizable transposons make up a considerable part of the C. difficile genome. While sequence analysis has identified a large number of these elements, experimental analysis is required to demonstrate mobility and function. This chapter describes the experimental methods utilized for determining function and transfer of mobile genetic elements in C. difficile including detection of the circular transfer intermediate and the analysis and confirmation of mobile genetic element transfer to recipient cells.
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Affiliation(s)
- Priscilla Johanesen
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, 3800, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Victoria, 3800, Australia.
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Knowles NJ, Wadsworth J, Bachanek-Bankowska K, King DP. VP1 sequencing protocol for foot and mouth disease virus molecular epidemiology. REV SCI TECH OIE 2017; 35:741-755. [PMID: 28332654 DOI: 10.20506/rst.35.3.2565] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleotide sequences of field strains of foot and mouth disease virus (FMDV) contribute to our understanding of the distribution and evolution of viral lineages that circulate in different regions of the world. This paper outlines a practical reversetranscription polymerase chain reaction (RT-PCR) and sequencing strategy that can be used to generate RNA sequences encoding the VP1 (1D) region of FMDV. The protocol contains a panel of PCR and sequencing primers that can be selected to characterise genetically diverse isolates representing all seven FMDV serotypes. A list of sequences is also described, comprising prototype sequences for all proposed FMDV topotypes, in order to provide a framework for phylogenetic analysis. The technical details and prototype sequences provided in this paper can be employed by FMD Reference Laboratories and others in an approach to harmonise the molecular epidemiology of FMDV.
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Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L. Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase. Nucleic Acids Res 2017; 45:9046-9058. [PMID: 28911121 PMCID: PMC5587808 DOI: 10.1093/nar/gkx633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.
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Affiliation(s)
- Rubén Agudo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
| | - Patricia A. Calvo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | | | - Luis Blanco
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
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Strobel EJ, Watters KE, Nedialkov Y, Artsimovitch I, Lucks JB. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. Nucleic Acids Res 2017; 45:e109. [PMID: 28398514 PMCID: PMC5499547 DOI: 10.1093/nar/gkx233] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/02/2017] [Indexed: 01/24/2023] Open
Abstract
RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq.
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Affiliation(s)
- Eric J. Strobel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA
| | - Kyle E. Watters
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yuri Nedialkov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA
- To whom correspondence should be addressed. Tel: +1 847 467 2943; Fax: +1 847 491 3728;
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Andreason SA, Arif M, Brown JK, Ochoa-Corona F, Fletcher J, Wayadande A. Single-Target and Multiplex Discrimination of Whiteflies (Hemiptera: Aleyrodidae) Bemisia tabaci and Trialeurodes vaporariorum With Modified Priming Oligonucleotide Thermodynamics. J Econ Entomol 2017; 110:1821-1830. [PMID: 28498951 DOI: 10.1093/jee/tox125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 06/07/2023]
Abstract
The whitefly species Bemisia tabaci (Gennadius) and Trialeurodes vaporariorum (Westwood) are worldwide agricultural pests and virus vectors. Bemisia tabaci, in particular, is often transported internationally via trade routes leading to potential introductions of exotic whiteflies or plant viruses. Quick identification of agriculturally important whiteflies can facilitate interventions that prevent these cross-border introductions. Polymerase chain reaction (PCR) primers were designed to amplify the mitochondrial cytochrome oxidase I gene (mtCOI) sequence of members of the B. tabaci complex, MEAM1, MED, and NW, and T. vaporariorum. Primers incorporated an A/T-rich overhang sequence at the 5' terminus (5' flap) to test for increased primer sensitivity and assay efficiency. Single-target and multiplex endpoint PCR assays with the eight primer sets were performed using genomic DNA template extracted from individual adult whiteflies. Resultant PCR amplicons obtained for B. tabaci MEAM1, MED, and NW, and T. vaporariorum primers with the 5' flap were 559-, 717-, 353-, and 258-bp, respectively, and without the 5' flap were 550-, 712-, 329-, and 252-bp in length, respectively. In single-target and multiplex reactions, specific amplification was achieved using both the unmodified and 5' flap-modified primers. Sequencing and phylogenetic analysis confirmed primer-target amplification specificity. Using these primer sets in single-target or multiplex PCR allows for quick discrimination and specific identification of B. tabaci complex members and T. vaporariorum, and the addition of 5'A/T-rich overhang sequences increases the sensitivity and amplification of some primer sets.
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Affiliation(s)
- Sharon A Andreason
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
- Department of Entomology, University of California, Riverside, CA 92521
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721
| | - Francisco Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Jacqueline Fletcher
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Astri Wayadande
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
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Zhang X, Shao M, Gao L, Zhao Y, Sun Z, Zhou L, Yan Y, Shao Q, Xu W, Qian H. A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP. Biochem Mol Biol Educ 2017; 45:299-304. [PMID: 28145107 DOI: 10.1002/bmb.21037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/31/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):299-304, 2017.
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Affiliation(s)
- Xu Zhang
- Department of Molecular Biology and Diagnostics, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
| | - Meng Shao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
| | - Lu Gao
- Experimental Teaching Center, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuanyuan Zhao
- Experimental Teaching Center, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zixuan Sun
- Department of Molecular Biology and Diagnostics, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Liping Zhou
- Department of Molecular Biology and Diagnostics, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Yongmin Yan
- Department of Molecular Biology and Diagnostics, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
| | - Qixiang Shao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
| | - Hui Qian
- Department of Molecular Biology and Diagnostics, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Zhenjiang, Jiangsu, China
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Chang Y, Peng Y, Li P, Zhuang Y. Practices and exploration on competition of molecular biological detection technology among students in food quality and safety major. Biochem Mol Biol Educ 2017; 45:343-350. [PMID: 28696055 DOI: 10.1002/bmb.21045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/22/2016] [Accepted: 01/13/2017] [Indexed: 06/07/2023]
Abstract
With the increasing importance in the application of the molecular biological detection technology in the field of food safety, strengthening education in molecular biology experimental techniques is more necessary for the culture of the students in food quality and safety major. However, molecular biology experiments are not always in curricula of Food quality and safety Majors. This paper introduced a project "competition of molecular biological detection technology for food safety among undergraduate sophomore students in food quality and safety major", students participating in this project needed to learn the fundamental molecular biology experimental techniques such as the principles of molecular biology experiments and genome extraction, PCR and agarose gel electrophoresis analysis, and then design the experiments in groups to identify the meat species in pork and beef products using molecular biological methods. The students should complete the experimental report after basic experiments, write essays and make a presentation after the end of the designed experiments. This project aims to provide another way for food quality and safety majors to improve their knowledge of molecular biology, especially experimental technology, and enhances them to understand the scientific research activities as well as give them a chance to learn how to write a professional thesis. In addition, in line with the principle of an open laboratory, the project is also open to students in other majors in East China University of Science and Technology, in order to enhance students in other majors to understand the fields of molecular biology and food safety. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):343-350, 2017.
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Affiliation(s)
- Yaning Chang
- East China University of Science and Technology, Fermentation Engineering Experiment Teaching Demonstration Center of Bioengineering College, No. 999 Haisi Road, Fengxian District, Shanghai, 201424, China
| | - Yuke Peng
- East China University of Science and Technology, Fermentation Engineering Experiment Teaching Demonstration Center of Bioengineering College, No. 999 Haisi Road, Fengxian District, Shanghai, 201424, China
| | - Pengfei Li
- East China University of Science and Technology, Fermentation Engineering Experiment Teaching Demonstration Center of Bioengineering College, No. 999 Haisi Road, Fengxian District, Shanghai, 201424, China
| | - Yingping Zhuang
- East China University of Science and Technology, Fermentation Engineering Experiment Teaching Demonstration Center of Bioengineering College, No. 999 Haisi Road, Fengxian District, Shanghai, 201424, China
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Bédarida S, Dussol B, Signoli M, Biagini P. Analysis of Anelloviridae sequences characterized from serial human and animal biological samples. Infect Genet Evol 2017; 53:89-93. [PMID: 28536071 DOI: 10.1016/j.meegid.2017.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 11/19/2022]
Abstract
Rolling-circle amplification-sequence-independent single primer amplifications (RCA-SISPA) and/or RCA-PCR-based approaches were applied to serial human plasma and animal (domestic cat) saliva samples. Complete SENV-H-related and PRA4 Anelloviridae genomes were characterized and analysed over time (~16 and 6.5years for human and animal samples, respectively). Genomic sequences and deduced putative coding regions were compared. Comparable values, i.e. ~2×10-4subs/site/year, were obtained for estimated rates of non-synonymous substitutions. A "hot-spot" of mutations located on the SENV-H-related ORF1 was identified. These results are first data concerning Anelloviridae evolution in a human and an animal host based on the analysis of complete sequences.
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Affiliation(s)
- Sandra Bédarida
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Bertrand Dussol
- Nephrology and Renal Transplantation Centre, CHU Conception, Marseille, France
| | | | - Philippe Biagini
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.
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Ma C, Zhang L, Gao M, Ma D. Construction of Lactococcus lactis expressing secreted and anchored Eimeria tenella 3-1E protein and comparison of protective immunity against homologous challenge. Exp Parasitol 2017; 178:14-20. [PMID: 28526337 DOI: 10.1016/j.exppara.2017.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 11/17/2022]
Abstract
Two novel plasmids pTX8048-SP-Δ3-1E and pTX8048-SP-NAΔ3-1E-CWA were constructed. The plasmids were respectively electrotransformed into L. lactis NZ9000 to generate strain of L. lactis/pTX8048-SP-Δ3-1E in which 3-1E protein was expressed in secretion, and L. lactis/pTX8048-SP-NAΔ3-1E-CWA on which 3-1E protein was covalently anchored to the surface of bacteria cells. The expression of target proteins were examined by Western blot. The live lactococci expressing secreted 3-1E protein, anchored 3-1E protein, and cytoplasmic 3-1E protein was administered orally to chickens respectively, and the protective immunity and efficacy were compared by animal experiment. The results showed oral immunization to chickens with recombinant lactococci expressing anchored 3-1E protein elicited high 3-1E-specific serum IgG, increased high proportion of CD4+ and CD8α+ cells in spleen, alleviated average lesion score in cecum, decreased the oocyst output per chicken compared to lactococci expressing cytoplasmic or secreted 3-1E protein. Taken together, these findings indicated the surface anchored Eimeria protein displayed by L. lacits can induce protective immunity and partial protection against homologous infection.
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Affiliation(s)
- Chunli Ma
- College of Food Science, Northeast Agricultural University, NO. 59 Mucai Street, Harbin 150030, China
| | - Lili Zhang
- College of Veterinary Medicine, Northeast Agricultural University, NO. 59 Mucai Street, Harbin 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, NO. 59 Mucai Street, Harbin 150030, China
| | - Mingyang Gao
- College of Veterinary Medicine, Northeast Agricultural University, NO. 59 Mucai Street, Harbin 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, NO. 59 Mucai Street, Harbin 150030, China
| | - Dexing Ma
- College of Veterinary Medicine, Northeast Agricultural University, NO. 59 Mucai Street, Harbin 150030, China; Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, NO. 59 Mucai Street, Harbin 150030, China.
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Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC. Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts. Biochemistry 2017; 56:1811-1814. [PMID: 28319368 PMCID: PMC10884885 DOI: 10.1021/acs.biochem.7b00128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
RNA molecules depend on structural elements that are critical for cellular function. Chemical methods for probing RNA structure have emerged as a necessary component of characterizing RNA function. As such, understanding the limitations and idiosyncrasies of these methods is essential for their utility. Selective hydroxyl acylation has emerged as a common method for analyzing RNA structure. Ester products as a result of 2'-hydroxyl acylation can then be identified through reverse transcription or mutational enzyme profiling. The central aspect of selective hydroxyl acylation analyzed by primer extension (SHAPE) experiments is the fact that stable ester adducts are formed on the 2'-hydroxyl. Despite its importance, there has not been a direct comparison of SHAPE electrophiles for their ability to make stable RNA adducts. Herein, we conduct a systematic analysis of hydrolysis stability experiments to demonstrate that furoyl imidazole SHAPE reagents form stable ester adducts even at elevated temperatures. We also demonstrate that the acylation reaction with the furoyl acylimidaole SHAPE reagent can be controlled with dithiothreitol quenching, even in live cells. These results are important for our understanding of the biochemical details of the SHAPE experiment.
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Affiliation(s)
- Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Yuran Zhen
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
| | - Ryan A Flynn
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine , Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine , Irvine, California 92697, United States
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Tsao SM, Lai JC, Horng HE, Liu TC, Hong CY. Generation of Aptamers from A Primer-Free Randomized ssDNA Library Using Magnetic-Assisted Rapid Aptamer Selection. Sci Rep 2017; 7:45478. [PMID: 28367958 PMCID: PMC5377317 DOI: 10.1038/srep45478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/28/2017] [Indexed: 01/20/2023] Open
Abstract
Aptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences. The Magnetic-Assisted Rapid Aptamer Selection (MARAS) is a newly developed protocol for generating single-strand DNA aptamers. No repeat selection cycle is required in the protocol. This study proposes and demonstrates a method to isolate aptamers for C-reactive proteins (CRP) from a randomized ssDNA library containing no fixed sequences at 5' and 3' termini using the MARAS platform. Furthermore, the isolated primer-free aptamer was sequenced and binding affinity for CRP was analyzed. The specificity of the obtained aptamer was validated using blind serum samples. The result was consistent with monoclonal antibody-based nephelometry analysis, which indicated that a primer-free aptamer has high specificity toward targets. MARAS is a feasible platform for efficiently generating primer-free aptamers for clinical diagnoses.
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Affiliation(s)
- Shih-Ming Tsao
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
- Sections of Infectious Diseases, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Ji-Ching Lai
- Institute of Electro-optical Science and Technology, National Taiwan Normal University, Taipei, Taiwan
- Research Assistant Center, Chang Hua Show Chwan Health Care System, Changhua, Taiwan
| | - Horng-Er Horng
- Institute of Electro-optical Science and Technology, National Taiwan Normal University, Taipei, Taiwan
| | - Tu-Chen Liu
- Department of Chest Medicine, Cheng-Ching General Hospital, Taichung, Taiwan
| | - Chin-Yih Hong
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, Taiwan
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