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Rund H, Wanzenböck J, Dobrovolny S, Kurmayer R. Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172281. [PMID: 38588740 DOI: 10.1016/j.scitotenv.2024.172281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.
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Affiliation(s)
- Hans Rund
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
| | - Stefanie Dobrovolny
- Department for Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
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2
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Paenkaew S, Jaito N, Pradit W, Chomdej S, Nganvongpanit K, Siengdee P, Buddhachat K. RPA/CRISPR-cas12a as a specific, sensitive and rapid method for diagnosing Ehrlichia canis and Anaplasma platys in dogs in Thailand. Vet Res Commun 2023; 47:1601-1613. [PMID: 36997812 PMCID: PMC10062689 DOI: 10.1007/s11259-023-10114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Rickettsial pathogens including Ehrlichia canis and Anaplasma platys are bacteria that cause parasitic infections in dogs such as canine monocytic ehrlichiosis (CME) and canine cyclic thrombocytopenia (CCT), respectively affecting mortality and morbidity worldwide. An accurate, sensitive, and rapid method to diagnose these agents is essential for effective treatment. In this study, a recombinase polymerase amplification (RPA) coupled with CRISPR-Cas12a methods was established to detect E. canis and A. platys infection in dogs based on the 16S rRNA. The optimal condition for DNA amplification by RPA was 37 °C for 20 min, followed by CRISPR-Cas12a digestion at 37 °C for one hour. A combination of RPA and the cas12a detection method did not react with other pathogens and demonstrated strong sensitivity, detecting as low as 100 copies of both E. canis and A. platys. This simultaneous detection method was significantly more sensitive than conventional PCR. The RPA-assisted cas12a assay provides specific, sensitive, rapid, simple and appropriate detection of rickettsial agents in canine blood at the point-of-care for diagnostics, disease prevention and surveillance.
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Affiliation(s)
- Suphaporn Paenkaew
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Nongluck Jaito
- Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Rd., Klong Luang District, Pathum Thani, 12120, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Korakot Nganvongpanit
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Puntita Siengdee
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, 10210, Bangkok, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand.
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3
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Lee S, Kim S, Kim S. A novel paper-based lysis strip for SARS-CoV-2 RNA detection at low resource settings. Anal Biochem 2023; 664:115037. [PMID: 36623679 PMCID: PMC9817428 DOI: 10.1016/j.ab.2023.115037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Infectious respiratory diseases such as COVID-19 are serious and global concerns from the past to the present. To isolate the spread of infectious diseases even in the absence of a health system, a simple, inexpensive, reliable, sensitive, and selective molecular diagnosis platform for Point of Care Test (POCT) is required. Especially, the nucleic acid extraction step is difficult to perform out of laboratory. Here, we propose a paper-based lysis (PBL) strip for nucleic acid extraction, especially in low-resource settings (LRS). PBL strips are suitable for isolating RNA from viruses with biological interference and inhibitors. We optimized the buffer compositions and membranes of the strip. A simple preparation method using a PBL strip could obtain an eluent for downstream inspection within 20 min. Overall, 104 copies/swaps were detected for 20 min for amplification in combination with Reverse Transcription Loop-Mediated Amplification (RT-LAMP).
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Affiliation(s)
| | | | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
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4
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Kumar S, Pany SPP, Sudhakar S, Singh SB, Todankar CS, Pradeepkumar PI. Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds. Biochemistry 2022; 61:2546-2559. [DOI: 10.1021/acs.biochem.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Satendra Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | | | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Sushma B. Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Chaitra S. Todankar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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5
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Colovas J, Bintarti AF, Mechan Llontop ME, Grady KL, Shade A. Do-it-Yourself Mock Community Standard for Multi-Step Assessment of Microbiome Protocols. Curr Protoc 2022; 2:e533. [PMID: 36066286 DOI: 10.1002/cpz1.533] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbiomes provide critical functions that support animals, plants, and ecosystems. High-throughput sequencing (HTS) has become an essential tool for the cultivation-independent study of microbiomes found in diverse environments, but requires effective and meaningful controls. One such critical control is a mock microbial community, which is used as a positive control for nucleic acid extraction, marker gene amplification, and sequencing. While mock community standards can be purchased, they can be costly and often include only medically relevant microbial strains that are not expected to be major players in non-human microbiomes. As an alternative, it is possible to design and construct a do-it-yourself (DIY) mock community, which can then be used as a positive control that is specifically customized to the protocol needs of a particular study system. In this article, we describe protocols to select appropriate microbial strains for the construction of a mock community. We first describe the steps to verify the identity of community members via Sanger sequencing. Then, we provide guidance on assembling and storing the DIY mock community as viable whole cells. This includes steps to create standard growth curves referenced to plate counts for each member, so that the community members can be quantified and later compared in terms of their "expected versus returned" relative contributions after sequencing. We also describe appropriate methods for the cryostorage of the fully assembled mock community as viable whole cells, so that they can be used as a unit in a microbiome analysis, from the lysis and nucleic acid extraction steps onwards. Finally, we provide an example of returned data and interpretation of DIY mock community sequences, discussing how to assess possible contamination and identify protocol biases for particular members. Overall, DIY mock communities serve to determine success and possible bias in a cultivation-independent microbiome analysis. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Strain identification and verification using Sanger sequencing Basic Protocol 2: Creation of glycerol stocks of each mock community strain for long-term cryostorage Basic Protocol 3: Assessment of strain freezer viability without cryoprotectant Basic Protocol 4: Creation of standard curve to determine CFU/ml of a liquid culture as a function of optical density Basic Protocol 5: Full mock community assembly using community concentration calculations and standard curves.
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Affiliation(s)
- Joanna Colovas
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Ari Fina Bintarti
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan
| | - Marco E Mechan Llontop
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan
| | - Keara L Grady
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan
- The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan
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6
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Single-tube collection and nucleic acid analysis of clinical samples for SARS-CoV-2 saliva testing. Sci Rep 2022; 12:3951. [PMID: 35273232 PMCID: PMC8913774 DOI: 10.1038/s41598-022-07871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
The SARS-CoV-2 pandemic has brought to light the need for expedient diagnostic testing. Cost and availability of large-scale testing capacity has led to a lag in turnaround time and hindered contact tracing efforts, resulting in a further spread of SARS-CoV-2. To increase the speed and frequency of testing, we developed a cost-effective single-tube approach for collection, denaturation, and analysis of clinical samples. The approach utilizes 1 µL microbiological inoculation loops to collect saliva, sodium dodecyl sulfate (SDS) to inactivate and release viral genomic RNA, and a diagnostic reaction mix containing polysorbate 80 (Tween 80). In the same tube, the SDS-denatured clinical samples are introduced to the mixtures containing all components for nucleic acids detection and Tween 80 micelles to absorb the SDS and allow enzymatic reactions to proceed, obviating the need for further handling of the samples. The samples can be collected by the tested individuals, further decreasing the need for trained personnel to administer the test. We validated this single-tube sample-to-assay method with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) and discovered little-to-no difference between Tween- and SDS-containing reaction mixtures, compared to control reactions. This approach reduces the logistical burden of traditional large-scale testing and provides a method of deployable point-of-care diagnostics to increase testing frequency.
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7
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Oñate-Sánchez L, Verdonk JC. Citrate-Citric Acid RNA Isolation (CiAR) for Fast, Low-Cost, and Reliable RNA Extraction from Multiple Plant Species and Tissues. Curr Protoc 2021; 1:e298. [PMID: 34874606 DOI: 10.1002/cpz1.298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
RNA isolation is routinely carried out in many laboratories for different downstream applications. Although protocols for this can vary between labs depending on the specific plant species and tissues under study and the preferences of their researchers, these protocols usually include the use of volatile organic and toxic chemicals. As an alternative, several companies offer less hazardous RNA extraction kits, but these kits significantly increase the cost per sample and are thus not affordable for every lab, especially when a large number of samples is to be processed. We have previously described a fast and efficient method for RNA isolation from plant vegetative tissues that requires only two home-made, simple, inexpensive, and nontoxic buffers. Both buffers have low concentrations of citric acid and its sodium salt. The first buffer also contains a detergent to help with nucleic acid solubilization while keeping RNases inactive. The second buffer has sodium chloride at high molarity to separate protein from nucleic acids. RNA is precipitated, and contaminating DNA can then be optionally removed. Here, we describe and expand on this approach, which we call the citrate-citric acid RNA isolation, or CiAR, method. We provide a detailed description of the protocol, describe a modification to make it compatible with non-vegetative tissues, and compile and extend the number of species and tissues to which it can be applied. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Julian C Verdonk
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
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8
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Lee H, Lee B, Kim DG, Cho YA, Kim JS, Suh YL. Detection of TERT Promoter Mutations Using Targeted Next-Generation Sequencing: Overcoming GC Bias through Trial and Error. Cancer Res Treat 2021; 54:75-83. [PMID: 33940787 PMCID: PMC8756133 DOI: 10.4143/crt.2021.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose Detection of telomerase reverse transcriptase (TERT) promoter mutations is a crucial process in the integrated diagnosis of glioblastomas. However, the TERT promoter region is difficult to amplify because of its high guanine-cytosine (GC) content (> 80%). This study aimed to analyze the capturing of TERT mutations by targeted next-generation sequencing (NGS) using formalin-fixed paraffin-embedded tissues. Materials and Methods We compared the detection rate of TERT mutations between targeted NGS and Sanger sequencing in 25 cases of isocitrate dehydrgenase (IDH)-wildtype glioblastomas and 10 cases of non-neoplastic gastric tissues. Our customized panel consisted of 232 essential glioma-associated genes. Results Sanger sequencing detected TERT mutations in 17 out of 25 glioblastomas, but all TERT mutations were missed by targeted NGS. After the manual visualization of the NGS data using an integrative genomics viewer, 16 cases showed a TERT mutation with a very low read depth (mean, 21.59; median, 25), which revealed false-negative results using auto-filtering. We optimized our customized panel by extending the length of oligonucleotide baits and increasing the number of baits spanning the coverage of the TERT promoter, which did not amplify well due to the high GC content. Conclusion Our study confirmed that it is crucial to consider the recognition of molecular bias and to carefully interpret NGS data.
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Affiliation(s)
- Hyunwoo Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Lee
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Deok Geun Kim
- Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Clinical Genomic Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon Ah Cho
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Jung-Sun Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon-Lim Suh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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9
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Abstract
In situ hybridization is a powerful technique that allows the visualization of specific RNA species in biological samples in exquisite detail. It has been particularly well explored in the field of developmental genetics. The spatial and temporal patterns of RNA expression provide us with critical information on likely gene function during embryonic development, and often inform the decision on whether to attempt further gene manipulation approaches. Furthermore, once a mouse strain with altered gene function has been created, in situ hybridization is a critical tool for revealing how the development of embryos with the mutation differs from that of wild-type embryos, and thus infer the function of the altered gene. Here, a well-tested protocol used to visualize RNA expression in whole-mount mid-gestation mouse embryos ranging from 8.5 to 14.5 days post-coitum (dpc) is described. © 2020 Wiley Periodicals LLC. Basic Protocol 1: RNA probe synthesis Alternate Protocol: Preparation of DNA template by PCR Basic Protocol 2: Embryo dissection Basic Protocol 3: Whole mount in situ hybridization Support Protocol: Generation of embryo powder.
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Affiliation(s)
- Annemiek Beverdam
- School of Medical Sciences, UNSW, Sydney, New South Wales, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
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10
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Hoellerbauer P, Kufeld M, Paddison PJ. Efficient Multi-Allelic Genome Editing of Primary Cell Cultures via CRISPR-Cas9 Ribonucleoprotein Nucleofection. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2020; 54:e126. [PMID: 32833346 DOI: 10.1002/cpsc.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas9-based technologies have revolutionized experimental manipulation of mammalian genomes. However, limitations regarding the delivery and efficacy of these technologies restrict their application in primary cells. This article describes a protocol for penetrant, reproducible, and fast CRISPR-Cas9 genome editing in cell cultures derived from primary cells. The protocol employs transient nucleofection of ribonucleoprotein complexes composed of chemically synthesized 2'-O-methyl-3'phosphorothioate-modified single guide RNAs (sgRNAs) and purified Cas9 protein. It can be used both for targeted insertion-deletion mutation (indel) formation at up to >90% efficiency (via use of a single sgRNA) and for targeted deletion of genomic regions (via combined use of multiple sgRNAs). This article provides examples of the nucleofection buffer and programs that are optimal for patient-derived glioblastoma (GBM) stem-like cells (GSCs) and human neural stem/progenitor cells (NSCs), but the protocol can be readily applied to other primary cell cultures by modifying the nucleofection conditions. In summary, this is a relatively simple method that can be used for highly efficient and fast gene knockout, as well as for targeted genomic deletions, even in hyperdiploid cells such as many cancer stem-like cells. © 2020 Wiley Periodicals LLC Basic Protocol: Cas9:sgRNA ribonucleoprotein nucleofection for insertion-deletion (indel) mutation and genomic deletion generation in primary cell cultures.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
| | - Megan Kufeld
- Antibody Discovery, Seattle Genetics, Bothell, Washington
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington
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11
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An efficient module-less synthesis approach for Digital Microfluidic Biochip. SN APPLIED SCIENCES 2020; 2:1442. [PMID: 32835163 PMCID: PMC7385941 DOI: 10.1007/s42452-020-3173-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/02/2020] [Indexed: 11/26/2022] Open
Abstract
Digital Microfluidic Biochips (DMFBs) will require error-free synthesis techniques which can function at much higher speed while implementing on real-time systems and capable of tackling more complex assay operations. Until now various bio-assays are successfully implemented based on different mixing modules present on such lab-on-chips. In present work, the concept of such dedicated virtual modules has been eliminated and a novel module-less-synthesis (MLS) method is proposed for accomplishing high-performance bio-protocols. Various shift-patterns (movements) of the micro-droplets are identified to accomplish entire mixing in lesser time compared to earlier module-based synthesis methods. We have also computed the percentage of mixing accomplishment for each directional-shift of the mixer-droplet. However, path congestion problem and operational errors are inevitable in MLS approach. Hence, the path congestion and washing problem in MLS is addressed by tweaking the earlier MLS approach and a new modified-MLS (MMLS) method is proposed. Finally, washing optimization technique on MMLS method is also given. Different real-life bio assays like PCR, IVD are tested with the proposed technique as well as synthetic benchmarks (hard test benches) are also incorporated in the experiments. For both kind of benchmarks synthesis performance improved with bioassay completion time ( T max ) significantly reduced compared to existing synthesis approaches on DMFB platform.
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12
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Barratt KS, Arkell RM. Production of Digoxigenin‐Labeled Riboprobes for In Situ Hybridization Experiments. ACTA ACUST UNITED AC 2020; 10:e74. [DOI: 10.1002/cpmo.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kristen S. Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical ResearchThe Australian National University Canberra ACT Australia
| | - Ruth M. Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical ResearchThe Australian National University Canberra ACT Australia
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13
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Wilkinson AA, Jagu E, Ubych K, Coulthard S, Rushton AE, Kennefick J, Su Q, Neely RK, Fernandez-Trillo P. Site-Selective and Rewritable Labeling of DNA through Enzymatic, Reversible, and Click Chemistries. ACS CENTRAL SCIENCE 2020; 6:525-534. [PMID: 32342002 PMCID: PMC7181315 DOI: 10.1021/acscentsci.9b01023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 05/02/2023]
Abstract
Current methods for bioconjugation rely on the introduction of stable linkers that lack the required versatility to perform sequential functionalizations. However, sequential manipulations are an increasing requirement in chemical biology because they can underpin multiple analyses of the same sample to provide a wider understanding of cell behavior. Here, we present a new method to site-selectively write, remove, and rewrite chemical functionality to a biomolecule, DNA in this case. Our method combines the precision and robustness of methyltransferase-directed labeling with the reversibility of acyl hydrazones and the efficiency of click chemistry. Underpinning the method is a new S-adenosyl-l-methionine derivative to site-selectively label DNA with a bifunctional chemical handle containing an acyl hydrazone-linker and a terminal azide. Functional tags are conjugated via the azide and can be removed (i.e., untagged) when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either rewritten to reset the original chemical handle or covalently reacted with a permanent tag. This ability to write, tag, untag, and permanently tag DNA is exploited to sequentially introduce two fluorescent dyes on DNA. Finally, we demonstrate the potential of the method by developing a protocol to sort labeled DNA using magnetic beads, with subsequent amplification of the sorted DNA sample for further analysis. The presented method opens new avenues for site-selective bioconjugation and should underpin integrative approaches in chemical biology where sequential functionalizations of the same sample are required.
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Affiliation(s)
- Andrew A Wilkinson
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Elodie Jagu
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Krystian Ubych
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Steven Coulthard
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Ashleigh E Rushton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Jack Kennefick
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Qiang Su
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, U.K., B15 2TT
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14
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Fernández A, Morín M, Muñoz‐Santos D, Josa S, Montero A, Rubio‐Fernández M, Cantero M, Fernández J, del Hierro MJ, Castrillo M, Moreno‐Pelayo MÁ, Montoliu L. Simple Protocol for Generating and Genotyping Genome‐Edited Mice With CRISPR‐Cas9 Reagents. ACTA ACUST UNITED AC 2020; 10:e69. [DOI: 10.1002/cpmo.69] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Almudena Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Matías Morín
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
- Servicio de Genética, Ramón y Cajal University HospitalIRYCIS Madrid Spain
| | - Diego Muñoz‐Santos
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Santiago Josa
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Andrea Montero
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Marcos Rubio‐Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Marta Cantero
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | - Julia Fernández
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
| | | | | | - Miguel Ángel Moreno‐Pelayo
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
- Servicio de Genética, Ramón y Cajal University HospitalIRYCIS Madrid Spain
| | - Lluís Montoliu
- National Centre for Biotechnology (CNB)CSIC Madrid Spain
- CIBER of Rare Diseases (CIBERER)ISCIII Madrid Spain
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15
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Keen P, Hastings AP, Agrawal AA, Van Eck J. Agrobacterium tumefaciens-Mediated Transformation of Three Milkweed Species (Asclepias hallii, A. syriaca, and A. tuberosa: Apocynaceae). ACTA ACUST UNITED AC 2020; 5:e20105. [PMID: 32150352 DOI: 10.1002/cppb.20105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Milkweeds have ecological significance for insect herbivores that rely on them as hosts for either part of or the entirety of their life cycles. Interesting interactions, some of which are not completely understood, have evolved over time. To develop these species as models to elucidate the interplay with insect herbivores, we established Agrobacterium tumefaciens-mediated transformation approaches for Asclepias hallii (Hall's milkweed), A. syriaca (common milkweed), and A. tuberosa (butterflyweed). The method is based on infection of stem internodal explants, which were more amenable to transformation than leaf explants. We found that addition of freshly prepared dithiothreitol was critical to prevent browning of stem explants. Depending on the species, the time from infection to the regeneration of transgenic lines ranges from 2 to 4 months. Transformation efficiency for A. hallii was 9%, whereas efficiencies for A. syriaca and A. tuberosa were 6% and 13%, respectively. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Agrobacterium tumefaciens-mediated transformation of Asclepias internodal stem explants Basic Protocol 2: Preparation of Agrobacterium glycerol stocks containing gene constructs.
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Affiliation(s)
| | - Amy Picard Hastings
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, New York.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York
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16
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Vazquez‐Vilar M, Gandía M, García‐Carpintero V, Marqués E, Sarrion‐Perdigones A, Yenush L, Polaina J, Manzanares P, Marcos JF, Orzaez D. Multigene Engineering by GoldenBraid Cloning: From Plants to Filamentous Fungi and Beyond. ACTA ACUST UNITED AC 2020; 130:e116. [DOI: 10.1002/cpmb.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Mónica Gandía
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Victor García‐Carpintero
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Eric Marqués
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | | | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Julio Polaina
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Paloma Manzanares
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Jose F. Marcos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos (IATA)Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Universitat Politècnica de València–Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
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17
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Bosch JA, Knight S, Kanca O, Zirin J, Yang-Zhou D, Hu Y, Rodiger J, Amador G, Bellen HJ, Perrimon N, Mohr SE. Use of the CRISPR-Cas9 System in Drosophila Cultured Cells to Introduce Fluorescent Tags into Endogenous Genes. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 130:e112. [PMID: 31869524 PMCID: PMC7213786 DOI: 10.1002/cpmb.112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The CRISPR-Cas9 system makes it possible to cause double-strand breaks in specific regions, inducing repair. In the presence of a donor construct, repair can involve insertion or 'knock-in' of an exogenous cassette. One common application of knock-in technology is to generate cell lines expressing fluorescently tagged endogenous proteins. The standard approach relies on production of a donor plasmid with ∼500 to 1000 bp of homology on either side of an insertion cassette that contains the fluorescent protein open reading frame (ORF). We present two alternative methods for knock-in of fluorescent protein ORFs into Cas9-expressing Drosophila S2R+ cultured cells, the single-stranded DNA (ssDNA) Drop-In method and the CRISPaint universal donor method. Both methods eliminate the need to clone a large plasmid donor for each target. We discuss the advantages and limitations of the standard, ssDNA Drop-In, and CRISPaint methods for fluorescent protein tagging in Drosophila cultured cells. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Knock-in into Cas9-positive S2R+ cells using the ssDNA Drop-In approach Basic Protocol 2: Knock-in into Cas9-positive S2R+ cells by homology-independent insertion of universal donor plasmids that provide mNeonGreen (CRISPaint method) Support Protocol 1: sgRNA design and cloning Support Protocol 2: ssDNA donor synthesis Support Protocol 3: Transfection using Effectene Support Protocol 4: Electroporation of S2R+-MT::Cas9 Drosophila cells Support Protocol 5: Single-cell isolation of fluorescent cells using FACS.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Shannon Knight
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Donghui Yang-Zhou
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Rodiger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Gabriel Amador
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
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18
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Li Z, Wang F, Li JF. Targeted Transcriptional Activation in Plants Using a Potent Dead Cas9-Derived Synthetic Gene Activator. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 127:e89. [PMID: 31237422 DOI: 10.1002/cpmb.89] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic tools for specific perturbation of endogenous gene expression are highly desirable for interrogation of plant gene functions and improvement of crop traits. Synthetic transcriptional activators derived from the CRISPR/Cas9 system are emerging as powerful new tools for activating the endogenous expression of genes of interest in plants. These synthetic constructs, generated by tethering transcriptional activation domains to a nuclease-dead Cas9 (dCas9), can be directed to the promoters of endogenous target genes by single guide RNAs (sgRNAs) to activate transcription. Here, we provide a detailed protocol for targeted transcriptional activation in plants using a recently developed, highly potent dCas9 gene activator construct referred to as dCas9-TV. This protocol covers selection of sgRNA targets, construction of sgRNA expression cassettes, and screening for an optimal sgRNA using a protoplast-based promoter-luciferase assay. Finally, the dCas9-TV gene activator coupled with the optimal sgRNA is delivered into plants via Agrobacterium-mediated transformation, thereby enabling robust upregulation of target gene expression in transgenic Arabidopsis and rice plants. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zhenxiang Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Fengzhu Wang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Feng Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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19
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Jain HV, Boehler JF, Nagaraju K, Beaucage SL. Synthesis, Characterization, and Function of an RNA-Based Transfection Reagent. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2018; 72:4.81.1-4.81.29. [PMID: 29927123 PMCID: PMC6020023 DOI: 10.1002/cpnc.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A synthetic 8-mer, amphipathic, trans-acting poly-2'-O-methyluridylic thiophosphate triester RNA element (2'-OMeUtaPS) can be prepared using solid-phase synthesis protocols. 2'-OMeUtaPS efficiently mediates the delivery of uncharged polyA-tailed phosphorodiamidate morpholino (PMO) sequences in HeLa pLuc 705 cells, as evidenced by flow cytometry measurements. In this cell line, 2'-OMeUtaPS-mediated transfection of an antisense polyA-tailed PMO sequence induces alternative splicing of an aberrant luciferase pre-mRNA splice site, leading to restoration of functional luciferase, as quantitatively measured using a typical luciferase assay. 2'-OMeUtaPS is also potent at delivering an uncharged antisense polyA-tailed PMO sequence in muscle cells of the mdx mouse model of muscular dystrophy; targeting the polyA-tailed PMO sequence against a splice site of the pre-mRNA encoding mutated dystrophin triggers an alternate splicing event that results in excision of the mutated exon (exon 23) from the pre-mRNA and production of functional dystrophin, as demonstrated by agarose gel electrophoresis. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Harsh V Jain
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Jessica F Boehler
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, District of Columbia
- The Institute for Biomedical Sciences, The George Washington University, Washington, District of Columbia
| | - Kanneboyina Nagaraju
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, District of Columbia
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton, New York
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
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20
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Gertsenstein M, Nutter LMJ. Engineering Point Mutant and Epitope-Tagged Alleles in Mice Using Cas9 RNA-Guided Nuclease. CURRENT PROTOCOLS IN MOUSE BIOLOGY 2018; 8:28-53. [PMID: 30040228 PMCID: PMC9249120 DOI: 10.1002/cpmo.40] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mice carrying patient-associated point mutations are powerful tools to define the causality of single-nucleotide variants to disease states. Epitope tags enable immuno-based studies of genes for which no antibodies are available. These alleles enable detailed and precise developmental, mechanistic, and translational research. The first step in generating these alleles is to identify within the target sequence-the orthologous sequence for point mutations or the N or C terminus for epitope tags-appropriate Cas9 protospacer sequences. Subsequent steps include design and acquisition of a single-stranded oligonucleotide repair template, synthesis of a single guide RNA (sgRNA), collection of zygotes, and microinjection or electroporation of zygotes with Cas9 mRNA or protein, sgRNA, and repair template followed by screening of born mice for the presence of the desired sequence change. Quality control of mouse lines includes screening for random or multicopy insertions of the repair template and, depending on sgRNA sequence, off-target mutations introduced by Cas9. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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21
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Woodman ME, Savage CR, Arnold WK, Stevenson B. Direct PCR of Intact Bacteria (Colony PCR). ACTA ACUST UNITED AC 2018; 42:A.3D.1-A.3D.7. [DOI: 10.1002/cpmc.14] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael E. Woodman
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine Lexington Kentucky
- Present address: Michael E. Woodman, Eli Lilly and Company Indianapolis Indiana
| | - Christina R. Savage
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine Lexington Kentucky
| | - William K. Arnold
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine Lexington Kentucky
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine Lexington Kentucky
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22
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Zhang N, Ding S. Imaging of Mitochondrial and Cytosolic Ca 2+ Signals in Cultured Astrocytes. ACTA ACUST UNITED AC 2018; 82:2.29.1-2.29.11. [PMID: 29357111 DOI: 10.1002/cpns.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This unit provides a step-by-step protocol for constructing cell type- and mitochondria-targeted GCaMP genetically encoded Ca2+ indicators (GECIs) for mitochondrial Ca2+ imaging in astrocytes. Mitochondrial Ca2+ plays a critical role in controlling cytosolic Ca2+ buffering, energy metabolism, and cellular signal transduction. Mitochondrial Ca2+ overload contributes to various pathological conditions, including neurodegeneration and apoptotic cell death in neurological diseases. Live-cell mitochondrial Ca2+ imaging is an important approach to understand mitochondrial Ca2+ dynamics and thus cell physiology and pathology. We implement astrocyte-specific mitochondrial targeting of GCaMP5G/6s (mito-GCaMP5G/6s). By loading X-Rhod-1 into astrocytes, we can simultaneously image mitochondrial and cytosolic Ca2+ signals. This protocol provides a novel approach to image mitochondrial Ca2+ dynamics as well as Ca2+ interplay between the endoplasmic reticulum and mitochondria. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nannan Zhang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri
| | - Shinghua Ding
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.,Department of Bioengineering, University of Missouri, Columbia, Missouri
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23
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Ramos AE, Muñoz M, Cortés-Vecino JA, Barato P, Patarroyo MA. A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA. Parasit Vectors 2017; 10:590. [PMID: 29187255 PMCID: PMC5707868 DOI: 10.1186/s13071-017-2549-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neospora caninum is a cyst-forming, coccidian parasite which is known to cause neurological disorders in dogs and abortion and neonatal mortality in cows and other livestock. This study reports the development of a loop-mediated isothermal amplification (LAMP) assay based on the Neospora caninum Nc-5 gene and compares its efficacy for detecting DNA to that of a semi-nested PCR test. RESULTS Six primers were designed based on the Nc-5 repeat region of N. caninum. Specific LAMP primers led to successful amplification of N. caninum DNA at 63 °C in 30 min. The LAMP assay was highly specific (i.e. it did not reveal cross-reactivity with other parasite species) and had a low N. caninum plasmid DNA limit of detection (1 fg), which is ten times higher than that for the semi-nested PCR. LAMP applicability was evaluated using a set of naturally-infected samples (59 from canine faeces and five from bovine abortions). Thirty-nine percent (25/64) of the naturally-infected samples were positive for N. caninum DNA by LAMP and 36% (23/64) by semi-nested PCR. However, the LAMP assay is much faster to perform than semi-nested PCR and provides results in 30 min. CONCLUSION The optimized reaction conditions described in this study resulted in a sensitive, specific and rapid technique for detecting N. caninum DNA. Considering the advantages of LAMP for detecting N. caninum DNA, further assays aimed at testing its usefulness on a wider range of field samples are recommended.
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Affiliation(s)
- Andrea Estefanía Ramos
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | - Marina Muñoz
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | | | - Paola Barato
- Corporación Patología Veterinaria (Corpavet), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia. .,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
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24
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Gelatin nanoparticles enhance delivery of hepatitis C virus recombinant NS2 gene. PLoS One 2017; 12:e0181723. [PMID: 28746382 PMCID: PMC5528829 DOI: 10.1371/journal.pone.0181723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/06/2017] [Indexed: 01/25/2023] Open
Abstract
Background Development of an effective non-viral vaccine against hepatitis C virus infection is of a great importance. Gelatin nanoparticles (Gel.NPs) have an attention and promising approach as a viable carrier for delivery of vaccine, gene, drug and other biomolecules in the body. Aim of work The present study aimed to develop stable Gel.NPs conjugated with nonstructural protein 2 (NS2) gene of Hepatitis C Virus genotype 4a (HCV4a) as a safe and an efficient vaccine delivery system. Methods and results Gel.NPs were synthesized and characterized (size: 150±2 nm and zeta potential +17.6 mv). NS2 gene was successfully cloned and expressed into E. coli M15 using pQE-30 vector. Antigenicity of the recombinant NS2 protein was confirmed by Western blotting to verify the efficiency of NS2 as a possible vaccine. Then NS2 gene was conjugated to gelatin nanoparticles and a successful conjugation was confirmed by labeling and imaging using Confocal Laser Scanning Microscope (CLSM). Interestingly, the transformation of the conjugated NS2/Gel.NPs complex into E. coli DH5-α was 50% more efficient than transformation with the gene alone. In addition, conjugated NS2/Gel.NPs with ratio 1:100 (w/w) showed higher transformation efficiency into E. coli DH5-α than the other ratios (1:50 and 2:50). Conclusion Gel.NPs effectively enhanced the gene delivery in bacterial cells without affecting the structure of NS2 gene and could be used as a safe, easy, rapid, cost-effective and non-viral vaccine delivery system for HCV.
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25
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Fang Y, Cui L, Gu B, Arredondo F, Tyler BM. Efficient Genome Editing in the Oomycete Phytophthora sojae Using CRISPR/Cas9. ACTA ACUST UNITED AC 2017; 44:21A.1.1-21A.1.26. [PMID: 28166383 DOI: 10.1002/cpmc.25] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Phytophthora is a filamentous fungus-like microorganism, but belongs to the oomycetes, in the kingdom Stramenopila. Phytophthora species are notorious as plant destroyers, causing multibillion-dollar damage to agriculture and natural ecosystems worldwide annually. For a long time, genome editing has been unattainable in oomycetes, because of their extremely low rate of homologous recombination. The recent implementation of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system in the soybean pathogen Phytophthora sojae, an experimental model for oomycetes, has opened up a powerful new research capability for the oomycete community. Here, we describe a detailed protocol for CRISPR/Cas9-mediated genome editing in P. sojae, including single guide RNA (sgRNA) design and construction, efficient gene replacement, and mutant-screening strategies. This protocol should be generally applicable for most culturable oomycetes. We also describe an optimized transformation method that is useful for other Phytophthora spp. including P. capsici and P. parasitica. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yufeng Fang
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, Virginia.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Linkai Cui
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Biao Gu
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Felipe Arredondo
- Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
| | - Brett M Tyler
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, Virginia.,Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon
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26
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Schilit SLP, Ohtsuka M, Quadros RM, Gurumurthy CB. Pronuclear Injection-Based Targeted Transgenesis. CURRENT PROTOCOLS IN HUMAN GENETICS 2016; 91:15.10.1-15.10.28. [PMID: 27727435 PMCID: PMC5123763 DOI: 10.1002/cphg.23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Microinjection of DNA expression cassettes into fertilized zygotes has been a standard method for generating transgenic animal models. While efficient, the injected DNA integrates randomly into the genome, leading to potential disruption of endogenous genes or regulatory elements, variation in copy number, or integration into heterochromatic regions that inhibit transgene expression. A recently developed method addresses such pitfalls of traditional transgenesis by targeting the transgene to predetermined sites in the genome that can safely harbor exogenous DNA. This method, called Pronuclear Injection-based Targeted Transgenesis (PITT), employs an enzymatic transfer of exogenous DNA from a donor vector to a previously created landing-pad site in the mouse genome. DNA transfer is achieved using molecular tools such as the Cre-LoxP recombinase and PhiC31-attB/P integrase systems. Here, we provide protocols for performing PITT and an overview of the current PITT tools available to the research community. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, Nebraska
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, Nebraska
- Developmental Neuroscience, Munroe Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska
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27
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Jurišić V, Obradović J, Tošić N, Pavlović S, Kulić M, Djordjević N. Effects of DMSO, glycerol, betaine and their combinations in detecting single nucleotide polymorphisms of epidermal growth factor receptor (EGFR) gene promoter sequence in non-small-cell lung cancer (NSCLC) patients. J Pharm Biomed Anal 2016; 128:275-279. [DOI: 10.1016/j.jpba.2016.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
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28
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Wakimoto H, Seidman JG, Foo RSY, Jiang J. AAV9 Delivery of shRNA to the Mouse Heart. ACTA ACUST UNITED AC 2016; 115:23.16.1-23.16.9. [PMID: 27366889 DOI: 10.1002/cpmb.9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RNA interference (RNAi) is a rapid approach to dissect loss-of-function phenotype for a gene of interest. However, it is challenging to perform RNAi in specific organs and tissues in vivo. Engineered viruses can provide a useful tool for delivery of small RNAs in vivo. Recombinant adeno-associated viruses (rAAVs) are the preferred method for delivering genes or gene modulators to target cells due to their high titer, low immune response, ability to transduce many types of cell, and overall safety. In this unit, we describe protocols for use of rAAVs as a cargo to deliver miRNA backbone-based shRNA controlled by a cardiac-specific promoter into the mouse heart. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Roger S Y Foo
- Cardiovascular Research Institute (CVRI), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jianming Jiang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Institute (CVRI), Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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29
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Sands B, Brent R. Overview of Post Cohen-Boyer Methods for Single Segment Cloning and for Multisegment DNA Assembly. ACTA ACUST UNITED AC 2016; 113:3.26.1-3.26.20. [PMID: 27152131 DOI: 10.1002/0471142727.mb0326s113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In 1973, Cohen and coworkers published a foundational paper describing the cloning of DNA fragments into plasmid vectors. In it, they used DNA segments made by digestion with restriction enzymes and joined these in vitro with DNA ligase. These methods established working recombinant DNA technology and enabled the immediate start of the biotechnology industry. Since then, "classical" recombinant DNA technology using restriction enzymes and DNA ligase has matured. At the same time, researchers have developed numerous ways to generate large, complex, multisegment DNA constructions that offer advantages over classical techniques. Here, we provide an overview of "post-Cohen-Boyer" techniques used for cloning single segments into vectors (T/A, Topo cloning, Gateway and Recombineering) and for multisegment DNA assembly (BioBricks, Golden Gate, Gibson, yeast homologous recombination in vivo, and ligase cycling reaction). We compare and contrast these methods and also discuss issues that researchers should consider before choosing a particular multisegment DNA assembly method. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Bryan Sands
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, Washington
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30
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Abstract
Visualization of single RNA molecules in living cells has enabled the study of synthesis, movement, and localization of mRNAs and has provided insight into gene regulation with sub-second temporal resolution and nanometer spatial resolution. Following transcription in single cells indicates that gene activity is heterogeneous between cells and also exhibits random variability over time even within single cells. Studies of mRNAs in yeast can take advantage of the powerful genetics available in this model organism and allow mechanistic questions to be addressed. In this chapter, we describe an approach for visualizing mRNA and transcription in live yeast cells. The method is based on binding of fluorescently labeled MS2 and PP7 coat proteins to stem loops sequences that are introduced into the gene of interest. We give detailed protocols for the construction of the necessary yeast strains, for image acquisition, and for validation.
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Affiliation(s)
- Tineke L Lenstra
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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31
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Wyatt LS, Earl PL, Moss B. Generation of Recombinant Vaccinia Viruses. CURRENT PROTOCOLS IN MICROBIOLOGY 2015; 39:14A.4.1-14A.4.18. [PMID: 26528782 PMCID: PMC5123791 DOI: 10.1002/9780471729259.mc14a04s39] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This unit describes how to infect cells with vaccinia virus and then transfect them with a plasmid-transfer vector or PCR fragment to generate a recombinant virus. Selection and screening methods used to isolate recombinant viruses and a method for the amplification of recombinant viruses are described. Finally, a method for live immunostaining that has been used primarily for detection of recombinant modified vaccinia virus Ankara (MVA) is presented.
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Affiliation(s)
- Linda S Wyatt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Patricia L Earl
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bernard Moss
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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32
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Hendriks WT, Jiang X, Daheron L, Cowan CA. TALEN- and CRISPR/Cas9-Mediated Gene Editing in Human Pluripotent Stem Cells Using Lipid-Based Transfection. ACTA ACUST UNITED AC 2015; 34:5B.3.1-5B.3.25. [PMID: 26237572 DOI: 10.1002/9780470151808.sc05b03s34] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Using custom-engineered nuclease-mediated genome editing, such as Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) RNA-guided Cas9 nucleases, human pluripotent stem cell (hPSC) lines with knockout or mutant alleles can be generated and differentiated into various cell types. This strategy of genome engineering in hPSCs will prove invaluable for studying human biology and disease. Here, we provide a detailed protocol for design and construction of TALEN and CRISPR vectors, testing of their nuclease activity, and delivery of TALEN or CRISPR vectors into hPSCs. In addition, we describe the use of single-stranded oligodeoxynucleotides (ssODNs) to introduce or repair point mutations. Next, we describe the identification of edited hPSC clones without antibiotic selection, including their clonal selection, genotyping, and expansion for downstream applications.
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Affiliation(s)
- William T Hendriks
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xin Jiang
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Laurence Daheron
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Chad A Cowan
- Harvard University, Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
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33
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Abstract
The large-scale production of recombinant G protein-coupled receptors (GPCRs) is one of the major bottlenecks that hamper functional and structural studies of this important class of integral membrane proteins. Heterologous overexpression of GPCRs often results in low yields of active protein, usually due to a combination of several factors, such as low expression levels, protein insolubility, host cell toxicity, and the need to use harsh and often denaturing detergents (e.g., SDS, LDAO, OG, and DDM, among others) to extract the recombinant receptor from the host cell membrane. Many of these problematic issues are inherently linked to cell-based expression systems and can therefore be circumvented by the use of cell-free systems. In this unit, we provide a range of protocols for the production of GPCRs in a cell-free expression system. Using this system, we typically obtain GPCR expression levels of ∼1 mg per ml of reaction mixture in the continuous-exchange configuration. Although the protocols in this unit have been optimized for the cell-free expression of GPCRs, they should provide a good starting point for the production of other classes of membrane proteins, such as ion channels, aquaporins, carrier proteins, membrane-bound enzymes, and even large molecular complexes.
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Affiliation(s)
- Kenneth Segers
- VIB Center for the Biology of Disease, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.,Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
| | - Stefan Masure
- Structural Biology Group, Biologics Research Europe, Janssen Research & Development, Beerse, Belgium
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34
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Gratz SJ, Rubinstein CD, Harrison MM, Wildonger J, O'Connor-Giles KM. CRISPR-Cas9 Genome Editing in Drosophila. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2015; 111:31.2.1-31.2.20. [PMID: 26131852 PMCID: PMC4506758 DOI: 10.1002/0471142727.mb3102s111] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The CRISPR-Cas9 system has transformed genome engineering of model organisms from possible to practical. CRISPR-Cas9 can be readily programmed to generate sequence-specific double-strand breaks that disrupt targeted loci when repaired by error-prone non-homologous end joining (NHEJ) or to catalyze precise genome modification through homology-directed repair (HDR). Here we describe a streamlined approach for rapid and highly efficient engineering of the Drosophila genome via CRISPR-Cas9-mediated HDR. In this approach, transgenic flies expressing Cas9 are injected with plasmids to express guide RNAs (gRNAs) and positively marked donor templates. We detail target-site selection; gRNA plasmid generation; donor template design and construction; and the generation, identification, and molecular confirmation of engineered lines. We also present alternative approaches and highlight key considerations for experimental design. The approach outlined here can be used to rapidly and reliably generate a variety of engineered modifications, including genomic deletions and replacements, precise sequence edits, and incorporation of protein tags.
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Affiliation(s)
- Scott J Gratz
- Genetics Training Program, University of Wisconsin-Madison, Madison, Wisconsin
| | - C Dustin Rubinstein
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Kate M O'Connor-Giles
- Genetics Training Program, University of Wisconsin-Madison, Madison, Wisconsin
- Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin
- Corresponding author: Kate M. O'Connor-Giles
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35
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Kaposi Sarcoma Herpesvirus Induces HO-1 during De Novo Infection of Endothelial Cells via Viral miRNA-Dependent and -Independent Mechanisms. mBio 2015; 6:e00668. [PMID: 26045540 PMCID: PMC4462627 DOI: 10.1128/mbio.00668-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Kaposi sarcoma (KS) herpesvirus (KSHV) infection of endothelial cells (EC) is associated with strong induction of heme oxygenase-1 (HO-1), a stress-inducible host gene that encodes the rate-limiting enzyme responsible for heme catabolism. KS is an angioproliferative tumor characterized by the proliferation of KSHV-infected spindle cells, and HO-1 is highly expressed in such cells. HO-1 converts the pro-oxidant, proinflammatory heme molecule into metabolites with antioxidant, anti-inflammatory, and proliferative activities. Previously published work has shown that KSHV-infected EC in vitro proliferate in response to free heme in a HO-1-dependent manner, thus implicating virus-enhanced HO-1 activity in KS tumorigenesis. The present study investigated the molecular mechanisms underlying KSHV induction of HO-1 in lymphatic EC (LEC), which are the likely spindle cell precursors. In a time course analysis of KSHV-infected cells, HO-1 expression displays biphasic kinetics characterized by an early transient induction that is followed by a more sustained upregulation coincident with the establishment of viral latency. A viral microRNA miR-K12-11 deletion mutant of KSHV was found to be defective for induction of HO-1 during latency. A potential mechanism for this phenotype was provided by BACH1, a cellular HO-1 transcriptional repressor targeted by miR-K12-11. In fact, in KSHV-infected LEC, the BACH1 message level is reduced, BACH1 subcellular localization is altered, and miR-K12-11 mediates the inverse regulation of HO-1 and BACH1 during viral latency. Interestingly, the data indicate that neither miR-K12-11 nor de novo KSHV gene expression is required for the burst of HO-1 expression observed at early times postinfection, which suggests that additional virion components promote this phenotype. While the mechanisms underlying KSHV induction of HO-1 remain unknown, the cellular mechanisms that regulate HO-1 expression have been extensively investigated in the context of basal and pathophysiological states. The detoxifying action of HO-1 is critical for the protection of cells exposed to high heme levels. KS spindle cells are erythrophagocytic and contain erythrocyte ghosts. Erythrocyte degeneration leads to the localized release of heme, creating oxidative stress that may be further exacerbated by environmental or other cofactors. Our previous work showed that KSHV-infected cells proliferate in response to heme and that this occurs in a HO-1-dependent manner. We therefore hypothesize that KSHV induction of HO-1 contributes to KS tumor development via heme metabolism and propose that HO-1 be evaluated as a therapeutic target for KS. Our present work, which aimed to understand the mechanisms whereby KSHV induces HO-1, will be important for the design and implementation of such a strategy.
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36
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Conte D, MacNeil LT, Walhout AJ, Mello CC. RNA Interference in Caenorhabditis elegans. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2015; 109:26.3.1-26.3.30. [PMID: 25559107 PMCID: PMC5396541 DOI: 10.1002/0471142727.mb2603s109] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNAi has become an essential tool in C. elegans research. This unit describes procedures for RNAi in C. elegans by microinjecting with dsRNA, feeding with bacteria expressing dsRNA, and soaking in dsRNA solution, as well as high-throughput methods for RNAi-based screens.
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Affiliation(s)
- Darryl Conte
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lesley T. MacNeil
- Programs in Systems Biology and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Albertha J.M. Walhout
- Programs in Systems Biology and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Craig C. Mello
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
- Howard Hughes Medical Institute
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Nishimura K, Kanemaki MT. Rapid Depletion of Budding Yeast Proteins via the Fusion of an Auxin-Inducible Degron (AID). ACTA ACUST UNITED AC 2014; 64:20.9.1-16. [PMID: 25181302 DOI: 10.1002/0471143030.cb2009s64] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The auxin-inducible degron (AID) system allows the rapid and reversible proteolysis of proteins of interest, and enables the generation of conditional mutants of budding yeast. The construction of budding yeast AID mutants is simple, and the effect of depletion of essential proteins on proliferation can be confirmed by analyzing their phenotype. In this protocol, we describe a procedure to generate AID mutants of budding yeast via a simple transformation using PCR-amplified DNA. We also describe methods to confirm the depletion of proteins of interest that are required for proliferation by serial-dilution and liquid-culture assays.
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Affiliation(s)
- Kohei Nishimura
- Center of Frontier Research, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka, Japan
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38
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Wang G, Liveris D, Mukherjee P, Jungnick S, Margos G, Schwartz I. Molecular Typing of Borrelia burgdorferi. CURRENT PROTOCOLS IN MICROBIOLOGY 2014; 34:12C.5.1-31. [PMID: 25082003 PMCID: PMC4317198 DOI: 10.1002/9780471729259.mc12c05s34] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens.
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Affiliation(s)
- Guiqing Wang
- Department of Pathology, New York Medical College, Valhalla, New York
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39
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Wang W, Pan Z, Hu X, Li Z, Zhao Y, Yu AX. Vacuum-assisted closure increases ICAM-1, MIF, VEGF and collagen I expression in wound therapy. Exp Ther Med 2014; 7:1221-1226. [PMID: 24940415 PMCID: PMC3991501 DOI: 10.3892/etm.2014.1567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/04/2014] [Indexed: 12/13/2022] Open
Abstract
Severe traumatic wounds are challenging to manage during surgery. The introduction of vacuum-assisted closure (VAC) is a breakthrough in wound management. The aim of the present study was to investigate the effect of VAC on cytokines in wounds during the management of severe traumatic wounds following initial debridement. VAC and conventional wound care (CWC) were independently applied to severe traumatic wounds on pigs. The expression levels of intercellular adhesion molecule-1 (ICAM-1), migration inhibitory factor (MIF), vascular endothelial growth factor (VEGF), basic fibroblast growth factor, collagen I and human fibroblast collagenase 1 were detected by quantitative polymerase chain reaction and western blotting. VAC significantly increased the expression of ICAM-1, MIF, VEGF and collagen I compared with that induced by CWC at the protein and mRNA levels. Therefore, the results of the present study indicate that VAC therapy is an effective method for treating severe traumatic wounds, as it increases the expression of cytokines in wounds. VAC significantly increases the expression of ICAM-1, MIF, VEGF and collagen I to manage severe traumatic wounds.
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Affiliation(s)
- Weiyang Wang
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zhenyu Pan
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiang Hu
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zonghuan Li
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yong Zhao
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Ai-Xi Yu
- Department of Micro-Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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40
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Jones JR. Nonrandom X chromosome inactivation detection. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 80:9.7.1-9.7.7. [PMID: 24510685 DOI: 10.1002/0471142905.hg0907s80] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
X chromosome inactivation patterns may be clinically useful in assessing tumor clonality, determining carrier status for certain X-linked disorders and evaluating the pathogenicity of a genetic variant identified in an X-linked gene. The protocols in this unit utilize the highly polymorphic trinucleotide repeat within the first exon of the human androgen receptor gene (AR) and the methylation-sensitive restriction enzyme HpaII to distinguish between the maternal and paternal alleles and simultaneously determine their methylation status. The data obtained from these protocols can be used to calculate the ratio of inactivation between the two alleles that ultimately reflects whether a female has a random or nonrandom pattern of X chromosome inactivation.
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Affiliation(s)
- Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
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41
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Basehore MJ, Friez MJ. Molecular analysis of fragile X syndrome. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 80:9.5.1-9.5.19. [PMID: 24510684 DOI: 10.1002/0471142905.hg0905s80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The gene responsible for Fragile X syndrome, fragile X mental retardation-1 (FMR1), contains an unstable sequence of CGG trinucleotide repeats in its promoter region. Expansions of >200 trinucleotide repeats are considered full mutations and typically lead to abnormal methylation of the region, resulting in loss of FMR1 expression. Males with loss of FMR1 protein are expected to be affected by Fragile X syndrome, while females may or may not clinically manifest features of the condition. The protocols in this unit outline the complementary use of polymerase chain reaction (PCR) and methylation-sensitive Southern blot hybridization to accurately measure trinucleotide repeat size and methylation status. These protocols are also used to evaluate CGG repeat size in two adult-onset conditions known for their association with FMR1 premutation alleles, Fragile X Tremor/Ataxia (FXTAS) syndrome and Premature Ovarian Failure (POF).
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42
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Obradovic J, Jurisic V, Tosic N, Mrdjanovic J, Perin B, Pavlovic S, Djordjevic N. Optimization of PCR conditions for amplification of GC-Rich EGFR promoter sequence. J Clin Lab Anal 2013; 27:487-93. [PMID: 24218132 PMCID: PMC6807403 DOI: 10.1002/jcla.21632] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/07/2013] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Polymerase chain reaction (PCR) is an extremely sensitive method that often demands optimization, especially when difficult templates need to be amplified. The aim of the present study was to optimize the PCR conditions for amplification of the epidermal growth factor receptor (EGFR) promoter sequence featuring an extremely high guanine-cytosine (GC) content in order to detect single nucleotide polymorphisms -216G>T and -191C>A. METHODS Genomic DNA used for amplification was extracted from formalin-fixed paraffin-embedded lung tumor tissue and PCR products were detected by agarose gel electrophoresis. RESULTS Results showed that addition of 5% dimethyl sulfoxide (DMSO), as well as DNA concentration in PCR reaction of at least 2 μg/ml, were necessary for successful amplification. Due to high GC content, optimal annealing temperature was 7°C higher than calculated, while adequate MgCl2 concentration ranged from 1.5 to 2.0 mM. CONCLUSION In conclusion, EGFR promoter region is a difficult PCR target, but it could be amplified after optimization of MgCl2 concentration and annealing temperature in the presence of DMSO and the DNA template of acceptable concentration.
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Affiliation(s)
- Jasmina Obradovic
- Faculty of Medical SciencesUniversity of KragujevacKragujevacSerbia
- Faculty of ScienceInstitute of Biology and EcologyUniversity of KragujevacKragujevacSerbia
| | - Vladimir Jurisic
- Faculty of Medical SciencesUniversity of KragujevacKragujevacSerbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
| | - Jasminka Mrdjanovic
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi SadSremska KamenicaSerbia
| | - Branislav Perin
- Institute for Pulmonary Diseases of VojvodinaClinic for Pulmonary OncologyFaculty of MedicineUniversity of Novi SadSremska KamenicaSerbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic EngineeringUniversity of BelgradeBelgradeSerbia
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43
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science, Graduate School of ScienceOsaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of ScienceOsaka Prefecture University Osaka Japan
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Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. ACTA ACUST UNITED AC 2013; 4:275-97. [PMID: 23788555 DOI: 10.1002/9780470559277.ch120019] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Knowledge of RNA structure is critical to understanding both the important functional roles of RNA in biology and the engineering of RNA to control biological systems. This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment. This protocol is applicable in a variety of conditions, and represents an important tool for understanding RNA biology. The protocol includes methods for the design and synthesis of RNA mixtures for study, and the construction and analysis of structure-dependent sequencing libraries that reveal structural information of the RNAs in the mixtures. The methods are generally applicable to studying RNA structure and interactions in vitro in a variety of conditions, and allows for the rapid characterization of RNA structures in a high-throughput manner. Curr. Protoc. Chem. Biol. 4:275-297 © 2012 by John Wiley & Sons, Inc.
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Affiliation(s)
- Stefanie A Mortimer
- Department of Molecular and Cell Biology, University of California, Berkeley, California
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45
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Huq A, Haley BJ, Taviani E, Chen A, Hasan NA, Colwell RR. Detection, isolation, and identification of Vibrio cholerae from the environment. ACTA ACUST UNITED AC 2012; Chapter 6:Unit6A.5. [PMID: 22875567 DOI: 10.1002/9780471729259.mc06a05s26] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recent molecular advances in microbiology have greatly improved the detection of bacterial pathogens in the environment. These improvements and a downward trend in the cost of molecular detection methods have contributed to increased frequency of detection of pathogenic microorganisms where traditional culture-based detection methods have failed. Culture methods also have been greatly improved, and the confluence of the two suites of methods provides a powerful tool for detection, isolation, and characterization of pathogens. While molecular detection provides data on the presence and type of pathogens, culturing methods allow a researcher to preserve the organism of interest for "-omics" studies, such as genomic, metabolomic, secretomic, and transcriptomic analysis, which are rapidly becoming more affordable. This has yielded a clearer understanding of the ecology and epidemiology of microorganisms that cause disease. In this unit, we present commonly accepted methods for isolation, detection, and characterization of V. cholerae, providing more extensive knowledge of the ecology and epidemiology of this organism. This unit has been fully revised and updated from the earlier version with the latest knowledge and additional information not previously included.
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Affiliation(s)
- Anwar Huq
- Maryland Pathogen Research Institute, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, Maryland, USA
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46
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Holland MM. Molecular analysis of the human mitochondrial DNA control region for forensic identity testing. CURRENT PROTOCOLS IN HUMAN GENETICS 2012; Chapter 14:Unit14.7. [PMID: 22786611 DOI: 10.1002/0471142905.hg1407s74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit highlights methods used to perform PCR amplification and sequence analysis of mitochondrial DNA (mtDNA) on pristine and highly degraded biological material. The focus is on applications to forensic casework, and a number of case examples are provided. Any laboratory working with DNA from old or "ancient" samples will benefit from this information.
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47
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. ACTA ACUST UNITED AC 2012; Chapter 17:17.3.1-17.3.35. [PMID: 22161546 DOI: 10.1002/0471143030.cb1703s53] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
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48
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Karginov AV, Hahn KM. Allosteric activation of kinases: design and application of RapR kinases. ACTA ACUST UNITED AC 2012; Chapter 14:14.13.1-14.13.16. [PMID: 22161545 DOI: 10.1002/0471143030.cb1413s53] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here we describe a method for the engineered regulation of protein kinases in living cells, the design and application of RapR (rapamycin regulated) kinases. The RapR kinase method enables activation of kinases with high specificity and precise temporal control. Insertion of an engineered allosteric switch, the iFKBP domain, at a structurally conserved position within the kinase catalytic domain makes the modified kinase inactive. Treatment with rapamycin or its non-immunosuppressive analogs triggers interaction with a small FKBP-rapamycin-binding domain (FRB), restoring the activity of the kinase. The reagents used in this method are genetically encoded or membrane permeable, enabling ready application in many systems. Based on the structural similarity of kinase catalytic domains, this method is likely applicable to a wide variety of kinases. Successful regulation has already been demonstrated for three kinases representing both tyrosine and serine/threonine kinase families (p38, FAK, Src). Procedures for designing and testing RapR kinases are discussed.
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Affiliation(s)
- Andrei V Karginov
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Golemis EA, Serebriiskii I, Finley RL, Kolonin MG, Gyuris J, Brent R. Interaction trap/two-hybrid system to identify interacting proteins. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.4. [PMID: 21462161 DOI: 10.1002/0471142301.ns0404s55] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The yeast two-hybrid method (or interaction trap) is a powerful technique for detecting protein interactions. The procedure is performed using transcriptional activation of a dual reporter system in yeast to identify interactions between a protein of interest (the bait protein) and the candidate proteins for interaction. The method can be used to screen a protein library for interactions with a bait protein or to test for association between proteins that are expected to interact based on prior evidence. Interaction mating facilitates the screening of a library with multiple bait proteins.
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Affiliation(s)
- Erica A Golemis
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA. EA
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Karched M, Furgang D, Sawalha N, Fine DH. Rapid identification of oral isolates of Aggregatibacter actinomycetemcomitans obtained from humans and primates by an ultrafast super convection based polymerase chain reaction. J Microbiol Methods 2012; 89:71-5. [PMID: 22326236 DOI: 10.1016/j.mimet.2012.01.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/23/2012] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
Abstract
Aggregatibacter actinomycetemcomitans is a Gram negative oral bacterium associated with localized aggressive periodontitis (LAP). Detection of A. actinomycetemcomitans in clinical samples is routinely done by PCR. Our aim was to develop a rapid and reliable PCR method that can be used as a chair-side tool to detect A. actinomycetemcomitans in clinical samples. Sensitivity and specificity assessment was performed on buccal and plaque samples obtained from 40 adolescents enrolled in an ongoing LAP study by comparing 20 A. actinomycetemcomitans-positive subjects and 20 who were negative. In a second study, A. actinomycetemcomitans presence was tested in oral samples from eighty-six primates that included rhesus monkeys, chimpanzees, marmosets, tamarins and baboons. All samples were processed for detection of A. actinomycetemcomitans by means of culture, conventional PCR (cPCR) and rapid PCR (rPCR) using a Super Convection based AmpXpress thermal cycler (AlphaHelix, Sweden). For human samples, culture, cPCR and rPCR showed perfect agreement. Using this method A. actinomycetemcomitans was detected in 27 of 32 rhesus monkeys, 4 of 8 chimpanzees and 1 of 34 marmosets. Rapidity of AmpXpress thermal cycler, combined with Ready-To-Go PCR beads (GE Life sciences), a quick DNA extraction kit (Epicentre Biotechnologies, Madison, Wisconsin, USA) and a bufferless fast agarose gel system, made it possible to obtain results on A. actinomycetemcomitans detection within 35 min. We conclude that AmpXpress fast PCR can be conveniently used as a chair-side tool for rapid detection of A. actinomycetemcomitans in clinical samples.
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Affiliation(s)
- M Karched
- Department of Oral Biology, New Jersey Dental School, University of Medicine & Dentistry of New Jersey, Newark, New Jersey, USA
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