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Weber E. Setup and Applications of Modular Protein Expression Toolboxes (MoPET) for Mammalian Systems. Methods Mol Biol 2024; 2774:15-29. [PMID: 38441755 DOI: 10.1007/978-1-0716-3718-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The design and generation of an optimal protein expression construct is the first and essential step in the characterization of any protein of interest. However, the exchange and modification of the coding and/or noncoding elements to analyze their effect on protein function or generating the optimal result can be a tedious and time-consuming process using standard molecular biology cloning methods. To streamline the process to generate defined expression constructs or libraries of otherwise difficult to express proteins, the Modular Protein Expression Toolbox (MoPET) has been developed (Weber E, PloS One 12(5):e0176314, 2017). The system applies Golden Gate cloning as an assembly method and follows the standardized modular cloning (MoClo) principle (Weber E, PloS One 6(2):e16765, 2011). This cloning platform allows highly efficient DNA assembly of pre-defined, standardized functional DNA modules effecting protein expression with a focus on minimizing the cloning burden in coding regions. The original MoPET system consists of 53 defined DNA modules divided into eight functional main classes and can be flexibly expanded dependent on the need of the experimenter and expression host. However, already with a limited set of only 53 modules, 792,000 different constructs can be rationally designed or used to generate combinatorial expression optimization libraries. We provide here a detailed protocol for the (1) design and generation of level 0 basic parts, (2) generation of defined expressions constructs, and (3) generation of combinatorial expression libraries.
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Affiliation(s)
- Ernst Weber
- Molecular Design & Engineering, Biologics Research, Bayer AG, Wuppertal, Germany.
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2
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Wang Y, Zhang R, Pu Y, Wang D, Wang Y, Wu X, Pan Y, Luo C, Zhao G, Quan Z, Zheng Y. Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project. Phenomics 2023; 3:300-308. [PMID: 37325707 PMCID: PMC10260709 DOI: 10.1007/s43657-023-00097-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00097-y.
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Affiliation(s)
- Yetong Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Ruyi Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Danqi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yanren Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Xuemei Wu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yujie Pan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Chen Luo
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200433 China
- Department of Cardiology, Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, 1609 Xietu Road, Shanghai, 200032 China
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3
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Rossotti MA, Trempe F, van Faassen H, Hussack G, Arbabi-Ghahroudi M. Isolation and Characterization of Single-Domain Antibodies from Immune Phage Display Libraries. Methods Mol Biol 2023; 2702:107-147. [PMID: 37679618 DOI: 10.1007/978-1-0716-3381-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Naturally occurring heavy chain antibodies (HCAbs) in Camelidae species were a surprise discovery in 1993 by Hamers et al. Since that time, antibody fragments derived from HCAbs have garnered considerable attention by researchers and biotechnology companies. Due to their biophysico-chemical advantages over conventional antibody fragments, camelid single-domain antibodies (sdAbs, VHHs, nanobodies) are being increasingly utilized as viable immunotherapeutic modalities. Currently there are multiple VHH-based therapeutic agents in different phases of clinical trials in various formats such as bi- and multivalent, bi- and multi-specific, CAR-T, and antibody-drug conjugates. The first approved VHH, a bivalent humanized VHH (caplacizumab), was approved for treating rare blood clotting disorders in 2018 by the EMA and the FDA in 2019. This was followed by the approval of an anti-BCMA VHH-based CAR-T cell product in 2022 (ciltacabtagene autoleucel; CARVYKTI™) and more recently a trivalent antitumor necrosis factor alpha-based VHH drug (ozoralizumab; Nanozora®) in Japan for the treatment of rheumatoid arthritis. In this chapter we provide protocols describing the latest developments in isolating antigen-specific VHHs including llama immunization, construction of phage-displayed libraries, phage panning and screening of the soluble VHHs by ELISA, affinity measurements by surface plasmon resonance, functional cell binding by flow cytometry, and additional validation by immunoprecipitation. We present and discuss comprehensive, step-by-step methods for isolating and characterization of antigen-specific VHHs. This includes protocols for expression, biotinylation, purification, and characterization of the isolated VHHs. To demonstrate the feasibility of the entire strategy, we present examples of VHHs previously isolated and characterized in our laboratory.
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Affiliation(s)
- Martin A Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Frederic Trempe
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
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4
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Payet R, Billmeier M. Small RNA Profiling by Next-Generation Sequencing Using High-Definition Adapters. Methods Mol Biol 2023; 2630:103-115. [PMID: 36689179 DOI: 10.1007/978-1-0716-2982-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Next-generation sequencing (NGS) of small RNA (sRNA) cDNA libraries permits the identification and characterization of sRNA species de novo. However, the method through which these libraries are constructed can often introduce artifacts such as over- or underrepresentation of specific sequences or adapter oligonucleotides due to sequence biases held by the enzymes used. In this chapter we describe a protocol for sRNA library construction making use of high-definition (HD) adapters for the Illumina sequencing platform, which reduce ligation bias. This protocol leads to drastically reduced direct 5'/3' adapter ligation products and can be used for the synthesis of sRNA libraries from total RNA or sRNA of various plant, animal, and fungal samples. This protocol also includes a method for total RNA extraction from plant leaf and cultured cells or body fluids.
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Affiliation(s)
- Rocky Payet
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Martina Billmeier
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
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Huang RR, Kierny M, Volgina V, Iwashima M, Miller C, Kay BK. Construction of an Ultra-Large Phage Display Library by Kunkel Mutagenesis and Rolling Circle Amplification. Methods Mol Biol 2023; 2702:205-226. [PMID: 37679621 DOI: 10.1007/978-1-0716-3381-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
An important contributor to the successful generation of recombinant affinity reagents via phage display is a large and diverse library. We describe, herein, the application of Kunkel mutagenesis and rolling circle amplification (RCA) to the construction of a 1.1 × 1011 member library, with only 26 electroporations, and isolation of low- to sub-nanomolar monobodies to a number of protein targets, including human COP9 signalosome subunit 5 (COPS5), HIV-1 Rev. binding protein-like protein (HRBL), X-ray repair cross-complementing 5/6 (Ku70/80) heterodimer, the receptor-binding domain (RBD) of SARS-CoV-2, and transforming growth factor beta 1 (TGF-β1).
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Affiliation(s)
| | | | - Veronica Volgina
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Makio Iwashima
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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6
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Handal-Marquez P, Koch M, Kestemont D, Arangundy-Franklin S, Pinheiro VB. Antha-Guided Automation of Darwin Assembly for the Construction of Bespoke Gene Libraries. Methods Mol Biol 2022; 2461:43-66. [PMID: 35727443 DOI: 10.1007/978-1-0716-2152-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein engineering through directed evolutison is facilitated by the screening and characterization of protein libraries. Efficient and effective methods for multiple site-saturation mutagenesis, such as Darwin Assembly, can accelerate the sampling of relevant sequence space and the identification of variants with desired functionalities. Here, we present the automation of the Darwin Assembly method, using a Gilson PIPETMAX™ liquid handling platform under the control of the Antha software platform, which resulted in the accelerated construction of complex, multiplexed gene libraries error-free and with minimal hands-on time, while maintaining flexibility over experimental parameters through a graphical user interface rather than requiring user-driven library-dependent programming of the liquid handling platform. We also present an approach for barcoding libraries that overcomes amplicon length limitations in next generation sequencing and enables fast reconstruction of library reads.
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Affiliation(s)
| | - M Koch
- Synthace Ltd., London, UK
| | | | - S Arangundy-Franklin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Sangamo Therapeutics Inc., Brisbane, CA, USA
| | - V B Pinheiro
- Rega Institute, KU Leuven, Leuven, Belgium.
- Institute of Structural and Molecular Biology, University College London, London, UK.
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7
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Vogt S, Stadlmayr G, Stadlbauer K, Stracke F, Bobbili MR, Grillari J, Rüker F, Wozniak-Knopp G. Construction of Yeast Display Libraries for Selection of Antigen-Binding Variants of Large Extracellular Loop of CD81, a Major Surface Marker Protein of Extracellular Vesicles. Methods Mol Biol 2022; 2491:561-592. [PMID: 35482205 DOI: 10.1007/978-1-0716-2285-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last two decades, yeast display methodology has served as a popular tool for discovery, humanization, stability improvement, and affinity maturation of antibodies and antibody fragments, but also for development of diverse non-antibody protein scaffolds towards the ability of antigen recognition. Yeast display is particularly well suited for multiparametric analysis of properties of derivatized proteins, allowing the evolution of most diverse protein structures into antigen binding entities with favorable expression, stability, and folding properties. Here we present the methodological basics of a novel yeast display-based approach for the functionalization of the large extracellular loop of CD81 into a de novo antigen binding unit. CD81 is intrinsically overrepresented on the surface of extracellular vesicles (EVs), naturally occurring nanoparticle units that act as cell-to-cell messengers by delivering their intracellular cargo from the source cell into a recipient cell. This amazing feature makes them of highest biotechnological interest, yet methods for their targeted delivery are still in their infancy. As a novel approach for introducing EV surface modifications enabling specific target cell recognition and internalization, we have prepared yeast display libraries of CD81 large extracellular loop mutants, which are selected towards specific antigen binding and resulting mutants conveniently clicked into the full-length EV surface protein. Resulting EVs display wild-type-like characteristics regarding the expression level and distribution of recombinant proteins and are hence promising therapeutic tools.
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Affiliation(s)
- Stefan Vogt
- acib GmbH (Austrian Centre of Industrial Biotechnology), Graz, Austria
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Gerhard Stadlmayr
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Katharina Stadlbauer
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Florian Stracke
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Madhusudhan Reddy Bobbili
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Research Center, Vienna, Austria
| | - Johannes Grillari
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Research Center, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Florian Rüker
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Gordana Wozniak-Knopp
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria.
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8
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Tourlousse DM, Narita K, Miura T, Sakamoto M, Ohashi A, Shiina K, Matsuda M, Miura D, Shimamura M, Ohyama Y, Yamazoe A, Uchino Y, Kameyama K, Arioka S, Kataoka J, Hisada T, Fujii K, Takahashi S, Kuroiwa M, Rokushima M, Nishiyama M, Tanaka Y, Fuchikami T, Aoki H, Kira S, Koyanagi R, Naito T, Nishiwaki M, Kumagai H, Konda M, Kasahara K, Ohkuma M, Kawasaki H, Sekiguchi Y, Terauchi J. Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements. Microbiome 2021; 9:95. [PMID: 33910647 PMCID: PMC8082873 DOI: 10.1186/s40168-021-01048-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/12/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. RESULTS In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. CONCLUSIONS The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.
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Affiliation(s)
- Dieter M Tourlousse
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Koji Narita
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Chitose Laboratory Corp., Kawasaki, Kanagawa, 216-0041, Japan
| | - Takamasa Miura
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Akiko Ohashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Keita Shiina
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Masami Matsuda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Daisuke Miura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Mamiko Shimamura
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yoshifumi Ohyama
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Atsushi Yamazoe
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yoshihito Uchino
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Keishi Kameyama
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Institute of Food Sciences and Technologies, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Shingo Arioka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Jiro Kataoka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Japan Tobacco Inc., Minato, Tokyo, 105-6927, Japan
| | - Takayoshi Hisada
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- TechnoSuruga Laboratory Co., Ltd., Shizuoka, Shizuoka, 424-0065, Japan
| | - Kazuyuki Fujii
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Infectious Diseases Unit, Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Tokushima, 771-0192, Japan
| | - Shunsuke Takahashi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- TechnoSuruga Laboratory Co., Ltd., Shizuoka, Shizuoka, 424-0065, Japan
| | - Miho Kuroiwa
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Masatomo Rokushima
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Laboratory for Innovative Therapy Research, Shionogi and Co., Ltd., Toyonaka, Osaka, 561-0825, Japan
| | - Mitsue Nishiyama
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Tsumura Kampo Research Laboratories, Tsumura & Co., Ami, Ibaraki, 300-1192, Japan
| | - Yoshiki Tanaka
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Biofermin Pharmaceutical Co., Ltd., Kobe, Hyogo, 650-0021, Japan
| | - Takuya Fuchikami
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Hitomi Aoki
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Satoshi Kira
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- CDM Center Division 4, Takara Bio Inc., Kusatsu, Shiga, 525-0058, Japan
| | - Ryo Koyanagi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Molecular Genetic Research Department, Advanced Technology Center, LSI Medience Corporation, Chiyoda, Tokyo, 101-8517, Japan
| | - Takeshi Naito
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- H.U. Group Research Institute G.K., Hachioji, Tokyo, 192-0031, Japan
| | - Morie Nishiwaki
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- H.U. Group Research Institute G.K., Hachioji, Tokyo, 192-0031, Japan
| | - Hirotaka Kumagai
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- JSR-Keio University Medical and Chemical Innovation Center, Shinjuku, Tokyo, 160-8582, Japan
| | - Mikiko Konda
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- JSR-Keio University Medical and Chemical Innovation Center, Shinjuku, Tokyo, 160-8582, Japan
| | - Ken Kasahara
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan
- Chitose Laboratory Corp., Kawasaki, Kanagawa, 216-0041, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroko Kawasaki
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, 292-0818, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan.
| | - Jun Terauchi
- Japan Microbiome Consortium (JMBC), Osaka, Osaka, 530-0011, Japan.
- Ono Pharmaceutical Co., Ltd., Osaka, Osaka, 541-8564, Japan.
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Abstract
RNA silencing plays a critical role in diverse biological processes in plants including growth, development, and responses to abiotic and biotic stresses. RNA silencing is guided by small non-coding RNAs (sRNAs) with the length of 21-24 nucleotides (nt) that are loaded into Argonaute (AGO) to repress expression of target loci and transcripts through transcriptional or posttranscriptional gene silencing mechanisms. Identification and quantitative characterization of sRNAs are crucial steps toward appreciation of their functions in biology. Here, we developed a step-by-step protocol to precisely illustrate the process of cloning of sRNA libraries and correspondingly computational analysis of the recovered sRNAs. This protocol can be used in all kinds of organisms, including Arabidopsis, and is compatible with various high-throughput sequence technologies such as Illumina Hiseq. Thus, we wish that this protocol represents an accurate way to identify and quantify sRNAs in vivo.
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Affiliation(s)
- Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- Graduate Program for Molecular and Environmental Plant Science, Texas A&M University, College Station, TX, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
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10
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Ouyang SQ, Park G, Ji HM, Borkovich KA. Small RNA Isolation and Library Construction for Expression Profiling of Small RNAs from Neurospora crassa and Fusarium oxysporum and Analysis of Small RNAs in Fusarium oxysporum-Infected Plant Root Tissue. Methods Mol Biol 2021; 2170:199-212. [PMID: 32797460 DOI: 10.1007/978-1-0716-0743-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Due to crucial roles in gene regulation, noncoding small RNAs (sRNAs) of 20-30 nucleotides (nt) have been intensively studied in mammals and plants and are implicated in significant diseases and metabolic disorders. Elucidation of biogenesis mechanisms and functional characterization of sRNAs is often achieved using tools such as separation of small-sized RNA and deep sequencing. Although RNA interference pathways, such as quelling and meiotic silencing, have been well-described in Neurospora crassa, knowledge of sRNAs in other filamentous fungi is still limited compared to other eukaryotes. As a prerequisite for study, isolation and sequence analysis of sRNAs is necessary. We developed a protocol for isolation and library construction of sRNAs of 20-30 nt for deep sequencing in two filamentous fungi, N. crassa and Fusarium oxysporum f.sp. lycopersici. Using 200-300 μg total RNA, sRNA was isolated by size-fractionation and ligated with adapters and amplified by RT-PCR for deep sequencing. Sequence analysis of several cDNA clones showed that the cloned sRNAs were not tRNAs and rRNAs and were fungal genome-specific. In order to validate fungal miRNAs that were imported into the host cell, we developed a straightforward method to isolate protoplasts from tomato roots infected by Fusarium oxysporum f.sp. lycopersici using enzymatic digestion.
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Affiliation(s)
- Shou-Qiang Ouyang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China. .,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China and Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.
| | - Gyungsoon Park
- Department of Electrical and Biological Physics, Plasma Bioscience Research Institute, Kwangwoon University, Seoul, Republic of Korea
| | - Hui-Min Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Katherine A Borkovich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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11
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Qian C, Qiu W, Zhang J, Shen Z, Liu H, Zhang Y. The long non-coding RNA MEG3 plays critical roles in the pathogenesis of cholesterol gallstone. PeerJ 2021; 9:e10803. [PMID: 33665015 PMCID: PMC7908887 DOI: 10.7717/peerj.10803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background Cholesterol gallstone (CG) is the most common gallstone disease, which is induced by biliary cholesterol supersaturation. The purpose of this study is to investigate the pathogenesis of CG. Methods Sixteen mice were equally and randomly divided into model group and normal control group. The model group was fed with lithogenic diets to induce CG, and then gallbladder bile lipid analysis was performed. After RNA-seq library was constructed, differentially expressed mRNAs (DE-mRNAs) and differentially expressed lncRNAs (DE-lncRNAs) between model group and normal control group were analyzed by DESeq2 package. Using the cluster Profiler package, enrichment analysis for the DE-mRNAs was carried out. Based on Cytoscape software, the protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were built. Using quantitative real-time reverse transcription-PCR (qRT-PCR) analysis, the key RNAs were validated. Results The mouse model of CG was suc cessfully established, and then 181 DE-mRNAs and 33 DE-lncRNAs between model and normal groups were obtained. Moreover, KDM4A was selected as a hub node in the PPI network, and lncRNA MEG3 was considered as a key lncRNA in the regulatory network. Additionally, the miR-107-5p/miR-149-3p/miR-346-3-MEG3 regulatory pairs and MEG3-PABPC4/CEP131/NUMB1 co-expression pairs existed in the regulatory network. The qRT-PCR analysis showed that KDM4A expression was increased, and the expressions of MEG3, PABPC4, CEP131, and NUMB1 were downregulated. Conclusion These RNAs might be related to the pathogenesis of CG.
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Affiliation(s)
- Changlin Qian
- The Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.,Department of General Surgery, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weiqing Qiu
- Department of General Surgery, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhang
- Department of General Surgery, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyong Shen
- Department of General Surgery, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Liu
- Department of General Surgery, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongjie Zhang
- The Second Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China
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12
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Puttamreddy S, Minion FC. Transposon Mutagenesis of Foodborne Pathogenic Escherichia coli. Methods Mol Biol 2019; 2016:73-80. [PMID: 31197710 DOI: 10.1007/978-1-4939-9570-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The Enterobacteriaceae, and in particular, Escherichia coli including foodborne pathotypes are particularly amenable to transposon mutagenesis. Here we describe the use of mini-Tn5 and Mu d1(Ap lac) to generate transposon inserts for analysis of enterohemorrhagic Escherichia coli EDL933. We also discuss how to array the library in 96-well plates and sequence individual clones for further analysis.
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13
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Abstract
The status of T cell receptors (TCRs) repertoire is associated with the occurrence and progress of various diseases and can be used in monitoring the immune responses, predicting the prognosis of disease and other medical fields. High-throughput sequencing promotes the studying in TCR repertoire. The chapter focuses on the whole process of TCR profiling, including DNA extraction, library construction, high-throughput sequencing, and how to analyze data.
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Affiliation(s)
- Huixin Lin
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Yonggang Peng
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Xiangbin Chen
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Yuebin Liang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Jialiang Yang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China.
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14
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Jakob V, Helmsing S, Hust M, Empting M. Restriction-Free Construction of a Phage-Presented Very Short Macrocyclic Peptide Library. Methods Mol Biol 2020; 2070:95-113. [PMID: 31625092 DOI: 10.1007/978-1-4939-9853-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phage display is a commonly used technology for the screening of large clonal libraries of proteins and peptides. The construction of peptide libraries containing very short sequences, however, poses certain problems for conventional restriction-based cloning procedures, which are rooted in the necessity to purify restricted library oligos. Herein, we present an alternative cloning method especially suitable for such very short sequences of about only 21 base pairs resulting in a 60 bp insert. The employed restriction-free hot fusion cloning strategy allows for facile library construction bypassing the need for purification of the small oligo. The library includes one well-defined disulfide bridge rendering the displayed macrocyclic peptide sequences as attractive scaffolds for novel active principles.
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15
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Lu W, Zhu M, Chen Y, Bai Y. A novel approach to improving hybrid capture sequencing targeting efficiency. Mol Cell Probes 2019; 46:101424. [PMID: 31336168 DOI: 10.1016/j.mcp.2019.101424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/08/2019] [Accepted: 07/19/2019] [Indexed: 11/28/2022]
Abstract
At present, approaches to hybrid capture sequencing have many limitations, from their significant complexity and labor requirements, to their low enrichment efficiency, resulting in their limited utilization. In an effort to overcome these drawbacks, we have developed a novel method that relied upon direct genomic DNA hybridization and single-stranded DNA library preparation. Using this novel protocol, we were able to achieve a targeting efficiency as high as 75%, and we found this approach to overall be an efficient and simple approach to DNA library construction.
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Affiliation(s)
- WenXiang Lu
- Department of R&D, Decode Genomics Incorporation, Nanjing, 210000, China; Department of R&D, AGCU ScienTech Incorporation, Wuxi, 214174, China
| | - Miao Zhu
- Department of R&D, Decode Genomics Incorporation, Nanjing, 210000, China
| | - Yi Chen
- Department of Obstetrics and Gynaecology, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, 215300, China.
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
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16
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Settele F, Zwarg M, Fiedler S, Koscheinz D, Bosse-Doenecke E. Construction and Selection of Affilin ® Phage Display Libraries. Methods Mol Biol 2018; 1701:205-238. [PMID: 29116507 DOI: 10.1007/978-1-4939-7447-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Affilin® molecules represent a new class of so-called scaffold proteins. The concept of scaffold proteins is to use stable and versatile protein structures which can be endowed with de novo binding properties and specificities by introducing mutations in surface exposed amino acid residues. Complex variations and combinations are generated by genetic methods of randomization resulting in large cDNA libraries. The selection for candidates binding to a desired target can be executed by display methods, especially the very robust and flexible phage display. Here, we describe the construction of ubiquitin based Affilin® phage display libraries and their use in biopanning experiments for the identification of novel protein ligands.
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Affiliation(s)
- Florian Settele
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Madlen Zwarg
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Sebastian Fiedler
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Daniel Koscheinz
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany
| | - Eva Bosse-Doenecke
- Navigo Proteins GmbH, Heinrich-Damerow-Straße 1, 06120, Halle (Saale), Germany.
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17
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Wei HY, Huang S, Wang JY, Gao F, Jiang JZ. Comparison of methods for library construction and short read annotation of shellfish viral metagenomes. Genes Genomics 2018; 40:281-288. [PMID: 29892802 DOI: 10.1007/s13258-017-0629-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022]
Abstract
The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI's NR and Uniprot's Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.
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Affiliation(s)
- Hong-Ying Wei
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.,Shanghai Ocean University, Shanghai, 201306, China
| | - Sheng Huang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.,Shanghai Ocean University, Shanghai, 201306, China
| | - Jiang-Yong Wang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Fang Gao
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.,Shanghai Ocean University, Shanghai, 201306, China
| | - Jing-Zhe Jiang
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
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18
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Wu J, Dai W, Wu L, Wang J. SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states. BMC Genomics 2018; 19:143. [PMID: 29439663 PMCID: PMC5811972 DOI: 10.1186/s12864-018-4530-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. RESULTS This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 105 to 500 cells. CONCLUSIONS This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China.
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19
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Abstract
Small RNAs (sRNAs) as key regulators of gene expression play fundamental roles in many biological processes. Next-generation sequencing (NGS) has become an important tool for sRNA discovery and profiling. However, NGS data often show bias for or against certain sequences which is mainly caused by adapter oligonucleotides that are ligated to sRNAs more or less efficiently by RNA ligases. In order to reduce ligation bias, High-definition (HD) adapters for the Illumina sequencing platform were developed. However, a large amount of direct 5' and 3' adapter ligation products are often produced when the current commercially available kits are used for cloning with HD adapters. In this chapter we describe a protocol for sRNA library construction using HD adapters with drastically reduced direct 5' adapter-3' adapter ligation product. The protocol can be used for sRNA library preparation from total RNA or sRNA of various plant, animal, insect, or fungal samples. The protocol includes total RNA extraction from plant leaf tissue and cultured mammalian cells and sRNA library construction using HD adapters.
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20
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Abstract
RNA sequencing (RNA-seq) can not only be used to identify the expression of common or rare transcripts but also in the identification of other abnormal events, such as alternative splicing, novel transcripts, and fusion genes. In principle, RNA-seq can be carried out by almost all of the next-generation sequencing (NGS) platforms, but the libraries of different platforms are not exactly the same; each platform has its own kit to meet the special requirements of the instrument design.
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Affiliation(s)
- Hong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Genetics and Development, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Genetics and Development, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Lei Cai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Genetics and Development, Shanghai Jiaotong University, Shanghai, 200240, China.
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21
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Abstract
Metabolomics based on mass spectrometry can provide quantitative and qualitative information of the pool of metabolites (metabolome) present intracellularly or extracellularly in a given biological system. A typical metabolomics workflow requires several key steps such as quick and robust sample preparations with quenching of metabolism, chemical derivatization if needed, instrumental measurement, data-processing with/without database information and further statistical analysis and interpretation. Here, we introduce general metabolomics workflows for global and targeted analyses using gas chromatography or liquid chromatography coupled with mass spectrometers.
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Affiliation(s)
- Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Heino M Heyman
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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22
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Haile S, Corbett RD, MacLeod T, Bilobram S, Smailus D, Tsao P, Kirk H, McDonald H, Pandoh P, Bala M, Hirst M, Miller D, Moore RA, Mungall AJ, Schein J, Coope RJ, Ma Y, Zhao Y, Holt RA, Jones SJ, Marra MA. Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing. BMC Genomics 2017; 18:515. [PMID: 28679365 PMCID: PMC5499059 DOI: 10.1186/s12864-017-3900-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/22/2017] [Indexed: 12/01/2022] Open
Abstract
Background RNA-Sequencing (RNA-seq) is now commonly used to reveal quantitative spatiotemporal snapshots of the transcriptome, the structures of transcripts (splice variants and fusions) and landscapes of expressed mutations. However, standard approaches for library construction typically require relatively high amounts of input RNA, are labor intensive, and are time consuming. Methods Here, we report the outcome of a systematic effort to optimize and streamline steps in strand-specific RNA-seq library construction. Results This work has resulted in the identification of an optimized messenger RNA isolation protocol, a potent reverse transcriptase for cDNA synthesis, and an efficient chemistry and a simplified formulation of library construction reagents. We also present an optimization of bead-based purification and size selection designed to maximize the recovery of cDNA fragments. Conclusions These developments have allowed us to assemble a rapid high throughput pipeline that produces high quality data from amounts of total RNA as low as 25 ng. While the focus of this study is on RNA-seq sample preparation, some of these developments are also relevant to other next-generation sequencing library types. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3900-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Haile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Tina MacLeod
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Steve Bilobram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Duane Smailus
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Philip Tsao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Heather Kirk
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Helen McDonald
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Miruna Bala
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Diane Miller
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jacquie Schein
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Robin J Coope
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Rob A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Steven J Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Richards B, Cao S, Plavsic M, Pomponio R, Davies C, Mattaliano R, Madden S, Klinger K, Palermo A. Detection of adventitious agents using next-generation sequencing. PDA J Pharm Sci Technol 2014; 68:651-660. [PMID: 25475640 DOI: 10.5731/pdajpst.2014.01025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED Next-generation sequencing has been evaluated at Genzyme as a means of identifying bioreactor contaminants due to its capability for detection of known and novel microbial species. In this approach, data obtained from next-generation sequencing is used to interrogate databases containing genomic sequences and identities of potential adventitious agents. We describe here the use of this approach to help identify the causative agent of a bioreactor contamination. We also present the results of spiking experiments to establish the limits of detection for DNA viruses, RNA viruses, and bacteria, in a background of Chinese hamster ovary cells, a cell line used for production of many human therapeutics. Using Illumina sequencing-based detection, all of the viruses included in this study were detected at less than 1 copy per cell, and bacteria were detected at 0.001 copy per cell. Thus, next-generation sequencing-based detection of adventitious agents is a valuable approach that can fill a critical unmet need in the detection of known and novel microorganisms in biopharmaceutical manufacturing. LAY ABSTRACT Because biological products are manufactured in cells, the living environment must be kept sterile. Any introduction of microorganisms into the culture vessel may affect the growth and other biological properties of the cells or contaminate the product. It is therefore important to monitor the culture for such contaminants, but many methods can only detect a specific microorganism. In this study, we show that next-generation sequencing-based detection is a sensitive and complementary approach that can potentially detect a wide range of organisms.
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Affiliation(s)
| | | | | | | | | | - Robert Mattaliano
- Biologics Research & Development, Genzyme, A Sanofi Company, Framingham, MA, USA
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