1
|
Huang Y, Zhang Y, Wu W, Wang Y, Qiu W, Zhang Z, Yu Y. Fast acoustic droplet ejection based on annular array transducer. ULTRASONICS 2024; 145:107448. [PMID: 39243532 DOI: 10.1016/j.ultras.2024.107448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/04/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024]
Abstract
Acoustic droplet ejection (ADE) has become the preferred method for liquid transfer in a variety of applications including synthetic biology, genotyping and drug discovery. Comparing with traditional pipetting techniques, the accuracy and data reproducibility of ADE based liquid transfer are improved, waste and cost are reduced, and cross-contamination is eliminated. The key component in the ADE system is the ultrasound transducer, which is responsible for generating focused ultrasound beam for droplet ejection. However, current ADE systems commonly utilize a single-element focused transducer with a fixed focal length that require mechanical movement to focus on the liquid surface, resulting in reduced liquid transfer efficiency. In this study, we first present a high-frequency annular array transducer for the ADE technology, which enables rapid and dynamic axial focusing to the liquid surface without mechanically moving the transducer, thereby accelerating liquid transfer. Experimental results show that the proposed 10 MHz, 5-element annular array transducer has good dynamic axial focusing ability, and can achieve accurate and stable droplet ejection of nanoliter volume at the designed focal length of 26-32 mm. Our results highlight the potential of the annular array transducer in advancing ADE system for rapid liquid transfer. This technology is expected to be useful in a variety of applications where precise and high-throughput liquid transfer is crucial.
Collapse
Affiliation(s)
- Youta Huang
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 508055 China; The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen 518055, China; National-Reginoal Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Ultrasound Imaging and Therapy, Shenzhen 518055, China
| | - Yang Zhang
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 508055 China; The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen 518055, China; School of Electrical Engineering, University of South China, Hengyang, China; Shenzhen Key Laboratory of Ultrasound Imaging and Therapy, Shenzhen 518055, China
| | - Weichang Wu
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 508055 China; The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Key Laboratory of Ultrasound Imaging and Therapy, Shenzhen 518055, China
| | - Yan Wang
- School of Electrical Engineering, University of South China, Hengyang, China
| | - Weibao Qiu
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 508055 China; The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Key Laboratory of Ultrasound Imaging and Therapy, Shenzhen 518055, China.
| | - Zhiqiang Zhang
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 508055 China; The Key Laboratory of Biomedical Imaging Science and System, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Key Laboratory of Ultrasound Imaging and Therapy, Shenzhen 518055, China.
| | - Yanyan Yu
- National-Reginoal Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518060, China.
| |
Collapse
|
2
|
Hernandez SI, Berezin CT, Miller KM, Peccoud SJ, Peccoud J. Sequencing Strategy to Ensure Accurate Plasmid Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586694. [PMID: 38585828 PMCID: PMC10996661 DOI: 10.1101/2024.03.25.586694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Despite the wide use of plasmids in research and clinical production, the need to verify plasmid sequences is a bottleneck that is too often underestimated in the manufacturing process. Although sequencing platforms continue to improve, the method and assembly pipeline chosen still influence the final plasmid assembly sequence. Furthermore, few dedicated tools exist for plasmid assembly, especially for de novo assembly. Here, we evaluated short-read, long-read, and hybrid (both short and long reads) de novo assembly pipelines across three replicates of a 24-plasmid library. Consistent with previous characterizations of each sequencing technology, short-read assemblies had issues resolving GC-rich regions, and long-read assemblies commonly had small insertions and deletions, especially in repetitive regions. The hybrid approach facilitated the most accurate, consistent assembly generation and identified mutations relative to the reference sequence. Although Sanger sequencing can be used to verify specific regions, some GC-rich and repetitive regions were difficult to resolve using any method, suggesting that easily sequenced genetic parts should be prioritized in the design of new genetic constructs.
Collapse
Affiliation(s)
- Sarah I. Hernandez
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Casey-Tyler Berezin
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Katie M. Miller
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Samuel J. Peccoud
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Jean Peccoud
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| |
Collapse
|
3
|
Uesaka K, Inaba K, Nishioka N, Kojima S, Homma M, Ihara K. Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2. PeerJ 2024; 12:e17126. [PMID: 38515459 PMCID: PMC10956519 DOI: 10.7717/peerj.17126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024] Open
Abstract
The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.
Collapse
Affiliation(s)
- Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Keita Inaba
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| | - Noriko Nishioka
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Aichi, Japan
| |
Collapse
|
4
|
Ramírez Rojas A, Brinkmann CK, Köbel TS, Schindler D. DuBA.flow─A Low-Cost, Long-Read Amplicon Sequencing Workflow for the Validation of Synthetic DNA Constructs. ACS Synth Biol 2024; 13:457-465. [PMID: 38295293 PMCID: PMC10877597 DOI: 10.1021/acssynbio.3c00522] [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: 08/25/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 02/02/2024]
Abstract
Modern biological science, especially synthetic biology, relies heavily on the construction of DNA elements, often in the form of plasmids. Plasmids are used for a variety of applications, including the expression of proteins for subsequent purification, the expression of heterologous pathways for the production of valuable compounds, and the study of biological functions and mechanisms. For all applications, a critical step after the construction of a plasmid is its sequence validation. The traditional method for sequence determination is Sanger sequencing, which is limited to approximately 1000 bp per reaction. Here, we present a highly scalable in-house method for rapid validation of amplified DNA sequences using long-read Nanopore sequencing. We developed two-step amplicon and transposase strategies to provide maximum flexibility for dual barcode sequencing. We also provide an automated analysis pipeline to quickly and reliably analyze sequencing results and provide easy-to-interpret results for each sample. The user-friendly DuBA.flow start-to-finish pipeline is widely applicable. Furthermore, we show that construct validation using DuBA.flow can be performed by barcoded colony PCR amplicon sequencing, thus accelerating research.
Collapse
Affiliation(s)
- Adán
A. Ramírez Rojas
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Cedric K. Brinkmann
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Tania S. Köbel
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Schindler
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-University
Marburg, Karl-von-Frisch-Str.
14, 35032 Marburg, Germany
| |
Collapse
|
5
|
Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
Collapse
Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
6
|
Brown SD, Dreolini L, Wilson JF, Balasundaram M, Holt RA. Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device. BMC Bioinformatics 2023; 24:116. [PMID: 36964503 PMCID: PMC10039527 DOI: 10.1186/s12859-023-05226-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/11/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Sequence verification is essential for plasmids used as critical reagents or therapeutic products. Typically, high-quality plasmid sequence is achieved through capillary-based Sanger sequencing, requiring customized sets of primers for each plasmid. This process can become expensive, particularly for applications where the validated sequence needs to be produced within a regulated and quality-controlled environment for downstream clinical research applications. RESULTS Here, we describe a cost-effective and accurate plasmid sequencing and consensus generation procedure using the Oxford Nanopore Technologies' MinION device as an alternative to capillary-based plasmid sequencing options. This procedure can verify the identity of a pure population of plasmid, either confirming it matches the known and expected sequence, or identifying mutations present in the plasmid if any exist. We use a full MinION flow cell per plasmid, maximizing available data and allowing for stringent quality filters. Pseudopairing reads for consensus base calling reduces read error rates from 5.3 to 0.53%, and our pileup consensus approach provides per-base counts and confidence scores, allowing for interpretation of the certainty of the resulting consensus sequences. For pure plasmid samples, we demonstrate 100% accuracy in the resulting consensus sequence, and the sensitivity to detect small mutations such as insertions, deletions, and single nucleotide variants. In test cases where the sequenced pool of plasmids contains subclonal templates, detection sensitivity is similar to that of traditional capillary sequencing. CONCLUSIONS Our pipeline can provide significant cost savings compared to outsourcing clinical-grade sequencing of plasmids, making generation of high-quality plasmid sequence for clinical sequence verification more accessible. While other long-read-based methods offer higher-throughput and less cost, our pipeline produces complete and accurate sequence verification for cases where absolute sequence accuracy is required.
Collapse
Affiliation(s)
- Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Lisa Dreolini
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Jessica F Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Miruna Balasundaram
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, SSB8166 - 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
- Department of Medical Genetics, University of British Columbia, C201 - 4500 Oak Street, 675 W 10th Ave, Vancouver, BC, V6H 3N1, Canada.
| |
Collapse
|
7
|
Pasin F. Assembly of plant virus agroinfectious clones using biological material or DNA synthesis. STAR Protoc 2022; 3:101716. [PMID: 36149792 PMCID: PMC9519601 DOI: 10.1016/j.xpro.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/29/2022] [Accepted: 08/26/2022] [Indexed: 01/26/2023] Open
Abstract
Infectious clone technology is universally applied for biological characterization and engineering of viruses. This protocol describes procedures that implement synthetic biology advances for streamlined assembly of virus infectious clones. Here, I detail homology-based cloning using biological material, as well as SynViP assembly using type IIS restriction enzymes and chemically synthesized DNA fragments. The assembled virus clones are based on compact T-DNA binary vectors of the pLX series and are delivered to host plants by Agrobacterium-mediated inoculation. For complete details on the use and execution of this protocol, please refer to Pasin et al. (2017, 2018) and Pasin (2021).
Collapse
Affiliation(s)
- Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain.
| |
Collapse
|
8
|
Hahaut V, Pavlinic D, Carbone W, Schuierer S, Balmer P, Quinodoz M, Renner M, Roma G, Cowan CS, Picelli S. Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq. Nat Biotechnol 2022; 40:1447-1451. [PMID: 35637419 PMCID: PMC9546769 DOI: 10.1038/s41587-022-01312-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/08/2022] [Indexed: 12/29/2022]
Abstract
We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying reduced strand-invasion artifacts. FS will be especially useful for characterizing gene expression at high resolution across multiple samples.
Collapse
Affiliation(s)
- Vincent Hahaut
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Dinko Pavlinic
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Walter Carbone
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sven Schuierer
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Pierre Balmer
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, University of Basel, Basel, Switzerland.
| |
Collapse
|
9
|
Emiliani FE, Hsu I, McKenna A. Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing. ACS Synth Biol 2022; 11:2238-2246. [PMID: 35695379 PMCID: PMC9295152 DOI: 10.1021/acssynbio.2c00126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Recombinant DNA is
a fundamental tool in biotechnology and medicine.
These DNA sequences are often built, replicated, and delivered in
the form of plasmids. Validation of these plasmid sequences is a critical
and time-consuming step, which has been dominated for the last 35
years by Sanger sequencing. As plasmid sequences grow more complex
with new DNA synthesis and cloning techniques, we need new approaches
that address the corresponding validation challenges at scale. Here
we prototype a high-throughput plasmid sequencing approach using DNA
transposition and Oxford Nanopore sequencing. Our method, Circuit-seq,
creates robust, full-length, and accurate plasmid assemblies without
prior knowledge of the underlying sequence. We demonstrate the power
of Circuit-seq across a wide range of plasmid sizes and complexities,
generating full-length, contiguous plasmid maps. We then leverage
our long-read data to characterize epigenetic marks and estimate plasmid
contamination levels. Circuit-seq scales to large numbers of samples
at a lower per-sample cost than commercial Sanger sequencing, accelerating
a key step in synthetic biology, while low equipment costs make it
practical for individual laboratories.
Collapse
Affiliation(s)
- Francesco E Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Ian Hsu
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States.,Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire 03756, United States
| |
Collapse
|
10
|
|
11
|
Fuchs M, Radulescu C, Tang M, Mahesh A, Lavin D, Umbreen S, McKenna J, Smyth M, McColgan E, Molnar Z, Baxter C, Skvortsov T, Singh A, Rogan F, Miskelly J, Bridgett S, Fairley D, Simpson DA. Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2. J Transl Med 2022; 20:105. [PMID: 35241105 PMCID: PMC8892412 DOI: 10.1186/s12967-022-03307-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic has highlighted the importance of whole genome sequencing (WGS) of SARS-CoV-2 to inform public health policy. By enabling definition of lineages it facilitates tracking of the global spread of the virus. The evolution of new variants can be monitored and knowledge of specific mutations provides insights into the mechanisms through which the virus increases transmissibility or evades immunity. To date almost 1 million SARS-CoV-2 genomes have been sequenced by members of the COVID-19 Genomics UK (COG-UK) Consortium. To achieve similar feats in a more cost-effective and sustainable manner in future, improved high throughput virus sequencing protocols are required. We have therefore developed a miniaturized library preparation protocol with drastically reduced consumable use and costs. RESULTS We present the 'Mini-XT' miniaturized tagmentation-based library preparation protocol available on protocols.io ( https://doi.org/10.17504/protocols.io.bvntn5en ). SARS-CoV-2 RNA was amplified using the ARTIC nCov-2019 multiplex RT-PCR protocol and purified using a conventional liquid handling system. Acoustic liquid transfer (Echo 525) was employed to reduce reaction volumes and the number of tips required for a Nextera XT library preparation. Sequencing was performed on an Illumina MiSeq. The final version of Mini-XT has been used to sequence 4384 SARS-CoV-2 samples from N. Ireland with a COG-UK QC pass rate of 97.4%. Sequencing quality was comparable and lineage calling consistent for replicate samples processed with full volume Nextera DNA Flex (333 samples) or using nanopore technology (20 samples). SNP calling between Mini-XT and these technologies was consistent and sequences from replicate samples paired together in maximum likelihood phylogenetic trees. CONCLUSIONS The Mini-XT protocol maintains sequence quality while reducing library preparation reagent volumes eightfold and halving overall tip usage from sample to sequence to provide concomitant cost savings relative to standard protocols. This will enable more efficient high-throughput sequencing of SARS-CoV-2 isolates and future pathogen WGS.
Collapse
Affiliation(s)
- Marc Fuchs
- Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen’s University Belfast, Belfast, UK
| | - Clara Radulescu
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Miao Tang
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Arun Mahesh
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Deborah Lavin
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Syed Umbreen
- Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen’s University Belfast, Belfast, UK
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
- School of Pharmacy, Queen’s University Belfast, Belfast, UK
| | - James McKenna
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
| | - Mark Smyth
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
| | - Eilís McColgan
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
| | - Zoltan Molnar
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
| | - Chris Baxter
- Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen’s University Belfast, Belfast, UK
| | | | - Aditi Singh
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Fiona Rogan
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Julia Miskelly
- Genomics Core Technology Unit, Faculty of Medicine and Health Sciences, Queen’s University Belfast, Belfast, UK
| | - Stephen Bridgett
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| | - Derek Fairley
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, UK
| | - David A. Simpson
- The Wellcome–Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast, UK
| |
Collapse
|
12
|
Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
Collapse
Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
Zulkower V. Computer-Aided Planning for the Verification of Large Batches of DNA Constructs. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2229:167-174. [PMID: 33405221 DOI: 10.1007/978-1-0716-1032-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Restriction digest analysis and Sanger sequencing are among the most commonly used techniques to check the sequence of synthetic DNA constructs. However, both require careful preparation to select restriction enzymes or DNA primers adapted to the expected constructs sequences. In projects involving manufacturing of large batches of synthetic constructs, the task can be tedious and error-prone. This chapter demonstrates the use of two free and open-source web applications providing fast and automated selection of enzymes and sequencing primers for DNA construct verification.
Collapse
Affiliation(s)
- Valentin Zulkower
- Edinburgh Genome Foundry, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
14
|
Guo Q, Su X, Zhang X, Shao M, Yu H, Li D. A review on acoustic droplet ejection technology and system. SOFT MATTER 2021; 17:3010-3021. [PMID: 33710210 DOI: 10.1039/d0sm02193h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pace of change in chemical and biological research enabled by improved detection systems demands fundamental liquid handling and sample preparation changes. The acoustic droplet ejection (ADE)-based liquid handling method has the advantages of improving precision and data reproducibility, reducing costs, hands-on time, and eliminating waste. ADE gradually replaced traditional aspiration-and-dispense liquid-handling robots in applications such as synthetic biology, genotyping, personalized medicine, and next-generation sequencing. This review emphatically introduces the setup of the ADE system and the critical technologies of each part, including acoustic droplet generation, optimized design of the source fluid wells, droplet coalescence, and power control. The advantages and disadvantages of these technologies are discussed, and the future development of acoustic droplet ejection technology is also predicted.
Collapse
Affiliation(s)
- Qing Guo
- State Key Laboratory of Precision Measurement Technology and Instruments, Tianjin University, Tianjin 300072, China.
| | | | | | | | | | | |
Collapse
|
15
|
Zhang J, Chen Y, Fu L, Guo E, Wang B, Dai L, Si T. Accelerating strain engineering in biofuel research via build and test automation of synthetic biology. Curr Opin Biotechnol 2021; 67:88-98. [PMID: 33508635 DOI: 10.1016/j.copbio.2021.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Biofuels are a type of sustainable and renewable energy. However, for the economical production of bulk-volume biofuels, biosystems design is particularly challenging to achieve sufficient yield, titer, and productivity. Because of the lack of predictive modeling, high-throughput screening remains essential. Recently established biofoundries provide an emerging infrastructure to accelerate biological design-build-test-learn (DBTL) cycles through the integration of robotics, synthetic biology, and informatics. In this review, we first introduce the technical advances of build and test automation in synthetic biology, focusing on the use of industry-standard microplates for DNA assembly, chassis engineering, and enzyme and strain screening. Proof-of-concept studies on prototypes of automated foundries are then discussed, for improving biomass deconstruction, metabolic conversion, and host robustness. We conclude with future challenges and opportunities in creating a flexible, versatile, and data-driven framework to support biofuel research and development in biofoundries.
Collapse
Affiliation(s)
- Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yongcan Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lihao Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bo Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| |
Collapse
|
16
|
Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
Collapse
Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
17
|
Zhao M, García B, Gallo A, Tzanetakis IE, Simón-Mateo C, García JA, Pasin F. Home-made enzymatic premix and Illumina sequencing allow for one-step Gibson assembly and verification of virus infectious clones. PHYTOPATHOLOGY RESEARCH 2020; 2:36. [PMID: 33768973 PMCID: PMC7990137 DOI: 10.1186/s42483-020-00077-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/13/2020] [Indexed: 05/06/2023]
Abstract
An unprecedented number of viruses have been discovered by leveraging advances in high-throughput sequencing. Infectious clone technology is a universal approach that facilitates the study of biology and role in disease of viruses. In recent years homology-based cloning methods such as Gibson assembly have been used to generate virus infectious clones. We detail herein the preparation of home-made cloning materials for Gibson assembly. The home-made materials were used in one-step generation of the infectious cDNA clone of a plant RNA virus into a T-DNA binary vector. The clone was verified by a single Illumina reaction and a de novo read assembly approach that required no primer walking, custom primers or reference sequences. Clone infectivity was finally confirmed by Agrobacterium-mediated delivery to host plants. We anticipate that the convenient home-made materials, one-step cloning and Illumina verification strategies described herein will accelerate characterization of viruses and their role in disease development.
Collapse
Affiliation(s)
- Mingmin Zhao
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Beatriz García
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Araiz Gallo
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Ioannis E. Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, USA
| | | | | | - Fabio Pasin
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
- University of Padova, 35122 Padova, Italy
| |
Collapse
|
18
|
High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
Collapse
|
19
|
Ip K, Yadin R, George KW. High-Throughput DNA Assembly Using Yeast Homologous Recombination. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2205:79-89. [PMID: 32809194 DOI: 10.1007/978-1-0716-0908-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Yeast homologous recombination is a reliable, low-cost, and efficient method for DNA assembly. Using homology regions as short as 24 base pairs, constructs of up to 12 unique parts can be assembled into a diverse range of vectors. The simplicity and robustness of this protocol make it amenable to laboratory automation and high-throughput operations. Here we describe a high-throughput protocol to generate DNA parts through PCR, assemble them into a vector via yeast transformation, and "shuttle" the resulting plasmid constructs into E. coli for storage and propagation. Though this protocol is intended for high-throughput workflows, it can be easily adapted for bench-scale DNA assembly.
Collapse
|
20
|
Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
|
21
|
Chiniquy J, Garber ME, Mukhopadhyay A, Hillson NJ. Fluorescent amplification for next generation sequencing (FA-NGS) library preparation. BMC Genomics 2020; 21:85. [PMID: 31992180 PMCID: PMC6988211 DOI: 10.1186/s12864-020-6481-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/10/2020] [Indexed: 01/29/2023] Open
Abstract
Background Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. Results In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. Conclusions We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.
Collapse
Affiliation(s)
- Jennifer Chiniquy
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,U.S. Department of Energy Agile BioFoundry, Emeryville, CA, USA
| | - Megan E Garber
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,U.S. Department of Energy Agile BioFoundry, Emeryville, CA, USA.
| |
Collapse
|
22
|
Christie W, Yadin R, Ip K, George KW. Highly Multiplexed, Semiautomated Nextera Next-Generation Sequencing (NGS) Library Preparation. Methods Mol Biol 2020; 2205:91-104. [PMID: 32809195 DOI: 10.1007/978-1-0716-0908-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
High-throughput, inexpensive DNA sequencing is an essential component of large-scale DNA assembly operations. Using traditional and acoustic liquid-handling robotics, Illumina's Nextera Tagmentation reactions can be miniaturized and paired with custom PCR index primers to produce highly multiplexed NGS libraries for pooled sequencing. This chapter describes a high-throughput protocol that enables the simultaneous sequencing of thousands of DNA constructs in a single sequencing run at a dramatically reduced cost compared to bench-top methods.
Collapse
|
23
|
Reif D. High-Throughput PCR for DNA Part Generation. Methods Mol Biol 2020; 2205:71-77. [PMID: 32809193 DOI: 10.1007/978-1-0716-0908-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This protocol describes a high-throughput approach to PCR for the generation of over a thousand amplicons in parallel. Modern liquid handling robotics are used to accelerate reaction setup, miniaturize reaction volumes, and dramatically reduce reagent and consumable cost. Although the focus is on generating DNA parts for use in DNA assembly techniques, this methodology can be applied to any workflow where the parallel production of hundreds or thousands of PCR amplicons is required.
Collapse
|
24
|
Hwang B, Heo S, Cho N, Seo H, Bang D. Facilitated Large-Scale Sequence Validation Platform Using Tn5-Tagmented Cell Lysates. ACS Synth Biol 2019; 8:596-600. [PMID: 30726053 DOI: 10.1021/acssynbio.8b00482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A typical molecular cloning procedure requires Sanger sequencing for sequence validation, which is cost-prohibitive and labor-intensive for large-scale clone analysis in genotype-phenotype studies. Here we present the cost-effective clone analysis platform TnClone, which uses next-generation sequencing based on Tn5 tagmentation to rapidly analyze a large number of clones from cell lysates. This method bypasses the extensive plasmid purification step. We also developed a user-friendly graphical user interface and provided general guidelines for conducting validation experiments. We tested our program with 1023 plasmids (222 from cell lysates and 801 from purified clones) and achieved 92% and 99.3% sensitivity with cell lysates and purified DNA, respectively. Our platform provides rapid turnaround with minimal hands-on time for secondary evaluation, as next-generation sequencing technology continues to evolve.
Collapse
Affiliation(s)
- Byungjin Hwang
- Institute for Human Genetics (IHG), Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143-0794, United States
| | - Sunghoon Heo
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - Namjin Cho
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - Hanna Seo
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, Korea
| |
Collapse
|
25
|
Suckling L, McFarlane C, Sawyer C, Chambers SP, Kitney RI, McClymont DW, Freemont PS. Miniaturisation of high-throughput plasmid DNA library preparation for next-generation sequencing using multifactorial optimisation. Synth Syst Biotechnol 2019; 4:57-66. [PMID: 30723818 PMCID: PMC6352296 DOI: 10.1016/j.synbio.2019.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 02/08/2023] Open
Abstract
High-throughput preparation of plasmid DNA libraries for next-generation sequencing (NGS) is an important capability for molecular biology laboratories. In particular, it is an essential quality control (QC) check when large numbers of plasmid variants are being generated. Here, we describe the use of the Design of Experiments (DOE) methodology to optimise the miniaturised preparation of plasmid DNA libraries for NGS, using the Illumina® Nextera XT technology and the Labcyte Echo® acoustic liquid dispensing system. Furthermore, we describe methods which can be implemented as a QC check for identifying the presence of genomic DNA (gDNA) in plasmid DNA samples and the subsequent shearing of the gDNA, which otherwise prevents the acoustic transfer of plasmid DNA. This workflow enables the preparation of plasmid DNA libraries which yield high-quality sequencing data.
Collapse
Affiliation(s)
- Lorna Suckling
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - Ciaran McFarlane
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Chelsea Sawyer
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - Stephen P. Chambers
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - Richard I. Kitney
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - David W. McClymont
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK
| | - Paul S. Freemont
- The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK,Department of Medicine, Imperial College London, London, SW7 2AZ, UK,Corresponding author. The London DNA Foundry, SynbiCITE, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
26
|
Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. PLoS One 2019; 14:e0206194. [PMID: 30629604 PMCID: PMC6328170 DOI: 10.1371/journal.pone.0206194] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/12/2018] [Indexed: 01/15/2023] Open
Abstract
Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.
Collapse
Affiliation(s)
- Madeline Y. Mayday
- UCSF School of Medicine, Benioff Children’s Hospital, Department of Pediatrics, Division of Critical Care, San Francisco, California, United States of America
| | - Lillian M. Khan
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
| | - Eric D. Chow
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
| | - Matt S. Zinter
- UCSF School of Medicine, Benioff Children’s Hospital, Department of Pediatrics, Division of Critical Care, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
27
|
Streamlined generation of plant virus infectious clones using the pLX mini binary vectors. J Virol Methods 2018; 262:48-55. [DOI: 10.1016/j.jviromet.2018.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/15/2018] [Accepted: 09/16/2018] [Indexed: 12/30/2022]
|
28
|
Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
Collapse
Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| |
Collapse
|
29
|
Saveliev A, Liu J, Li M, Hirata L, Latshaw C, Zhang J, Wilson JM. Accurate and Rapid Sequence Analysis of Adeno-Associated Virus Plasmids by Illumina Next-Generation Sequencing. Hum Gene Ther Methods 2018; 29:201-211. [PMID: 30051733 DOI: 10.1089/hgtb.2018.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sequence validation of plasmid DNA is a crucial quality control step that must occur prior to adeno-associated virus (AAV) vector packaging through plasmid transfection. AAV cis-plasmids present unique challenges to sequence analysis, as they contain inverted terminal repeats and are prone to sequence rearrangements. An accurate and rapid next-generation sequencing approach has been established to analyze full-length sequences of AAV cis-plasmids within 3.5 days. Here, a step-by-step protocol is described that can reliably detect and identify the location and frequency of sequence variants commonly observed in AAV cis-plasmids.
Collapse
Affiliation(s)
- Alexei Saveliev
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Juan Liu
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Mingyao Li
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Lee Hirata
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Caitlin Latshaw
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Jia Zhang
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - James M Wilson
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| |
Collapse
|
30
|
Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
Collapse
Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
| |
Collapse
|
31
|
Whitehead E, Rudolf F, Kaltenbach HM, Stelling J. Automated Planning Enables Complex Protocols on Liquid-Handling Robots. ACS Synth Biol 2018; 7:922-932. [PMID: 29486123 DOI: 10.1021/acssynbio.8b00021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Robotic automation in synthetic biology is especially relevant for liquid handling to facilitate complex experiments. However, research tasks that are not highly standardized are still rarely automated in practice. Two main reasons for this are the substantial investments required to translate molecular biological protocols into robot programs, and the fact that the resulting programs are often too specific to be easily reused and shared. Recent developments of standardized protocols and dedicated programming languages for liquid-handling operations addressed some aspects of ease-of-use and portability of protocols. However, either they focus on simplicity, at the expense of enabling complex protocols, or they entail detailed programming, with corresponding skills and efforts required from the users. To reconcile these trade-offs, we developed Roboliq, a software system that uses artificial intelligence (AI) methods to integrate (i) generic formal, yet intuitive, protocol descriptions, (ii) complete, but usually hidden, programming capabilities, and (iii) user-system interactions to automatically generate executable, optimized robot programs. Roboliq also enables high-level specifications of complex tasks with conditional execution. To demonstrate the system's benefits for experiments that are difficult to perform manually because of their complexity, duration, or time-critical nature, we present three proof-of-principle applications for the reproducible, quantitative characterization of GFP variants.
Collapse
Affiliation(s)
- Ellis Whitehead
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Hans-Michael Kaltenbach
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| |
Collapse
|
32
|
Gao Y, Tian W, Han X, Gao F. Immunological and virological characteristics of human immunodeficiency virus type 1 superinfection: implications in vaccine design. Front Med 2017; 11:480-489. [PMID: 29170914 DOI: 10.1007/s11684-017-0594-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/30/2017] [Indexed: 02/04/2023]
Abstract
Superinfection is frequently detected among individuals infected by human immunodeficiency virus type I (HIV-1). Superinfection occurs at similar frequencies at acute and chronic infection stages but less frequently than primary infection. This observation indicates that the immune responses elicited by natural HIV-1 infection may play a role in curb of superinfection; however, these responses are not sufficiently strong to completely prevent superinfection. Thus, a successful HIV-1 vaccine likely needs to induce more potent and broader immune responses than those elicited by primary infection. On the other hand, potent and broad neutralization responses are more often detected after superinfection than during monoinfection. This suggests that broadly neutralizing antibodies are more likely induced by sequential immunization of multiple different immunogens than with only one form of envelope glycoprotein immunogens. Understanding why the protection from superinfection by immunity induced by primary infection is insufficient and if superinfection can lead to cross-reactive immune responses will be highly informative for HIV-1 vaccine design.
Collapse
Affiliation(s)
- Yang Gao
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Wen Tian
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China.
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China. .,Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
| |
Collapse
|
33
|
Chao R, Mishra S, Si T, Zhao H. Engineering biological systems using automated biofoundries. Metab Eng 2017; 42:98-108. [PMID: 28602523 PMCID: PMC5544601 DOI: 10.1016/j.ymben.2017.06.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 05/22/2017] [Accepted: 06/05/2017] [Indexed: 11/19/2022]
Abstract
Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges.
Collapse
Affiliation(s)
- Ran Chao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Shekhar Mishra
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Tong Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Departments of Chemistry, Biochemistry, Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
| |
Collapse
|
34
|
Goodman DB, Kuznetsov G, Lajoie MJ, Ahern BW, Napolitano MG, Chen KY, Chen C, Church GM. Millstone: software for multiplex microbial genome analysis and engineering. Genome Biol 2017; 18:101. [PMID: 28545559 PMCID: PMC5445467 DOI: 10.1186/s13059-017-1223-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/26/2017] [Indexed: 11/10/2022] Open
Abstract
Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.
Collapse
Affiliation(s)
- Daniel B Goodman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA
| | - Gleb Kuznetsov
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Program in Biophysics, Harvard University, Boston, MA, USA
| | - Marc J Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA
| | - Brian W Ahern
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael G Napolitano
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Kevin Y Chen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Changping Chen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
35
|
Nguyen Quang N, Perret G, Ducongé F. Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers. Pharmaceuticals (Basel) 2016; 9:ph9040076. [PMID: 27973417 PMCID: PMC5198051 DOI: 10.3390/ph9040076] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS.
Collapse
Affiliation(s)
- Nam Nguyen Quang
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
| | - Gérald Perret
- LFB Biotechnologies, 3 avenue des Tropiques, 91958 Courtaboeuf CEDEX, France.
| | - Frédéric Ducongé
- CEA, DSV, I²BM, Molecular Imaging Research Center (MIRCen), 18 route du panorama, 92260 Fontenay-aux-Roses, France.
- Neurodegenerative Diseases Laboratory, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Université Paris-Sud, UMR 9199, 92260 Fontenay-aux-Roses, France.
| |
Collapse
|
36
|
Walter JM, Chandran SS, Horwitz AA. CRISPR-Cas-Assisted Multiplexing (CAM): Simple Same-Day Multi-Locus Engineering in Yeast. J Cell Physiol 2016; 231:2563-9. [PMID: 26991244 DOI: 10.1002/jcp.25375] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/11/2016] [Indexed: 01/21/2023]
Abstract
Demands on the industrial and academic yeast strain engineer have increased significantly in the era of synthetic biology. Installing complex biosynthetic pathways and combining point mutations are tedious and time-consuming using traditional methods. With multiplex engineering tools, these tasks can be completed in a single step, typically achieving up to sixfold compression in strain engineering timelines. To capitalize on this potential, a variety of yeast CRISPR-Cas methods have been developed, differing largely in how the guide RNA (gRNA) reagents that direct the Cas9 nuclease are delivered. However, in nearly all reported protocols, the time savings of multiplexing is offset by multiple days of cloning to prepare the required reagents. Here, we discuss the advantages and opportunities of CRISPR-Cas-assisted multiplexing (CAM), a same-day, cloning-free method for multi-locus engineering in yeast. J. Cell. Physiol. 231: 2563-2569, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
|
37
|
Abstract
Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis.
Collapse
Affiliation(s)
- Simone Picelli
- a Eukaryotic Single Cell Genomics Facility , Science for Life Laboratory , Tomtebodavägen , Solna , Sweden
| |
Collapse
|
38
|
Hora B, Keating SM, Chen Y, Sanchez AM, Sabino E, Hunt G, Ledwaba J, Hackett J, Swanson P, Hewlett I, Ragupathy V, Vikram Vemula S, Zeng P, Tee KK, Chow WZ, Ji H, Sandstrom P, Denny TN, Busch MP, Gao F. Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites. PLoS One 2016; 11:e0157340. [PMID: 27314585 PMCID: PMC4912073 DOI: 10.1371/journal.pone.0157340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/29/2016] [Indexed: 12/20/2022] Open
Abstract
HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.
Collapse
Affiliation(s)
- Bhavna Hora
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheila M. Keating
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
| | - Yue Chen
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ana M. Sanchez
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ester Sabino
- Instituto de Medicina Tropical, Sao Paolo Brazil
| | - Gillian Hunt
- National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Johanna Ledwaba
- National Institute of Communicable Diseases, Johannesburg, South Africa
| | - John Hackett
- Abbott Laboratories, Infectious Diseases Research, Abbott Park, Illinois, United States of America
| | - Priscilla Swanson
- Abbott Laboratories, Infectious Diseases Research, Abbott Park, Illinois, United States of America
| | - Indira Hewlett
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Viswanath Ragupathy
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Sai Vikram Vemula
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Peibin Zeng
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Kok-Keng Tee
- Centre of Excellence for Research in AIDS, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Zhen Chow
- Centre of Excellence for Research in AIDS, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hezhao Ji
- National HIV & Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Thomas N. Denny
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | | |
Collapse
|
39
|
Wilson EH, Sagawa S, Weis JW, Schubert MG, Bissell M, Hawthorne B, Reeves CD, Dean J, Platt D. Genotype Specification Language. ACS Synth Biol 2016; 5:471-8. [PMID: 26886161 DOI: 10.1021/acssynbio.5b00194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We describe here the Genotype Specification Language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.
Collapse
Affiliation(s)
- Erin H. Wilson
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Shiori Sagawa
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - James W. Weis
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Max G. Schubert
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Michael Bissell
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Brian Hawthorne
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Christopher D Reeves
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Jed Dean
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| | - Darren Platt
- Amyris, Inc., 5885 Hollis Street, Suite 100, Emeryville, California 94608, United States
| |
Collapse
|
40
|
Mora-Castilla S, To C, Vaezeslami S, Morey R, Srinivasan S, Dumdie JN, Cook-Andersen H, Jenkins J, Laurent LC. Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing. ACTA ACUST UNITED AC 2016; 21:557-67. [PMID: 26891732 PMCID: PMC4948133 DOI: 10.1177/2211068216630741] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 11/15/2022]
Abstract
As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing.
Collapse
Affiliation(s)
- Sergio Mora-Castilla
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Cuong To
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soheila Vaezeslami
- TTP Labtech Ltd., Melbourn Science Park, Melbourn, Royston, Hertfordshire, UK
| | - Robert Morey
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Jennifer N Dumdie
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joby Jenkins
- TTP Labtech Ltd., Melbourn Science Park, Melbourn, Royston, Hertfordshire, UK
| | - Louise C Laurent
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|