scholarly journals Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly—present and future challenges

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Ian K Blaby ◽  
Jan-Fang Cheng
Keyword(s):  
Department Of Energy ◽  
Joint Genome Institute ◽  
Biological Engineering ◽  
Iterative Design ◽  
Synthetic Dna ◽  
Crucial Component ◽  
Design Build ◽  
Future Challenges ◽  
Engineering Projects ◽  
Energy Joint Genome Institute

Abstract The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design–build–test–learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.

scholarly journals The Genome Portal of the Department of Energy Joint Genome Institute

2011 ◽  
Vol 40 (D1) ◽  
pp. D26-D32 ◽  
Author(s):  
I. V. Grigoriev ◽  
H. Nordberg ◽  
I. Shabalov ◽  
A. Aerts ◽  
M. Cantor ◽  
...  
Keyword(s):  
Department Of Energy ◽  
Joint Genome Institute ◽  
Energy Joint Genome Institute

scholarly journals The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

2013 ◽  
Vol 42 (D1) ◽  
pp. D26-D31 ◽  
Author(s):  
Henrik Nordberg ◽  
Michael Cantor ◽  
Serge Dusheyko ◽  
Susan Hua ◽  
Alexander Poliakov ◽  
...  
Keyword(s):  
Department Of Energy ◽  
Joint Genome Institute ◽  
Energy Joint Genome Institute

scholarly journals Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains

2019 ◽  
Vol 40 (3) ◽  
pp. 125
Author(s):  
William B Whitman ◽  
Hans-Peter Klenk ◽  
David R Arahal ◽  
Rosa Aznar ◽  
George Garrity ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Transcriptome Sequencing ◽  
Department Of Energy ◽  
Joint Genome Institute ◽  
The Us ◽  
Prokaryotic Species ◽  
Type Strains ◽  
Genomic Encyclopedia ◽  
Energy Joint Genome Institute

Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new project GEBA VI extends these efforts to functional genomics, including pangenome and transcriptome sequencing and exometabolite analyses. As part of this project, investigators with interests in specific groups of prokaryotes are invited to submit samples for analysis at JGI.

scholarly journals Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals

2021 ◽  
Vol 9 (5) ◽  
pp. 1079
Author(s):  
Alec Banner ◽  
Helen S. Toogood ◽  
Nigel S. Scrutton
Keyword(s):  
Enzymatic Degradation ◽  
Consolidated Bioprocessing ◽  
Carbon Sources ◽  
Cellulolytic Enzymes ◽  
Waste Biomass ◽  
Chemical Production ◽  
Iterative Design ◽  
Biomass Feedstocks ◽  
Advanced Fuels ◽  
Design Build

The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.

scholarly journals Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Andrew Currin ◽  
Neil Swainston ◽  
Mark S Dunstan ◽  
Adrian J Jervis ◽  
Paul Mulherin ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Dna Sequencing ◽  
Cost Effective ◽  
Polymorphism Analysis ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Synthetic Dna ◽  
Design Build ◽  
Hardware Costs

Abstract Synthetic biology utilizes the Design–Build–Test–Learn pipeline for the engineering of biological systems. Typically, this requires the construction of specifically designed, large and complex DNA assemblies. The availability of cheap DNA synthesis and automation enables high-throughput assembly approaches, which generates a heavy demand for DNA sequencing to verify correctly assembled constructs. Next-generation sequencing is ideally positioned to perform this task, however with expensive hardware costs and bespoke data analysis requirements few laboratories utilize this technology in-house. Here a workflow for highly multiplexed sequencing is presented, capable of fast and accurate sequence verification of DNA assemblies using nanopore technology. A novel sample barcoding system using polymerase chain reaction is introduced, and sequencing data are analyzed through a bespoke analysis algorithm. Crucially, this algorithm overcomes the problem of high-error rate nanopore data (which typically prevents identification of single nucleotide variants) through statistical analysis of strand bias, permitting accurate sequence analysis with single-base resolution. As an example, 576 constructs (6 × 96 well plates) were processed in a single workflow in 72 h (from Escherichia coli colonies to analyzed data). Given our procedure’s low hardware costs and highly multiplexed capability, this provides cost-effective access to powerful DNA sequencing for any laboratory, with applications beyond synthetic biology including directed evolution, single nucleotide polymorphism analysis and gene synthesis.

scholarly journals Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
Dylan Parks ◽  
In-Hwa Chung ◽  
In kyu Lee ◽  
Eui-Joong Kim ◽  
Sarbjeet Niraula ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Vitamin K2 ◽  
Department Of Energy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Bacillus Subtilis Natto ◽  
High Production ◽  
Energy Joint Genome Institute

Bacillus subtilis strain natto VK161 was selected for its high production of vitamin K2. Its genome was sequenced and annotated in the Department of Energy-Joint Genome Institute (DOE-JGI) annotation pipeline. It resulted in a chromosome of 4,073,396 bp, which is composed of 4,332 protein-coding genes, 23 rRNA genes, and 77 tRNA genes.

The Analysis of Passive Design in Zero-Energy Buildings: A Case Study of Solar Decathlon

2013 ◽  
Vol 689 ◽  
pp. 119-124
Author(s):  
Cheng Chen ◽  
Rong Wen Du ◽  
Hao Zhang
Keyword(s):  
Department Of Energy ◽  
Zero Energy ◽  
Solar Decathlon ◽  
Living Space ◽  
Design Build ◽  
Passive Design ◽  
Ecological Landscape ◽  
Solar House ◽  
Zero Energy Buildings

In order to promote the development of the zero-energy buildings, the U.S. Department of Energy Solar Decathlon is held biennially, in which every team is required to design, build and operate an energy-efficient house powered by the sun. This paper is focused on the innovative passive design in the Solar Decathlon 2011 in following five categories: the indoor and outdoor space, the envelop, the ecological system as well as the shading structure. Based on the case studies, it is suggested that the solar house is emphasizing more flexible living space, the multifunctional envelop and the ecological landscape.

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