A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the journal has recommended the use of SBOL in their publications.
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http://dx.doi.org/10.1042/BST20160347 | DOI Listing |
J Am Chem Soc
January 2025
Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza 50018, Spain.
DNA nanotechnology is a powerful synthetic approach to crafting diverse nanostructures through self-assembly. Chemical decoration of such nanostructures is often required to tailor their properties for specific applications. In this Letter, we introduce a pioneering method to direct the assembly and enable the functionalization of DNA nanostructures using an azide-bearing functional polyamine.
View Article and Find Full Text PDFAppl Microbiol Biotechnol
January 2025
Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
Lignin, the most abundant renewable source of aromatic compounds on earth, remains underexploited in traditional biorefining. Fraxetin, a naturally occurring flavonoid, has garnered considerable attention in the scientific community due to its diverse and potent biological activities such as antimicrobial, anticancer, antioxidant, anti-inflammatory, and neurological protective actions. To enhance the green and value-added utilization of lignin, Saccharomyces cerevisiae was engineered as a cell factory to transform lignin derivatives to produce fraxetin.
View Article and Find Full Text PDFPlant J
January 2025
College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China.
The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified.
View Article and Find Full Text PDFThe concentrations of individual proteins vary between cells, both developmentally and stochastically. The functional consequences of this variation remain largely unexplored due to limited experimental tools to manipulate the relationship of protein concentration to activity. Here, we introduce a genetically encoded tool based on a tunable amyloid that enables precise control of protein concentration thresholds in cells.
View Article and Find Full Text PDFJ Clin Exp Hepatol
December 2024
Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute, Giza, Egypt.
Background: Liver fibrosis is a serious global health issue, but current treatment options are limited due to a lack of approved therapies capable of preventing or reversing established fibrosis.
Aim: This study investigated the antifibrotic effects of a synthetic peptide derived from α-lactalbumin in a mouse model of thioacetamide (TAA)-induced liver fibrosis.
Methods: analyses were conducted to assess the physicochemical properties, pharmacophore features, and docking interactions of the peptide.
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