Asmparts: assembly of biological model parts.
Ontology highlight
ABSTRACT:
SUBMITTER: Rodrigo G
PROVIDER: S-EPMC2553328 | biostudies-other | 2007 Dec
REPOSITORIES: biostudies-other
Similar Datasets
Project description:There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity.
| S-EPMC3563576 | biostudies-literature
Project description:UnlabelledCombinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment.Availability and implementationBioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilderContactjoel.bader@jhu.eduSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4803390 | biostudies-literature
Project description:The BioBricks standard has made the construction of DNA modules easier, quicker and cheaper. So far, over 100 BioBricks assembly schemes have been developed and many of them, including the original standard of BBF RFC 10, are now widely used. However, because the restriction endonucleases employed by these standards usually recognize short DNA sequences that are widely spread among natural DNA sequences, and these recognition sites must be removed before the parts construction, there is much inconvenience in dealing with large-size DNA parts (e.g., more than couple kilobases in length) with the present standards. Here, we introduce a new standard, namely iBrick, which uses two homing endonucleases of I-SceI and PI-PspI. Because both enzymes recognize long DNA sequences (>18 bps), their sites are extremely rare in natural DNA sources, thus providing additional convenience, especially in handling large pieces of DNA fragments. Using the iBrick standard, the carotenoid biosynthetic cluster (>4 kb) was successfully assembled and the actinorhodin biosynthetic cluster (>20 kb) was easily cloned and heterologously expressed. In addition, a corresponding nomenclature system has been established for the iBrick standard.
| S-EPMC4203835 | biostudies-literature
Project description:We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.
| S-EPMC3044748 | biostudies-literature
Project description:BackgroundThe design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea.Methods/principal findingsBy analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified.Conclusions/significanceOrganizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.
| S-EPMC2441434 | biostudies-literature
Project description:The properties of biological networks, such as those found in the ocular lens capsule, are difficult to study without simplified models. Model polymers are developed, inspired by "worm-like" curve models, that are shown to spontaneously self assemble to form networks similar to those observed experimentally in biological systems. These highly simplified coarse-grained models allow the self assembly process to be studied on near-realistic time-scales. Metrics are developed (using a polygon-based framework) which are useful for describing simulated networks and can also be applied to images of real networks. These metrics are used to show the range of control that the computational polymer model has over the networks, including the polygon structure and short range order. The structure of the simulated networks are compared to previous simulation work and microscope images of real networks. The network structure is shown to be a function of the interaction strengths, cooling rates and external pressure. In addition, "pre-tangled" network structures are introduced and shown to significantly influence the subsequent network structure. The network structures obtained fit into a region of the network landscape effectively inaccessible to random (entropically-driven) networks but which are occupied by experimentally-derived configurations.
| S-EPMC7918283 | biostudies-literature
Project description:We are still far from being able to predict organisms' shapes purely from their genetic codes. While it is imperative to identify which encoded macromolecules contribute to a phenotype, determining how macromolecules self-assemble independently of the genetic code may be equally crucial for understanding shape development. Pollen grains are typically single-celled microgametophytes that have decorated walls of various shapes and patterns. The accumulation of morphological data and a comprehensive understanding of the wall development makes this system ripe for mathematical and physical modeling. Therefore, pollen walls are an excellent system for identifying both the genetic products and the physical processes that result in a huge diversity of extracellular morphologies. In this piece, I highlight the current understanding of pollen wall biology relevant for quantification studies and enumerate the modellable aspects of pollen wall patterning and specific approaches that one may take to elucidate how pollen grains build their beautifully patterned walls.
| S-EPMC9292386 | biostudies-literature
Project description:Kluyveromyces marxianus is a non-conventional yeast whose physiology and metabolism lends itself to diverse biotechnological applications. While the wild-type yeast is already in use for producing fragrances and fermented products, the lack of standardised tools for its genetic and metabolic engineering prevent it from being used as a next-generation cell factory for bio-based chemicals. In this paper, we bring together and characterise a set of native K. marxianus parts for the expression of multiple genes for metabolic engineering and synthetic biology. All parts are cloned and stored according to the MoClo/Yeast Tool Kit standard for quick sharing and rapid construction. Using available genomic and transcriptomic data, we have selected promoters and terminators to fine-tune constitutive and inducible gene expression. The collection includes a number of known centromeres and autonomously replication sequences (ARS). We also provide a number of chromosomal integration sites selected for efficiency or visible phenotypes for rapid screening. Finally, we provide a single-plasmid CRISPR/Cas9 platform for genome engineering and facilitated gene targeting, and rationally create auxotrophic strains to expand the common range of selection markers available to K. marxianus. The curated and characterised tools we have provided in this kit will serve as a base to efficiently build next-generation cell factories from this alternative yeast. Plasmids containing all parts are available at Addgene for public distribution.
| S-EPMC6515861 | biostudies-literature
Project description:This paper presents a set of performance metrics, test methods, and associated artifacts to help progress the development and deployment of robotic assembly systems. The designs for three task board artifacts that replicate small part insertion and fastening operations such as threading, snap fitting, and meshing with standard screws, nuts, washers, gears, electrical connectors, belt drives, and wiring are presented. To support the evaluation of robotic assembly and disassembly operations, benchmarking protocols and performance metrics are presented that leverage these task boards. Finally, robot competitions are discussed as use cases for these task boards.
| S-EPMC7537423 | biostudies-literature
Project description:Host cell invasion is monitored by a series of pattern recognition receptors (PRRs) that activate the innate immune machinery upon detection of a cognate pathogen associated molecular pattern (PAMP). The RIG-I like receptor (RLR) family of PRRs includes three proteins--RIG-I, MDA5, and LGP2--responsible for the detection of intracellular pathogenic RNA. All RLR proteins are built around an ATPase core homologous to those found in canonical Superfamily 2 (SF2) RNA helicases, which has been modified through the addition of novel accessory domains to recognize duplex RNA. This review focuses on the structural bases for pathogen-specific dsRNA binding and ATPase activation in RLRs, differential RNA recognition by RLR family members, and implications for other duplex RNA activated ATPases, such as Dicer.
| S-EPMC4070197 | biostudies-literature