Biology subjects

Mante, J.

Publications and source records attributed to Mante, J..

4 recordsLinked to original sources

bioRxiv2023

SeqImprove: Machine Learning Assisted Creation of Machine Readable Sequence Information

The progress and utility of synthetic biology is currently hindered by the lengthy process of studying literature and replicating poorly documented work. Reconstruction of crucial design information through post-hoc curation is highly noisy and error-prone. To combat this, author participation during the curation process is crucial. To encour-age author participation without overburdening them, an ML-assisted curation tool called SeqImprove has been developed. Using named entity recognition, named entity normalization, and sequence matching, SeqImprove creates machine-readable sequence data and metadata annotations, which authors can then review and edit before sub-mitting a final sequence file. SeqImprove makes it easier for authors to submit FAIR sequence data that is findable, accessible, interoperable, and reusable.

bioinformatics↗

bioRxiv2022

Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories

Accelerating the development of synthetic biology applications requires reproducible experimental findings. Different standards and repositories exist to exchange experimental data and metadata. However, the associated software tools often do not support a uniform data capture, encoding, and exchange of information. A connection between digital repositories is required to prevent siloing and loss of information. To this end, we developed the Experimental Data Connector (XDC). It captures experimental data and related metadata by encoding it in standard formats and storing the converted data in digital repositories. Experimental data is then uploaded to Flapjack and the metadata to SynBioHub in a consistent manner linking these repositories. This produces complete connected experimental datasets that are exchangeable. The information is captured using a single template Excel Workbook, which can be integrated into existing experimental workflow automation processes. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/520467v1_ufig3.gif" ALT="Figure 3"> View larger version (50K): org.highwire.dtl.DTLVardef@1c5f886org.highwire.dtl.DTLVardef@3f2a6dorg.highwire.dtl.DTLVardef@fa6cb2org.highwire.dtl.DTLVardef@f63236_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

Standards support synthetic biology research by enabling the exchange of component information. However, using formal representations, such as the Synthetic Biology Open Language (SBOL), typically requires either a thorough understanding of these standards or a suite of tools developed in concurrence with the ontologies. Since these tools may be a barrier for use by many practitioners, the Excel-SBOL Converter was developed to allow easier use of SBOL and integration into existing workflows. The converter consists of two Python libraries: one that converts Excel templates to SBOL, and another that converts SBOL to an Excel workbook. Both libraries can be used either directly or via a SynBioHub plugin. We illustrate the operation of the Excel-SBOL Converter with two case studies: uploading experimental data with the studys metadata linked to the measurements and downloading the Cello part repository. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/505873v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@c06d7aorg.highwire.dtl.DTLVardef@153724eorg.highwire.dtl.DTLVardef@1758791org.highwire.dtl.DTLVardef@11779c2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

Building artificial plant cell wall on lipid bilayer by assembling polysaccharides and engineered proteins

The cell wall constitutes a fundamental structural component of plant cells, providing them with mechanical resistance and flexibility. Mimicking that wall is a critical step in the conception of an experimental model of the plant cell. The assembly of cellulose/hemicellulose in the form of cellulose nanocrystals and xyloglucans as a representative model of the plant cell wall has already been mastered, however, those models lacked the pectin component. In this work, we used an engineered chimeric protein designed for bridging pectin to the cellulose/hemicellulose network, therefore achieving the assembly of complete cell wall mimics. We first engineered proteins, i.e. carbohydrate-binding module from Ruminococcus flavefaciens able to bind oligo-galactorunan, resulting in high-affinity polygalacturonan receptors with Kd in the micromolar range. A Janus protein, with cell wall gluing property, was then designed by assembling this CBM with a Ralstonia solanacearum lectin specific for fucosylated xyloglucans. The resulting supramolecular architecture is able to bind fucose-containing xyloglucans and homogalacturonan ensuring high affinity for both. A two-dimension assembly of an artificial plant cell wall was then built first on synthetic polymer and then on supported lipid bilayer. Such artificial cell wall can serve as a basis for the development of plant cell mechanical models and thus deepen the understanding of the principles underlying various aspects of plant cells and tissues. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=123 HEIGHT=200 SRC="FIGDIR/small/501355v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@18af594org.highwire.dtl.DTLVardef@ec3dorg.highwire.dtl.DTLVardef@95d44aorg.highwire.dtl.DTLVardef@a47bea_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗