ATG’s molecular BioDesign Services are based on genome mining, analytics and rationally derived gene statistics


ATG’s molecular BioDesign Services are based on genome mining, analytics and rationally derived gene statistics


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Products & Services | ATG:biosynthetics GmbH

Overview

The genomic informational space that contains the accumulated treasure of 3.5 billion years of life form evolution. This forms a huge and highly complex world with many virtual continents still to be discovered.

Primary comparative genomic data provide the keys for exploring and exploiting this world through ‘genome mining’ – bioinformatics research in genomic data. This can unearth valuable and precise formal-functional information to exploit this information in vitro as well as in combination with constructive molecular biodesigns in vivo.

Comparative genomic analyses combine newly gained evolutionary information with thorough genome statistics for identifying pattern of analytically meaningful genetic diversity and experimentally and constructively exploitable formal functionality.

ATG:biosynthetics offers advanced molecular analytics and biodesign services as well as its realization through gene synthesis based on rational genomic data by exploiting its proprietary platform technology EvoMAGIS2.0 .

Using genome statistical data for functional gene design and realization by gene synthesis

Pan-genetic and Pan-genomic data, the exploration of favorable gene functions like enzymatic activities encoded by individual single genes, can be efficiently performed, enabling the creation of gene clusters that form functional pathways coding for enzymatic cascades like physiologically active compounds (e.g. PKS/ NRPS).

The data also yields valuable information about the molecular parameters influencing functional expression of target genes, which can be delineated from genomes using comparative gen(om)e statistics RNA seq and proteomics analyses.

Genomic primary data in combination with pan-genome mining can provide excellent informational sources for rational molecular designs to drive forward development of bio-analytical technologies and bio-production processes.

Desired synthetic biological applications can thus be programmed that closely match the rationally determined formal-functional requirements of an expression target organism.

Example 1: Epitope signal hits of Mycoplasmal surfome derived peptides arranged in high density peptide array immune analytics by use of serum of infected animal's in life vaccine development.

Example 1: Epitope signal hits of Mycoplasmal surfome derived peptides arranged in high density peptide array immune analytics by use of serum of infected animal’s in life vaccine development.

Bioinformatic analysis for vaccine development

ATG is directly involved in the highest scoring EU Synthetic Biology project MycoSynVac started in 2015. The final objective of MycoSynVac is the generation of life vaccines against veterinary Mycoplasmal pathogens which are self-growing for simple, easy and cost-effective bio-production.

The combination of thorough comparative genomic analytical efforts and finally the generation of molecular constructions for displaying antigenic determinants on the surface was the task of ATG, realized in collaboration with its MycoSynVac project partners. The bacterial chassis for this purpose is under substantial genetically modification (in terms of safety and security issues of its deployment).

In addition, ATG provides computational tools for the analysis of molecular data, database developments for molecular and experimental data integration, stratifying and evaluating results for the generation of valuable information.

As well as providing life vaccine development targets, epitopes are also good for monoclonals and the design of specifically and selectively targeting and binding peptides.

Example 2:  Course of relative codon index values along a bacterial gene sequence. In red: mid to low frequency codons, in blue: higher to high frequency codons (upper image) pre codon calculations (lower image) after codon calculations

Example 2: Course of relative codon index values along a bacterial gene sequence. In red: mid to low frequency codons, in blue: higher to high frequency codons (upper image) pre codon calculations (lower image) after codon calculations

Biochemical pathway engineering

For some years, ATG has been involved in biochemical pathway engineering efforts partly in funded projects in collaboration with the Helmholtz-Institute for Pharmaceutical Research (HIPS) in Saarbrücken, Germany.

Initially these projects have been highly informative in imprinting for ATG’s in-house research and software developments. The projects have used comparative source genome analytics of a variety of different biochemical gene clusters of genes integrated in PKS/NRPS pathways. Thoroughly analyzed gene statistics, sequence compositions, distance parameters, secondary structural data (mRNA, protein), sequence motive, codon usage, ribosomal kinetics and other data are used to back-translate the protein. This allows biochemical gene clusters to be recalculated and modulated to fit the most rational target organism molecular requirements.

ATG has developed the algorithms for pathway engineering for a variety aiming on the bioproduction of different molecules like epothilone, argyrin, myxochromides, PUFAs and many more.

Resources

Click on ATG Molecular BioDesign Services for Gene Syntheses for more information.
Click on ATG to contact the company directly.
Click on Cluster Design for more information on design criteria and parameters.


Supplier Information
Supplier: ATG:biosynthetics GmbH
Address: Weberstrasse 40, 79249 Merzhausen, Germany
Tel: +49 (0) 761 888 9424
Fax: +49 761 888 9425
Website: www.atg-biosynthetics.com/


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