SteinBlog

Proud members of Microverse Cluster of Excellence

We are thrilled to announce that the proposal “Balance of the Microverse” has been selected as a cluster of excellence by the Excellence Commission, consisting of the members of the international Committee of Experts and the research ministers of the federal and state governments of Germany. Group leader Prof. Christoph Steinbeck is one of the principle investigators of the proposal. The cluster will be funded with 50 mio Euros over 7 years. The mission of the Balance of the Microverse Cluster is to understand microbial balance from the molecular to the ecosystem level and to develop detection and manipulation technologies to create beneficial impact.

 


Slides of my talk on NMR data sharing at ACS Boston, August 2018

The slides of my talk on NMR data sharing at ACS Boston, August 2018, can be found at https://doi.org/10.6084/m9.figshare.6984314

The submitted abstract was:

NMR spectroscopic data is a cornerstone in the structure elucidation and identification of organic molecules. In publications on newly synthesised compounds and their intermediates as well as in the characterisation of novel natural products, NMR data are indispensable components of experimental sections, albeit typically reported in ways which destroy information. This talk reports on two current community efforts to a) create an open, distributed and internationally adopted repository for raw NMR data (McAlpine2018) and b) the new NMReData format, a lightweight description of curated NMR data and their assignment to chemical structures (Pupier2018).

Raw NMR data only reaches its maximum potential usefulness if it is universally accessible. While molecular biology has paved the way through the establishment of open data repositories in many of its subfields, developments in areas overlapping with chemistry, such as metabolomics, have shown that the technology for a repository for open raw NMR data is at our fingertips and we will discuss aspects leading towards the creation of such an archive. Furthermore, here is no standard file for the NMR data relevant to structure elucidation. With NMReData, a file format is introduced and presented here, to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds with the assigned chemical structure. NMReDATA descriptions include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times and diffusion rates. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, automating the verification of published result, and for assisting the constitution of open-access structural databases.

We believe that the combination of these two grassroots movements as well as a requirement from publishers to deposit the raw NMR data in open access repositories, as is customary and well accepted in genetics, crystallography and other fields, will have a substantial impact on the reproducibility of chemistry studies and aid the development of new and better tools for dereplication and structure verification.

References:

[tpsingle key=”Pupier:2018jo” link=true]

[tpsingle key=”McAlpine:2018ee” link=true]

 


Steinbeck group joins ChemBioSys to lead INF project

With effect from 1 July 2018, we are proud members of the collaborative research center ChemBioSys to lead the informatics project. ChemBioSys, composed of 18+ research groups and PIs at the University of Jena, the Leibniz Institute for Natural Product Research and Infection Biology and the Max-Planck-Institute for Chemical Ecology,  investigates the regulation, activity and function of natural products in complex communities.


Current Challenges in Plant-Ecometabolomics

Our new overview article entitled “Current Challenges in Plant-Ecometabolomics” has just appeared in the International Journal of Molecular Sciences [tpcite key=”Peters:2018cv”]. As we explain in the abstract, “[t]he relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms.”

[tpref link=true]