Science News Past Items

New Publication: Adaptations to the Calvin cycle by genome comparison

Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes is published in PLoS Computational Biology.

In this computational work, Johannes found one thousand non-cyanobacterial genomes containing the Calvin cycle, and compared them to close relatives that lacked the Calvin cycle. We wondered how bacteria integrate a newly-acquired Calvin cycle into their metabolism. Using multiple analyses, including a machine learning algorithm, he found some key differences in the abundance of genes and protein family domains between these two groups. The software he developed for this analysis is RedMAGPIE, for "Reductive pentose phosphate pathway Machine-Assisted Genomic Pattern Identification and Evaluation." Perhaps most interesting are genes and protein domains of unknown function that were revealed to be of high importance. Some of these likely play a role in regulating the Calvin cycle, and could be targets for metabolic engineering. RedMagPie_striking RedMAGPIE ranks genetic adaptations to the Calvin cycle to construct a recipe for an autotrophic microbe.

Our new website

Behold! We have for a while wanted our own website. It was important for us to be able to share our software, data, and publications in a coherent way, so as to make a faithful impression on visitors. We are so pleased with the layout and imagery! This website was designed and built by Balthazar Berling Kelpe. We use Cirrus Cumulus by Clara Sambot for our logo.

Conference: AlgaeEurope 2020

Paul gave a 2 minute pitch at the AlgaeEurope 2020 (virtual). The conference was focused on cultivation and engineering of microalgae for economical production of chemicals. You can see the pitch here.

Kiyan Shabestary, Ph.D.

Kiyan successfully defended his Ph.D. thesis, Improving cyanobacteria productivity: From theory to assay. The defense was held over Zoom. The opponent was Danny Ducat from Michigan State. Thanks for getting up so early! The committee was Karin Stensjö from Uppsala, Carl Johan Franzén from Chalmers, and Veronique Chotteau from KTH. Congratulations to Kiyan! Kiyan defense party

Conference: 11th European Workshop on Molecular Biology of Cyanobacteria

We attended the 11th European Workshop on Molecular Biology of Cyanobacteria, which is held every two years. This time it was organized by Paula Tamagnini of Porto, but was virtual. While we were bummed not to be able to visit Porto, the conference went off well with three days of new research in the cyanobacteria world. Paul and Michael gave talks (see Resources page). Markus and Jan gave posters.

New Funding: Agenda 2030 Research Centre in Plant Biotechnology

Our group will be part of a new Center for Plant Biotechnology, funded by SSF (Swedish Foundation for Strategic Research) as one of four Agenda 2030 Research Centers. Our center is led by Prof. Åsa Strand of Umeå University and will focus on enhancing the rate photosynthesis in plant by engineering both the Calvin cycle and light protection. Other center partners are Alizee Malnoe of Umeå University and Alexey Amunts of Stockholm University/SciLifeLab. The center will begin in Fall 2020. See Press Release from SciLifeLab.

Globala målen 2030

New Funding: Novo Nordisk Foundation Ascending Investigator

Paul was granted an Ascending Investigator in Biotechnology-Based Synthesis and Production Research award by Novo Nordisk Fonden, as part of their Research Leadership Program. This is an honor! We will work on high-throughput screening of Calvin cycle variants. Read more about ours and the other awards in the area of Biotechnology-based synthesis and production here. NNF research leader logo

Presentation: The Nordic Algae Symposium

Ivana presented at this year's Nordic Algae Symposium in Uppsala. The topic was CRISPR technologies in cyanobacteria. The NAS is arranged yearly by the NordAqua Nordforsk Center of Excellence.

Presentation: Moving Across

Paul presented at the Moving Across, Art is Science event at Stallet, Kungsträgården. It was a short presentation about our work on cyanobacteria, and there was an improv group who interepreted our ideas with skits. Thanks to Sandra Petrus-Reurer and the organizing committee from Karolinska Institutet for this invitation! Paul Hudson 2018 Moving Across Moving Across Logo

New publication: CRISPRi libraries in Synechocystis

Lun and Kiyan's paper on pooled CRISPRi libraries in cyanobacteria was published in Nature Communications. Thank you to Johannes for RNA-Seq analysis, and to Sara Björk and Håkan Jönsson for the collaboration with droplet microfluidics technology. Michael led data analysis and also was the figures guru. Michael's visualization of Synechocystis gene fitness is available on our Resources page. Johannes's RNA-Seq data workup software RiboPipe is available on our Software page.