The workshop is designed to provide a solid understanding of the nuances of experimentation and data analysis on picocyanobacteria. Open to both novices and experts alike, it will be a forum for sharing established protocols and omics tools as well as those under development. All the sessions will be method-oriented and include videos of hands-on experiments and time for discussion with participants on technical questions.
Laboratory topics will include: Strategies for culturing in large and small volumes, continuous and semi-continuous cultures, co-culture with heterotrophs, cryopreservation, isolating cells from natural seawater, agar plating; cyanophage methods such as plaque assays, or how to knock out genes in the cyanophage genome; progress in the development of genetic tools for both Prochlorococcus and Synechococcus, the lessons to be learned and discussion of paths forward, with recent examples of applications from their ‘model’ sister, Synechocystis; the challenges of working with picocyanobacteria lipids and vesicles. The aim is to disseminate expertise in working with these fascinating (but finicky) microbes!
As a bonus, participants will also have an opportunity to select from a large diversity of characterized cultured strains across the diversity of the genus which will be mailed to them after the conference.
In parallel, a separate track will feature the most relevant bioinformatics databases and tools available to handle the ever-growing amount of ‘omics’ data and metadata available on these microbes – presented by their developers: the IMG database, the new home for Proportal; “Planet Microbe”, a marine-specific portal for iMicrobe/muSCOPE; The BioCyc database collection gathering 14,735 pathway/genome databases, plus software tools for exploring them; “Cyanorak”, a manually curated database of clusters of orthologs built from 97 picocyanobacteria genomes; and CMAP, a visualization platform for oceanic datasets.
|WORKSHOP||Laboratory track||Computational track|
|8:30-9:00||Registration of workshop attendants / Welcome tea, coffee, etc|
|9:00-11:00||Culturing picocyanobacteria Organizer: Allison Coe Contributors: Lisa Moore, John Waterbury||Rekha Seshadri: "Comparative Genomics for Gene Discovery using Integrated Microbial Genomes (IMG)"|
|11:00-11:30||Coffee break||Coffee break|
|11:30-13:00||Marine Cyanophages Organizer: Debbie Lindell Speakers: Dror Shirtrit||Bonnie Hurwitz: “Planet Microbe: a Cyberinfrastructure for marine sciences and analytics"|
|14:00-15:30||Genetics in Cyanobacteria Organizer: David Kehoe Contributors: David Lea-Smith||Peter Karp: The BioCyc Database Collection|
|15:30-16:00||Coffee break||Coffee break|
|16:00-17:00||Genetics in Cyanobacteria (cont.)||Frédéric Partensky: Cyanorak v2, a scalable information system for the visualization and expert curation of picocyanobacteria genome|
|17:00-18:00||Vesicles and Lipids Organizer: Steven Biller Contributors: María del Carmen Muñoz-Marín||E. Virginia Armbrust: CMAP, an open-source data service to retrieve, visualize, and analyze oceanic datasets|
|17:30-19:00||Welcome of other participants of the conference / Drinks + appetizers - Caballerizas Reales|
|Evening||Dinner in town (attendees on their own)|