Micro-Eco Discussion Group

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MBL MICRO-ECO DISCUSSION GROUP

Meets Thursdays, 2:30-3:30 PM, Lillie 103, unless otherwise stated

MBL Micro-Eco Discussion Group, Fall 2018

Sept. 20: Organizational meeting

Last spring, we all decided we'd like to have a rotating set of 3 kinds of sessions. We'll mix :

--Looking into the statistics used in microbiomes/microbial community analysis - compare, contrast, understand the strengths and weaknesses of various techniques
--Hearing project and research updates from members -- whether projects that came out of MicroEco discussions, or projects that people are working on separately, or practice talks for meetings or jobs, etc.
--Pulling in new literature on varied topics that have caught people's eyes - journal-club like

For stats, we've started a google drive folder where papers could be added. Everyone should have view and edit access using this link:

https://drive.google.com/drive/folders/18ozoHpeLn8TjXlitW_LfdXE6vQ7mdvEk?usp=sharing

A book we might find helpful is "Modern Statistics for Modern Biology", by Susan Holmes and Wolfgang Huber
http://web.stanford.edu/class/bios221/book/index.html#Home

For new literature, here's another google drive folder where papers can be added. Again, all should have view and edit access using this link:

https://drive.google.com/drive/folders/1tZp-YVcA0fPLUjBPUpqERWHytSmGr_6M?usp=sharing

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Sept. 27 ___ Rut Pedrosa-Pamies _research talk

Rut will tell us about her work work analyzing lipid biomarkers (of e.g. phytoplankton, zooplankton, and bacteria) associated with suspended particles in the ocean. She'd like to discuss with you all the big opportunities she sees for combining organic molecular geochemistry (her expertise) and metagenomics.

Please read the abstract, the introduction, the discussion sections 4.1-4.3 and conclusions in PedrosaPamies et al. (in press) . (The other two papers below are "gravy" for discussion -- eyeball if you're interested!)

Pedrosa-Pamies R, Conte MH, Weber JC, and Johnson R (2018) Carbon cycling in the Sargasso Sea water column: Insights from lipid biomarkers in suspended particles. Progress in Oceanography 167 (in press).

Metfies K et al. (2017) Protist Communities in Moored Long-Term Sediment Traps (Fram Strait, Arctic)–Preservation with Mercury Chloride Allows for PCR-Based Molecular Genetic Analyses. Front. Mar. Sci. 4:301. doi: 10.3389/fmars.2017.00301

Mestre et al. (2018) Sinking particles promote vertical connectivity in the ocean microbiome. PNAS 115 (29): E6799–E6807

Oct. 4 ___ Jessica Mark Welch ___new literature

Bar-On YM, Phillips R, and Milo R (2018). The biomass distribution on Earth. PNAS www.pnas.org/cgi/doi/pnas.1711842115

Oct. 11 ___ Peter Larsen___ ( Argonne Natl. Lab) Machine learning with omics datasets. (Ashley Bulseco-McKim, host)

Focus on:

Larsen PE, Dai Y (2015) Metabolome of human gut microbiome is predictive of host dysbiosis. GigaScience 4:42 DOI 10.1186/s13742-015-0084-3

And these two papers (below) are also relevant:

Larsen PE et al. (2015) Satellite remote sensing data can be used to model marine microbial metabolite turnover. The ISME Journal 9:166-179.

Larsen PE et al. (2016)Multi-Omics approach identified molecular mechanisms of plant-fungus mycorrhizal interaction. Front. PlantSci.6:1061. doi: 10.3389/fpls.2015.01061

Oct. 18 ___No meeting -- NSF grant-writing discussion later in afternoon!_______________