Slideshow of Otters at the UC Davis Riparian Preserve

Made a slideshow of the otters I saw at the UC Davis Riparian Preserve yesterday. See

Videos of Talks from the JGI "NeLLi (New Lineages of Life)" Meeting Now Available

Recently the DOE JGI Hosted the "NeLLi" meeting on New Lineages of life.  See agenda here: https://usermeeting.jgi.doe.gov/2021-nelli/2021-nelli-agenda/ 

There were a whole series of interesting talks in this program and now the videos are available on Youtube. 

See Youtube Channel or the embedded video link below.

Wall Street Journal Podcast on the Downfall of uBiome, part 1 and 2

Part 1 of "The Journal" podcast featuring story by Amy Marcus et al on the downfall of uBiome.  Includes interviews with multiple people including myself.

What went wrong at uBiome, Part 1. 

 

Part 2 has now been posted

 

Some recent posts of interests from my lab blog and MicroBEnet

So I have been lax in blogging these days as I spend a lot of time on Twitter. And when I do write blog posts, I don't always post here - I also post blog posts to a few other places including my lab blog and the microBEnet blog. Here are a few moderately recent posts from these places

Lab Blog

• The tale of the blue soy products – from contaminated soy milk to a new publication
• The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies (talk video and slides)
• New paper from the Eisen lab (with many others) on Global biogeography of chemosynthetic symbionts

microBEnet blog

• Metagenomic Binning / Assembly
• Wanted: Workers for the COVID19 Mass Testing Operations for UC Davis and Healthy Davis Together 
• Compiling Information about COVID19 transmission, masks, filtration, schools, etc.
• Wanted – science driven guidelines for deciding if and how to keep open / reopen schools re: #COVID19

Some thoughts on the CDC new mask guidance

 

See this thread 

I am with @kprather88 here. Really vexed by what @CDCDirector and @CDCgov have done here. I mean, I get the general idea of trying to return to normal and encourage vaccination. But here are some thoughts for why I am still a bit vexed. https://t.co/tTzdFYoTqU

— Jonathan Eisen (@phylogenomics) May 14, 2021

Made into a thread reader thread here: https://threadreaderapp.com/thread/1393025234303741954.html 

Compiling some of my Twitter comments about the evolution and origins of SarsCoV2/ COVID19

 News Stories Quoted in

• UC Davis Aggie: Emerging SARS-CoV-2 variants raise concern for the future of the pandemic
• 9/15/2020. Newsweek. Fact-check: Does a New Study Give Evidence that the Coronavirus Was Made In a Lab?
• May 17, 2020. Newsweek: Scientists Shouldn't Rule Out Lab As Source of Coronavirus, New Study Says
• April 27, 2020. The controversial experiments and wuhan lab suspected of starting the coronavirus pandemic. Newsweek. 

Twitter Threads

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Relating to the lab vs natural origin theory of #SarsCOV2. I would like to call attention to the history of the anthrax attack investigation. Circumstantial evidence, that seemed so strong to so many people, was used to falsely accuse multiple people. https://t.co/olpDu8sKT9

— Jonathan Eisen (@phylogenomics) March 27, 2021

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Reading: Why the COVID lab-leak theory in Wuhan shouldn't be dismissed

By ⁦@alisonannyoung⁩ in ⁦⁦@USATODAY⁩ . #covid19 https://t.co/u42TxLOcHe

— Jonathan Eisen (@phylogenomics) March 22, 2021

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This is a fascinating deep look into theories about the origins of #B117 #SARSCoV2 variant:

A lone infection may have changed the course of the pandemic https://t.co/jKNgWth63T

By @mattsreynolds1 w/ comments from @EvolveDotZoo, @LauringLab @firefoxx66 @GuptaR_lab @jcbarret

— Jonathan Eisen (@phylogenomics) February 10, 2021

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Worth reading / rereading - on the risks of gain of function research from 2014 from The Cambridge Working Group #covid19 #GainOfFunction https://t.co/PfTd32nNHe

— Jonathan Eisen (@phylogenomics) May 19, 2020

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Yes, as I told @newsweek it is theoretically possible that a Chinese lab accidentally released #SARSCoV2 https://t.co/90qFnFcKJc but preponderance of evidence so far supports all natural events and the evidence actually supporting "lab release" is shown in this pic #Covid19 pic.twitter.com/TyqAiFnQuf

— Jonathan Eisen (@phylogenomics) May 3, 2020

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Reading: Scientists shouldn't rule out lab as source of coronavirus, new study says https://t.co/cZIyRXczrY - personally I do not find the analysis in this new paper remotely convincing 1/n

— Jonathan Eisen (@phylogenomics) May 17, 2020

New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

See Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum 

Paper based on PhD thesis work of Katie Dahlhausen and wrap up of analysis led by Laetitia Wilkins. 

Full citation:

Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LGE. 2020. Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ8:e10177 https://doi.org/10.7717/peerj.10177

Acknowledgements. We thank Céline Caseys ORCID: 0000-0003-4187-9018 for her idea to search eggNOG annotations against KEGG Class 1.11 Xenobiotics biodegradation and metabolism pathways; Chris Brown ORCID: 0000-0002-7758-6447 for his script to download assemblies in batch from GenBank; Cassandra L. Ettinger ORCID: 0000-0001-7334-403X for valuable comments on the pangenome analysis and help with revising the figures. We also thank Dr. Joseph Gillespie ORCID: 0000-0002-5447-7264, Dr. Raphael Eisenhofer ORCID: 0000-0002-3843-0749 and two anonymous reviewers for comments on the submitted manuscript. Isolate 16S Sanger sequencing was performed at the UC Davis College of Biological Sciences DNA Sequencing Facility.