Tuesday, October 20, 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. 2020Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumPeerJ8:e10177 https://doi.org/10.7717/peerj.10177

Acknowledgements. We thank CĂ©line 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.

Monday, August 24, 2020

Great horned owl at #YoloBypass


Went for a walk at Yolo Bypass 8/23/2020 early in the AM and got a nice view of a Great Horned Owl. Here are some pics.

Saturday, June 20, 2020

Introducing "Hammerhead Man" - the superhero you did not know you needed.

So I was digging through some old school papers because my daughter asked me what books they had use write reports on in high school and, well, I have a lot of my English papers from high school in a box in a closet.  

And in digging through this box I found a short story I wrote for a creative writing class from freshman year in college, which was taught by Catherine Tudish. 

Now, mind you, I was not in a good place when I wrote this as I was reading from the death by suicide of my father.  And, possibly related to that I truly have almost no memory of writing this, other than the concept of the assignment. But I read it to my kids. And, well, I actually like it.  It has a lot of issues.  But I think it should be expanded on. I may just revisit this.

So - here is the official first release of "Hammerhead Man".  With corrections and comments from Catherine Tudish. 

Saturday, June 06, 2020

Brief summary of the gear I use for photography (of mostly birds)

So - many people have asked what gear I use for my photography (mostly of birds). Here is a quick summary. See some of my pictures here: https://jonathaneisen.smugmug.com

Camera: Nikon D500

 Lenses Birding: Nikkor 200-500 f/5.6

 Macro: Nikkor 105 mm f/2.8

Based on review of Mark Smith.

See more detail in this blog post here. "Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500.

Wednesday, April 22, 2020

Slides I have used for "Biodiversity and the Tree of Life" at @ucdavis

I have posted the slides I have used so far in remote teaching for "Biodiversity and the Tree of Life" - aka Bis2C - at UC Davis and I thought I would share them here.

Many of the figures are from "Life v 11" by Hillis et al. which is the textbook we have been using for the class. I have been told in the past by the publishers that this was OK to do so I am assuming it is still OK. Hope there are not too many errors ... for some reason Lecture 10 will not upload - working on it

Saturday, April 04, 2020

Today's stay at home activity - virtual tour of the Dali museum

Love that the Dean of the College of Biological Sciences Mark Winey sent out a suggestion to check out this virtual tour of the Dali Museum in his regular message to the college.  And it is pretty cool. Check it out: Visit the museum as you have never done before! | Fundaci� Gala - Salvador Dal�

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Resource for #NatureAtHome: California Academy of Sciences

OK have not been posting much to this blog for a few weeks due to the disruption from the coronavirus but I am going to start posting again when I find things that may be of use for the new world of social distancing, etc.

Today I am posting about the California Academy of Sciences which has a nice page compilation information and resources they have for activities at home: Academy @ Home | California Academy of Sciences

Thanks Cal Academy.

Tuesday, March 17, 2020

Collecting some of my comments about Sacramento County's poor response to COVID19

Posted this rant on March 9

And then another rant
And this one
And then Placer and Yolo County came out with their somewhat more aggressive plan
And more
And this
And another And this And another And another

Tuesday, March 10, 2020

My posts about #UCDavis and #Covid19

Going to use this page to keep track of some of what I have been posting about what is going on at UC Davis in regard to the coronavirus.  Will add more later ... but just going to use this to keep track.

February 26

Things blew up at @ucdavis with reports that the 1st community acquired case of COVID19 was at our hospital. I received an email about this that I eventually posted to Twitter (I waited to post until I saw others reporting this)
Tons of stories came out over the next few weeks about this and I will add some links to them. But eventually, attention went elsewhere as the 1st large clusters of cases that were detected in the US ended up being in other locations.

March 7.

Actions from UC Davis announced regarding COVID19 was, well, better than nothing but pretty limited.

March 10. 

UC Davis expanded actions.

Monday, March 09, 2020

Some of my favorite books about infectious disease, viruses, bioweapons in relation to #Coronavirus #COVID19

I posted some pics of my books I brought home from work to look over in relation to the current coronavirus outbreak and some people asked if I could post a list. So here is a collection. I will update with other books.

I used Amazon links here b/c, well, that was really simple.

Infectious Diseases


Biological Warfare


General Information about Viruses


Thursday, March 05, 2020

What's worse than not cancelling your conference during #COVID19? How about a #MANEL #YAMMM during #COVID19.

Well got invited to this meeting "Non-Coding RNAs In Biology & Medicine Conference".  And I looked up the meeting so I could see if the meeting was still on and if yes, to then encourage the organizers to encourage them to postpone the meeting to help reduce the spread of the coronavirus going around.

And alas, the meeting still on - April 2-4, 2020
As a side note, it is around the corner from where I used to work (it is in the same general area as where TIGR used to me).

And, alas, on top of the meeting apparently still being on, it is also what appears to be a MANEL - a meeting with a highly skewed gender balance of speakers.  I say "what appears to be" since I just do not have time right now to do what I frequently do which is to look up people's personal websites to see how they describe themselves in terms of gender.  So I am basing this entirely on names and appearance but it does not look like a good balance.

Not a good look Johns Hopkins and USUHS,

#1 - due to #COVID19 this conference should be cancelled
#2 - due to the apparently extreme gender skew for the speakers, this conference is one I would encourage people to not attend anyway.

Monday, February 24, 2020

Reading Relevant to Contributions to Diversity, Equity and Inclusion Statements (by Prof. Dawn Sumner)

Dawn Sumner, a colleague and friend of mine who is a Professor at UC Davis, sent me this document she has written up on readings of relevance to DEI statements and I thought it would be useful broadly and offered to post it here.  See below:

Reading Relevant to Contributions to Diversity, Equity and Inclusion Statements
By Dawn Sumner

Summary: the state of knowledge on diversity, equity and inclusion in universities, with all their intricacies: “An Inclusive Academy – Achieving Diversity and Excellence” by Stewart and Valian. This is a long read at something over 400 pages. It is very good and presents the issues with nuance and discussions of what unknown.  The library provides free digital access: https://direct.mit.edu/books/book/4114/An-Inclusive-AcademyAchieving-Diversity-and

Chapter 5 is specifically about faculty hiring. It includes a good list of design principles for avoiding bias in hiring. Diversity statements are mentioned as one aspect. It also explains the context for why there is such a huge drop between the available pool of underrepresented candidates and those who actually apply to faculty jobs at UCD.

Morality and Diversity:This article describes 3 moral approaches to diversity, including the intrinsic conflict between 2 of them that reflect the debate we are currently having over DEI statements. The third (new) approach is to focus on the virtues/skills that someone needs to have to do their job well and the values of the organization to shape fair practices that promote excellence. https://link.springer.com/article/10.1007/s10551-012-1434-z

What’s in DEI Statements?Some of the arguments against requiring DEI statements relate to their contents. Here are some analyses of what's in real statements from applicants. (Note that I saw on twitter tonight some complaints about plagiarized DEI statements - so it is certainly true that there are problems.)
To me, the combination of using a virtues-and-values–focused framework for considering diversity, placed in the context of understanding how academic processes are discriminatory with an understanding of what’s communicated in diversity statements shows: 1) the potential value of DEI statements; and 2) how they should be used appropriately to help inform the process of finding colleagues who possess the skills (virtues) to promote our values (as we express them).

DEI statements can help us find the best colleagues. Misusing them can be very damaging. We need to work on setting appropriate standards for how to effectively use DEI statements to level the playing field, promote equity, and ensure excellence.

Saturday, February 01, 2020

A month of #DailyINat - observations posted to @inaturalist every day for January 2020

I posted a thread to Twitter about this topic. See
if you want to see this on Twitter but am reproducing it here.

OMG I pulled it off. I did daily observations that I posted to @inaturalist for all of January - see my Calendar - this was not trivial since I was on jury duty for almost three weeks (with some time off in the middle) 1/n


In total I made 1841 observations for the month - see inaturalist.org/observations?d - might go up a little as I got through a few more pictures #DailyiNat 2/n


My observations were predominantly (97%) of birds (for those who KNow me I am sure you are shocked, shocked by this) inaturalist.org/observations?d #DailyiNat 3/n


All of these observations were in the general area near #DavisCA and #SacramentoCA #DailyiNat 4/n


Most amazing to me was that I reported >120 species of birds during this time - including a few lifers #DailyiNat inaturalist.org/observations?d 5/n


Incredibly grateful to @inaturalist @LMGerhart @ReaderMeter @ShannonSkalos @talonDNA @tvanlaarmicro @calacademy and many many others for inspiration and all the people doing IDs to help me out inaturalist.org/observations?d #DailyiNat 6/n


One of my favorite observations during this time: Prairie Falcon - inaturalist.org/observations/3 my 1st time seeing one #DailyiNat 7/n


Also seen a few ferruginous hawks which are becoming one of my favorite birds - inaturalist.org/observations?d #DailyiNat 8/n


Also fun - my 1st pics of a golden crowned kinglet inaturalist.org/observations?d #DailyiNat 9/n


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