Sunday, September 11, 2022

Lake Arrowhead Microbial Genomics Meeting History

Making a page here with information on the history of the Lake Arrowhead Microbial Genomes meeting.  Please post in comments any additional links to other information.
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Friday, August 19, 2022

Wanted - comments on the current @ucdavis COVID plans

 So - I have been publicly and privately critical of some of the recent @ucdavis practices regarding COVID. If you want to know more about my areas of concern see for example this Twitter thread which I posted today: 

After I posted that, The Chancellor of UC Davis Gary May posted an article with some details of current UC Davis COVID plans. See https://leadership.ucdavis.edu/news/checking-in-with-chancellor-may-planning-ahead 

What he wrote is below - but rather than comment myself right now, I am wondering - what do people out there (especially those at UC Davis) think of all of this?

Coronavirus

Davis campus students are required to be compliant with the UC Vaccine Policy by Sept. 21 either by being up to date on vaccines and boosters or submitting a religious or medical exception request. Students who are not in compliance by Sept. 21 will receive a registration hold on their accounts for fall quarter. Please visit the Information for Students and Families page on the Campus Ready website for additional details about the vaccine policy compliance process. The vaccine policy also applies to employees.

It’s clear that COVID-19 will be with us for some time. UC Davis continues to monitor for the virus through weekly wastewater testing, which helps inform our decision making. We have reviewed the scientific literature and heard from many people, and, at this point, we are not likely to increase the frequency of wastewater testing given that Davis is not a large urban center. Also please note: We have access to daily test results from Stanford’s Sewer Coronavirus Alert Network (SCAN).

We encourage our students, faculty and staff to get tested regularly for COVID-19. The Davis campus testing kiosk — offering free, asymptomatic testing (saliva-based) — remains in operation, although in a new location: Human Resources Administration Building (1050 Blue Ridge Road), across La Rue Road from the ARC. The kiosk is open from 8:30 a.m. to 4:30 p.m. Sunday through Thursday (closed Fridays and Saturdays). Testing is by appointment only through the Health-e-Messaging portal. Please note: Testing appointments are limited from Sept. 13 to 15, due to move-in.

At-home antigen tests are available for free as follows:

  • By mail from the federal government.
  • From no-charge vending machines around Yolo County. The machines are accessible 24 hours a day at the Mary L. Stephens Davis Branch Library, 315 E. 14th St.; West Sacramento City Hall, 1110 W. Capitol Blvd.; Winters City Hall, 318 1st St.; and Esparto Regional Library, 17065 Yolo Ave. (with one more to be installed in Woodland).
  • From Yolo County libraries during open hours.

I would also like to recognize the effects of long COVID and the impact it continues to have on people. We are learning more about it every day, in UC Davis Health’s Post-COVID-19 Clinic, which opened in November 2020; and in our research and clinical studies, including one assessing the risks for children.

Students affected by long COVID should work with the Student Disability Center for resources and support. Employees should work with Disability Management Services. These units are busy, so please reach out to begin the interactive process as soon as you can.

Masking and air filters

I recognize that there is still some anxiety about masking. While the Davis campus does not have a mask mandate in place, we strongly recommend that people wear masks indoors to reduce risk.

Free masks are coming soon. The university plans to distribute one N95 mask to every student and employee this fall quarter, with this one-time distribution to take place in September. For more information about the distribution, students should contact their major departments, and employees should contact their departments or units. See “Directions for departments” on how to acquire mask supplies.

Remember that a proper mask fit is especially important. A 10-minute video is available for students on how to properly use N95 masks, also called respirators. They are rated to filter out 95% of particles.

Employees are required to complete a 10-minute video training about the proper use of N95 masks.

Yolo County also offers video guidance on masking. Further information can be found at Campus Ready and through the California Department of Public Health.

If you’re concerned about air filtration at home, a Corsi-Rosenthal Box is a cost-effective device that can be built with just a few components. The box was co-invented by Richard Corsi, dean of the College of Engineering, and has received acclaim nationwide. Visit this link to learn how to build your own Corsi-Rosenthal Box.




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Sunday, June 05, 2022

Best pics from Trip to Monterey - Day 1 - May 25, 2022

 

Went on a brief trip to Monterey, CA last week. Took lots of pics. Here are some of the better ones. Also see postings with identifications at iNaturalist.

 
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Monday, May 16, 2022

Videos about using the UCSC Genome Browser for analysis of SarsCOV2

 These look pretty useful and thought I would post here. Text is from the UCSC Youtube channel

This 5-part video series is for virologists and public health researchers interested in leveraging the UCSC Genome Browser and web interface to UShER (Ultrafast Sample placement on Existing tRees). These tools are a 'one-stop shop' to understand SARS-CoV-2 through genome annotations as well as track variants by placing your samples in a phylogenetic tree with millions of other SARS-CoV-2 sequences. Use the SARS-CoV-2 Genome Browser: http://bit.ly/sarscov2browser Visit our SARS-CoV-2 Genome Browser and UShER quick start page with videos, scripts and more: http://bit.ly/ucsccovidbrowser COVID-19 Research at UCSC: https://genome.ucsc.edu/covid19.html 'The UCSC SARS-CoV-2 Genome Browser' publication: https://www.nature.com/articles/s4158... 'Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic' publication: https://www.nature.com/articles/s4158... UShER documentation, installation, source code:: https://github.com/yatisht/usher https://usher-wiki.readthedocs.io/en/... COVID-19 Genomic Epidemiology Toolkit module "Realtime Phylogenetics with UShER: https://www.cdc.gov/amd/training/covi... Learn more about the UCSC Genome Browser: http://genome.ucsc.edu https://twitter.com/genomebrowser Learn more about the UCSC Genomics Institute: https://twitter.com/ucscgenomics https://genomics.ucsc.edu/

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Saturday, April 23, 2022

Endosymbiosis Animations for "Biodiversity and the Tree of Life"

So I am in the midst of co-teachign a very large introductory biology course at UC Davis "BIS2C - Biodiversiy and the tree of Life". I cover much of microbial diversity in this class and also the large scale structure of the Tree of Life. 

As always, I spent a lot of time working on slides and such for this class and recently posted some animations based on these slides to Twitter and Facebook and thought I would share some of them here. For today, I am sharing the animations I made on Endosymbiosis. I posted a first version of this to Twitter last week. Note - I added music - Mussorgsky - Night on Bald Mountain for drama ... I also posted it to Facebook:

  

And boy am I glad I did. Because multiple people commented and pointed out parts that were, well, not correct. I had lecture too soon to fix them so I told my students about this and that I would update the slides. I then spent a day updating everything and made a new version which I think is much much better.

 
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Tuesday, April 05, 2022

A good bye to my beloved Clover

 

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Monday, March 28, 2022

The ongoing saga with the UC Health Insurance Pharmacy "Benefits" Via Navitus

Well the saga continues. Here is an update.


It all started March 7. See here for a long thread and also responses. See this thread in an easier to read format here: https://threadreaderapp.com/thread/1500934973775249412.html See this thread in an easier to read format here https://threadreaderapp.com/thread/1506297722776657920.html And then I got told Navitus was going to be instructed to cover my insulins by UCOP but the message clearly was not recieved. And finally and thankfully today I was told my insulins would be covered. I am now interested in what is happening to others out there who have been harmed by the UC / Navitus system.
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Wednesday, March 23, 2022

Some links to articles about Diabetes and COVID19

Posted some links to Twitter that I am compiling here too about type 1 diabetes and COVID19 with a focus on recommendations for diabetics in current COVID situation



See also


Independent risk factors of COVID-19 pneumonia in vaccinated Mexican adults

Risk Factors for Severe COVID-19 Outcomes Among Persons Aged ≥18 Years Who Completed a Primary COVID-19 Vaccination Series — 465 Health Care Facilities, United States, December 2020–October 2021

Age, Underlying Conditions Top Factors in Breakthroughs

 A Wall Street Journal analysis found that among fully vaccinated people, the ones most likely to be hospitalized with breakthrough infections of COVID-19 are the elderly and those with specific underlying medical conditions.

“In particular, people with diabetes, chronic lung disease, kidney disease and compromised immune systems were at risk of serious outcomes from breakthrough cases,” The Journal reported.











 

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Lots of useful responses to question "What should high risk people do in face of relaxed masking requirements"?

 

So I posted this to Twitter.
And got lots of useful resposnes. Rather than compile them here if interested people should browse the responses.
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Tuesday, March 22, 2022

The ongoing disaster of the new UC Health Insurance Pharmacy "benefits"

Recently I posted to Twitter about the disastrous new University of California Pharmacy Benefits system.
In summary, I got a letter in March that warned me of something that was about to happen in January (that is, in the past).  And what was about to happen was bad - cutting off coverage of my insulin.  And the system in place for trying to even find out what was going on and what to do about this was a disaster.

I note, this generated an enormous response and it was clear that this was not just me experiencing the disaster of their system.

I used the threadfreader app to make this into a more easily readable thread here: https://threadreaderapp.com/thread/1500934973775249412.html

A few people pointed me to some contacts at UC Davis to reach out to and I did.  They were both great and very helpful.  They told me that the UC was working on dealing with many of these issues and some of those responses were rolled out quickly. 

And I posted about how these efforts were sort of helpful but not ideal. For example




On March 21, I got a detailed email from the University of California apologizing for the situation and detailing many changes to apparently try and help fix things.  I mean, they never should have done this and used this incredibly cheap, low grade system.  But at least they are trying to fix things.

Below is the email from UC. More about this in a bit but I wanted to share the full text for people to see here.

An important message from UC about your pharmacy benefits

Dear Jonathan,

We are writing to acknowledge — and apologize for — the problems many members of the UC community are experiencing with Navitus Health, a new administrator of pharmacy benefits for UC employee and Medicare PPO plans, and to let you know what we are doing to fix the problems.

Last year, University of California Health (UCH) and UC Systemwide Human Resources selected Navitus Health to administer pharmacy benefits, starting Jan. 1, 2022. This decision was made following an extensive formal bid process, conducted by a committee with representatives from UCH, Systemwide HR, UC faculty with pharmacy expertise and UC’s retiree association. 

Navitus was selected as the partner that could provide UC with the best overall flexibility, service, and affordability. However, since UC’s transition to Navitus Health, we have heard from too many members who have been negatively impacted by this change. 

Some members have had to change prescription drugs, been required to complete time-consuming authorization processes and experienced denials by Navitus, causing unnecessary anxiety and frustration. Navitus failed to meet the scheduled target date for mailing a clinical transition letter, causing hardship and worry for faculty, staff, retirees and their family members.  

Additionally, like many employers Navitus has faced customer service staffing challenges, leading to wait times that far exceed Navitus’ standards and UC performance guarantees. Among other things, this has put undue pressure on benefits professionals at UC locations and in the UC Retirement Service Center and the UCPath Center, as they have worked to provide support that should be handled by Navitus.

We take these problems — and our responsibility to ensure that members of UC health plans have access to the prescriptions they need — very seriously. UCH and UC Systemwide Human Resources have been in constant communication with Navitus, and we want to let you know what we are doing to fix these problems.

Support with member transitions
  • Due to the delay in mailing clinical transition letters, Navitus has provided an extended transition period to the end of April for drugs that are not covered. Extension letters and an email campaign were recently initiated.
  • Navitus will call members who need to transition to new medications directly and offer help with authorizations, denials, and appeals. Those who have experienced a denial for a Not Covered/Non-Formulary medication will also receive a phone call offering help. 
  • UCH, Alliant (a UC consultant) and Navitus will audit and review the protocols Navitus uses for denials to ensure they are in alignment with Navitus internal guidelines, industry standards and Medicare guidelines – and to identify and correct any gaps. 

Customer service improvements
  • Navitus has committed to adding an additional 35 customer service representatives (an increase from 125 to 160) by the end of April, and hopes to add another 15 staff after that, along with additional support for UC benefits professionals.
  • Navitus has also added two more personnel with pharmacy clinical expertise to help UC benefit professionals support members.
  • In addition, Navitus is exploring a concierge-type customer service model to ensure UC members receive the dedicated assistance they need.

Again, we sincerely apologize for any difficulties you or your family members have experienced during this transition. We are committed to you receiving the critical health care you deserve, without unnecessary inconvenience or frustration.

Sincerely,
 
Cheryl Lloyd                                                    Dr. Carrie Byington
Vice President                                                 Executive Vice President
Systemwide Human Resources                      University of California Health


Please do not reply to this message. Replies to this message are routed to an unmonitored mailbox. 
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Saturday, March 19, 2022

Baby Hummingbirds at Yolo Bypass

 

So I got a glimpse of a hummingbird nest at Yolo Bypass And then I went back and got a better look at it , with babies ... And I posted some videos too





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Friday, February 11, 2022

A field guide to SarsCOV2

 

Gave a talk on SarsCOV2 to the Yolo County Community of Practice group. I basically discussed how the concept of a field guide can be useful for thinking about SarsCOV2. Here are my slides I will try to post the recording of the talk at some point.
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Wednesday, February 09, 2022

Northern Harrier at Yolo Bypass

 Some pics ...



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Monday, January 10, 2022

Best Pics from Nimbus Fish Hatchery

Went to Sacramento for a Doctor's appointment and then had a 2 hour Zoom call. Decided to do the call while walking around the Nimbus Fish Hatchery which I have never been to. I heard that people had seen a rare duck there so went on over. And it was awesome. I then messaged a grad student in my lab, Alonna Wright who lives nearby and she came over for a walk after lunch. Here is a link to a slideshow of some of the pics I got
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Friday, January 07, 2022

Some thoughts on Omicron and COVID19 in the last week or so

 

Some recent Tweets and threads from me on Omicron and related topics
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Tuesday, December 28, 2021

Tribute to EO Wilson

 

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Sunday, December 12, 2021

Video and slides of my talk for the Microbiome Virtual International Forum posted

I gave a talk last week for the Microbiome Virtual International Forum. https://www.microbiome-vif.org/ Title: Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically underappreciated)" 

 See the Youtube video:  

 Slides:


Also see this Twitter thread for some more info:
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Wednesday, November 17, 2021

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
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Saturday, November 06, 2021

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.


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Friday, November 05, 2021

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

 
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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
microBEnet blog
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Sunday, May 16, 2021

Some thoughts on the CDC new mask guidance

 

See this thread 

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

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Saturday, March 27, 2021

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

 News Stories Quoted in


Twitter Threads


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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. 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.

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Monday, September 21, 2020

Green heron at Yolo Bypass

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A ton to be thankful for -- here is one part of that - all the acknowledgement sections from my scholarly papers

So - it is another Thanksgiving Day and in addition to thinking about family, and football, and Alice's Restaurant, I also think a lot a...