Category Archives: Daily

Laboratory In A Pandemic

This past year has been remarkable in terms of the impact that COVID-19 has wrought, as well as its impact upon everyone in the team.  I am proud of the resiliency and huge efforts that people have gone through to keep science in the lab going, and cannot possibly relate how grateful I am to everyone.  They have struggled through working remotely, human resources problems, child-care issues, logistical issues related to access of research tools and data, equipment downtime due to maintenance issues, personal COVID infections, and outbreaks in their families, not being able to attend meetings, duties to the department and university to assist with the COVID-19 response, volunteering of time, money and resources to assist the COVI-19 response, having to be responsive to new IT demands, and so much more.

I had been tracking COVID-19 since January, but by March, I became particularly alarmed and shut the lab down, sending everyone home with computers in short order.  Having no idea how this would turn out, I did have visions of being able to get all caught up and do a ton of reading that I’ve not been able to do, and more.  2020 being 2020, that was just not possible, and the bureaucratic overhead of reporting and constant emails and videoconferencing has eaten up massive amounts of time.  This year, despite the global pandemic, we’ve still managed to publish 6 manuscripts, 3 pre-prints, 2 abstracts, and 1 chapter, and secured a new NSF grant.  We’ve continued to mentor graduate students, undergraduate students, and post-docs.  Again, I am incredibly proud of this team.

The danger with all this productivity in the face of a global pandemic is that we are burning our team out.  So, the plan was to take a couple weeks off, spend time with the closest people in our lives, recharge our batteries, and hit the ground running again in the New Year.  Reality intruded for me at least however, and I discovered a water leak from one of the electron microscope chillers that leaked into the walls.  I am investigating this now, but we are clearly down with half of our ultrastructural infrastructure unavailable until we can either get the chiller/microscope repaired or equipment replaced.  2020 just will not let go…  The lab is still working from home, but I’ve had to go into work and get some things done related to the water leak.

Outside of equipment failures and water leaks, working in the lab during 2020 has been a challenge.  After getting approval to have some people return to campus, we decided to bring technicians back for part time work in the lab and part time work at home, so long as they could keep distances while wearing masks while in the lab.  Not being able to be in the lab full time, and having to maintain physical distance from all others and wear masks and personal protective gear constantly has absolutely been an added burden.  However, we are fortunate in that we have space to spread out, but it has still been a massive challenge, getting work done.

Our lab has helped with the COVID-19 response by taking temperatures and performing health screenings of visitors and patients/visitors to the Moran Eye Center, a task all of our labs in the Moran Eye Center have been participating in.  It takes us away from our research duties, but also helps in some small way with the COVID-19 response.

Staying up on the work from students and post-docs has, like everything else, gone virtual.  This slows everything down of course and contributes to the sense of isolation.  Both Crystal @CSigulinsky and Becca @BeccaPfeiffer19 have been critical in this mentoring effort.  I can’t wait until we get this thing back under control and can meet in person again…

I’m also grateful for the Kevin Mcilwrath from JEOL @JEOLUSA who helped us maintain the microscopes and keep them up and running.  And when they went down, I am so grateful that Kevin could come in and help us get them back up and running.  We definitely had downtime as a result of the pandemic, but we would have had more, if it were not for Kevin Mcilwrath.  We will need him again, to get back up and running after the Christmas Eve chiller failure, and I am grateful for him and JEOL for making the efforts to keep us running.

We’ll see what the New Year brings.  The list of things to do starting in a few days is formidable.  Even though the vaccines are just now starting to roll out, we are still in the middle of a pandemic and will not be returning to normal functioning in the lab for months yet.  We have to perform repairs to our infrastructure, finish a manuscript I am working on, edits to a colleagues manuscript, getting a couple of manuscripts from post-docs going, a couple of new genetic models to create, a grant renewal to write, data to process for collaborations, getting our light microscopes back up and running, a grad student starting a rotation, undergrads presenting their research, and then completing work on all the other stuff that we normally have to do.

I am so grateful for Jia-Hui, Jamie, Hope, Nat, Crystal, Becca, Jeebika, Jessica, Selena and Olivia. You all made getting through this year possible.  Thank you for your teamwork, and your *hard* work.  Also, my undying gratitude to my chairman, and all the colleagues in my department.  What a brutal year, and my hopes are for more normalization, better leadership at the federal level, and mitigation of the COVID-19 pandemic as vaccines start to roll out.

Happy Weird Holidays, 2020 From The Marclab For Connectomics

Happy Weird Holidays, 2020 to you all from us here at the Marclab for Connectomics.

What a strange, and fundamentally challenging year this has been for so many.  It has been lonely, frustrating, painful, and discouraging for many of us, and I encourage all to be a bit more patient, kind, and compassionate to those around you, as you don’t know what they are dealing with.

This pandemic has exacerbated the challenges that many are dealing with financially, socially, and emotionally. It has led to incredible bureaucracy for many of us trying to run labs. Personnel issues as folks in labs struggle with the issues in their lives not only working from home, but working from home during a pandemic, including child care, or care for other family members. Struggles with personal illness (COVID and otherwise). Financial issues related to employment. Struggles with depression and isolation. Inability to collaborate, or attend meetings that are critical to ongoing projects. Loss of research resources. Inability to get equipment or service on equipment… For some, this pandemic has resulting in a complete cessation of research activities.

Lab productivity has certainly been hugely impacted for many labs and the implications of that for their NIH or NSF funding is still unclear. Our productivity has certainly suffered this year, and we are absolutely behind on promised data generation. I don’t know how we are going to deal with that yet. The goal is to try and catch up, and while our lab is nominally working right now, all undergraduate, and graduate students are working remotely. Postdocs are partially working in the lab, and technicians are splitting their time. Until all the vaccines roll out, it is unclear how much longer this will have to continue. Fortunately for us, we are heavily computational and we’ve been able to still be productive on existing data. We also have generous lab space that we can spread out in for those who are working on campus. So, for now, we are forging ahead, managing as best as we can and attempting to be helpful to others where we can by processing tissues for other labs where we can to help them with their productivity problems for instance, and as always, reviewing manuscripts and grants in-between trying to get our manuscripts and grants in.

This pandemic has exacerbated the challenges that many are dealing with financially, socially, emotionally, and scientifically. And while this life gives and it takes, it also gives us opportunities to make decisions that allow us to help improve the lives of others, and be a force for good.

Happy Holidays from the Marclab for Connectomics.

Jessica Garcia Is This Year’s Student Veteran Of The Year

Jessica Garcia is this year’s University of Utah Student Veteran of the Year. Jessica is an undergraduate student in the lab exploring the OFF-layer branches of ON cone bipolar cells in early retinal degeneration.

Jessica came to us by way of service with the US Navy, where she served as an aviation technician before attending the University of Utah.

Congratulations Jessica! We are so proud of you.

Teleworking In Response to COVID-19

The Marclab for Connectomics is immediately implementing teleworking strategies, moving many functions off campus in response to the COVID-19 outbreak/pandemic.

I am feeling fortunate in the much of our work is computational, but we do have a substantial wet lab component in addition to the ultrastructural data capture component.

We are not shutting down completely, yet. All students and postdocs will be working from home.  We have limited capacity to process tissue as only one person at a time will be in the laboratory proper, sectioning, performing immuno procedures, or capturing ultrastructural data.

I will be working intermittently from home and the laboratory office and working to determine where we are at from a personnel standpoint and how we will be impacted by NIH funding decisions. The good news is that NIH, I believe will honor charging salaries to grants, even if we cannot maintain our planned effort.  This means no job losses for the time being.

The COVID-19 outbreak is getting bigger and bigger.  I have cancelled all of my travel for the year to date, including a trip with friends to Lisbon in two weeks to walk around with cameras that I was planning on being the highlight of my year.  Trips to California, Italy, Sweden, and Germany are also off the table, at least through May/June.  ARVO has been cancelled. FASEB has been cancelled.


– COVID-19 is far more infectious than the flu.

– COVID-19 is far more deadly than the flu. On the order of 300-1000x more deadly. The difference is that it is not as common as the flu… yet.

-Our current Surgeon General just said on the 9th that the outbreak was already “contained”. I don’t even know where to start with this one as it is gross misinformation.

-I am seeing a level of buildup in the outbreak community and in the military that I’ve never seen before. This buildup is stymied by an administration that keeps talking it down. But I’ve never before seen a military response (calling out National Guard units specialized in biowarfare management) for an outbreak. At the same time, there is no coordination between the services that I can see. Navy is not talking with Army for instance, which is bizarre.

-The President has not invoked the Defense Production Act yet… I have no idea why.

-There is nobody at CDC that is coordinating all the information from the individual states as of today. This infrastructure *used* to exist. I don’t know why it is not there and that scares me, and makes me more angry than ever with the Trump administration.

HHS is estimating that a “moderate” outbreak will have 200,000 hospitalizations required for respiratory distress from COVID-19. We only have 100,000 ICU beds total in the United States, and some percentage of those are already in use, being optimized for markets. That looks to me like Italy’s situation right now, and their advanced medical system (among the best in Europe) is starting to fail which is why Italy has just extended their quarantine to the entire country.

-Per the Johns Hopkins dashboard, there is effectively no screening being done in Africa. No screening being done in Russia, with one backchannel report to me of at least 300 active cases in Moscow, but the doctors are not allowed to report it.

-No screening being done in the former Russian republics either.

-In all of India, there are only 43 reported cases. That does not make any sense to me.

-The lack of reporting for an infectious disease that is far more infectious than the flu indicates to me that COVID-19 is already in the population and is already spreading.

-Because it is relatively asymptomatic amongst much of the younger populace, it is not being seen/found. And as such, is a potent vector for spreading rapidly in communities.

-Universities around the country (not just my institution, the University of Utah) are prohibiting travel.

All of this means that if this is in fact as bad as it sounds, then we need to take active measures to limit the spread and the impact upon our healthcare infrastructure that is already going to be strained and we need to flatten the curve.


This *feels* very different from previous outbreaks, and the lack of coordination from the White House to CDC and .mil folks is astoundingly disturbing. Don’t forget, back in 2018, the Trump administration shut down the CDC foreign disease outbreak monitoring program.  This was the program that helped monitor foreign disease outbreaks and help define what sequences vaccine makers should use.

We have thus been relying upon WHO for information, and they even offered us primers for COVID-19 to make test kits.  But someone in the Trump administration told the CDC not to take them and we’d develop our own. My information says that those US developed primers had problems recognizing the epitope, and now people want to know *why* we rejected WHO primers. Speculation is that they wanted to use IP from the US made primers to capitalize on those markets.

This is infuriating and another example of why we should not be using economic models to address disease outbreaks, a position I’ve been taking on Twitter for some time now.

The WHO certified this outbreak as a pandemic on the 11th.  I have some real concerns, as some, like the former CDC director are advising that in a worst case scenario, up to 1.6 million Americans could be killed by COVID-19.  My concern is that from his numbers, even if this outbreak is just 1% infectious, and just moderately severe, that means 16,350 possible deaths.  That is not the bad part though. More importantly, 16,350 deaths will likely mean ICU beds are needed, and we only *have* 100k beds in the US.  Additionally, optimal occupancy for intensive care units (ICU) in the United States is accepted to be 70-75%. This means that at 1% infection rate, and moderately severe mortality rates, ALL of our ICU bed capacity could be occupied by COVID-19.  If it is worse, and the numbers from Italy’s example suggest it is, this could reach crisis levels quickly.

For all these reasons, I am taking active measures to reduce the exposure of people in my laboratory and help to reduce pressure on our healthcare systems.


Bryan William Jones, PhD


Kevin Rapp At TEM1

This is Kevin Rapp, a technician in the lab running some test captures on our original JEOL transmission electron microscope.  This microscope is likely the highest use electron microscope on planet Earth, having been run effectively non-stop for over a decade.  This microscope, purchased through a generous gift from Martha Ann Dumke Healey made possible our entire connectomics initiatives.

From Jonesblog.


Becca Pfeiffer At TEM2

This is Becca Pfeiffer setting up a test capture on our new JEOL electron microscope. We’ve customized this scope, like our previous scope, and it is taking us a little while to track down some variables with a piece of equipment this complex and hammer them down. My thanks to Becca, Jamie and Kevin for working through this together.

From Jonesblog.

Tracing Neurodegenerative Disease

This is one of our undergraduates Jeebika Dahal, working to annotate in one of our pathoconnectomics databases.  This work is helping us to understand how neural degenerative disease changes wiring, and corrupts processing in neural systems.  We work in retina, but the principles apply to all neural systems with implications for Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis, epilepsy, and more.

Originally posted on Jonesblog.

Marclab Off To ARVO2019

The Marclab is off to ARVO 2019 and eager to share some of what we’ve been up to over the past year.  We have undergraduate Jeebika Dahal presenting her work on the AII Amacrine Cell Connectivity Changes In Degenerating Retina on Sunday (see poster B0013 Abstract Number: 551 – B0013).  Undergraduate Selena Wirthlin will present her work on the Comparative Anatomy and Connectivity Of The AII Amacrine Cell In Mouse And Rabbit Retina on Sunday (poster B0010 Abstract Number: 548 – B0010). Undergraduate and US Navy veteran Jessica Garcia will present her work Sunday on OFF-layer Branches Of ON Cone Bipolar Cells In Early Retinal Degeneration (B0017 Abstract Number: 555 – B0017). And postdoc Crystal Sigulinsky will present her work on Coupling Architecture Of The Aii/ON Cone Bipolar Cell Network In Degenerate Retina in a platform presentation on Thursday at 11:15am (Abstract Number: 6441).

We hope to see you there!