All posts by Jonathan Eisen

About Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Today at #UCDavis: Giulio De Leo “Planetary Health: novel ecological solutions for the control of environmentally transmitted diseases”


Dr. Giulio De Leo is the seminar speaker for the Ecology and Evolution Seminar Series Today Thursday, Feb. 22nd at 4:10pm in 2205 Haring Hall.

His talk is entitled: “Planetary Health: novel ecological solutions for the control of environmentally transmitted diseases”

Abstract: In the past few decades, the unprecedented rate of technological innovation has contributed to the decline of diseases that have afflicted humanity for centuries. Yet, for diseases with obligate environmental transmission, such as malaria and schistosomiasis, targeting pathogens in the human host through vaccines and drugs might not be enough. In my talk, I present empirical evidence and theoretical considerations from a field project based in Senegal to promote a more holistic approach that acknowledges the ecological complexities driving disease dynamics and investigates the interactions of people and the environment. The ultimate goal is to identify "ecological levers" we can use to develop cost-effective solutions that can improve human health and protect the environment.

For more information on Giulio and his current work, please see the De Leo lab website, https://deleolab.stanford.edu/ .

mofofospoomics Solves #TomBrady “Injury” Mystery

So – there is great controversy surrounding the “Injury” to New England Patriots quarterback Tom Brady.  See for example:

And much much more.

So – in the interest of showing the power of science and the power of microbiome science, I have decided to tackle (so to speak) the topic.  If you are not familiar with the power of microbiome science in addressing Tom Brady related controversies then you must check out the use of microbial forensics to solve the #deflategate controversy.

See “Secret microbiome forensic study reveals #deflategate culprit” and the amazing video below

So given this prior record of the value of mofofospoomics (microbiome forensics for sports)  I decided to see what we could learn about Tom Brady’s injury.

I started, as any goo microbiome study does, with collecting all the relevant hypotheses to test and not in any way doing an exploratory analysis.  So I surveyed the internet by Googling, and searched around Twitter for 3-4 minutes and I found the following plausible hypothesis:

A: Brady was really injured in practice and got a cut that was then treated with stitches and topical antibiotics.

B. Brady had surgery to add an additional finger to hold a future Super Bowl championship ring. In addition, one would assume that oral or IV antibiotics were given as part of the post surgery treatment.

See for example:

https://platform.twitter.com/widgets.js

https://platform.twitter.com/widgets.js

C. Brady and Bill Belichick are faking it to force Jacksonville to alter practice plans.

All three seem completely plausible.  I would give them each equal wait in a Bayesian prior sense. So the key question was – could one develop some ways to use a mofofospoomics approach to test for which of these three hypothesis was most likely to be correct.


The first thing to do was to make some mofofospoomics related predictions based on each hypothesis.  This actually was relatively easy.

Under hypothesis A, I would expect one key mofofospoomics related signature.  Assuming the topical antibiotics were only applied to his right hand then one would expect his right hand to have a different microbiome than his left and to look abnormal like all antibiotic treated skin samples do.   So to test for this hypothesis A all we would need would be some hand microbiome samples from him.

Under hypothesis B, I would expect two mofofospoomics related signatures.  First, one would expect Brady’s hand to show the typical signature of post surgical changes in the microbiome (see for example Grice 2014). In addition, one would expect there to be affects of the antibiotics used.   The oral or IV antibiotics would be expected to affect all of his microbiome – skin and gut for example. Thus both his hands should look like apocalypse happened relative to the microbiome.   Also we might expect the new finger to look different from the other fingers since translated parts look more like the donor than the recipient. So to test for this hypothesis B all we would need would be some hand microbiome samples from him and also possibly a fecal sample.

Under hypothesis C,  I would expect no mofofospoomics related signatures. That his, his hands should look normal.  Or maybe they should look normal for a superstar athlete.  So one would need to compare to other well known athlete microbiome signatures.

So – from examination of the possible tests for the three hypothesis it seemed that getting hand microbiome samples for Brady would allow us to use a mofofospoomic approach to determine which of the three was best.

Thus the next issue was – how to get hand microbiome samples from Mr. Brady.  First, we tried to get the gloves he has been wearing since the “injury” assuming we could turn them inside out and do all sorts of cool things.  Alas, apparently, he has not taken them off at all.rom Boston Globe

So we were left with one alternative possibility.  It is well known that before every major game, Mr. Brady destroys his cell phones to make sure that nobody can find directions to his house.  Or for some other reason. Well this is key because it is well known that phones contain a signature of the users finger microbiome whereby one can identify individuals using the phones for criminal or other investigations (see also this).

So all we would need would be to get his latest phone. To do this, we placed fake garbage cans on the path from the parking area to their training facility yesterday and .. voila .. Brady walked by and tossed something into the can.  Using our patented SmartGarbage sample collector, what he threw in was sealed inside sterile, DNA free plastic.  And later in the evening we collected it and … voila voila .. we had a smashed phone itself in a plastic bag (I guess Brady does not want people to get exposed to the cell phone dust).  Thanks Tom.

So we took the phone back to our private lab and we asked one key question that was critical to whether we could proceed.  Will it blend?  And it did.

So then we took the cell phone dust and did standard mofofospoomic analysis on it (DNA isolation, both rRNA gene PCR and sequencing and shotgun metagenomic sequencing, de multiplexing, QC).  Kit and other controls were included in every step. And we also downloaded and added sequences from studies of human skin, hands, antibiotic treated or not, cell phones, and also some controls like sports objects.

And then we we fed all the data into the new integrated MAQDADDY pipeline (a combination of Mothur, Anvi’o, QIIME, and DADA).  And we used it to test the three hypotheses.  Amazingly none of them showed a good match to the data.

For example, the Brady phone sample did not really even resemble a phone well

So this was really disappointing.  But as one last ditch effort, we decided to download all of the available microbiome data from any sample on the planet.  Like all of it.  We then reran the MAQDADDY pipeline and found an amazing result.

What I think this means is that Tom Brady had a Luke Skywalker operation.  That is, his hand is robotic.  So cool.

I just love mofofospoomics.

 

Today at @ucdavis: Katie Hinde ” More than food: how hormones in mother’s milk organize infant behavior”

​Updated with location …

This week’s Animal Behavior Graduate Group seminar:

More than food: how hormones in mother’s milk organize infant behavior

Dr. Katie Hinde

Associate Professor, Arizona State University

Friday, January 19th, 12:10 pm in Young Hall 194
Coffee and cookies will be available

"Dr. Hinde’s research focuses on how mother’s milk contributes to infant development and behavior in socially complex taxa, particularly humans and monkeys. This includes not only provision of energy and materials for growth, but also milk constituents that shape immunological, neurobiological, and behavior development. She investigates how variation in mother’s milk and behavioral care influences infant outcomes from post-natal life and into adulthood, and subsequent generations.” – The Evolution Institute

For more information on Dr. Hinde’s research: http://mammalssuck.blogspot.com/?view=classic

At #UCDavis 1/19: Katie Hinde “More than food: how hormones in mother’s milk organize infant behavior”

This week’s Animal Behavior Graduate Group seminar:
**please note that the location will be announced prior to Friday’s seminar**

More than food: how hormones in mother’s milk organize infant behavior

Dr. Katie Hinde

Associate Professor, Arizona State University

Friday, January 19th, 12:10 pm – LOCATION TO BE DETERMINED
Coffee and cookies will be available

"Dr. Hinde’s research focuses on how mother’s milk contributes to infant development and behavior in socially complex taxa, particularly humans and monkeys. This includes not only provision of energy and materials for growth, but also milk constituents that shape immunological, neurobiological, and behavior development. She investigates how variation in mother’s milk and behavioral care influences infant outcomes from post-natal life and into adulthood, and subsequent generations.” – The Evolution Institute

For more information on Dr. Hinde’s research: http://mammalssuck.blogspot.com/?view=classic

1/24 and 1/25 at #UCDavis: Peter Mumby, Storer Lecturer, on Coral Reefs

Posting as requested:

PLEASE POST AND DISTRIBUTE:

We are pleased to announce that Peter Mumby, Professor of Marine Spatial Ecology Laboratory from the University of Queensland in Australia, will be presenting two lectures in the Storer Lectureship in Life Sciences Series, “The Future of Coral Reefs,” at 4:10 p.m. on Wednesday, January 24, 2018 in the Alumni and Visitors Center and “The Connectivity, Ecosystem Overfishing and Rebuilding of Coral Reef Fisheries” at 4:10pm on Thursday January 25, 2018 in Haring Hall. Please see the attached flyer for additional information.