Showing posts with label outreach. Show all posts
Showing posts with label outreach. Show all posts

Saturday, November 03, 2018

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:






And I have on and off carved pumpkins on sciency themes every once in a while.




So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.





And I posted about it to Twitter.


But something seemed lacking.  So I went and got another pumpkin


And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

 Assembling the long piece pumpkin shotgun was easy.



Linking assembly.

 Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.




We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.


Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

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Wednesday, April 24, 2013

Guest post: Kevin Carpenter on his new microbial photo exhibit at the Exploratorium in SF #SoCool

Special guest post from Kevin Carpenter who has microbe photos featured at the Exploratorium.

One of my colleagues who does research on the microbes that live in the hindguts of lower termites once remarked that interesting organisms can be found in the most unusual of places. And the lower termite hindgut, by almost anyone’s estimation, is certainly an unusual place. It is also a fascinating place for anyone interested in biology, ecology, evolution, biochemistry, or beautiful natural forms and patterns.

Since my undergraduate days in the early 90s, I have had a deep interest in the tree of life, especially eukaryote phylogeny. After a Ph.D. in Plant Biology at U.C. Davis, I headed off to the University of British Columbia to work in Patrick Keeling's lab to pursue these interests. Anyone who has this peculiar obsession (actually, I think it's peculiar not to have this obsession!) knows that the eukaryote tree comprises mostly protists, and they arguably encompass greater structural, cell biological, biochemical, (and certainly evolutionary!) diversity than all plants, animals, and fungi combined.

In Patrick's lab I developed methods for SEM and TEM imaging of these microbes to investigate their phenotypic character evolution, functional morphology, and symbioses with bacteria in the light of molecular phylogenetic data. In addition to a number of publications (with more to come) and talks in Russia, Germany, Norway, etc. my electron micrographs have been featured on numerous journal covers, textbooks, and invited artistic presentations in Canada and Germany.

On 17 April 2013, a collection of 11 of my scanning electron micrographs of lower termite hindgut protists and their bacterial symbionts will go on permanent exhibit at the Exploratorium museum as they open their new $300 million dollar location on Pier 15 in San Francisco. This is a large (12' x 4') installation in the East Gallery (overlooking the bay):




The waterfront location, the architecture, the exhibits, and sustainable technology (rooftop solar panels, etc) are all amazing, and I encourage anyone with any interest in science/biology, art, experimentation, tinkering, and beautiful views to come out for a visit. For more information on the exhibit, the organisms, additional images and other resources (including a blog!), please visit my website at: KevinJCarpenter.com

As for the organisms...

The hindgut of wood-feeding lower termites--comprising approximately 1000 species (out of a total of several thousand species of termites)--is densely packed with symbiotic protozoa (protists), many of which engulf and enzymatically degrade wood fragments making their way to the termite hindgut. Far from being parasites, numerous studies have shown this to be a mutualsitic symbiosis, by demonstrating that the termites will starve and die if deprived of their protist symbionts. The symbiosis between lower termites and their hindgut protists is one of the longest-studied and best-known examples of microbial symbiosis, dating back nearly a century and a half to the work by Joseph Leidy and others.

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Tuesday, January 03, 2012

Wow - Sacramento Zoo Education Team incredibly impressive

Went to the Sacramento Zoo yesterday with my brother, our wives, and our kids.  We met up there at 2:15 PM because my brother's 2 year old daughter is obsessed with orangutans and there was a educational talk scheduled for 2:15.


The talk was impressive and when it was over and the Zoo "Animal Ambassador" team started heading to the anteaters, well, we followed them.  And then, when that was over, we followed them to the clearing near the reptile house where they did an outdoor show with their Harris Hawk Saguaro.

The woman leading the show was one of the best public-science-education speakers I have ever seen.  Really.  She had a perfect temperament, explained complex topics, showed incredible respect to children asking bizarre questions, and showed a deep respect for the hawk that really blew me away (they realized that their activities with the hawk had been too repetitive and that it was getting bored so they were trying many new things to diversify it's life, for example).  We lingered and lingered soaking up everything she was doing.  I wish I could remember her name to give her extra props but I will figure it out.

Here are some pics --- most by me, some by my brother


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