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

Graveyards of America mapped

It’s Halloween. Joshua Stevens mapped all the graveyards:

Right away I was struck by the geography. The pattern, however, makes a great deal of sense in the context of American history. Some of the deadliest battles of the Revolutionary and Civil Wars took place in Georgia, Kentucky, Mississippi, New York, South Carolina, Tennessee, and Virginia.

Get the print version here.

Tags: ,

Graveyards of America mapped

It’s Halloween. Joshua Stevens mapped all the graveyards:

Right away I was struck by the geography. The pattern, however, makes a great deal of sense in the context of American history. Some of the deadliest battles of the Revolutionary and Civil Wars took place in Georgia, Kentucky, Mississippi, New York, South Carolina, Tennessee, and Virginia.

Get the print version here.

Tags: ,

Crowdsourcing plant phenomic data, bacterial niche construction abilities, protocell evolution, microRNA target prediction

  Crowdsourcing plant phenomic data, bacterial niche construction abilities, protocell evolution, microRNA target prediction Posted August 13, 2018 by post-info Check out our Editors-in-Chief’s selection of papers from the July issue of PLOS Computational Biology. Crowdsourcing image analysis

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Author Interview: Kimi Chapelle & Massospondylus Skull Anatomy

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Storify of #UCDmicroBOOmes Halloween Symposium at #UCDavis on #microbiomes

Halloween Rules of the Road

Parent taking children trick or treating on Halloween.

Halloween is an exciting time for kids and adults – the delight of dressing up in a fun costume, all of the spooky decorations, and of course let’s not forget the candy. Traditionally, kids trick-or-treat at night – going house-to-house in their costumes. On average, children are more than twice as likely to be hit by a car and killed on Halloween than on any other day of the year. Children are at Trick-or-Treat Checklist: first aid kit, warm clothes, water, cell phone, emergency contact card, trick-or-treat route, reflective strips or tape, well-fitting costume, comfy shoes, flashlight or glow sticks, trick-or-treat baggreater risk of injury than adults because they are small, have trouble judging distances and speeds, and have little to no experience with traffic rules.

On the Trick-or-Treat trail?

As a parent or caregiver, there are a few important things you can do to protect your trick-or-treaters on the Halloween trail.

  • Light the way. Bring glow sticks or a flashlight with extra batteries so your trick-or-treater can see (and be seen) in the dark.
  • Be visible. Put reflective tape on clothes, costumes, and trick-or-treat bags so your trick-or-treater can be seen by passing motorists.
  • Use the crosswalk. Cross the street at a crosswalk or intersection. Never cross the street from between parked cars and don’t assume you have the right-of-way.
  • Stay on the sidewalk. If available, use the sidewalk. Otherwise walk on the shoulder facing traffic.
  • Pay attention. Distracted walking can be as hazardous as distracted driving so watch where you are going.
  • Review traffic safety. Talk to your trick-or-treater about basic traffic laws before leaving the house.

Driving on Halloween?

  • Remove distractions. The Spooky Truth: In 2015, 5,376 people died while walking along roads – 26 percent of those deaths happened at night. Nearly 1/3 of the deaths that happened in the fall months (i.e., September, October and November) of that year occurred in the evening hours between 6 and 9 p.m. Put your phone in the glovebox or the back seat.
  • Practice defensive driving. Be cautious and stay alert to reduce your risk of getting into a crash. Enter and exit driveways and alleys carefully.
  • Watch your speed. Pay attention to the speed limit and drive slower when you are around pedestrians.
  • Be prepared to stop. Trick-or-treaters may ignore crosswalks and traffic signals so stay alert. Do not pass a vehicle stopped at a crosswalk – they may be stopped for a pedestrian.
  • Do not drive under the influence. Every 51 minutes, one person in the United States dies in a motor vehicle crash that involves an alcohol-impaired driver.
  • Properly buckle kids no matter how short the trip. Properly buckling children in their car seats, booster seats, and seat belts when transporting them and making sure that their costumes don’t interfere with them being properly buckled.

Learn more

Have a fun and safe Halloween!

Don’t Be Scared, Be Prepared!

Little girl in witch costume playing in autumn park. Child having fun at Halloween trick or treat. Kids trick or treating. Toddler kid with jack-o-lantern. Children with candy bucket in fall forest.

Jack-o’-lanterns glow on the front porch. Children wait anxiously in their costumes, ready to go house-to-house collecting buckets of treats. For kids (and, yes, adults too), Halloween can be a time of excitement and imagination. But as a parent, you need to protect your little ones from some very real dangers. What if they get separated from you? Are they prepared to safely cross the street? Did you remind them to not eat the candy before you check it?

Glow in the DarkTrick or treat checklist.

From chilling tales to creepy costumes, lots of things can be scary on Halloween night. But the real danger for children is walking in the dark. On average, children are more than twice as likely to be hit by a car and killed on Halloween than on any other day of the year. Make sure children know the rules of the road and are as visible as possible at night.

Here are some tips to help you prepare:

  • Travel together. Avoid letting children walk alone. Always walk in large groups with a responsible adult
  • Brighten up. Fasten reflective tape to kids’ costumes and treat bags so drivers can see them at night. Brightly-colored costumes are better for kids
  • Look both ways. Tell your child to look both ways before crossing the street and to use crosswalks
  • Stay on sidewalks. Walk on sidewalks whenever possible, or on the far edge of the road facing traffic to stay safe
  • See and be seen. Give children a flashlight or glow stick to hold while trick-or-treating to help them see, and to help others see them while they walk – never run! – from house to house

Caution with Costumes!Trick or treat safety kit.

Your little princess or goblin is itching to hit the trick-or-treat trail. Their costume looks spook-tacular… but is it safe? The right costume will allow your child to see and move safely while they’re out and about.

Using makeup instead of masks can help kids watch the action around them. When painting little faces, always test make-up in a small area first, and remove it before bedtime to prevent possible skin and eye irritation.

Avoid trips and falls by making sure costumes and shoes are well fitted. Swords, knives, and other costume accessories should be short, soft, and flexible. For extra safety, slip an emergency contact information card in your child’s pocket or treat bucket in case they get lost or separated from the group.

While beautiful, candles and luminaries can be a Halloween hazard. Check that everyone’s costumes are flame-resistant, and don’t walk near anything that’s lit. Use battery operated lights whenever you can to keep others safe.

No Tricks, Only Treats

As children’s candy buckets fill up, tiny fingers may struggle to resist temptation: “Just one piece will be okay…”

Or is it? Remind your trick-or-treaters not to eat anything until they get home and you can inspect it. Feed your children dinner or a snack to keep them from wanting to pilfer the treats while they’re out.

Bellyaches are no fun! While inspecting the candy, look for evidence of tampering, make sure it’s in the original wrapper, and throw away treats that look homemade. Does your child have food allergies? Don’t forget to check all the labels.

Have a Fa-boo-lous Halloween!

Halloween is about making memories: haunted houses, carving pumpkins, costumes, and the search for full-size candy bars. Keeping children safe throughout the festivities depends on everyone – parents and kids, drivers and pedestrians – being thoughtful, attentive, and careful.

Visit the CDC website for more tips on how you can prepare, and have a fun and safe Halloween!

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