Genomes, Environments and Traits Confrence!

Jason Bobe moderates a discussion with George Church and Geraldine Hamilton about personalized medicine microfluidic devices

Today I attended the Genomes Environments and Traits Conference.  It was awesome!  There were talks on all manner of technical breakthroughs from faster and cheaper sequencing, to single-cell sequencing (WITH 3D protein/DNA localization on the intracellular level!!!), to hackable drug delivery kits for 3rd world countries.

The more exciting part for me personally was running into all kinds of DIYBiologists.  It was awesome to finally meet them in person!  Ellen Jorgensen from GeneSpace was there, as well as Joseph Jackson from BioCurious, and (obviously) Jason Bobe from the Personal Genome Project.  There were also some people from the BOSSLAB group there (woo! not sure if they want to be mentioned by name).  I even found somebody from Olins’ neighbor college, Wellesley, and I spotted at least one Babson Jacket in the crowd.

Anyways, this conference got me more excited about biology and science, and this summer at BOSSLAB.

Mini-Maker Faire @ Cambridge Science Festival!

Really bad photo. I apologize…

I was at the mini-maker faire today representing DIYBIO Boston, and all I got was this really bad photo…

Just kidding!  I also talked to a bunch of AWESOME MAKERS and excited participants.  I even got to help Gui and Molly of Artisans Asylum lift a giant motorized barbers chair onto a truck, and see a bunch of <6 year olds run dyes from M&Ms in agarose gels.

If you are looking for my bio work because you met me at the festival, click here to see the things I have done with biology.

Baby Sea-Animals, Everywhere.

What happens when you let your saltwater tank evaporate off for a month or so, then do a water change?

The punchline here is BABIES.  It turns out that some sea animals, in this case featherdusters, some kind of worm, and snails all like to reproduce when they are put under stress.  Specifically the salinity dropped from 40+ PPT (S.G. 1.032) to 28-30 PPT (S.G. 1.021), the temperature probably dropped as I added room temperature or colder water.  I also agitated the tank with a turkey baster to help the filter pick up snail waste and to dislodge some stubborn algae.

Anyways, here are some pictures of the creatures I noticed, including some nocturnal bristleworm looking things, and copeopods, which I missed in my last post about the denizens of the tank.

Baby snail!

These guys crop up with some regularity actually.  I suspect some of them dont make it, and others rapidly grow up.  Occasionally I see some that are just 1-2mm long, this one was about twice that size.

Just a blurry view of my aquarium…or is it?

At first glance, this is just a really bad photo of the aquarium where the AF decided to focus on the glass.  But when I looked closer…

Upon closer inspection, there is a baby tube worm/featherduster!

 

 

 

I noticed teeny tiny feelers coming out of this guy.  When I tapped the glass, he snapped back into his coil-thing, just like the featherduster!  I can only assume that they are related.  I can’t wait for these to grow up; there are a whole bunch of them sprinkled around the aquarium.

This appears to be a bifurcated bristleworm

This guy may not be a baby, but it certainly caught my attention with its weirdly bifurcated body.  It seems to be due to trauma and not genetic, because one side is much longer and the bifurcation did not seem to be symmetrical.

Last but not least, a copeopod

This guy (to the right of the pink thing in the middle) is a copeopod.  These are ALL OVER the tank, and they feed on pretty much anything.  They like to pester the featherdusters (the burrow/shell of which can be seen directly below the ‘pod).

Thats all for now.  Tomorrow I may go chiton hunting somewhere on the shore of mass, so there may be forthcoming posts about that!

Deizens of the Saltwater Tank

Despite having added only live rock and snails, the 5 gallon hex tank is showing an amazing amount of macro biodiversity.  This is a short post to document what is growing in there!

A multitude of dwarf cerith snails

These guys are the workhorse of the algae fighting army.  There are many of them, in many shapes and a variety of sizes.  They like to crawl up and down the sides of the tank, and will occasionally congregate there.  Sometimes they hitch a ride on the back of larger snails!

This big guy is a florida cerith!

If I had to pick the coolest looking species of snail in the tank, it would be the Florida cerith.  Between their green coloration and rippled shell, they are hard to beat!  Not to mention these snails can self-right themselves!  These are are the largest snails in the tank.

This is the nassarius snail, in the middle. it looks like he is hitching a ride on a Florida cerith

If you zoom in you can tell this is a nassarius on a florida cerith snail.  The nassarius is easily distinguished by its single long stalk that probes for algae.  These guys are speedy!

Heres a nerite snail

My nerites are identifiable by the deep grooves that run along their round shells.  they have two long feelers, unlike the nassarius.  These guys are also very speedy.  Here, the nerite is harassing a dwarf cerith.

This is a featherduster

This guy was quite the find! It came as a hitchhiker on some live rock I bought.  It seems to have grown some since the rock was introduced, and it certainly is less skittish now.  there is another one on the same rock with a green/purple coloration, but it is hard to get a picture of that one because it is shy and very well hidden.

Cyanobacteria!

I thought this stuff was algae, but I was wrong!  It turns out to be purple cyanobacteria.  Its HUGE, and the snails seem to nibble at it from time to time.  I really don’t mind it, although it is considered a pest.

Thats all for now!  Maybe I will notice more stuff as time goes on.

 

 

GFP Project Week Three: DNA!

Lets DIYBIO!

Well, the GFP Project has come full circle.  It started out about a month ago with the idea that a few people could get together and do some science together.  I would say that it has been a success.  In the past few weeks we have covered what I believe to be the “Hello World” of DIYBIO, which is to transform a plasmid into a bacteria, do something with the modified bacteria, and then get the plasmid back out.  Yesterday we closed the loop and extracted the plasmid.

Overnight Culture

The plasmid extraction went smoothly.  The Idea behind plasmid extraction is pretty simple, and it starts with an overnight culture.

Spun down cells

Then we centrifuge the tubes to pellet the cells.  This allows us to pour off the supernatant, as the cells will stick to the bottom of the eppendorfs.  The next step is to re-suspend the cells in “resuspension buffer”.

Resuspended Cells

Here are some resuspended cells!  Looking pretty good.  This is necessary so that the next few buffers can get to all the cells.

Lysed Cells

Here the cells are lysed.  As you can see, the lysis buffer seems to denature the GFP, as the tube is no longer very green.  The lysis allows the plasmid DNA to get out of the cell, and it also helps break down the genomic dna.  The plasmid DNA is a little tougher because of its circular shape.

Halted Lysis

Now we halt the lysis, and this causes a change in the solubility (and probably pH and salinity), causing the extra cell ‘junk’ to fall out of solution.  As you can see, the GFP has returned!

Pelleted Cell Debris

Now we pellet the cell debris in the centrifuge.  This should get rid of quite a bit of the cell debris, leaving us with the plasmid DNA and some other junk in solution.

Spin Column

The supernatant (liquid) in the tube with the pelleted cell lysate is applied to the top of the spin column, and then centrifuged so that the DNA is bound to the matrix (solid white stuff) in the column.  Whatever passes through is junk.  To remove some of the other cell bits stuck to the column, two “wash” buffers are applied to the top of the column and centrifuged through the column.  This removes other chemicals that have a negative charge like DNA, but that are not DNA.

Elution!

The final step is to elute the plasmid DNA from the column by applying (you guessed it) an elution buffer.  This washes the DNA out of the column.  In this picture, the spin column has been placed in a clean eppendorf that will hold the final purified plasmid DNA solution.

Purified plasmid DNA

Once centrifuged, you have purified plasmid DNA!

 

The GFP Project: One Step Backward, Two Steps Forward

Oops.  After a week off for spring break, I returned to the GFP project and realized we had to do another transformation, because last time we had accidentally used up all our stocks of transformed bacteria.

So we did another transformation, and we also plated some of the leftover bacteria we had on a plate from the first transformation.  Hopefully we can use one of these sources to grow an overnight culture and extract GFP from.

We also had some interesting visitors!  We had Jonathan, an anthropologist in the science and technology field, who knew Mac Cowell from way back, and that we had some DIYBIO screens hidden away at BOSSLAB!  Time to make some T-Shirts!

We also had Kris Constable and Megan who are starting BioSpace, a which is exactly what it sounds like (a bio-hackerspace) up in Canada.  It was cool to meet international DIYBIO folks!

The other good news is that the stickers are finally in the envelopes and addressed!  They should go out this week.