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.


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: DNA Quantification

This is the nanodrop, a machine for quantifying DNA.

So now that we have grown up and extracted our plasmid DNA, the next question is how much do we have?  And how the heck do you measure the concentration and purity (amount of unwanted protein to amount of DNA) of nanograms of DNA dissolved in microliters of volume?

The answer is that we do these things with spectrometry magic.  It turns out that proteins (which are all made of amino acids) tend to absorb light at 280nm, while nucleic acids tend to absorb light at 260nm.  The concentration can be determined by the absorbence at 260nm (A260), and it turns out that “pure” nucleic acid samples have an A260/A280 absorbence ratio of 1.8 or higher.

This can be done with a spectrophotometer and nice quartz cuvettes, but this means you need enough liquid to fill the bottom of the cuvette, so you have to do a dilution.  This means more math to figure out the actual concentration, and it means that you have to do the figuring of the ratio and concentration by hand.  Fortunately, the lab at school recently got a nanodrop DNA quantification machine.  To use it you just drop 2uL between the silver jaws, and hit “measure”.

The interface for the nanodrop. The prep from BOSSLAB is at the top of the queue!

It turns out our prep went OK.  The stats are:

  • A260=.887
  • A280=.675
  • 260/280 1.31
  • concentration=44ng/ul

To give you an idea of how much DNA that is (and that is quite a bit of DNA!), the plasmid used for the initial transformation was at a concentration of 5ng/ul.  So this prep is almost 9x the concentration.  The volume of DNA from Carolina was 200uL; the volume of the prep we did was (if I recall correctly) 100uL (or more).  So we have now purified 4.5x  the amount of DNA we started with!  Pretty impressive.  The question is- now what do we do with it?

GFP Project Week Three: DNA!


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.


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.

GFP Project Week 2: Extract(ifying) GFP

GFP! GFP has an excitation peak in the blue light spectrum. Unfortunately, the blue LED is comparatively bright. Gotta find a green pass filter!

This week was Week 2 of the GFP project!  The extraction of the Green Fluorescent Protien (GFP) from the transformed host cells, using Hydrophobic Interaction Chromatography (HIC).  We used a kit from Carolina because I have not ever done this before, and I didn’t really know what to buy to do this completely DIY style.  Nonetheless, it was a success and a clear demonstration of the central dogma of biology (DNA–>RNA–>Protein), and a good way to add some value to our transformation.  Now we have not only altered the bacteria, but made something pseudo-useful, but definitely cool, with our alteration.

At a high level, the way HIC works is by selectively binding the protein to a “bead” (more like a fine powder) resin.  Once the cell has been lysed (the cell walls are broken up), the GFP-bearing lysate is mixed with a high salt binding solution.  This gently and reversibly denatures the GFP so that the hydrophobic (water fearing) inside is exposed to the solution.  This water fearing end acts like oil in water; it is attracted to other hydrophobic bits, so the bits all clump together.  Since the beads have hydrophobic sites, they bind to lots and lots of proteins that are hydrophobic.  At this stage, the liquid that contains non-binding proteins is removed from the matrix, so we remove it.  Then a medium-salt wash buffer is added, which removes some of the hydrophobic proteins that re-fold in lower salt, and are therefore less “sticky” than the gfp.  The extra liquid holding these proteins is then removed, and this is when the final low-salt TE buffer is added.  The low salt buffer is also known as the elution buffer, because it elutes (washes out with a solvent) the GFP from the matrix by allowing the GFP to re-nature (fold back into its original configuration), and hide its hydrophobic sites.  Then the liquid contains GFP!  The process is described in more detail below.

Overnight cultures fluorescing! You want to use only a few mls for these, to increase the amount of oxygen-per-volume in each culture.

The first step is to grow overnight cultures of the transformants.  To do this, aseptically pick off a colony from a plate of transformants that are (ideally) only a few days old, and use it to inoculate an LB+ampicillin liquid broth culture .  The antibiotic keeps the selection pressure on the transformed cells, and doing it a few days after the transformation helps ensure that you do not pick satellite colonies or have e. coli that have dropped the plasmid.  These are literally grown overnight, for about 12-16 hours in a shaker.  It is important that the cells are exposed to oxygen, because it is critical to the development of the GFP.  The cells should fluoresce brightly when blue light is shone on them.  In the picture above, the middle and right tube are fluorescing green, but the rightmost tube is not.

HIC resin and equilibration buffer

The next thing to do is to equilibrate the HIC resin with the equilibration buffer.  This is just some salt so that when you add your bound GFP (cell lysate in high-salt solution), the water that the hydrophobic beads are suspended in does not bring the salinity down.  To equilibrate, we added 300ul of HIC resin to 1mL of equilibration buffer, and centrifuged, removing the supernatant.  The supernatant is the liquid remaining on top of the pellet (the mass of solids at the bottom of the microcentrifuge tube) once it has been centrifuged.  Definitely remove the supernatant with a pipettor, because it is runny, so you need to keep the tube upright.

You can see the large green pellet at the bottom of the tube, after it has been centrifuged. The stuff on top is the supernatant.

The next steps you do twice.  Add 1mL of overnight culture to a microcentrifuge tube, spin down for ~2 min at max RPM, being sure to balance the centrifuge.  Then pour off the supernatant.  Repeat for another 1mL

The big green thing at the bottom is a huge pellet of cells!  Notice that the supernatant has been removed, and the cells are kind of stuck to one side of the tube.  That is the side of the tube the was facing outwards.

At this point, we have a great big lump of green cells.  Now we want to harvest the GFP, which is inside the cell membrane in the cytoplasm, with all the other cellular proteins.  To get it out, we add a lysis buffer.  I suspect that in this kit, it is SDS because it got bubbly/sudsy when we pipetted it.

Washboard technique!

The secret to lysing pelleted cells quickly is using the washboard technique.  It works better (for me) than vortexing, and way better than flicking or pipetting up and down.  What you do is grab the top of the eppendorf, and run it along the top of a tube rack, like you would run a stick against a washboard for musical effect.  This subjects the tube to a lot of sudden shocks, and really blasts the pellet off the side of the tube.  When this is done, the pellet and lysis buffer should not be clear; it should have a milky green consistency.

Lysate on ice. you can see the pale green lysate in the tubes.

Another factor in support of the lysis buffer being SDS and not lysosome enzymes is that the ice would slow the enzymatic reactions, while icing cells without any kind or cryoprotectant (like glycerol) is reputed to break up the cell membrane by forming ice crystals, which would further our goals in this stage.

Pellet again! This time the supernatant lysate is green, and contains the GFP we are trying to extract,

The lysate is taken off ice and centrifuged after 15 minutes, and 250 ul of supernatant is pipetted into a clean eppendorf.  In this tube, we add the binding buffer, which gently denatures the GFP.  It is called binding buffer because it allows the GFP to bind to the HIC resin, not because it binds to the GFP.  It gets cloudy in this step, but still retains some greenness.

supernatant lysate in a clean tube.  Note bubbles from (probably) SDS

After the binding buffer has been added

The next step is to add the GFP bearing lysate in the binding buffer to the HIC resin.  You will want to mix this thoroughly to ensure that the GFP binds to the resin.

GFP in binding buffer sitting on the HIC resin

Once the beads and the lysate are mixed, you put the tubes into the centrifuge and pellet out the HIC resin, which is now bound to the GFP and many other proteins.  As you can see in the picture below, the supernatant is not fluorescent, so it does not contain any significant amount of GFP.

The resin glows now, but the supernatant does not!

Now the supernatant is pipetted off, and the wash buffer is added.  The wash buffer is a less salty buffer than the binding buffer, so some of the proteins that are less sensitive to salt change configuration and “hide” their hydrophobic sites from the HIC resin, making them fall back into solution.  This is centrifuged and the supernatant removed and discarded much like the binding buffer was.

The final step is to elute (to wash out with a solvent) the GFP from the resin with the TE (low salt) buffer.  This makes the GFP fall off of the resin and into the solution.  Then we pipetted the supernatant (now containing GFP) into a clean eppendorf.  Here are some shots of the results:

left tube is the extract, right tube is the crude cell lysate

with blue light from my arduino!

Now next weekend the GFP project will be on hiatus, because I will be away for spring break.  However, the sunday after that it will be back in full effect, probably with a plasmid DNA extraction adventure!




The GFP Project Week 1: A Lesson in Patience and Ingenuity

Arduino: the alternative lighting platform for molecular biology

It had been two days since the transformation yesterday, and I had not seen any growth on my plates.  I was becoming concerned.  It can be tricky to orchestrate the teaching and the actual transformation procedure, and I have had less than optimal results with this media, strain, and plasmid before.  I was not sure what I would do on Sunday if there were no transformants!  It would be a disaster, and very demoralizing.

I had a meeting to go to that would result on me being on the red line, so on the way back I stopped by and took a look at the cultures with my blue LED.  Nothing was growing, except for what appeared to be some e. coli growing on the ampicillin plate, which I took to be an ill omen.  I left my blue LED and some batteries there, because I figured that if there were transformants, they would be more likely to grow on the multitude of plates at sprout instead of the two that I had.

I wasn’t sure what to do there, so I grabbed a few items for doing another transformation and headed home, convinced that I would have to do another transformation.  Upon my return home, I obsessively checked again.

Perfect little colonies!

When I returned from dinner, I decided to take one last look.  I was greeted with two plates full of transformants, in perfect little green colonies.  Having left my sole blue LED at sprout, I initially thought that I would have no way of testing the fluorescence, until I spied my arduino nano on my desk.  I remembered that it had a blue LED on it, so I plugged it into my laptop and used it to light the plates, which indeed fluoresced.


Lessons learned:  Be patient.  Synch your life to the organism you are studying, not the other way around.  Also arduinos are good for many things.

cell growth phase chart, found via the google

The final question you may have is “why did they take so long to grow?”.  The answer there is something I should have recognized!  I totally forgot that there is often a “lag phase” of growth in bacteria.  This is the phase where bacteria are generating the needed metabolites and substrates to adjust to their surroundings.  The colonies are also growing (in this case) from a single bacteria!  So it makes sense that there was a pretty big lag from when they were plated, until  I could see them.

The GFP Project Week 1: Hands-on Transformation!

The shirt says it all.

The GFP project rolls forward!  Powered (funded) by the people doing the work, I managed to order all the materials that we would need for a transformation this weekend (by that, I mean today).  There was an awesome turnout; some new people came out, a lot of supporters came out, and a good time was had by all.

From left to right: LB broth, LB agar, 50 mM CaCl solution, alcohol burner, tape, streaked plate, arduino, pipettes in a fancy box, ziplock-o-wires

To start out, we had to sterilize some media and CaCl2 solution.  We made 200 ml of LB agar, 80 ml of LB broth, and 500 ml of 50mM CaCl2 salt solution.  The LB agar was used to make LB+ ampicillin plates.  These were prepared by adding 2 ml of 1% ampicillin to the still-molten agar once it had cooled to “warm enough to hold”, and then pouring it into sterile petri dishes.

The Calcium Chloride solution and the LB broth were needed for the transformation.  You only need 250 ul of each per-transformation.  We prepared the LB broth in bulk because it is useful to have on hand, and we prepared way to much CaCl2 because our scale was not sensitive enough to measure out a smaller quantity that would make a 50mM solution.  We could have made a 1M solution and diluted it, but it seemed simpler to just make 500ml.

Totally legit ice-bucket of science

The other necessities for the transformation that had to be prepared were the ice bath, and the 42 C water bath.  The ice bath was created using the insulated shipping crate that the plasmid and ampicillin came in by throwing some ice in the larger (bottom) container.  The water bath I have successfully made before by nuking (microwaving) the water and then  guesstimating that it was hot enough (more than body temperature, but cool enough to hold, between 37-50C).  Today I used what seemed to be a much more reliable method, which was a hot plate and a submersible temperature probe.

(Hot) Water bath setup. Sensor in falcon tube taped to beaker, arduino connected to sensor and computer

The temperature probe was improvised with my arduino mini, a DS1820 digital temperature sensor, some long wires, and a 15 ml falcon tube.  I submerged the falcon tube in the water bath, and stuck the temperature sensor (which had been soldered to the long wires) into the tube, allowing it to (hopefully) measure the temperature of the bath.  This was reporting the temperature back to my computer with some script I got to work a while ago.  A better way to set this up physiclly would be to cram the sensor in to a thin-wall reaction tube (PCR tube) and fill it with milliQ water (non conductive, very DI RO water), stick the sensor in the water and waterproof all that with sugru or epoxy.  This way there would be no air gap, and the sensor would be safe in DI water.

The game plan for the transformation in flowchart doodle format

During all of that setup we were also preparing the bacteria for heat shock, teaching people how to pipette and streak bacteria, and talking about biology in general.  Our transformation protocol, officially was this:

Gather all the things! Everything didn’t fit in this picture, but this is a lot of stuff!

1.  Gather reagents (LB broth, 50mM CaCl2, LB+Amp plates, e. coli plate, eppendorf tubes), prepare ice bath and water bath, and gather your tools (flame, inoculation loop, pipettes and tips)

Use your sweet pipetting skills to add salt solution to your eppendorf. keep on ice.

2.  add 250 ul of 50 mM CaCl2 to an eppendorf tube, and chill on ice

Scrape e. coli off your source plate. Be careful not to pick up any agar!

3.  scrape off some e. coli (enough to see on the loop) with a flame sterilized loop, and swish the loop around in the iced CaCl2 in the eppendorf.  Make sure they fall off into the CaCl2.

flick! flick! done!

4.  flick the tube until the bacteria are no longer clumped together.  The solution should be cloudy now.  Chill tube on ice for 1-5 min.

Adding tiny amounts of DNA means tiny pipette tips!

5. Add 20ul of plasmid DNA at .005ug/ul to the eppendorf.  This is .1ug of DNA.  Return tube to ice, incubate for 5 min

Heat shock!

6. heat shock at 42C for 90 seconds

7. add 250ul of LB broth

Spread the bacteria around with the sterile loop

8. plate 100ul on LB+Amp plates.  Pipette 100ul on to the plate, then flame loop and cool in agar somewhere that you did not pipette onto.  Use loop to spread pipetted transformant mixture.

With all of that done, we cleaned up and headed off to wherever.  Some people had to leave early, but most everyone seemed like they would be back!  There should be results on if this worked in just a few days.

DIYBIO: Streaking Plates to Isolate Colonies

Isolated colonies. Also note initial thick streaks in to the top of the plate, and then the less continuous sreaks in the bottom right, and the thinnest concentration of isolated colonies on the bottom left

So, you want to isolate that plastic degrading, or bioluminescent, or plasmid-bearing microbe from the rest of a mixed sample.  Or maybe you want to grow up a colony from a single bacteria for a clean PCR sample, or to inoculate a liquid culture.  To do this you will need to streak a plate!  There are many techniques for this, but there are really two key ideas:

  • Work cleanly; don’t contaminate your sample.  Use an open flame
  • You want to thin out the amount of bacteria on your loop

My technique for this is to heat my loop up to orange-hot, then cool it in the agar of the sample I am taking the colony from, being careful not to touch any of the colonies on the plate.  Once quenched (So I don’t heat-kill the bacteria),  I rub it on the target colony or area on the sample plate.  Then I close the sample plate and open the target plate.  I like to do 3 streaks.  The first one is to spread out the bacteria I picked up on the top 1/3 of the plate.  Once this is done, I sometimes flame and cool the loop in the target agar, although it is ok to skip this step.  Either way, I then make another zig-zag, starting in the area that I spread the bacteria in, and then moving out onto an unused third of agar.  The last streak takes up the last third, and starts in the last area I covered.

Good, isolated colonies

If everything works out, you should have isolated colonies like in the picture above.  A few common pitfalls are:

Clear streaking pattern, but there are too many bacteria, and it looks like I overlapped my first zig-zag with my last zig-zag! oops.

  1. TOO MUCH bacteria.  Bacteria are very small, and if you pick up too many, you will end up with a bacterial “lawn”, which is useless for isolating colonies.
  2. Accidentally killing your sample bacteria by sticking your red-hot loop into them (doh!).
  3. Streaking back into an already streaked area.  This defeats the purpose of streaking, which is to spread out the bacteria.  If you go back from a low concentration area to a high concentration area, and then back to the low concentration area, you risk bringing extra concentrated bacteria that would form a lawn into an area where you want single colonies.