Wrapping Up

This week all that I have left to do is prepare two presentations to give the BU community and the rest of the RET participants information on just what Jared and I accomplished this summer.  I'm in the middle of setting up a poster right now, but figured I'd stop to share some random reflective thoughts.

I'm really happy that I was able to get good data on my experiment, and even happier that the data confirms our hypothesis.  I've also learned to appreciate how rare it is for that to happen, so I feel pretty lucky.  The major downside of the data story though is that we didn't collect more of it.  Mainly this was because neither Jared nor I know how to use the software which processes the data that we collected with the high-magnification IRIS.  One of the students who works in the lab did it for us on just two of our images, and he did things so quickly that we had no chance of being able to do it on our own.  In fact, while we have data which supports our hypothesis, our data isn't that convincing because we didn't collect enough of it.  Imagine people voting for president: 100 million votes are usually cast in an election, but imagine that whoever is in charge only looked at 1,000 of them before deciding who won the election.  That's what our data is like.

I'd say that the major hurdle to getting research done at first was a lack of supervision.  We were mainly working with Carlos, who was sadly also in charge of helping two other RET teams.  He ended up not having a ton of time for us at first, so we didn't really start working independently in the lab until the very last week, when in fact we could have started a week earlier.  We wasted a lot of time in that first week just waiting for him to have a free moment to work with us, and that held us back.

Instead of giving you a final word, I'll end with a quote that sums up pretty much the main thing I learned this summer.

"If I find 10,000 ways something won't work, I haven't failed. I am not discouraged, because every wrong attempt discarded is another step forward."
-Thomas Alva Edison

Success!

Today, a story of success.  I know, just about the last thing you'd expect, right?  Same here.

Yesterday we looked at our latest batch of chips.  Our gold beads have anti-HGH attached to them, which means that the beads should want to stick to the chips that have HGH on them, but not stick to any other chips.  We took a lot of pictures of the chips yesterday and saw a lot of white spots on the HGH-coated chips, so we assumed that those were the gold beads and left the lab feeling really good.  On the last day of working in the lab, it seemed like we had finally accomplished our goal.

Today we got some help from a undergrad students in the lab, Joey.  He used some specialized software to look at our images, and he analyzed the same regions of the chips that we did.  When he saw the white spots though, he was instantly skeptical that they were in fact beads, and our hearts fell.  Had we failed after all?  In a sense, yes.  The spots were actually dirt of some kind, perhaps salt crystals or some other debris, but they were clearly too big to be the gold beads.  However, rather than give up, Joey decided to study part of the chip that appeared to have nothing on it, just to see what would happen.  Turns out it had nearly 100 gold beads on it.  Finally, we have tasted success, and I can only hope that the rest of the research groups were able to feel the same.

As this experience comes to a close, I can say that I have changed.  No longer do I see research as a process of speed, where scientists are continuously at work in a lab working on machines, pipetting solutions, or furiously completing calculations.  I understand that most of the work is expected to fail, and that successes come well spaced.  I feel that in my time I have mostly acclimated to the process but lack deep background on the content of the lab's work.  If I were placed in a microbiology lab I would doubtless have been more effective from the start, but would likely have learned less, and so I am glad that this lab expanded my horizons.  I pepper my teaching with stories of science, and now that I have some personal experience with research, I can add it to my growing repertoire.  I know my students will appreciate it.

Hard to be an Optimist

I woke up yesterday morning feeling really good.  I had a full day of experiments planned, and I was really happy that there wouldn’t be too much down time.  So I got to lab and got started, full of positive energy.  Some of our steps required us to wait for a chemical reaction to happen, so we didn’t mind stepping away from lab to participate in the weekly lab meeting. 

That was the beginning of the end of my good mood.

The meeting predictably started 40 minutes late.  Neither of the senior lab members were there, so one of the graduate students finally got things started.  We’d wrapped up all of the issues when the lab head arrives, a full 75 minutes late.  He made us go through the entire thing all over again so he could give his input.  At this point I was itching to get back to lab.  We’d lost a lot of time and I wasn’t looking forward to staying late.  I figured if I cut my lunch really short I’d still be able to finish everything, so I started to get up, determined and focused. 

Then the lab director had us all stay put so that we could have another meeting, but not just yet.  He went outside to talk to a graduate student for 15 minutes, leaving Jared and me in the meeting room with four other students.  When he came back, we had a second meeting on developing the curriculum for an outreach program that the lab was running starting next week.  First, it amazed me that they were going to lead a program that started in four days and hadn’t planned for any of it.  Second, I couldn’t believe that the professor started by outlining a plan whereby the outreach participants (all high school students) would listen to presentations for two hours straight on Monday as a nice introduction.  I don’t know anyone who would be excited to listen to lecture for two hours without a break, so I gave input to that effect.  This had an unintended consequence.

I suggested they do an activity in the middle of the first day to break up the lecture segments.  Jared agreed and suggested a fun disease-spread simulation that would tie in with one of the points they would be making about global health.  They loved the idea, and he helped explain it to them, and then at the end the lab director told us that we would be presenting it.  Wow.  This is their outreach program, not ours.  We’re here to do research, not to take over their commitments. 

Well, message received on that number.  Jared and I wisely kept our mouths shut for the rest of the meeting so as to not get any more responsibilities, and it finally concluded at 1:45 pm.  Neither of us had eaten lunch, and there was no longer any chance that we were going to get all of our work done in time.  We went back to the lab, hungry, to do what we could.  Our hope was to hurry to get to a step that required us to wait for two hours, and then we could have a late lunch then. 

On returning, we picked up our chips, which had chemical spots placed on them.  We needed to verify the position of the spots underneath the IRIS, a high power microscope of sorts.  Both of us looked and looked, but sadly it appeared that all of the spots had vanished when we rinsed the slides.  This was unexpected, and Carlos couldn’t explain how it happened. 

That threw our plan completely out the window.  I blamed the lack of spots on the four hour lab meeting, since we had immersed our chips in water for far longer than usual.  Now we had to completely rethink our plan.  We took some new chips, coated them with a polymer to allow proteins to stick to them, and then put them in the vacuum chamber to keep them until Monday.  This wouldn’t have taken long, except that we had to make the polymer first and that took a while. 

All in all we ended up leaving the lab at about 4:00.  We created a very basic list of things to do next week, and since all are exceedingly simple it should be no problem getting all of it done in time for the end of the program.  Hopefully there won’t be any major surprises next week.  

Productivity: Optional

Since this program started, Mondays have been my least productive day.  They always start the same: a trip to the clean room to work on our photolithography project.  I go with four other teachers and one of the program directors who takes us through the steps to make... something.  I understand what we're making, but I'm still not sure why.  We seem to be doing a lot of things to help us get acquainted with the materials and machines in the clean room, and a lot of these procedures are related to the types of things that many of the labs in the building do on a regular basis, so that's useful.  However, it has practically no bearing on my immediate project, the gold nanobeads.

Still, it is a lot of fun to do the experiments.  Today we took glass plates that we'd etched with chemicals the week before.  On top we added a mixture of PDMS, which looks a lot like clear Jell-O when it hardens.  It essentially formed an impression of our glass plates, and then we peeled it off and shined lasers through it.  They made some really cool patterns on the floor.  I'd take a picture, but the laser is making my dog go nuts, and I don't have enough hands to handle everything besides.

But now I have a jello-like disc that I can use in class to impress my students.  That should be good for a light demo.

Frustration Anew

We thought things were going to work today, and by all rights they should have.  We had prepared the gold nanobeads last week with a coating of MUA.  The MUA was supposed to have served as a glue to which we would attack proteins, with the goal of making a gold bead covered in proteins.  However, before we could add the proteins we had to first change the MUA with a brief chemical reaction to make it sticky.

We prepared the chemicals and mixed them with the gold.  Instantly we knew there was a problem though; instead of remaining a light pink, the gold solution turned clear at first, and then slightly yellowish.  It wasn't supposed to do that, but we thought the experiment might work anyway, so we continued to the next step.  Now the gold was sitting in a chemical solution, and we needed to rinse it, so we had to separate the gold from the chemicals.  To do this we had to use a centrifuge, which spins the mixtures around really fast like a merry-go-round moving at warp speed.

Centrifuge:

So we spun the gold mixture for a bit, and then took it out.  Imagine our shock when the solution showed no change at all.  I know it's hard to imagine, but this result was about as surprising as if you had shot a pistol at a piece of paper and had the bullet bounce back at you!  Thinking that maybe a higher setting on the centrifuge would fix things, we set it to it's maximum speed and let the gold solution stay in it for 20 minutes.  The gold particles were feeling a force roughly 16,000 times stronger than gravity, so surely they would separate from the solution this time.

They didn't.

Success...comes in incredibly small doses

Today was a good day.  After a lab meeting Jared and I sat down and hashed out a short term plan that would hopefully bring us one step closer to our eventual project goal: coating gold beads with proteins and making them stick to a silicon chip.

We decided that we needed to make sure the first step in our process would work.  Yesterday our first step seemed to have gone well, but when we showed up to lab this morning, it was apparent that we had failed.  We had mixed gold beads and a chemical called MUA together, and the MUA was supposed to coat the gold.  However, what happened instead was that all of the MUA and all of the gold spheres stuck together in giant lumps, and that won't work for us: we need them to be separated, individual gold spheres.

Today we decided to test MUA and gold in two different liquids: ethanol and water.  Ethanol is the scientific name for what we commonly call alcohol; it's what gets you drunk.  Water, less so.  Then we went a step further: we also decided to change the amount of MUA that would be added to each sample of the beads, so in total we had eight different vials of beads and MUA to study.  Add in the two control vials, and we had a total of ten.  Here's how they looked after 50 minutes.

The ones on the left are mixed with water and the ones on the right are mixed with ethanol.  You can see the color difference between the two.  We were hoping to see a nice light pink, so it looks like water is the chemical to use.  Next week we'll have to test out phase two of the experiment, which will be adding two more chemicals to the MUA-covered gold: NHS and EDC.  Yes, it's going to get very technical with the acronyms.

Here's how the ideal, perfect, bestest ever situation would play out:
Tuesday: We successfully coat the gold beads with a cow protein called BSA.
Wednesday: We prepare a chip with antibodies that like BSA.
Thursday: We mix the BSA-coated gold and the chip together, and the gold sticks to the chip.  We confirm this using IRIS, a fancy machine I'll get into later.
The following week: We repeat this basic process using gold rods instead of beads, and it works the same.  Then we do the beads and rods at the same time and the IRIS can see a difference between the two.

So, that's my fantasy.  I wonder what reality will look like.

The Devil in the Details

Carlos sure does have a lot of faith in us.  I've been out of school for six years, and Jared for about twice as long, but tonight both of us will be scouring the internet for information on how to make microscopic gold beads sticky.  That doesn't sound like such a difficult task, but it is.  This is a basic procedure, we think, and so the answer likely resides in the heads of scientists around the world; however, because it's so basic, none of them have bothered to publish a nice complete and super-basic article anywhere on the internet explaining how to do it.  So it's up to both of us to read dozens of journal articles tonight to see if we can find clues and references as to how to make gold sticky.

But this isn't easy either.  Consider the following sentence, which is a pretty typical example of what I'm speed-reading:

"The MUA-attached, gold nanoparticle-deposited substrate was immersed in an aqueous solution containing 0.1 M 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (WSC, Dojindo) and 0.1 M N-hydroxysuccinimide (NHS, Tokyo Kasei Kogyo) for 2 h."

Or how about this one?

"Antibody-binding events were examined by measuring the transmission spectra of the gold nanoparticle-deposited substrate functionalized by BSA and HSA before and after incubation in anti-BSA (from pig) and anti-HSA (from goat, vector) solutions, respectively."

It's hard to get back into the rhythm of being able to read these once and understand them.  I know I could do it in college because I had to do it frequently then, but that was a long time ago.  Now I'm having to stop every few words to look up a term.  I'm also not really finding the solution to the problem I'm working on, at least not a specific one.

Hopefully I can dig something workable out of the internet by tomorrow.  Stay tuned to see if I did.