July 28, 2011

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.  

July 25, 2011

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.

July 19, 2011

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.


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.

July 14, 2011

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.

July 11, 2011

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.

July 7, 2011

Men and Tools

It's been a week full of new people and new toys.  I have a good feel for how research is performed on a day to day basis, and I've been introduced to a number of cool toys, many of which cost tens of thousands of dollars.  More to come on that later.  First the people.  Dr. Ünlü is the professor in charge of the entire lab, which consists of about 15 people.  There are researchers who work at the school and run the day to day projects in the lab.  Dr. Lopez (Carlos) is my go-to guy, and he's one of them.  Then there are post-doctoral fellows, who have their PhDs and are continuing to do research, but with guidance from the researchers and Dr. Ünlü.  Lower on the food chain you have graduate students working on masters and doctoral degrees, and then finally a couple undergraduates.  At the very bottom you have me and my partner, Jared.  Thankfully it's rare for everyone to show up at the same time because the lab room itself is actually rather small.

But it's quite impressive what can be fit into such a small space.  The main attraction is the pride and joy of the lab, a one-of-a-kind instrument that these people have developed.  It's called IRIS, the Interferometric Resonant Imaging Sensor.  Sounds fancy, but it's just a set of LED lights, prisms, mirrors, and a video camera.  It's special because it can use light to measure the thickness of the tiniest amounts of stuff (proteins, dirt, blobs of liquid) on a slide.  One day they hope to be able to identify viruses and determine the amount of virus by using this instrument on living tissue.  Perhaps a blood sample.  Right now I'm helping them test it on "simulated" virus particles, which in this case means gold beads.  Yes, I'm playing with pure gold.  It's not worth much though, since the gold beads are so small you would need an incredibly powerful microscope to see them.

Good thing the lab has one of those too.

July 6, 2011

A Mission

I've been feeling a little worried about the program lately since it seemed like no one in the lab really knows what to do with us.  On the two occasions that we've been shown equipment for a demo process, the equipment has broken down.  Our coordinator's time is limited, and while he clearly wants to do what's best for us, I'm not sure he knows what that is.

Today though at the end we spent some time with him, and we finally got a clear mission: learn how to functionalize gold nanobeads.  This is going to be a lot of research, pouring through journal articles and the internet in general, but this is what I signed up for, and I hope that maybe I can make a small contribution to the lab through it.

July 5, 2011

Day 1

Today was a pretty perfect counter-example to the ideas we have in our head of research.  When I think of research, I imagine seasoned veterans with PhDs and white hair diligently pipetting solutions into well plates.  I imagine whiteboards covered in incomprehensible equations.  What I got today was not any of that.

After meeting with our head researcher to discuss our project, we followed a grad student to the clean room to practice making one of the basic components that we would need for our experiment to work.  It was the equivalent of learning how to pump gas so that you could drive a car.  No gas, no working car.  So we get dressed up for the clean room, and that means bunny suits.  You can see how they got that name:

We have to wear these to protect the materials from dust and other particles that our bodies give off.

So anyway we go the lab, get dressed, and then start the process of making our materials.  Today that means we need to make a silicon wafer, which I'll just call "the chip."  First we clean the chip, which is easy.  Just wash it with some chemicals and then dry it off by blowing nitrogen gas on it.  But we go to blow the gas and it turns out that the lab is out of gas.  The nitrogen comes out with such little pressure that it won't dry the chip.  Oh well, we think, we'll try another lab station.  So we hit another one, but same result.  Guess we have to use a paper towel.  This is horribly against the rules because it will make it impossible to get a proper chip created, but we do it anyway because this is just a practice run, and we need to get to the rest of the steps.

Next we have to put photoresist on the chip.  This is a fun chemical that reacts to light.  We open the cabinet, and while it appears to be overflowing with bottles of photoresist, none is the correct type for our chip.  We pick one that seems "close enough" and use it anyway.  After applying it to the chip using a special spinning machine, it appears that the photoresist was not applied correctly, and the chip is a complete loss.  Whatever, we think, let's go through the steps anyway just to get practice.  So we go to the machine that we need next, but it happens to be giving a loud beeping error message: lamp overheating.  Why?  Turns out that the same nitrogen which we needed to dry our chip is also used to keep the lamp cool in this machine.  So we turn the machine off since no one can use it.

Error after error after error, and no one was really at fault.  That's research for you.  Sometimes things work, sometimes they don't.  Tough luck.