Friday, July 26, 2013

RET 2013: The IRIS

My research this year is on viral detection and viral sizing. I scan chips that have been spotted with various antibodies, then incubate these chips with virus and re-scan them afterwards. These scans are done on the IRIS, Interferometric Reflectance Imaging Sensor. I will go into how we capture the virus and what viruses I am looking at in more detail in another post (I need to find out what information is OK for public consumption!), but for now I want to talk about how the IRIS works.

Here is a photo of the machine. It is called the SP-IRIS. SP stands for single particle because our pictures are magnified enough to see single viral particles attached to antibodies on the surface of our chip. The drawings below explain what is going on. The first picture is a drawing of the device you see in the photograph above. See the green light in the photo above? In the pic below it is the green line going through two 'lenses.' See Jyothsna's hands in the photo (she has on blue gloves)? She is moving the stage around to place a chip in the correct spot under the objective. Find the objective in the photo below. The box labeled CCD is a camera. It is the white roundish box in the photo above.

The SP IRIS works by shining LED light at a Si/SiO2 chip. See the chip in the picture above? It is blue and grey with red lines coming off of it? Below is what it really looks like. The very small dots are antibody spots.

We put that under the objective and shine green LED light on it. The light reflects off of the different layers on the chip causing interference (look at part (b) below- the grey thing is the chip with light reflecting off of it. The red and green symbols are particles attached to the chip. They change how the light interferes with itself as it bounces off of the chip. When additional materials (for example antibodies and antigens) are adhered to the chip, the resulting height difference changes how the light interferes. The CCD camera images the difference in how the light interacts, thereby indicating how much biomass is adhered to the chip.

    By taking images of the light bouncing off the chip we can tell where the particles are. On our screen we see large light gray spots (see (c)) where we placed the antibodies and if we zoom (see below) in we see small white dots. The white dots are individual viral particles. 

We can count these viral particles to see how many adhered and we can determine how large these particles are by how the interference of the light changed. Most viruses I've looked at are around 70-120 nanometers in length. How big is a nanometer?!?!? The ruler below has centimeters graduated into millimeters, A nanometer is 1 millionth the size of that millimeter. It is SMALL!.

Wednesday, July 24, 2013

RET 2013: A night at the observatory

Last week the five of us RETers had a little bonding night! First we went to Zumba - which was crazy hot and lots of fun... and then we took advantage of our summer at BU by heading up to the BU observatory.
The BU observatory as seen from my desk across the street in the Photonics Center
The Observatory is open every Wed night from 8:30-9:30 and has students there guiding us from one telescope to another explaining what we are seeing.

This is a telescope inside the mini-museum - the ones we looked through are a bit less old school

This is a telescope inside the mini-museum - the ones we looked through are a bit less old school

Once outside (and loving the breeze given it was the middle of the 97 degree heatwave and we'd just finished an hour of dancing around on the 2nd floor of an un-airconditioned old church) we had a great view of Cambridge across the Charles River and of downtown.
This is the view from the top of the building across the Charles River!
We looked through three telescopes while up there. The first, and the one with the longest line, was pointed at Saturn. I tried taking a pic with my iPhone pressed up to the view finder but it didn't work out. To my eye Saturn looked like a tiny paper cut out of a circle with a ring around it. It's hard to believe I was looking at the real thing!

The next telescope had two stars (I forget their names). They burn at different energies so they are different colors (one red and one blue). This picture didn't come out ether, so you'll just have to imagine it.

Finally we got to the telescope pointed at the moon. How beautiful the moon is up close! The pictures below are what came out when I let my iPhone do the looking through the telescope.

If you look closely you can see some craters - many more were visible  when I looked through the 'scope directly!

Here I zoomed in for you!

PS. I just discovered that the observatory has a twitter feed here!

If you are around you should definitely check this out! It's free and you do not need a BU ID!

Wednesday, July 17, 2013

RET 2013: My fellow RETers and labmates

Here's an introduction to the teachers in this year's RET program. There are five of us this year and we are all returning champions! If you click on the links to our old blogs you will get a good sense of what this RET program has looked like over the last three years.

The 2012 Cohort of RET teachers
The three of us from last year's RET program:

1)  Michelle (here's her blog: Michelle is in the front of the picture to the right with a blue cardigan.
2) Maureen is on the left (next to me) in a black shirt and glasses. Her blog from last year is:  
3) and myself (my blog from last summer: ). Can you see my head poking out next to Maureen?

The two participants from years before that:

1) Ashley (her 2010 blog) who participated in the program in 2010 with my department head Gary Smith (his 2010 and 2011 blog; Gary participated two years in a row)
2) and Jessica who was an RET teacher summer of 2011. Her blog from that summer:

Michelle and Maureen are in Dr. Bifano's lab, as they were the year before, working with lasers and deformable mirrors. I am also in the same lab I was the year before continuing my work with viruses and the IRIS. Ashely and Jessica are both in new labs. Jessica is learning a lot of new material and Ashely is working on designing hands-on a classroom project to help teach her middle school students something about nanotechnology.

Here's a funny little video trailer my RET partner and I made last year:

Monday, July 15, 2013

RET 2013: Labels in the lab

RET SUMMER 2013 has begun!

This summer I decided to go back to the lab - again! In fact all of the RETs are returning participants. We are all coming back to this having enjoyed it a lot last summer and determined to do more research and help make the program even better for the next group. This first blog is just to orient readers with what I see in the lab everyday.

Here is where most of the magic happens:

This one wet bench is used by basically everyone in Dr. Selim Unlu's OCN lab. OCN stands for Optical Characterization and Nanophotonics lab. In this first blog I'm not going into detail on what I have been working on yet, but I want to point out a few highlights in this picture.

Let's start at the bottom. You've probably noticed the refrigerator with the biohazard sign on it. labeling is important because this one lab bench is used by about 25 different people in any given day. We each take a few minutes to set up an experiment and while that experiment runs or washes or incubates, someone else is working on theirs. Labels are an absolute necessity.
 In this lab we work with a number of viruses, all inoculated with UV light so not dangerous, and other biological products that should not be eaten or stored near eatables. You will also notice that all of the drawers are labeled with their contents (though I'm pretty sure that drawer on the right does not have Margo inside of it).

Speaking of labels check out the row of glass bottles on the shelf on the upper right. Each one contains a different clear liquid. Almost every liquid we use in the lab looks just like water to the naked eye. Without labels it would be all too easy to grab the wrong stuff. Each label contains a lot of information. Most have the name of the substance inside the bottle, the concentration (often measured in molarity) of that substance, as well as the initials of the person that prepared it and the date prepared. Can you find all this information on the labels below?


 A few other labels are really important and found throughout the lab. Here are some examples:
This is the label on the door outside the lab. This label tells the fire and safety department all of the hazards they may encounter entering the lab. The diamond on the left gives an assessment of risks (more detail in next picture). The green PPE box denotes the Personal Protective Equipment one is expected to wear in the lab: googles, aprons, gloves. The third box reminds those who enter not to eat or drink and the last box on the right is a warning that this lab uses lasers!

This diamond, created by the National Fire Protection Association, indicated the hazards contained in this lab. The hazards assessed are health (blue), flammability (red), reactivity (yellow), and other hazards (ex. the W means there are substances in the lab that react with water). The numbers go from 0-4 with zero being no hazard and 4 being high risk. I don't love using a wikipedia link but it's much clearer that the NFPA links so, click here if you want to learn more about this symbol.
This is a bottle of deionized water. What do you think that means? Remember what an ion is? What ion is added to public water supplies for the benefit of your dental health? Notice the NFPA symbol has all zeros. 

This is a sharps and biohazard disposal container. We cannot just toss anything we use in the trash or recycling! These barrels tell us where we can put sharps (like glass slides) and where we can dispose of materials we used to test virus.

Now I've made the lab sound a bit dangerous, but it is all these precautions that make it safe to work with these materials in this laboratory!