Frederick Douglas Academy III

December 12th, 2008

The BioBus just finished an amazing week at FDA III in the Bronx. On the first day, we brought all of the 10th grade students through the bus. The rest of the week we brought interested students from the first day back to the bus for a day of lab work. In the lab work we had two major goals – first, to figure out the nature of the bright spots in the hoechst labeling (labels DNA) of our fixed cells, and second to identify and make movies of some locally collected cells. For now, I will post one image and one movie, but soon I will make a new page with all of the hypotheses and data that the students came up with over the week.

Hoechst (DNA, blue) and phalloidin (actin cytoskeleton, green)

Hoechst (DNA, blue) and phalloidin (actin cytoskeleton, green). Sample prep by Tomas, microscopy by Wilson & analysis by Bo and Chris.


 

Dividing Bacteria from Crotona Park Pond. (Movie is in real time). Made by Princess and Taccara (P&T Productions).

First Fluorescence

December 5th, 2008

No, I’m not talking about the birth of food production in the Fertile Crescent (can you tell I’ve been reading Guns, Germs, and Steel?), I’m talking about the first digital images of fluorescence taken on the BioBus. The generous donations of a camera from Edmund Optics along with a lens adapter from Olympus have enabled us to start making still pictures, time-lapse sequences, and video-rate movies of cells. Below is one of the first composite images I took with the camera. Composite means that the picture is actually two images added together: the blue shows where DNA is and the green shows filaments of actin protein. These filaments form a spider’s web-like network in the cell’s cytoplasm that allow the cell to do things like move and eat. Each blob of blue is the DNA of a different cell. Do you count 6 separate blobs?

Green actin with blue DNA

Green actin with blue DNA

The microscope slide I used to make this picture was donated to the BioBus by Tomas Perez at Columbia University. Tomas uses fluorescently labeled cells in his research to let him track the whereabouts of certain proteins inside the cell. For instance, in the above image you see that the blue stained DNA is located at the center of the green-stained cytoplasmic network of actin. Do you know why DNA stays in the center of the cell and doesn’t spread out into the cytoplasm? Hint: it starts with the letter ‘N’.

These cells came from petri dishes that Tomas keeps full of so called ‘immortalized’ mouse cells. Immortalized means that these cells can grow forever on a petri dish, without ever needing to be in a mouse again! Tomas then chemically ‘froze’ or fixed the cells in place, after which he stained the cell with special chemicals designed to recognize only certain cell structures (in this case the structures of DNA and actin filaments) and make them glow. This is like putting fluorescent colored clothes on certain parts of the cell and then shining a black light on it, like you might do at a party! And believe me, cells CAN dance.

Our ability to take digital fluorescent images is also exciting since we are working on a grant to fund building a large library of fixed and stained samples for the BioBus in order to see all the different organelles and structures (like mitochondria and ribosomes). We can also look for differences between cells from different places. Perhaps student-researchers aboard the BioBus will discover a difference between cancer and non-cancerous cells? It’s not impossible.

If you are a scientist and you have fluorescently-labeled samples you would like to donate to the BioBus, please contact me (ben@biobus.org). We currently have filter cubes for UV, GFP, and Rhodamine excitable dyes.

Amazing Waving Cells

November 17th, 2008

A new article published today in PLOS One from Columbia University and Cell Motion Labs (the non-profit that runs the BioBus) gives new insights into how cells move. And, even if you’re not into the gory details of what a cell is doing when it spreads out like a pancake on the microscope, you might still be interested in just playing through the movies, like this one:

All PLOS journals are free, and you can even comment on and rate articles! So please support this work and open-science by going to the article, browsing around, and giving your two-cents.

Wheel Well Step

November 16th, 2008

Gaylen has done a bang-up job on the wheel well cover. Instead of making two steps as in Ray’s original design, we made just one on the bottom and left the curve of the wheel-well alone, which I think looks really nice and is perfectly functional. The wood was all reused – it came partly from the organ in grace church and partly from Gary’s original wheel well cover that I still had in storage. The structure holds an uncanny resemblance to a gigantic plant cell, and it would  be fun to paint it like that! Next project up: better cabinets for the wet-lab.

Back Home!

October 29th, 2008

The tour was a real success, but of course it is very nice to be back home in New York! The bus is back at Grace Church in Jersey city, in fact, just across the river from Manhattan. We are finishing up the painting here and also making some improvements to the interior based on our experience on the tour. In addition, this Sunday we will have BioBus Sunday as a way to give thanks to the church for its generosity in letting the bus park in the driveway while we paint it.

Sketch of Wheel Well Stand

Sketch of Wheel Well Stand

Tomorrow, my friend Gaylen will help me add a step/seat on the left-front wheel well, based on the design by Ray Naula (at right). This will add to the useable space in the front of the bus. The wood is coming from the old organ in Grace Church that Donald is currently taking apart – it was made of beautiful hard-wood and will make a very sturdy, and handsome, addition to the lab.

One of the things I have found quite gratifying while working on the bus has been our ability to get many of the materials we need second-hand or sometimes even out of the garbage. It is incredible how much stuff we throw away that is perfectly good and useable, if you can just find the person who needs it! It is true that you can usually furnish your apartment just by spending a few days looking at the trash piles on the street. I’d like to take this opportunity to promote one of my favorite, slightly more organized, recycling resources, called Freecycle. On the NYC list, there are about 100 items people are giving away for free on the list every day – it is an amazing resource whether you are running a shoe-string non-profit or trying to help save the planet by reusing things that would end up in a land-fill, instead of buying them new.

 

Francisco

Francisco

Francisco came by last night and did an amazing job cleaning the microscope and wet lab. Francisco is gifted in many things – he not just cleaned the bus, he started teaching me how I could keep the bus clean myself more easily! Typically the bus gets cluttered with tools and parts until I have students coming on board and I clean it just for these occasions. But I need to develop a system for storing things and keeping things neat so that the bus is always ready for action. Francisco also came up with a very neat idea about how to use the space in the computer lab at the back of the bus that is atop the vegetable oil tanks. This is a large platform, about 7 foot long and 6 feet wide, with about 5 feet between the platform and the ceiling. Francisco’s idea is to put cushions along the walls around the sides of the platform and add a low table in the center of the platform. Students would sit cross-legged or with their legs under the table. The number of students that could sit would range between 4 and 10, depend on whether they were big high schoolers or smaller kindergardeners. I think it is a really nice way to utilize the space, and I will also try to make the table adjustable height so that it can accommodate different sized people, as well as drop down all the way when the platform needs to be used as a bed.

It is getting cold again, and the wood stove is heating everything up nicely. I have gotten good at making smoke-free fires, and the stove is big enough to really heat up the entire bus. There are still places that need to be better insulated, but otherwise I am happy. I am still considering replacing the wood-stove with much more convenient and space-saving propane heat, but there are also good reasons not to do it. First, wood-heat is very cheap! Second, it is carbon-neutral. Third, it makes the bus have a really nice atmosphere. On the other hand, propane can be turned on and off instantly, and replacing the wood-stove with a propane heater would make enough room for another microscope station.

Back on Track

October 20th, 2008

Had a two day delay in Macedonia and Twinsburg, Ohio – the veggie system still needs a little work. Translation = I’m back on diesel. The good news is that I ran about 100 miles on veggie oil and I think I know how to fix the system for good this time.

I have also just come to an agreement with the Frederick Douglas Academies in the Bronx to do a week of teaching in December. On the first day all of their science classes will come on, and then each day for the rest of the week five students will spend an entire day on the bus. It should be really fantastic!

Photo Log from N&W Garage

October 18th, 2008
Left to right: Beak, Beak's son, David Newsome, Conley Newsome, Ben   Me with the N&W Gang

The garage I was at for the last few days is a really special place. Conley Newsome is the owner, and his son David and daughter Anita help him run the business, along with CC and his brother-in-law Beak (Anita and CC are missing from the photo. Conley is an 8 time motorcycle hill-climbing champion (here he is in a Sports Illustrated article), and is tough as nails and strong as an ox – he broke apart some of the pipe fittings that I was having trouble with. Whenever I had a question about something or needed to borrow a tool, they were always there to help, and the coffee they brewed in the morning kept me going. I am hoping that their business might actually pick up because of the economic downturn, since people might start fixing their old vehicles instead of trading in for new ones.

I got to see a little bit of Columbus, including the COSI science center, thanks to my school friend, Sam. And there was a really nice yard sale nearby that I stopped at twice, where I bought a little hand held vacuum for the bus.

Well, do you want to see what working on the bus? Here is a little photo journal of the work I did this week at N&W, including hooking up the ‘slobber tube’ collecting pan, reinforcing the waste water tanks, and putting together the veggie valve assembly.

One of the reasons to go to a garage is that you can put the bus over a pit or up on a ramp, making it much easier to get underneath of the thing. This particular ramp actually tilts back when the bus gets on it – it is a peculiar feeling when the bus starts tilting back. Once the bus was up there we ran it for a while to try to see where the oil leak was (the engine is hanging off the ramp at the back of the bus). We thought that the leak was just coming from the slobber tubes, which are designed to drain oil out of the air box. As Sam put it, the bus ‘sweats oil’. 

Slobber Tubes and Collector Can

Slobber tubes and collector can

Well, what do with someone who slobbers too much???

No guesses? Well in this case the bus was definitely slobering too  much, and since lots of people with these buses don’t like the idea of leaving a trail of noxious slime behind them, there are special kits that will collect the oil and also prevent it from going back into the air box which can be bad. I was able to remove one of the old tubes easily, however the other one was directly beneath a big metal compressed air tube, so for that one a just extended the existing tube. Then both tubes clamp onto the drain box. You could do this using a milk jug too, but it doesn’t look as good, though milk jugs are very cheap.

Of course, I will still need to drain the can whenever it is full, but I can recycle the oil properly instead of leaving it to runoff into our already too-polluted waters. You should see the gigantic catfish that Conley and his grandson caught in the pond right next to the garage! These guys know how to run a green garage.

Gray water support

Here is a very exciting picture of the new support I put in for the gray water waste tank. You can’t see the tank – what you see is the drain line for the tank, and the thin steel ribbon I added to keep it from sagging down. The bus has two 50 gallon waste water holding tanks, one for the two sink drains (gray water) and one for the toilet (black water). In the future, I would like to try to recycle the gray water so that it is used to flush the toilet, since that water doesn’t need to be clean for that purpose. Daniel had actually set up this kind of system at the Flowershop (Daniel appeared in some of the very early posts here). Can you imagine how much water we could save if every house had a system like that? And it is not all that difficult to setup.

Every night in Columbus there were beautiful sunsets and beautiful moon-rises. Here is a picture of the bus where I was parked most of the time, in front of the garage’s ‘wrecker’ tow-truck. Well, no towing for me this time! (Knock on wood.)

The bus’ paint job is supposed to represent the sun, the water and the sky – one reason I like this picture, because you can see the colors of the bus in the colors of the sky. Soon we will start putting murals of molecules, cells, and ecosystems on the blue parts of the bus. The idea is to eventually use the outside of the bus as a teaching aid.

Valve assembly

Valve (dis) assembly

The first two photos here are the valve assembly that I diagrammed in an earlier post. In the first picture you see how I’ve disassembled it, in the second you see it put together. The metal rods in the first picture get covered by the black blocky things in the second picture – the blocks are solenoid electromagnets that pull up on the valve stem that is inside the rod, opening the valve underneath. Depending on which of the valves are turned on, you either use vegetable oil or diesel, and you can also choose where the unburned, ‘return’ fuel from the engine goes. This allows you to put diesel in your veggie tank if you would like to dilute it before burning it. The fifth valve is ‘magic’ – but since this is a science bus I shouldn’t talk about magic, so I won’t.

Veggie system installed

Finally, I stuck the entire assembly into the engine compartment, in about the only free space there is, which happens to be a very inconvenient space for working! But after some fiddling, I got everything connected and the thing bolted onto the firewall (that’s the metal mesh in the background).

I’m not showing you pictures of the electrical system, which I also did a bunch of work on. But if you thought pictures of a bunch of valves stuck together were boring, imagine photos of a mess of dull colored wires. I’m just not a good enough photographer to make that look at all compelling… yet!

Spending the night near Cleveland, but I hope to make it to Ithaca by tomorrow night. I prefer not to drive at night if I don’t need to, and I’m not in a big rush right now, which is a nice change! So when it got dark, I found a place to park, lit a fire in the wood stove, baked an acorn squash, and enjoyed a beautiful fall night.

na yuo raed tihs? (and now for sotmeingh cmepoltley dffienert)

October 18th, 2008

I cdnuolt blveiee taht I cluod aulaclty uesdnatnrd waht I was rdanieg. The phaonmneal pweor of the hmuan mnid. it dseno’t mtaetr in waht oerdr the ltteres in a wrod are, the olny iproamtnt tihng is taht the frsit and lsat ltteer be in the rghit pclae. The rset can be a taotl mses and you can sitll raed it whotuit a pboerlm. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. Azanmig huh? yaeh and I awlyas tghuhot slpeling was ipmorantt!

Grease Machine

October 18th, 2008

The bus is drinking veggie oil! Heading to Ithaca now. It is a great day to be alive!

Go Veg Go!

October 17th, 2008

The system is installed and seems to be working well so far… took a very short trip to the parking lot next to N&W, not enough time to build up heat to actual switch to veggie oil, but at least I know that the diesel system is functioning. Tonight I reassembled all the control circuits, and tomorrow morning I will test by driving around the lot a few hundred times! If I pass that test, then I think I can safely claim that the BioBus is fully operational. Will post pictures soon.