Mind, Hand, and Heart

MIT’s motto Mens et Manus means Mind and Hand, and at first glance this sounds like a good thing. This motto implies that we not only think about great things, but we also do great things. As engineers we build things and as scientists we conduct experiments. However, this past semester showed me that MIT needs a slightly different motto: Mens Manus et Corde or Mind, Hand, and Heart. I think MIT could use a step up, and I think iHouse offers some hope.

Continue reading

Our September Speaker Series

It was great to have Dr. Sujata K. Bhatia from Harvard join us for our September speaker series this past Tuesday! She shared an interesting way of how she has been involved in international development. She started by explaining how for her work in biomedical engineering she is encouraging the use of biopolymers made from natural (agricultural) materials for medical applications. The rationale is that natural polymers and substances react best with natural people!

So how is this related to international development? Well, one of her *undergraduates* a few years back wrote a thesis about how developing nations are filled with the agricultural potential to be powerhouses for high-end medicine projection. This inspired Dr. Sujata and others at Harvard who are now offering workshops targeted towards the brightest minds in developing countries to realize the potential of natural agricultural products in medicine. Continue reading

Conquering Concrete

In America concrete is an exact science. Every quantity of material is weighed exactly and mixes are specifically designed for certain jobs. When hand-mixing concrete in rural Uganda, concrete is more of an art. We initially planned to make a 1:2:4 mix of concrete with one part cement, two parts sand and four parts aggregate or gravel. However, the gravel we found was too large so we had to adjust the mix to 1:2:2. It worked out well after a bit of trial and error. We also had to compromise between the Ugandan method of making concrete with lots of water and the American method with minimal water. We ended up with a decent mix of concrete that was not too wet or too dry. Mixing the concrete and pouring it was a lot of labor. We were especially sad that Valerie and Lawrence had to leave in the middle of the day so we lost two laborers. Some local teenagers in the village helped out but everyone was exhausted by the end of the day. We did successfully finish one concrete lid! Only four more to go. We will definitely enlist more local labor to help out or bring Ivan, Mrs. Muwanika’s grandson, with us everywhere.

-Marisa

(This blog post is also posted on the EWB-MIT’s blog site: http://ewbmit.blogspot.com/)

Also, farewell to Valerie and Lawrence!

We are all sad that two of our teammates had to leave to go back to their jobs. Valerie, our mentor for the first part of the trip, is reluctantly going back to work in Boston. Lawrence, a Ugandan student and friend of EWB-MIT Daphne, heads back to job training in northern Uganda. We are sad to see them go but we are happy that Valerie will finally get to read all about the royal baby and get a real shower.

Lots of Progress!

Sorry for the delay in blogging! We have made good progress despite some minor illnesses and injuries. Noam and Valerie had colds but are feeling much better and Marisa (me) sprained her ankle but it is also much better. Everyone is enjoying the weather and food in Ddegeya.

We are replacing the existing wooden lids with concrete lids and currently most of the formwork, wood to support the concrete, is complete. Many of our team members are now experts with saws. We also worked with the community to clean the tanks before we pour the new lids. Most people were eager to clean out their tanks. A few tanks had lizards but most of the contamination was dirt. Hopefully the concrete lids will be more secure.

We’ve also began work to fix some of the gutters that were placed in the wrong direction. Removing the existing gutters is a lot of work because they are nailed in tightly. Undoing the work from last year has been tough so far since everything is built so solidly. We’ve also put the new pumps together but the small screws went missing so we need to buy more. Scott, Leone and I are in Masaka today to pick up some more materials. Now that everyone is healthy construction should proceed smoothly.

-Marisa

(This blog post is also posted on the EWB-MIT’s blog site: http://ewbmit.blogspot.com/)

Reaching Ddegeya

On Wednesday Noam, Scott and I (Marisa) got up around 5am to get ready to pick up Valerie from the airport. Unfortunately our driver was late and instead of leaving at 6am we left around 6:45am. Valerie had to wait a bit but we made it. We then went back into Kampala to pick up Sarah and Leone, the students assisting us from Makerere University. We were glad to have a private van and not the public taxi, especially with all of our luggage. We had a tasty lunch at the equator and took pictures we will upload when we get faster internet. We finally reached Ddegeya around 2pm. After a bit of settling in the girls, Valerie, Leone, Sarah, and me went out to Kinoni, a nearby town to buy food and supplies. Upon our return we visited each tank.

The main problems we found were:
1. Pumps were not working, mostly because of broken valves. There were also broken T-joints and broken handles.
2. Lids were cracked and warped and rotting in some cases.
3. People must stand on the lid because the pump is too far in.
4. The gutters are overflowing. Each gutter has a long edge and a short edge and in some cases the short edge is on the outside. Schematic to come if we get faster internet!

Our solutions:
1. Replace wood valves with rubber.
2. Replace wooden lids with concrete.
3. Move pumps closer to edge to reduce stress on T-joints, possibly build stairs to reach the pump handles
4. Secure handles with joints, not just drilling holes
5. Replace gutters to get long edges on the outside in all cases and increase gutter supports to prevent bending.

After our long day of travel and visiting tanks we had a delicious dinner of potatoes, onions and tomatoes with tea. We all enjoyed it but most of us could not finish it all.

Everyone slept well on Wednesday night and we then set out to buy supplies and repair the tanks! We are currently in Masaka buying supplies. Stay tuned for more updates!

-Marisa

(This blog post is also posted on the EWB-MIT’s blog site: http://ewbmit.blogspot.com/

OLI OTYA FROM KAMPALA!

Scott and I (Marisa) have arrived safely in Uganda after many hours of flying late last night. We are excited to pick up Noam later this evening and to get Valerie tomorrow and head to Ddegeya.

This morning we slept in to make up for the pains of traveling. We are staying at Red Chilli’s hostel with many other travelers. Most of them got up early to go on trips so we had the place mostly to ourselves at breakfast. We shared the dining room with the resident dog and cat. Three years ago Shavi and I called the dog “Dug” after the dog in up, but I learned that his name is actually Nero. I think Dug suits him better.

After sleeping in we have been busy in Kampala running errands. We now have phones and can call people! We also met with Leone to discuss how we will meet with the Makerere students and get to Ddegeya tomorrow. We plan to hire a private car and pick up Valerie en route to Ddegeya. We also purchased mosquito nets and explored the supermarket, which is similar to Target.

-Marisa

 (This blog post is also posted on the EWB-MIT’s blog site: http://ewbmit.blogspot.com/)

Bromeando Duro

We strapped on our boots, and it’s a good thing Noam Angrist and I brought them from the states. Our hostess Ana Ojeda laughed at the idea of me finding size 12 boots in Bluefields. After a brisk 2 mile walk up the stone and mud path to el sitio where the trucks dump the garbage they collect. The four of us myself, Noam, Camila Caballero, and Malika Flanagan got our first glimpse of the working conditions of the women in the collaborative, Luz del Futuro.

Ten women carrying poles with makeshift hooks divide themselves into groups of five around two piles of garbage. They stand on a slurry of mud and garbage about a foot off the ground stabbing and pulling at the piles with their palos. They spread out the pile looking for aluminum cans and plastic bottles that they can get clean.  A woman sees a beer can, she picks it up, taps it against the palo to knock off some of the sticky mixture of paper, mud and who knows what else, that covers everything in the piles, then she throws it into the bag for aluminum and scrap metal. Organic waste, tin cans, and glass bottles are ignored or shoved out of the way. On the surrounding hills is an audience of zopilotes (vultures) silently watching the women, or picking at mortizos in the tracks that the garbage trucks have made in the muddy ground. The dogs on the other hand join the women in digging through the trash as they look for a meal. Every once in a while nature’s silence is broken by small black birds calling to each other.

When we arrived we stood around awkwardly for a bit wondering how to start. Noam and Camila moved towards the near pile, and I walked around to join the second group of women. Malika had cut her toe earlier, and so she became the designated videographer for the day. Margarita (president of Luz del Futuro) told me to use the Bernarda’s palo. Bernarda motioned to me. I took the tool and asked her what I was looking for. She pointed to a couple things that I should pick up, and I began to imitate the dragging motion of the other women. The women began to laugh a little as I struggled at first with the palo and asked Bernarda many questions about what should go into each bag. I began to get the hang of it and it would be quiet for a minute before a women would notice something in the trash and make a comment. The others would laugh and respond in kind. After we had been working for half an hour or so, Bernarda got my attention and told me the names of each of the women. Going around the circle, I repeated everyone’s name 3 or 4 times until I was sure that they would stick, which the women found amusing. Then, I commented that this was good I’d probably remember their names for the next 15 minutes or so eliciting another chuckle from the group. Feeling reasonably comfortable at this point, I asked if the women always laughed this much or it was just me. Bernarda answered, “Bromeamos duro.” I was floored, as I translated in my head, “We joke hard.” Through my laughter, I responded that my goal for the end of the trip would be to understand a few of their jokes.

To be continued later…

Anthony McHugh from Bluefields, Nicaragua on the events of 6/12/13

Tamale Take 2

Hello, everyone! This is Yiping and Coyin here! Today was our second full day here at Tamale and boy did we have a lot of new experiences! My day started off again with the wondrous baa-ing of the goats in our neighborhood (which have been my alarm clock for my time here in Tamale MIRIM CAULI). Afterwards, I wrestled my mosquito bed net in an epic duel in order to get out so I could eat breakfast and do stuff. But yeah! It was an early start today. We woke up around 7AM, got dressed and the usual stuff, before eating a breakfast of Ghanaian peanut butter and bread (and oatmeal too for Coyin)! Then, we chilled for a little bit and met some more Pure Home Water employees! Including PHW’s housemaid, Zainab. She’s this bubbly young women, who has a cell phone, can speak English (and the local language), who is Muslim, who is currently studying to be a school teacher, who has been working with Susan since 2007, and who got married last year (lucky guy ;). Coyin talked last time about finding someone who could help us carry on the project after we leave, and we think Zainab could be a potential match! More updates on that later though.

After our meeting with Zainab, we went on a tour of Susan’s ceramic water filter factory (Pure Home Water’s factory). We saw the place where the women have to get water everyday, and it was quite an eye opening experience. We are approaching the end of the dry season, so the little pond was almost completely dried up. The water was opaque and there was feces littering the pond’s surroundings. And this is the water the community of 800 people use. Water is so precious; I’ve always known that, but today, I gained a newfound understanding of exactly how precious a resource water actually is.

We also toured the eco-san latrine and the physical factory and we met all the women! However, they spoke no English and we did not speak their native tongue either (a language called Dagbani). For the first time in my life, I’ve felt a block due to the language barrier. But we made due with our sign language and smiles and there was also this SUPER CUTE BABY. However, the baby was scared of us and cry whenever we approached him. And then the baby would smile and wave us byebye because he wanted us to leave. But whenever we got close to the baby, he would start crying again. :( But other cool things: we had a legit Ghanaian meal cooked by the PHW cook. It was a rice/bean dish with a fish/tomato paste, and it was yuuummmmmyyyyyyyyy. We then went to hang out with the women, take pictures, and tried to learn as much of their language as possible. For example, we learned that ayule means “What is your name?”

In the afternoon, we had a community meeting in Taha (the village). All the elders there were….elderly. But they were nice. We didn’t know that in the Islam religion (Taha is a Muslim village), it was inappropriate for females to shake a male’s hand or something like that. So that was why everyone started laughing at us when we started shaking people’s hand. We were so embarrassed but good thing the elders didn’t take it too seriously. They had a good laugh and were quite understanding. We were there because one of the fellow students, John, was there to build them a toilet block and he wanted community input on what the toilet block would be like. It took them legit 15 minutes to decide!! SO EFFICIENT!! One of Susan’s friends traveling with us joked that in America, that decision would take 3 months. But yeah, then we went to the chief’s house and the chief gave us kola nuts so now we will live forever (lol jk but they are cool looking nuts).

We then went into town and boy, was driving crazy. But I bought a pair of sneakers by the roadside (I don’t think I got ripped off TOO much), and we drove around town with a PHW employee (Michael aka our Ghanaian father). We then had dinner (cooked by Daniel), and it was some legit fried chicken!! Then, the power went out (woohoo flashlights #prepared). So Michael then took us out to his sister’s place called club savanna with some flashing Christmas lights and lots of plastic tables/chairs set up outside. Coyin and I had gizzard on a stick, which was really delicious. It tasted like the ones I ate back home in China in my youth!

The power came back on when we got back to the house, and all of us started trying to get our new wifi-router to work (which is why we are able to post this in the first place)!! It worked. We checked email. Exciting stuff. Then we called it a night.

Overall, it was an awesome day. I got to see a whole new world. The Ghanaian people are so kind it’s unbelievable sometimes. Michael (PHW employee) left 70 cedis with a random kiosk counter guy whom he never met before to give to his daughter in 2 hours time, and the daughter actually managed to pick up the money in time. And then when we were driving to town, two random women jumped onto the back of our truck, and when I asked Michael if he knew them, he said no. They just want a ride into town, that’s all: normal stuff.

Coyin and I are doing well. Project wise, we are going to go hunt for Black Soldier Flies while we wait for our fly attracting buckets to attract them. So fingers crossed!

Lots of Love,

Yiping (on behalf of Coyin too)

Wunam (on behalf of Wunpini too)

P.S. Those are our official Dagbani names given to us by the community

Chill day in Tamale

(I’ve really got to be more creative with my blog post titles, so far it has just been __ day in ___ ………. very smart Coyin, very smart.)

Thursday – June 6, 2013

After the long journey last night, we decided to spend today in a more “chillax” way! Yiping and I gladly had our 12-hour sleep for the night, considering we barely slept well at all for the past four days due to non-stop traveling.

We woke up at 10:30AM, Yiping due to the non-stop baa-ing of the goats/lambs (HELLO MIRIM WE MISS CAULI HERE), and me probably just after a good night’s rest. We then got directions from Daniel, the house manager for Pure Home Water, and walked around the neighborhood. He pointed us to MyComm, the local Internet café, for Internet access and Relax Lodge, one of the local hotels/lodges for food. But food prices at the latter were a bit pricey, so we only had two lemon-flavored Fanta. The Internet café was sort of run down with slow computers, but it minimally served our purpose, so that was good. It was quite reasonably priced too, only 30 Pesewas for 15 minutes, 60 Pesewas for 30 minutes, 80 for 45 minutes, and a Cedi for an hour.

Lunch at home then was Ghanaian peanut butter and Ghanaian honey homemade sandwiches. The peanut butter came in a big, or rather huge blue tub, and the Ghanaia honey was contained in this semi-sketchy plastic bottle. We also made fruit salad as a healthy option. Thanks to Aditi / Carolina / Marisa’s training on me when making the two watermelon salads a week before that, I think I actually managed cutting up this HUGE Ghanaian watermelon pretty well. There is this particular type of watermelon here with no stripes!!!! I thought they were some giant melons at first, okay I guess they sort of still are melons. The mangoes here are also HUGE. And so sweet too. Oh dear they are the best mangoes I have ever had.

I think the rest of the day just passed by with us planning things, talking to Susan, and making changes to our project plans for the next few days. Then it was dinner time! We made tomato paste mixed vegetables with rice, and beans, but then towards the end of the dinner Bhavna brought us this REALLY YUMMY Indian yellow rice and some sort of spicy cake-like thing. Delicious. We also found out that Susan does this thing called “check-ins”, so at dinner time towards the end of the day we each tell everybody on the dinner table about our day.

One issue about our project that Yiping and I have been really scratching our head about is, who in the local community would take over the project and relay data back to us when we are gone? We wanted somebody who would fit these criteria: speaks English, has a cellphone, literate, knows how to weigh things and write down data, is willing to work with waste and flies, and last but not least is sincere and hardworking. So this is our problem to-solve for the day, since we decided it would be best for this person to work alongside us from the beginning, so s/he would feel a stronger sense of ownership over the project and would more likely be doing the work for the project when we were gone.

Any ideas, people?

Till then.

love, Coyin (and I think on behalf of Yiping again)

Summer= UROP

Hey guys! 

Hope you all have been having a wonderful summer so far (I sure have!), and I just wanted to share what I’ve been/ what I’m going to be up to this summer =)

To begin, I’m Prakriti (or Parki), a rising junior, and I have the amazing privilege of working at the Phillip Sharp Lab at the Koch Institute for Integrative Cancer Research at MIT. The Sharp Lab is a pure biology lab, aiming to understand the very foundations of molecular biology, with an emphasis on anything RNA-related and the processes of alternative splicing and RNA interference. Given the fundamental nature of the research, the research has significant downstream consequences in understanding various disease mechanisms and pathology and will be useful in coming up with innovative treatments to them. Thus, it is extremely exciting for me to be surrounded my grad students and postdocs who are going after such interesting questions, constantly discussing their research, and to even be a part of the research process!

I’ll talk about what I’m doing and some other lovey-dovey things about lab <333 (maybe I’ll save that part for a second blog)

What I’m slaving at pipetting and tissue culture for <333- Overview

1)    Understanding how RbFox2 is co-regulating alternative splicing that leads to Nonsense-Mediated Decay for RNA binding proteins.

2)    Understanding how chromatin-remodeling influences alternative splicing patterns regulated by RbFox2.

3)    Cloning Setd2 and Dot1L (histone methyltransferases), and other RNA-binding proteins.

Okay, so there’s a lot of jargon, but hopefully I can make the terms clear to understand!

  1. RbFox2= Fox2 is an RNA binding protein. It generally binds to a UGCAUG motif, and plays a crucial role in regulating alternative splicing.
  2. Alternative Splicing: When you transcribe your DNA to make mRNA, the mRNA consists of introns and exons. Introns are long non-coding sequences (they don’t contribute to making protein) that need to be spliced out of the transcript to create a contiguous sequence of exons. However, not all of the exons are always included in the final transcript, so alternative splicing is where you have different patterns of exons in the final transcript, because they have different levels of inclusion.
  3. Nonsense-Mediated Decay (NMD): Mature mRNA transcripts have a 5’ G-cap, 5’ UTR, coding region, 3’ UTR, 3’ poly-A tail, and a stop codon before the 3’UTR. When you have a premature stop codon (PTC), a stop codon that appears before it should, the mRNA transcript gets degraded instead of translated into truncated protein. This prevents the buildup of toxic proteins that are detrimental to the cell.

What I’m slaving at pipetting and tissue culture for <333- In detail

1)    Sometimes, the transcripts produced from alternative splicing introduce a premature stop codon, which then undergo NMD= AS-NMD. Research contends that the presence of these transcripts don’t always represent “noise” in the alternative splicing process, but actually represent a functional process. It turns out that AS-NMD is used to regulate protein levels (especially for splicing factors like SR proteins/ hnRNPs), plays a role in development (you want to express certain proteins at certain times of development), and can be involved in negative feedback loops for protein expression. In summary, AS-NMD is an important post-transcriptional gene control mechanism, and naturally, its misregulation can lead to downstream issues.

It turns out that RbFox2 actually binds to these transcripts for other RNA-binding proteins! We hypothesize that it co-regulates the NMD process for these proteins, and we want to understand trends across different genes and tissues, and perhaps even uncover the mechanism by which it does so.

2)    Chromatin describes the state of DNA interaction with various proteins (histones). The state of “openness” of the DNA is important because it affects what processes the DNA can undergo. The more open DNA is, the more able it is to undergo replication and transcription. Since splicing is mostly co-transcriptional (it actually happens at the same time as opposed to after transcription), we want to understand how different chromatin states affect alternative splicing patterns that are regulated by RbFox2. This is actually really important. Believe it or not, but adding methyl or acetyl groups to certain amino acid residues on histone proteins influences, or at least correlates with, different molecular processes and even disease phenotypes. The chromatin landscape is very dynamic and while the significance of many of the chromatin states are not well understood yet, you can bet there is a lot to uncover and understand the connections between those states and molecular biology processes that they affect.

3)    Finally, I’m cloning histone methyltransferases! And I’m SO much better at cloning than I was last year!! These are enzymes that add methyl groups to lysine residues on specific histone proteins (details not so important), and our hope is to see how overexpression of these methyltransferases can affect alternative splicing mechanisms =)

***

And thus is a brief (it wasn’t very short though) summary of my research! It excites me SO much, and has been keeping me in lab for 10 hours a day, reading and re-reading papers and reviews to better understand the intricacies of what I’m investigating, and to really, appreciate the big picture of where my research fits into the larger network of questions and answers of molecular biology. I really love what I’m doing.

A pretty exciting thing is happening next week! My grad student Mohini is presenting her poster at the RNA Society Conference in Switzerland next week, and she’s featuring some of the data that I produced! And my name is on her poster… right next to Phil Sharp’s- just the association blows my mind ><

Anyways, I hope you guys followed/ enjoyed what I was saying, and if I was able to give you the tiniest appreciation for molecular biology, then I would say the past hour writing this was super worth it ;)

Till more lab adventures next time!
Parki =)