August Update

August 11, 2015

Well, I was able to create all the Cas9 plasmids in order to knockout the genes involved with 7SK snRNP, however I have attempted to transfect these plasmids into an A2 Jurkat cell line, and it has failed all three times. I used the same apparatus and protocols as I used in Berkeley, and in Berkeley, I was able to do the transfection protocol in my first attempt under the instruction of Zichong, my Berkeley mentor, yet here in China nothing seems to work in my favor. In Berkeley I was even able to do the transfection protocol under no supervision, yet here it won’t work. It is very disheartening, and I am beginning to question if research is the right thing for me. I naively thought I was destined for research prior to my departure. I planned on applying to graduate school this fall, but I feel I need more education, experience, and practice in molecular biology before applying since I had so much trouble doing a simple transfection. I am not going to have any data at all once this project finishes, and I feel like a complete failure.

A small amount of time has passed since I wrote the last paragraph, and I was able to transfect the proper cell line with the Cas9 plasmids. I am not going to be able to verify a successful knockout before I leave China, but hopefully someone will pick up my work and be able to continue from where I left off.  I have loved every moment I have spent in China thus far, minus the troubles in lab, and I don’t want to leave and I must enjoy these last 10 days I have here in Xiamen.

Cheers,

Alex

July Update

July 10th,  2015

Welcome to this second installation of my experience in China. The Copa America, taking place in Chile, has kicked off not too long ago, and it has already concluded with Chile taking the spoils. Also, the US women’s national team defeated Japan in the Women’s World Cup Finals!!!  Hope Solo, and Olympic Gold Medalist, reminds me of Tim Howard and her goalkeeping abilities are simply phenomenal, and she was essential in the US taking home the trophy.

I recently went to the main island and checked out an electronic store, containing 5 stories, where I was able to purchase a pretty sweet Xiaomi smart phone for 120USD. I plan on giving it to my little brother as a gift. I wanted to get him a shirt, but I am sure this will exceed his expectations. While on the Island I also visited a coworker’s home. He showed me the room he grew up in, and I was able to meet his mother. We had a bunch of delicious food: fried sardines, dumplings, a potato dish, a pork rib dish, fried octopus and zongzi, in celebration of the dragon boat festival which commemorates the famous Chinese scholar Qu Yuan. He also showed me his guitar, which he learned how to play himself, and he played some Green Day songs such as Good Riddance (Time of your Life) and Wake me up when September Ends, while I attempted to sing. This day was an experience I will never forget.

I have been having some difficulties in the lab in extracting plasmids since the kits here are rather cheap and they are not as efficient and clean as the Qiagen plasmid extraction kits in Professor Zhou’s Berkeley lab, though a coworker gave me some tips and tricks to increase the purity to since the instructions included in the kit are not in English. I used these tips and still no success.  More recently, I discovered that the Cas9 plasmid I was using was not an actual plasmid after verification on a DNA gel. Well, there went a couple weeks of work, but that is biology for you, I guess.

Until again,

Alex

August Updates

Hello again! I’ve been in Uganda for almost two months now, and I have a lot of updates since the last time I posted.

The residents of our house have been shifting– my lab-mate Jordan left about a month ago, and Hannah and Melissa have moved in. Hannah is a second year medical student at UCSF and Melissa is a postdoctoral fellow in Dr. Rosenthal’s lab. Our house has become much more lively especially with our neighbors rushing in and out of our house. Did I mention that they range from the age of 1 to 9? They are the cutest, yet most devilish bunch. They come to us whenever they are hungry (they’re a huge fun of our digestive cookies, Pringles, and other snacks), but we are teaching them how to say “please” when they ask for food. They also enjoy playing with us in games such as “Run away from the mzungu, even when they’re not chasing you” and working out with Nike Training Club. Our larger neighbors are also fun– we’ve been playing Uganda’s Way on nights after work, and I’ve been winning a couple of games. They are funny, and it’s very amusing to see them lecture the munchkins.

Ariana, Sherina, and Shalome at Sherina’s 4th birthday party!
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Sherina, Shalome, and Jayden “working out”
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My neighbors and housemates

Our lab has also been shifting with visits from many of the UCSF researchers. Pras, an assistant professor and postdoctoral fellow at UCSF, came for a week in June and it was fun meeting another fellow Cal graduate. Dr. Grant Dorsey also came for a week in July (he arrived with Hannah) and we had a couple dinners and our Birth Cohort 1 party to celebrate the completion of the Birth Cohort 1 study. The party took place at Green Meadows, a very nice hotel that Grant stayed in, and it was very fun! The food was especially delicious; I must go back for dinner before I leave. After Grant left, Dr. Phil Rosenthal visited for a weekend and we had a meeting and dinner at our house. Dr. Cooper left last week, and my labmate Stephanie will be leaving on Monday. Besides the steady stream of researchers in and out of the lab, work has been steady– we haven’t had any malaria cases in the past month due to the recent insecticide spraying over the summer, but we’ve kept busy with the cases we have received in June and early July. I’ve learned a lot over the past few months, and I will be working mostly by myself for the next three weeks (of course, there will be frequent sarcastic comments from Sam, excited outbursts from Thomas, and fun with the lab technicians in the microscopy room.)

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The silly announcement for our Birth Cohort 1 party taped outside the microscopy room
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My housemates and I at the BC1 party (before Jordan left and Melissa arrived)
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The parasitology group at BC1 party! From left to right: me, Stephanie, Dr. Cooper, Patrick, Oswald, and Jordan.
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Group photo after our meeting with Dr. Rosenthal
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Dinner with our guests from the U.S. and Europe

Outside of lab and lab dinners, I recently visited Kampala with my housemate Hannah. One of my friends from Cal is Ugandan and staying in Kampala for a summer internship, so she and her family hosted us for the weekend. Last Friday afternoon, we drove to Kampala with Richard, Able, and Hajerah; Richard and Able are doctors at the Tororo Hospital and Hajerah is the administrator. It was an enjoyable trip, and I also tried grilled plantain for the first time when we took a food break. We arrived to Kampala at night, and my friend Yvette picked us up and brought us to her beautiful home. The next day was an adventure: we visited Mengo Palace, Gaddafi Mosque, Acacia Mall for lunch and gelato, the local crafts market, Cassia Lodge for a night view of Lake Victoria, and a few bars at the Kololo District. After a few hours of sleep, we set out on Sunday to find a store to print group photos for our housekeeper Agnes, eat breakfast at the Cafe Javas in Oasis Mall, and buy snacks at Nakumat to bring back to Tororo. It was a lovely weekend with Hannah, Yvette, her sisters Yvonne and Laura, and their personal driver Sampala! When it was time to head home, we met with Hajerah and Bena for the 4 hour drive to Tororo. We stopped by Jinja along the way to visit Hajerah’s aunt; the kids were fascinated by me and took turns touching my skin. We also stopped to see the baboons along the side of the road and our car was even attacked by one! The weekend trip was a fun break from work, and we’re planning on visiting Sipi Falls in Mbale for a day trip this Saturday. It is sad that I only have three weeks left, but we are trying to do and learn as much as we can. My housemates and I are learning how to make chapati from our housekeeper soon so we can bring a piece of Uganda back home with us (plus, we love eating chapati and rolexs, so how can we live without them?!) I will write again closer to my leave– until then!

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Mengo Palace!
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Gaddafi Mosque
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The beautiful view of Kampala from the top of the mosque!
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Group photo with Hannah, Yvonne, and Yvette
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Our Western lunch at Caffiserie in Acacia Mall!
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Breathtaking night view of the city and Lake Victoria
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Passed by Jinja on the drive back to Tororo

27 June 2015

So India is still great. Caroline just had a birthday on Wednesday and I got her a cake and a birthday hat and we celebrated with some foreigners in the hostel. The cake had four types of fruit on it: kiwi, black currant, guava, and I think mango. The fruit here is definitely in my top 10 favorite things about this experience so far. Growing up in a Cuban household, we eat mango and guava for dessert as often as we can find it and here mango and guava are accessible EVERYWHERE. There is a mango tree right outside the hostel and people use a big stick to knock them down. I started to do that and got in trouble one day. I found out that chocolate is expensive here so if you give the security guards chocolate, you have made instant friends. And now I have endless access to mangoes. Something else I have tried is using chocolate to haggle with the auto rickshaw drivers – it doesn’t usually work, but it has worked before! If we’re in the same-ish range, then the chocolate helps me get an extra 10 rupees off generally.

I have e. coli food poisoning currently, but I’m recovering. I’m mainly sleeping and laying in my bed in the hostel- fortunately, it looks like it will only affect about 5 days of the trip and only 2 of those are workdays. I’m not the only patient in the hostel – there happens to be patients who are recovering (generally orthopedic and plastic surgery patients it seems) that are staying in the hostel. I met an elderly man named Thomas from Mangalore. He is very friendly and walks up and down the hallways each day helping his knee to recover; he is recovering from a knee replacement. I brought him yogurt and water for when he takes his medication and I’ve given him chocolate a couple of times to boost patient morale! He told me one day that he thinks his doctor is wrong about taking three medications at once and that it is hurting his stomach – he said he thinks its better to take them at three different times of the day and then he showed me a newspaper article about overdose causing nausea to back up his claim. He wanted my opinion/validation about how he should take them an hour apart and I told him to listen to the doctor. He seemed intent that the doctor was wrong however, so I told him, “you know, you’re right. Take one pill and then wait five minutes and then take the other and then wait five minutes and then take the other. Eat some yogurt and drink lots of water before and after.” He was really pleased when I said this and said, “See, I was right- its better to space it apart.” And I replied, “Yes, you’re right, but NO MORE than five minutes apart.” We found a middle ground without obeying doctor’s orders.

Anyway, I’m not so sure why I told that story. I think it’s because those moments make me feel like me. And by that I mean I felt like a nurse. Listen to patients, meet them at their level, talk it over, find a healthy solution that works for all parties involved.

In terms of the research, it was going very smoothly at first and now we have hit a few bumps. The focus group discussion for the husbands did not go well- the husbands were very unresponsive so we are going to give it a second attempt. The surveys have been completed and in a week or so we will be starting our cleaning the data and analyzing – right now we are entering data. We have started working on our in-depth interview guides- there are nine in total and the people interviewed will be one person that stood out from each FGD group and then 4 administrative staff to see their perspective on how the program/training went. The 4 administrative staff interviews will be conducted by myself since they are in English.

Anyway, that’s all for now. More to come!

It has been nearly a month since my arrival in Bangalore. This blog post is long overdue…

Bangalore has been absolutely wonderful thus far and surprisingly easier to adjust to than I anticipated. From day 1, there was preparation work to be done for my research project, a substudy of Dr. Ekstrand’s original HIV stigma behavioral study.

The original Dristi HIV stigma study had nursing and ward staff as participants. The study has expanded to multiple hospitals in South India and a few in the north as well with a total of 3,600 participants. Because of the scale of the project, there are many people and multiple teams at St. John’s and UCSF who are involved. I was able to meet the team at UCSF before arriving at Bangalore as well.  In Bangalore, I met the members of the team that administer the assessments, the intervention team, the health informatics team who help manage the IT portion of the project, the onsite principal investigator Dr. Srivnivsan (who also happens to be the dean of the medical school at St. Johns), and numerous others. So the first week was primarily going around and meeting everybody.

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My study would be on a continuation of the current Dristi study but on a much smaller scale with about 120 medical student participants. I only have two and a half months to conduct 120 interviews/intervention sessions. Working with the tight timeline seemed very daunting, especially when I would be using the first week to jumpstart the study and navigate around both the campus and research staff/ medical school administrators. Luckily, when I came, this was not an issue. Everyone here has been extremely kind and helpful with showing me the ropes of the original study and assisting me with starting my own. I even have my own cubicle :D. Even though I technically do not have any lab/project mates, the health informatics team have become my work friends since my cubicle is within their office space. There is Divya, Rhadika, Dhina, Shaju, Benedict, Murthy, and Varun. I spend most of my mornings and lunches with them. We even celebrated a birthday this past week. While I am the youngest amongst my coworkers, it is still a delight to talk with them about anecdotes from their daily lives, memorable experiences, culture, and food. Working at the health informatics office has given me a feel for workplace culture in South India. The vibe seems a lot more relaxed, unlike my experience in the US.

I’m excited at the progress I am making in the project and completing it seems more of a reality now.

My second weekend here, I was able to schedule a trip with Remy and Catherine (from Rice University). We took a bus tour around the major sites in Bangaluru. We visited a couple temples, Tippu Palace, Lahbagh gardens, and Cubbon park. Overall, it was a nice, relaxing trip and we were able to see many of famous landmarks in Bangaluru.

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My third weekend here I was able to visit Coorg, a hill station in Karnataka, with Catherine. Despite severe rain that would never cease, the landscape was breathtaking with lush greenery surrounded my thick layer of mist. I regret not bringing a better quality camera so my camera on my phone will have to do. Our homestay was on a coffee plantation (which is what Coorg is known for) so we had access to great coffee 24/7 further fueling my coffee addiction.  We also visited Bylakuppe, a Tibetan settlement in Karnataka containing one of the largest Buddhist monasteries I have ever seen, on our trip to Coorg. Even though the rain prevented us from doing much, the trip was very relaxing and much needed after a long week of work.

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And this past weekend I went on a trip to Hampi, a small town full of historical ruins of an empire that once one of the most populated cities in the world during its time.  I went with multiple people that I have met through St. John’s Research Institute as well as a medical students. We went visited the ruins via bicycle and Moped which both were quite the experience (also a great reminder of how much I need start going to RSF more often). We stayed in the bazaar which was right across the temples which meant that every morning we would hear music sounding from the Virupaksha Temple and watch the temple elephant walk towards the river for a daily bath. Before this blog becomes too long-winded, I will just post pictures of the trips.

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The food here is amazing and relatively inexpensive. There are so many Southern Indian dishes here that I have never tried at home. But it took a while for my stomach to get used to thus during my 2nd week here I was recovering from a minor illness. Occasionally, I do miss home food so I am on the lookout for a good Vietnamese restaurant.

On a side note, I celebrated my birthday last week with both my coworkers and friends I have met here. Thanks for the cake Remy!

That’s all for now!

I’ve been in Uganda for a week already– time passes by so quickly, I can’t believe it was just a week ago that I said goodbye to my family and two weeks ago that I was at my cousin’s wedding in China. I spent the first day in Kampala, where I bought a SIM card and mobile internet and Stephen from the MoLab showed us around Makerere University and the “ghetto” (I’m not sure why he was so excited to show us this area.) On the second day, Stephanie, Jordan and I took the IDRC truck to Tororo, where we will be staying for the remainder of the summer and conducting our research. Steph and Jordan are two students of Dr. Cooper at Dominican University and the four of us will be working together at the Tororo District Hospital. Here are a few pictures from our truck ride and our first meal in Tororo!

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We are renting the house of another IDRC driver, and we also have a friendly maid, Agnes, who will be cleaning the house and preparing our meals. Agnes seems to be quite amused by my fear of cockroaches (especially when we found seven in my room) and by my Asian snacks. We have been working everyday for about a week now, as more malarious patients trickle into the hospital. It is quite busy, but we have found some time to explore. We tried the rolexes, which are eggs fried with chapati, at Crystal Hotel, and last night we went to Mzuri to try their pork. Dr. C goes on and on about how good the pork at Mzuri is, and it was actually very good. It was the softest meat I’ve had so far in Tororo. Later today, I am hiking the Big Rock with Steph and Jordan, and we hope to go rafting in the Nile River sometime when lab gets less busy.

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Tororo is a very beautiful town. Interestingly, it reminds me of some of the rural towns in China and my childhood stays in Zhongshan. Most of the roads are composed of red dirt and disorganized driving by cars and boda-bodas. The buildings are quite old, with some of them having pretty designs, and they are set against a gorgeous backdrop of rolling blue skies and endless green. The sky is a beautiful baby blue, and I can see the stars clearly at night. The sunsets are my favorite time of day– it is as though the sky is on fire and the orange-stained clouds are chasing the sun as it sets into the horizon.  There are cows, chickens, turkeys, roosters, goats, and generally a wide array of animals on the sides of the streets. I pass by them everyday when I leave for lab, and it makes for a lively morning walk. I also enjoy the corn fields on the roadsides– corn is one of my favorite foods, and I am hoping that I will have it for lunch or dinner soon. It would be a nice change from our usual rice, beans, matoke, tough meat, and what I call the mystery vegetable (I hope to go with Agnes to the market sometime to see what it is for myself.) The Ugandan food is very heavy on carbohydrates; I have not eaten so much rice in my life! The fruit though is delicious, especially the pineapples and mangoes. I am really excited to try more of the local food and explore the surrounding nature. I have two and a half months in my new home, and I look forward to growing scientifically, culturally, and personally.

Until next time!
Christine

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Even though WordPress is blocked by the People’s Republic of China, I will not let that defer me from writing and posting this blog because I believe, in addition to my Chinese friend who provided me with the software to bypass the Great Firewall of China, that the internet should not be censored. Period. I hate politics, almost as much as I hate economics, so that is all I have to say regarding this issue. The flight here was difficult because it was so long and it was my first time flying since I developed a memory. I had flown once when I was three from Sac to Spokane, but I cannot recollect that experience. I was not nervous or anything since flying is statistically safer than driving; I just did not know what to expect.

I am staying at the Xiang’an campus, and it is about 30 km away from the main campus on Xiamen Island. From what my coworkers have said, I do not want to be on the main campus because it is extremely crowded and noisy. It is quiet here on the Xiang’an campus, and I have more space than I know what to do with. There are two soccer pitches with goals that have nets, are rare occurrence in the states, and over 20 basketball courts.  I have utilized both numerous times already. It is also very humid here, and hot. I have never experienced humidity before, and it sucks. If it is 80 degrees Fahrenheit outside, it feels like 999 degrees due to the humidity. Okay, 110 degrees.  But you get the point. Lab work has been solid; biology is the same everywhere so there was no surprises with that aspect. Plus, I can wear shorts in the lab with flip flops since that is what everyone else does here, in every lab, though I still have to wear a lab coat when working with human cells, as it should be.  Everyone knows about CRISPR/Cas9, and a few individuals know about the Berkeley and Broad Institute quarrel. I am going to do some co-immunoprecipritations while I am here, and I am excited since I have already done this in the Kathleen Ryan lab, and it is an experiment I quite enjoy.

I have visited the closest village outside of the university when two lab members took me out to dinner and shopping. A lot of people stared at me and did double takes, but I blame the red hair. Some people do that in the states when my hair is long, but not to the level I experienced in China. I did not care since this is there space, and who the hell am I to say what is acceptable or not in a culture I know very little of. It is way safer here in China than compared to the states, in my neighborhood in Sacramento I have to be cautious of violence, especially since anyone can be carrying a gun and especially since two guys tried to rob a friend and me two years ago during summer break. That simply won’t happen here, people don’t have guns and the punishments for violent crimes are enough to deter people from trying anything. Even if you get caught with the possession of a knife on the streets, without registering it, you can land yourself in some deep-shit.  I have been told to pay attention for pick-pocketing though. There is also a safe guard on almost every intersection and at the entry of every housing complex to keep the students on the university safe. I am safe here in China.

On the first Friday I was here, the lab took me out to dinner at a local restaurant, and everything I ate was something I had not had before. The duck was delicious, and so was the twice fried pork. Everything was delicious, and the restaurant even had a pool table, so we took part in a few games after dinner. I had a great time, and we are going to go out as a lab at least once more before I depart.  Well, I have spent a majority of my time here in the lab, so there is not much more to report, yet. I still plan on visiting the main island and Gulangyu. I also plan on visiting Shenzhen and Hong Kong. I do not know if I am going to visit my cousin in Seoul, who is serving in the military on a base near the border between North and South Korea, since the tickets are expensive and he is returning to the states in October. That concludes this blog, until I write again, cheers.

Alex