Archive for the ‘The Latest’ Category
Hello from the lab!!! Things in lab have recently taken off because we have acquired a second gel box and a second PCR machine, doubling the number of reactions we can run and process each day. These acquisitions have dramatically increased microbiology lab morale! We now hope to complete data collection on our set of samples within the next couple of weeks.
It is hard to believe that we have only two weeks remaining- time has gone by so quickly!
This upcoming weekend we have reservations at Hans Cottage Botel, a few kilometers from Kakum National Park. Kakum is known for its canopy walk (30m high) and its populations of birds, monkeys, and butterflies. We are excited to visit the rainforest and will post pictures upon our return.
Equally exciting is our lodging for the weekend: The Botel is located on a lagoon containing Nile crocodiles!
We will probably spend our last weekend in Ghana closer to Accra. We are looking into day trips, but there are plenty of places in Accra which we have not yet explored… so much to see!
There is one thing we have been exploring since arriving in Ghana, and that is the food. Fortunately, we all like groundnuts (peanuts) and have experienced many of the groundnut related delicacies available: groundnut soup, groundnut cakes, groundnut paste, etc. We have also tried many of the traditional dishes, including fufu (a ball of mashed cassava or plantain, roughly the texture of bread dough), banku (similar to fufu, but fermented), palava sauce (spicy, cooked spinach with variable other unidentified ingredients), yams (dense, white potato-like starch), and goat kebabs (self-explanatory).
We’ve also enjoyed trying all of the Ghanaian snack foods. Favorites include Choco FanIce, essentially frozen chocolate milk, and “rock pies”, which resemble muffins but taste more like a biscuit with a little nutmeg and pineapple juice.
In the beverage category, we’ve enjoyed Alvaro sodas—one is pineapple flavored and contains malt, as well as pineapple juice with “a hint of ginger”, as the bottle describes.
At our hostel, we typically cook dinner and one of our specialties we have called “orange-orange”, which we like to think is a close cousin of the Ghanaian bean and fried plantain dish with the name “red-red”. We’ll keep the recipe a secret, but will say that its distinct color derives from a can of tomato paste.
Thats all for now! Stay tuned for pictures from the rainforest!
It has been a while since our last post so we wanted to update everyone on our activities in Ghana- both in and out of lab. The past week brought some good news and some bad news regarding our two projects in lab. As for the bad news- sadly, the A6 cell line was not able to survive and it will be another couple weeks before we can get the next shipment of cells. However, the good news is that, so far, we have made great progress with the PCR aspect of our research. We have approximately 260 DNA samples and for each we must run a total of about 6 PCR reactions. Initially, we had a few problems with some of the reactions but, now that most of our troubleshooting is done we are moving right along. The department of Microbiology at the University of Ghana Medical School has been doing an incredible job of making sure we are as comfortable and productive as possible in lab and for this we are very appreciative.
As for life outside of lab we have been busy exploring the capital city of Accra and surrounding areas. Last week we went to an outdoor sports bar to watch Ghana and Uruguay face off in the quarterfinals of the World Cup. Unfortunately, Ghana lost to Uruguay in a penalty shoot out but, the match was a great one to watch especially when surrounded by hundreds of die-hard football fans covered from head to toe in Ghana’s red, green, and gold. This past weekend the four of us traveled to Cape Coast which is about 2 hours west of Accra by bus. There, we toured Cape Coast Castle and Elmina Castle both of which were built by Europeans and used for slave trade during the 18th century.
During the past week we have also visited some notable sites right in Accra. We visited the National Museum and the Kwame Nkrumah Mausoleum, a park and museum dedicated to the 1st President of Ghana. We have also visited the Arts and Cultural center of Accra, an outdoor market where you can buy all traditional African crafts including masks, drums, cloth, carvings, beads and much more.
The end of this week will mark the halfway point of our 6 week stay in Ghana. Laura, who only joined us for 3 weeks, is already back in the US. As for this weekend Nora, Catherine, and I plan to continue exploring Accra and hopefully relax at the beach so we can rest up for yet another productive week in lab beginning on Monday.
Between settling into a new city and new lab, our first week in Ghana has been extremely busy! After our arrival last Friday, we were able to take a little break from science and become accustomed to our new surroundings over the weekend. We explored a big market, called Kaneshie market, near where we live, and have also found several places near the International Student’s Hostel, where we’re staying, to buy food. Our hostel had a communal kitchen that we can cook in, and have had some successful and delicious dinners of rice and cooked vegetables.
Our first full day in lab was this past Monday, and we got a tour of the University of Ghana’s Microbiology Department. Our lab is extremely nice, and our hosts have done a wonderful job of making sure that we have everything that we need.
So far, we’ve been able to get lots of work done and haven’t encountered too many problems. We have lots of different PCRs to run on many different samples, so hopefully we’ll be able to get all the data gathered during our time here. Also, it seems so far that our A6 cells are alive, though they are growing slowly. Hopefully we’ll be able to have a happy culture of cells growing soon.
We made it! The flight was approximately nine hours, and unfortunately we weren’t able to sit with each other, but we made it safely. Today we’re mostly meeting new people and seeing the labs that we’ll be working in. Even though we were all tired and groggy, one of the first things we had to do after arrival was head to lab to make sure that our cells were alive. We have high hopes that they will be fine, since the luggage was able to keep all our flasks cold. Right now, however, I think we’ll be in search of some food, and then maybe settle into our housing at the International Students Hostel. We’ll update more soon!
With only nine days left before we fly to Accra, everyone is working hard to prepare for our time at the University of Ghana. Nora, Marina, and Catherine have been analyzing wild type strains of E. coli from Nigeria with a technique called Polymerase Chain Reaction, or PCR. PCR is an extremely helpful tool for molecular biology research, since it allows for researchers to determine genes contained within strains of E. coli. We’ll use PCR to detect different categories of E. coli and the resistance genes within those strains. However, PCR requires particular conditions in order to work, so a lot of time can be spent troubleshooting so that the PCR will give accurate and reliable results. Fortunately, things have been going well so far.
My project, with the A6 cells from Xenopus, is also going well so far. Maintaining tissue cultures isn’t too difficult, but it’s critical that everything remains sterile so that the cells do not become contaminated. Contamination is a lot easier to prevent, however, when one has the proper equipment. We’re lucky enough to have large tissue culture hoods with ventilation to prevent unwanted microbes interfering with our cells. In Ghana, we won’t have these types of hoods, and instead will work in smaller, wooden cabinets with a glass front.
There’s a lot still to do, both in and outside the lab. Since we’re going to West Africa, we’ve all had to acquire the necessary vaccines, anti-malarial pills, and visas (and our visas have just arrived safely!). Fortunately, our science center helped us obtain our visas and plane tickets. Now all we have to do is finish familiarizing ourselves with necessary techniques for lab, and pack!
Hi, everyone! Welcome to our blog and very first post. We’re very excited about this project and are looking forward to beginning work in Ghana. The four of us are currently at Haverford and are already running experiments. Catherine, Marina, and I (Nora) are new to Professor Iruka Okeke’s lab, and so we are getting used to E. coli and the new protocols. Laura conducted her senior research in Iruka’s lab, so is familiar with everything and is helping us get adjusted. We will leave for Accra, Ghana on June 17th. Before our departure, we plan to get started on our projects and run through the molecular microbiology workshop that we will help to teach to university students while in Ghana.
Before going any further, it would be helpful to know exactly what we’re doing! The four of us are working on two separate projects, both of which have to do with the bacterium E. coli. (Click here for a brief overview of this incredible and well-studied organism.) Laura will be spearheading a very exciting project and introducing a new cell line to the lab in Ghana, which comes from a frog species known as Xenopus laevis, another model organism. These cells are used to detect different kinds of diarrhea-causing E. coli (not all types are harmful). In the US, human cells are typically used for these tests, but require special conditions for maintenance which are not available in resource-poor settings such as Ghana. Introducing the frog cell line will allow Ghanaian scientists to perform these tests and differentiate between E. coli types, allowing for more effective and specific treatment.
The second project we’re working on is a bit more complicated. Iruka’s colleague in Ghana, Mr. Opintan, has collected several hundred samples of E. coli (from workers in the food-industry who are required to be tested for Salmonella infection) that we will work with. We will test these samples both for resistance to antibiotics and for pathogenicity, or the ability to cause disease. We are mainly interested in tracking the presence of a resistance gene located on a plasmid– a small ring of DNA separate from the chromosome that is easily transferred between bacteria cells. Last year, Laura and Amy Labar ’10 went with Iruka to Nigeria, where they performed similar experiments. They found a high prevalence of the resistance gene in pathogenic E. coli in samples collected in Nigeria, and comparing these results to what we find in Ghana will give us a clue to the regional distribution of E. coli resistance.
Together with the frog cell line, these studies will hopefully help scientists and health workers detect and provide better treatment for diarrhea caused by E. coli, which remains a leading cause of death in young children.
Catherine Smith ’11, Marina Zambrotta ’11, Nora Proops ’10 and Laura VanArendonk ’10 will be visiting the Department of Medical Microbiology, University of Ghana. They will be applying skills they gained in Superlab (Bio300) and their senior research experiences to laboratory research there in an on-going collaborative study by Iruka Okeke (HC), Professor Mercy Newman (UGMS) and Japheth Opintan (UGMS).