Friday, 15:00

Seminar over. By all accounts it was a very productive and stimulating meeting. Scientists at the MRC Gambia are very keen to exploit genome-level studies through next-generation sequencing in their work, with organisms as diverse as Chlamydia (which causes blindness through the devastating disease trachoma), Mycobacterium africanum, malaria and HIV-2. The metagenome concept, presented this morning by Karen Nelson and George Weinstock is a rich potential source of new knowledge, and the MRC has an incredible resource of patient and epidemiological information, samples and isolates to exploit. These can prime many very exciting metagenome level projects. An existing project is the nasopharyngeal metagenome in babies, through using a combination of Sanger and 454 sequencing by Brenda Kwambana, in collaboration with the University of Leicester. There is excitement about extending the study further.

We had a long discussion about how genomics and next-generation sequencing could be applied to Africa. There was agreement that the MRC Gambia are well posed to ask very interesting questions, borne out of their wide-ranging and long-term surveillance projects taking place across the country and neighbouring countries. This is the area of greatest strength and confidence. The group felt that the MRC Gambia was not quite ready to get its own next-generation sequencer, but that was a clear aspiration for the future. Important right now is to build up strengths in the bioinformatics and subsequent data analysis. Some Linux servers hosted locally would help immensely because their Internet (provided by satellite link) is too slow to use services like NCBI BLAST satisfactorily. I have offered to help them with this as much as we can – perhaps donating a few older servers and sending DVD-ROMs of the latest software and databases to get under way. Karen, George and myself have offered to host Gambians interested in bioinformatics to gain more skills.

Will write more on the contents of the seminars soon and upload pictures from today. However, now it is time to relax a little bit, perhaps have a swim – it is very hot today and the skies are clear for the first time. Karen Nelson and her husband have decided to visit Dakar in Senegal, an 800km drive, in a ‘bush taxi’ which is pretty much the bravest (or stupidest) thing I’ve ever heard. They plan to visit Goree Island, the departure point of the slave ships to the USA and an important ‘roots’ tour destination.

Update 13/12/08

A few pictures of the conference:

Dinner at Ngala Lodge before the conference started
Dinner at Ngala Lodge before the conference started
George Weinstock giving a talk on the international human microbiome
George Weinstock giving a talk on the international human microbiome
Martin Antonio in full flow
Martin Antonio in full flow
The conference group photo
The conference group photo, in the centre bottom row is Hilton Whittle, virology legend and head of MRC Gambia

Thursday, 18:00

It’s going to be another rapid update I’m afraid. We’ve just finished Day 1 of 2 of the inaugural MRC Gambia genomics conference, and it was certainly crammed full of interesting talks. A wide-ranging programme took in the genomics and genetics of viruses, malaria (and their hosts), pneumococcus, mycobacteria and even Helicobacter. My slight headache is most likely to be caused by malaria, but I suppose it might also be the 6 cups of coffee. Bouka, the local infectious diseases physician doesn’t take malaria prophylaxis during the dry season – which it currently is – preferring instead to do thick and thin films every time she spikes a temperature! That’s pretty hardcore…

I’ve taken copious notes, and some photographs and even a short video of the conference, but I think I am just too tired and headachey to start writing it up now. And besides, we are off to dinner at the Gambia’s premiere Indian restaurant – the Clay Oven, shortly.

Food update: lunch was benichin, a kind of biryani style rice with stewed vegetables and meat (probably goat). A little bit spicey and rather good, in fact. I have yet to try afra, the Gambian take on a kebab, where a whole meat joint is hung on a hook – you point at which bit you want and they chop it and barbecue it and serve in Gambian bread with spices and mustard.

Tomorrow is the last day of the seminar and I so in the PM I am looking forward to doing a little bit of relaxing with some JulBrew at the pool. George has moved into the African Village and I am going there too later.

Wednesday 17:30

Mainly a picture update for you today of a visit down to Bakau Market. There were plenty of ‘bumsters’ here which we had been warned about. Some bumsters are nicer than others. Some are keen to show you around and provide useful tour guide services. Others just want money and are not afraid to tell you that. George happily received a friendship bracelet. It was relatively easy to shake most of them off with a firm “no thank you”. Invoking the name of MRC is also helpful in this situation.

Some MRC Accommodation
Some MRC Accommodation
The local beauty salon
The local beauty salon
Tiffany and an old friend in Bakau Market
Tiffany and an old friend in Bakau Market
George and his new friend (and bracelet)
George and his new friend (and bracelet)
Typical Gambian menu - I want some SupaKanja!
Typical Gambian menu - I want some SupaKanja!
Whittling drums to sell at Bakau Market
Whittling drums to sell at Bakau Market
The Taxi Menu - Wrestling is an improbably popular sport in the Gambia
The Taxi Menu - Wrestling is an improbably popular sport in the Gambia
I like to think the rifle is a visual metaphor for genomics
I like to think the rifle is a visual metaphor for genomics

 

Cipro might be a better choice...
Cipro might be a better choice...

Tonight: Dinner at Ngala Lodge with conference organiser Richard Adegbola (Head of Bacterial Diseases at MRC Gambia) and the other delegates.

Tuesday, 23:30

First impressions of The Gambia:

  • the driving over here makes this morning’s dash to the airport this morning look pretty weedy – think pulling out directly into the path of oncoming vehicles and then neither driver attempts adjust their speed
  • there are little kids everywhere on the sides of the road and all are wearing beautiful and immaculate brightly coloured clothes because it is currently Eid al-Adha, known locally as Tabaski. Gambia is a predominantly Muslim country (95%), but tolerant of other faiths and even has its own brewery.
  • at the airport and car park you are surrounded by scores of people wanting your old newspapers, trying to help with your luggage, or just wanting cash from you just because. The local scam is to pretend that they know you already “hey, I’m from your hotel” or to pretend they previously did a service for you which you didn’t pay for “we took all your bags to the car and you didn’t pay us”. I gave a chap 40p to take my bag (it was all I had!) and he looked at it with sheer contempt. Perhaps he’s been reading those old newspapers about the British economy…

Dinner at Martin’s was great, we drank the local beer JulBrew which is a fairly standard lager for tourists and ate a starter made from battered and fried black-eye bean paste. Martin and his wife Joyce are Ghanaian. Jouce made a vast dinner including a specialty of kimke – a fermented corn maize dough which is wrapped in corn leaf and boiled.

We are staying in the MRC Gambia compound which is large (1 mile around) and enclosed in a private compound with high security. There is a hospital on site and the patients queue in the mornings to be triaged by a nurse, who then refer to the outpatient department if there is need. This is also a way of recruiting patients to the various MRC clinical trials which are conducted here. Inside, the offices are modern with good Internet and office facilities.

Tomorrow: market, crocodiles and I finish preparing my 3 talks ready for the start of Thursday’s conference!

Gambia Fact: The extent of the Gambia border was determined by the range of a patrolling British gun-boat going up and down the River Gambia!

Banjul's NASA-registered airport, and "Slok Air"
Banjul's NASA-registered airport, and "Slok Air"
This plane welcomes you at the airport
This plane welcomes you at the airport
Karen Nelson, Tony, George, Bouke, Tiffany, Sebastien, Joyce
From left: Karen Nelson, Tony, George, Bouke, Tiffany, Sebastien, Joyce and Kinke!

Tuesday, 15:00

We’re in a high-altitude Geordie nightclub, 30000ft above West Africa as I write this. Karaoke refrains ring out, distracting from the turbulence. The flight consists of mainly sun-starved British tourists, plus some native West Africans, some in traditional dress. And of course, 3 tired genomics conference travellers: myself, George Weinstock from Washington University, and Tiffany-Marie Williams from Baylor College of Medicine. Despite a 5:30am start, spirits are high. The flight, minus our diversion via Manchester will take 6 hours in total, meaning we go South long enough for the average temperature to raise at least 20 degrees centrigrade to 31 degrees.

We are hoping to be met off the plane by Martin Antonio, our host from the the MRC Gambia and an ex-students of Mark. He has invited us round for a traditional Gambian dinner. The guidebook states that a traditional meal will be served in pots which are passed around the guests who are seated. Each person dips in (strictly using the right hand) with some bread and passes it on. I have no idea whether this will be the case, or whether we are in for a more Western experience.

It looks like we will be staying in the MRC Gambia compound as the African Village hotel we had booked is apparently “below standard”. Shame, as the guide book promised a pool-bar, but I am sure we will make up for it in other ways…

"Hamburg International" - no, neither have I
"Hamburg International" - no, neither have I
George contemplates the Geordies
George contemplates the Geordies
Indiana Jones style red line
Indiana Jones style red line