On Sunday I went to the U2 concert in Boston with some friends. The event took place at the Gillette Stadium, located South of Boston and capable of hosting more than 68000 people. Most of the stadium was filled, and that, together with the poorly designed exit routes, made coming out of the concert a nightmare.
If I knew that before I would have thought twice about parking at the Stadium. I was kind of startled that for a stadium which costed $325 million they did not even build underground tunnels so that the crowd would not have to cross the road to get to the parking lot. I had to wait more than two hours in the parking lot before the line even started moving. I could not believe I had to pay $40 only for parking. This again, goes along the well practiced way to do business, once they get you to pay, there is no more incentive for a good service.
That said, there was a bright side in the story. Once out of the parking lot, I had in front of me a four lanes line of cars. The idea to be stuck there was as startling as the two hours waiting in the parking lot. While in line, I checked on the GPS program I bought for my phone for $35 and I noticed that there was a little road, S Walpole St, heading back south and joining the highway a couple of miles away. Moved by desperation and a sense of "if I don't try I will never know", I exited the line, and in less than five minutes I was driving 80 miles an hour on I-95, in the complete darkness of the night, since street lamps are not common in American highways. I was amazed, but the best part of it was when I-95 crossed the road where the line was. Around 2am I could see all the cars stuck on top of the flyover. The view was just beautiful.
As I would say in Italian, "un mondo di pecore!"
Tuesday, September 22, 2009
Monday, September 14, 2009
Chromosome 17
I wished there was a book with fun facts about genetics. Actually, there might be. I have not even looked out of laziness. Nevertheless, this is still a good reason to talk about fun facts. Let me start from the beginning.
Since the completion of the human genome project, every once in while the Genome Reference Consortium updates what is called the human reference genome. Each one of us carries two sets of chromosomes, each made of about 3.2 billions nucleotides. Now, if you wanted to store that information, you could do so by writing down all the nucleotides. You probably know that most of the genome is the same across people, and it is mostly the same across great apes and humans. On average, one nucleotide out of 100 is different between a chimpanzee and a human being. So it is much more efficient to have a reference sequence and to store, for each one of us, the differences between our genome and a consensus reference sequence.
The consensus reference sequence was the goal of the human genome project and, even if it is mainly complete, it gets updated every now and then. In the last update, hg19, 9 regions have been marked as special, because they have what is called an alternate assembly. What happened is that, for different reasons, nine long sequences have diverged so much that they have irrevocably parted and cannot recombine with each other anymore. So, the reference genome takes into account the possibility, at this nine loci, for these alternative sequences.
One of these caught my interest today. It is a two million nucleotides long sequence on chromosome 17. It is thought that at some point, around two million years ago, an inversion event took place, that is, these two million base pairs got inverted in direction. This does not affect the functionality of the sequence, since the cells have no predilection for sequence direction. Although, it affects the ability of the sequence to recombine with the version with the inverted version. Among the genes in this sequence, the most famous is MAPT. It is known that mutations at this gene are responsible for some neurological disorders.
The interesting part of the story is that the inverted version of the sequence is present only in Europeans, with a prevalence between 20% and 30%. It is not clear why and some hypothesize that it might be the legacy of the Neanderthal people, who, before extinguishing, managed to interbreed with homo sapiens. That would explain why the two versions of the sequence are so different from each other and have a coalescence time, that is, an expected age from their most recent common ancestor, of about two million years.
Some of you might already understand why this is a touchy subject. It has all the ingredients for racial discrimination. The sequence is known to influence the brain, in some unknown way, and one version of it is present only among Europeans. I do not want to debate this aspect, although I expect that eventually scientist will perform the due experiments to unveil any possible hypothesis. In the meanwhile, be assured that the Neanderthal project will indeed unveil if the alternative sequence on chromosome 17 was contributed by Neanderthal people or not. Even if it is not, though, it will not rule out that it was instead contributed by home Erectus in Asia or some other unknown extinguished hominid for which no fossils are known.
In the meanwhile, I had to know, as a European, what do I have? It turns out that with 23andme you can check, if you look at the right SNP. In particular SNP rs1864325 is a predictor for the two sequences. A C at the SNP corresponds to the typical African haplotype, while a T at the SNP corresponds to the mysterious European haplotype. It turns out that I have a C and a T. So, whatever it means, I know that I have one of each sequences in my pair of chromosomes 17.
In a more romantic way, I can say to be one of those many million of Europeans within which the two sequences, after million of years of separation, have come together to shape me. Whatever that means. But I am confident I will not have to wait long to know.
Since the completion of the human genome project, every once in while the Genome Reference Consortium updates what is called the human reference genome. Each one of us carries two sets of chromosomes, each made of about 3.2 billions nucleotides. Now, if you wanted to store that information, you could do so by writing down all the nucleotides. You probably know that most of the genome is the same across people, and it is mostly the same across great apes and humans. On average, one nucleotide out of 100 is different between a chimpanzee and a human being. So it is much more efficient to have a reference sequence and to store, for each one of us, the differences between our genome and a consensus reference sequence.
The consensus reference sequence was the goal of the human genome project and, even if it is mainly complete, it gets updated every now and then. In the last update, hg19, 9 regions have been marked as special, because they have what is called an alternate assembly. What happened is that, for different reasons, nine long sequences have diverged so much that they have irrevocably parted and cannot recombine with each other anymore. So, the reference genome takes into account the possibility, at this nine loci, for these alternative sequences.
One of these caught my interest today. It is a two million nucleotides long sequence on chromosome 17. It is thought that at some point, around two million years ago, an inversion event took place, that is, these two million base pairs got inverted in direction. This does not affect the functionality of the sequence, since the cells have no predilection for sequence direction. Although, it affects the ability of the sequence to recombine with the version with the inverted version. Among the genes in this sequence, the most famous is MAPT. It is known that mutations at this gene are responsible for some neurological disorders.
The interesting part of the story is that the inverted version of the sequence is present only in Europeans, with a prevalence between 20% and 30%. It is not clear why and some hypothesize that it might be the legacy of the Neanderthal people, who, before extinguishing, managed to interbreed with homo sapiens. That would explain why the two versions of the sequence are so different from each other and have a coalescence time, that is, an expected age from their most recent common ancestor, of about two million years.
Some of you might already understand why this is a touchy subject. It has all the ingredients for racial discrimination. The sequence is known to influence the brain, in some unknown way, and one version of it is present only among Europeans. I do not want to debate this aspect, although I expect that eventually scientist will perform the due experiments to unveil any possible hypothesis. In the meanwhile, be assured that the Neanderthal project will indeed unveil if the alternative sequence on chromosome 17 was contributed by Neanderthal people or not. Even if it is not, though, it will not rule out that it was instead contributed by home Erectus in Asia or some other unknown extinguished hominid for which no fossils are known.
In the meanwhile, I had to know, as a European, what do I have? It turns out that with 23andme you can check, if you look at the right SNP. In particular SNP rs1864325 is a predictor for the two sequences. A C at the SNP corresponds to the typical African haplotype, while a T at the SNP corresponds to the mysterious European haplotype. It turns out that I have a C and a T. So, whatever it means, I know that I have one of each sequences in my pair of chromosomes 17.
In a more romantic way, I can say to be one of those many million of Europeans within which the two sequences, after million of years of separation, have come together to shape me. Whatever that means. But I am confident I will not have to wait long to know.
Tuesday, September 8, 2009
Coming back to Boston
I have finally moved, about one week ago, to my new place in Cambridge. I like it a lot, there is a big kitchen and a nice living room and I have half bathroom all for myself. Overall, it is quite a treat. There are two very sweet cats which periodically come to me asking to be scratched on the neck.
After spending the week in Montreal and Hanover, I drove back today at night, listening to radio Kiss 108. This was the first time I drove back to my new place. Driving through the city and parking right in front of my place was relaxing and stress free. Not even two months have gone by, but I think I have already adjusted.
After spending the week in Montreal and Hanover, I drove back today at night, listening to radio Kiss 108. This was the first time I drove back to my new place. Driving through the city and parking right in front of my place was relaxing and stress free. Not even two months have gone by, but I think I have already adjusted.
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