Dec 22, 2013

London's mold of doom

Before you travel to a new country you probably will hear a lot of things in advance: about the weather, the transport system, the language, the currency, or the myths and legends about how people are and the nuances of their culture. There are things however, you will never find out until you get there!

One of the most surprising things about London, perhaps the entire UK, is a black mold, a fungus so pervasive that nothing can escape it. It terrifies me because in my three decades of life I have not seen any life form so aggressive and resilient, besides Homo sapiens and cyanobacteria. I swear it! For the Brits it makes already part of their daily lives and their natural landscape, so they don't make a big deal of it, rarely mention it and seem to be pretty oblivious to its existence, but it is nonetheless one nasty fungus.

At the beginning of the autumn, when it was getting cold, I decided to wear one of my winter jackets for the first time in that season to go to the shop one Saturday morning, when I take a look at the jacket it had been completely colonized by the m****f***ing fungus. How disgusting, NAAASTY!

I had never experienced anything like it.

This fungus grows everywhere, it lives within a rubber that is used to seal tile corners in the shower and sinks, it grows within the fibers of the curtain shower, it grows within every wall where it probably feeds from the paint, it grows in pretty much every surface of any material you find in a house. It has completely invaded my flat-mate's shaving razor and she does not seem to realize it at all. I have seen this fungus in the lid of plastic lunch boxes from some people at work. It invades your clothing hanging in the closet if you leave it unattended for just a few weeks. It grew on the plastic lenses of a pair of 3D glasses I forgot in a drawer. The nasty fungus also thrives in the cold rooms of our laboratory and probably every laboratory in the UK, so it clearly loves the low temperatures and high humidity. Every so often, it needs to be bleached, but that will not stop it from invading once again! Nothing can escape this fungus of doom.

I must say that during the five years that I lived in Sweden, I never experienced a fungus like that in my apartment... not even during summer time. Neither in my hometown in Montería nor Bogotá I saw a mold so nasty, and that is the tropics! In Paris, I never had to worry about anything like this and the building where I first lived was probably a couple of hundred years old.

I have asked people around and I have seen other apartments and I'm sure this is not an isolated problem of my house, but a quite common occurrence. 

I think this has to do perhaps with the fact that the UK is an island, so the humidity in general is very high and the temperature rarely goes below freezing, at least in the south. Who knows.

Nasty.


Dec 11, 2013

Journey to myself - 23andMe, health results (Part 4)

I might have been one of the last customers of 23andMe to have received health information from the DNA sequencing service they offered. Although initially I was most interested in exploring my ancestry, the main reason I chose this service rather than any other ancestry service was because I could get the additional health information. Unfortunately, FDA has ordered 23andMe to stop providing health data and who-knows-when they will be able to do so again. As controversial as it is the interpretation of our individual genome data now, because we know so little, I think it is the right direction the world should move towards. Eventually, we should be able to access our genome data whenever we want, and have clear and extensive information of any risk for developing any diseases or condition before they have happened, so that we could act in advance before it is too late... at least if it is within the limits of our own possibilities and the available technologies. In an ideal world, this genome data should be used fairly for the improvement of people’s well-being, but it does raise concerns about whether ‘your genome’ becomes another product to be sold for profit, misused, and taken advantage of.

Several of my close relatives have died of cancer, my grandfather died of throat cancer, and three uncles have succumbed to different forms of the diseases before they reached sixty years old. So, I was very interested about what the results would tell me. I must say most of the results were totally unexpected.

23andMe provided Health information divided into four sections. These were: health risks (122 risk reports), inherited conditions (53 different ones), traits (60), and drug response (25). Depending on how much research has been done on the disease, condition, or trait, they calculate a confidence factor. If there is a lot of research done in the genetic basis of particular diseases, they mark it as four stars. If research has only been done in a very limited number of patients, they mark it with one star. For the health conditions which are marked with four stars a risk percentage is calculated, and this could be above average (higher risk), below average (lower risk), or average (typical risk).

In my report I was surprised to find that I have an above average risk for Coronary Heart Diseases (CHD). This is one of the diseases for which a lot of research has been done. Fifteen genetic markers have been identified over the years, and they show you in a plot which particular genetic markers you got and whether they are likely to increase or decrease your risk for the diseases (see the figure below). They have calculated that for men, the average risk of CHD is 46.8%; and this was calculated for men of European ethnicity. In their own words, “46.8 out of 100 men of European ethnicity will develop Coronary Heart Disease between the ages of 45 and 79”.

In my personal case, I was calculated to have 60.2% risk… meaning that 6 out of 10 people with my genetic markers will develop CHD. That is not a very positive prognosis!

Fuck genetics goddammit!

23andMe health results
My genetic markers for CHD, what is that large red bar? WHY TO ME!!!
 
For each genetic marker associated with the disease you will get an explanation of what it means, a summary of the research that it has been done specific for that marker, and you will be able to access further scientific literature in the matter. I think that is quite nice. 

In addition to CHD, I was calculated higher than average risk for a number of other health problems including type 2 diabetes, psoriasis, age-associated macular degeneration, atrial fibrillation, gout, and ulcerative colitis. I might say that my grand-mother had diabetes, and uncle suffers of gout, and on my dad’s side there has been a lot of “eye” related problems. My grandma’s sister became blind, my dad suffered retina detachment, and some of my aunts have undergone already eye surgeries for several eye-issues. Could that be related to my genetic markers for macular degeneration? Who can tell. As far as it concerns me, I should just take good care of myself and keep a healthy diet and lifestyle.

On the other hand, one of my “traits” results relates to Adiponectin levels, it says:

Adiponectin is a hormone that is secreted by fat cells. It regulates the breakdown of fats and sugars and influences the body's response to insulin. Lower levels of adiponectin may increase the odds of obesity while higher levels are thought to be beneficial and may reduce the risk of cardiovascular disease, type 2 diabetes, and related conditions. Many factors are likely to influence adiponectin levels, including genetics.

I was found to have two genetic markers that have been linked to higher levels of adiponectin, according to some research performed in Asian populations. So how will this affect my chances of CHD or diabetes remains to be seen!

Besides that, I was also found to have some genetic markers that have been associated to higher risk in other diseases, but the research is not extensive enough to calculate a risk percentage. Some scary examples are basal cell carcinoma, nasopharyngeal carcinoma, meningioma, and sarcoma. I also have some mutations that might increase my chances of developing bipolar disorder (funny).
  
On the positive side I was calculated to have a lower than average risk for Alzheimer’s, colorectal cancer, melanoma, rheumatoid arthritis, esophageal squamous cell carcinoma, stomach cancer, type 1 diabetes, among many others.

Another interesting part of the analysis is the drug response study. I was found to have higher than average sensitivity to a drug called Warfarin, and anticoagulant. It might also be that a drug called Clopidogrel will have lower efficacy in me... and funny enough this drug is used to treat CHD. They also found that I was a fast Caffeine metabolizer and I have higher odds of becoming addicted to heroin than average: oops, I better don’t try it out then.

On the traits part of the study I was found to have higher odds of detecting the smell of asparagus metabolites in pee. I don’t often eat asparagus so I can't tell you whether this is correct or not now, but perhaps I should add some asparagus into my healthy-heart menus. I also have mutations that gives me lower odds of developing chronic hepatitis B if infected with the virus, and I also learned that I have no resistant to HIV/AIDS or noroviruses, what a bummer!

I have one mutation that according to a study of 4405 individuals of European ancestry was associated with less freckling. I have another mutation that was found to be associated with typical number of freckles and moles in Anglo-Celtic people: how about freckles in Latinos?

On a more interesting note than freckling, I also have a mutation that gives me a “slightly increased episodic memory”, mutations that reduce my sensitivity to sweaty odors (lucky?), and I have a mutation that was linked to much less efficiency at learning to avoid errors, according to an study on 26 healthy German subjects. I also have the muscle performance of Usain Bolt and if I had been a woman, I may have had smaller than average tits.

Dec 5, 2013

Journey to myself - 23andMe, ancestry composition (Part 3)


I have finally gotten the full results of my ancestry, and as a good Latino I’m an extraordinary mix of peoples from all over the world.

53% of my genome is of European Ancestry, mostly Southern Europe: likely Spain but with a fraction of Ashkenazi Jew, which is a big surprise!

21.9% Native American! I so would like to know which tribes exactly. Hopefully, one day I could narrow my search to a particular Native American group.

5.3% Sub-Saharan African, mostly from West Africa. The health results also shows that I have the mutation that makes Africans great sprinters! I might give birth to the next 100 m World Record breaker.

0.5% North African or Middle Eastern, probably from my surprising Jewish ancestry.

And last but not least 19% unassigned awesomeness.

In conclusion, a true Colombian.


Dec 4, 2013

Journey to myself – 23andMe, ancestry results (Part 2)

So, who are we really? Where do we come from? It boggles me how little we know about our past and the history of our ancestors. How short our memories are to the point that we might know absolutely nothing about our great-grandparents. That is at least my case on either side of my family, I do not know who they were and where in Colombia they were from. Finally, today I started figuring out the surprising journey of my ancestors in the book of human evolution!

The results of my DNA sequencing are partially in! At the moment I only have information on my father's line through the Y chromosome, which is inherited only from men to sons; and from my mother's line through the mitochondrial DNA (mtDNA), which is inherited only from women to their daughters and sons. I have added links to relevant wikipedia pages where you can read more about things that may be hard to understand.

Y chromosome (paternal line)
On my paternal line, I am haplogroup E1b1b1c1a, which is a subgroup of haplogroup E1b1b1c. Most people who are E1b1b1c can trace their ancestry to the Near East (Iraq, Iran, Palestina, Jordan, Lebanon, Turkey) where it originated around 15000 years ago... that is about 500 generations ago, give or take. Sephardic and Ashkenazi Jews carry this haplogroup. However, people carrying this haplogroup are also found in North Africa (Egyptians, Algerians, Tunisians), where it entered in the 7th century AD with the Arab conquest.

E1b1b1c1 is rare in Europe but can be also found among populations bordering the Mediterranean Sea. According to the site around 5% of people in Sicily and Sardinia have it. It is also found at low levels on Corsica. It is also found in low levels in people from Portugal and Galicia, around 4% of the population. And it says in the website it could have gotten there from an early migration from the Near East immediately after the Ice Age or arrived with Sephardic Jews before the Spanish inquisition.

A few months ago I asked my father if he knew anything about the origin of his parents, he said that her mother had relatives who were of Jewish ancestry. According to the legend a group of about ten brothers, the ancestors of my grandmother, arrived at the Caribbean cost of Colombia sometime at the end of the XIX or beginning of the XX century. However, these results are from the Y chromosome, which does not originate from my dad's mother, but on his father side, which is then a bit mysterious.

This image shows the distribution of people with the haplogroup E1b1b1c1. The scale bar and colors are the percentage of people that in that region have that particular haplogroup. So in this case is no more than 20% of the population in any region of the world.

Mitochondrial DNA (maternal line)
In a previous post I had told you, dear reader, that about 90% of Colombian mestizos in certain regions of the country had mitochondrial DNA originating from Native American populations, according to some research, suggesting that some of the first Spanish settlers, mostly men, mated with the only women they could fine: Native American women. My results confirmed this, after sequencing 14% of my mitochondrial DNA I know for certain now that I had an ancestral Native American mother at some point (within the last 500 years), carrying the haplogroup A2.

Haplogroup A2 is common in Asia, Siberia, and the Americas. It originated 50000 years ago somewhere in China perhaps. It is found among 10% of Tibetans and other Chinese ethnic groups like the Dong and Yi people, and about in the same proportions in the Koreas and Japan. This might be why I like ramen and manga so much. About 90% of Eskimos have this haplogroup and this might explain why I felt so at home living in Sweden. It might also explain my extraordinary snowboarding talents.

It is also very widespread in Native American populations all the way from Canada to Perú and Brazil, but it is not found in the southernmost part of the continent, like Argentina or Chile. You find it in Mohawk, Navajos, Aztecs, Incas, and in about 50% of most Colombian Native American groups.

Map for the distribution of people with haplogroup A2. Black means that 100% of the native people in that region have that particular mtDNA.
Ice Maiden, an Inca mummy, also has haplogroup A2.
As I was saying, the results are not yet complete. I look forward to see the results from the other parts of the genome, so that I can check out the percentages of the different ethnic groups I am made from. The funny thing is that I never imagined one day I would create a folder in my computer named “My Genome” to store all my DNA sequences. That makes me happy.

In my next blog-post I will write about the health section of the results, so that you can see the kind of information this technology could give you. I found some extremely unexpected results, such as an absurdly high risk for Coronary Heart Disease. On the good side, I also found that I have a much lower risk of getting Alzheimer’s compared to the average person. It's a very detailed report so I may take a while before my next post.

See you next time!