shotgun sequencing is...

This is going to be a short post because I have to go to bed in preparation for my 8AM class tomorrow(wheeee), but I'm taking this bioinformatics course under the stat department, where we learn how the immense amount of data has been organized to be study-able.

I found this description of shotgun sequencing, which is so concise and easy to understand:

Before any analysis of a DNa sequence can take place it is first necessary to determine the actual sequence itself, at least as accurately as is reasonably possible. Unfortunately, technical considerations make it impossible to sequence very long pieces of DNA all at once. Instead, many overlapping small pieces are sequenced, each on the order of the 500 bases (nucleotides). After this is done the problem arises of assembling these fragments into one long "contig". One difficulty is that the locations of the fragments within the genome and with respect to each other are not generally known. However, if enough fragments are sequenced so that there will be many overlaps between them, the fragments can be matched up and assembled. This method is called "shotgun sequencing.

- Statistical Methods in Bioinformatics by Ewens and Grant

How easy and simple is this description? Non-biology people are sure to be able to pick it up and understand this explanation. I didn't fully understand the concept of shotgun sequencing from textbooks until recently. This is how I want to be able to present science to others.

altitude on breathing, drinking.

I am back from Denver, and already in Houston to begin my new year. I just had my first classes today, and luckily, my entire afternoon is free.

Denver:

Beautiful weather, really sunny sunshine(my friend and I got sunburned-sneakily!), Mt. Evans is beautiful, and I loved seeing the mountains in the distance. It's calming and reassuring. My friends are just so lovely, and I was so happy to have spent relaxing and laughter-filled times with them before school started.

Flipping through the hotel welcome book, we found that the book warned us about staying hydrated and drinking mildly, all because we're in the Mile High city(5280 feet above sea level). We took the advice to heart, and wondered, what is it about higher altitude that makes us more prone to being dehydrated and more drunk?

First, staying hydrated is important because Denver has much drier air than other places due to high altitude and low humidity. 

Since the altitude is higher, the atmospheric pressure is lower, which also lowers the partial pressure of O2. Now, human lungs function best at sea level, where the partial pressure of oxygen is about 20.9%. When the partial pressure of O2 is lower, hemoglobin's ability to take in oxygen is compromised, and therefore, consuming alcohol which interferes with oxygen consumption by the tissues, is magnified up here, among the mountains.

Yep, we definitely felt it. We took a tour up to Mt. Evans and hiked the last 10 minutes up the top, and wow, it was extremely difficult to breathe though we were only briskly walking.

Beautiful views. The drive was winding and fun, our tour guide Ron was funny, and the mountains. Just beautiful, beautiful, beautiful.

happily(freezingly) at the top!

peer pressuring apple.

Umma-bear (as I've been calling her lately) checked out this amazing book from the library called "How to Boil Water" (Food Network Kitchen). In it are great tips about how to wean yourself off take-out and restaurants, including necessary items for a functional kitchen and tutorials on basic culinary skills (using knives, cutting veggies, boiling eggs, etc). 

In the section about fruits, it mentioned that to ripen an avocado or a pear, put it in a brown paper bag with a ripe apple or banana. I had never heard of this before: I have had to eat many unripened peaches and avocados!

When fruits ripen, they produce ethylene gas (C2H4, the simplest dikene with a single double bond) which acts as a plant hormone. Ethylene gas activates regulatory genes called ethene-responsive-elements(ERE's) which in turn regulate other genes leading to the plant ripening, including breaking down chlorophyll, breaking down acids and pectin, and turning starch into sugars. Placing fruits in a brown bag(so moisture goes out) with a ripe apple/banana allows them to be exposed to ethylene and ripen faster.

Both of these are ethene-insensitive, but still delicious!

Farmers take advantage of this gas by picking fruits when not yet ripe, then exposing them to ethylene just before putting them out on markets. On the flip side, ethene not only ripens fruit but also causes senescence(death), which means farmers/transporters have to be extra careful to separate fruits producing ethylene from those that are sensitive, so that fruits arrive in their best state. Ethene can penetrate paper, cardboard boxes, and even concrete walls. Ethylene producing fruits include apples, apricots, avocados, bananas, mangos, melons, peaches, and pears.

I tried to think of a witty analogy for this (my favorite pastime activity). So far the most obvious and available one is that peer pressure= ethylene. I have found out (happily) that I've picked up new habits from the very friends I adored them in! My sleep schedule is a perfect example. Living with my lovely roommate last year,  I usually went to bed at midnight and woke up before 8.

One useful tip for those flower-receivers: if you add ethanol to the water flowers are standing in, the flowers will last longer before petal senescence. Ethanol interferes with synthesis of ethene!  Heins and Blakely

meatless mondays.

I heard about Meatless Monday on the radio this morning. The movement began in 2003 to encourage beef-happy carnivores to cut out their consumption of meat by beginning their work week meatless.

From their website:

Meatless Monday is a non-profit initiative of The Monday Campaigns, in association with the Johns Hopkins’ Bloomberg School of Public Health. We provide the information and recipes you need to start each week with healthy, environmentally friendly meat-free alternatives. Our goal is to help you reduce your meat consumption by 15% in order to improve your personal health and the health of the planet.

This movement challenges participants to give up meat one day a week(15%), for themselves and for the environment. 

Baltimore City Public schools adopted Meatless Mondays for its 80,000 students last year as a way to cut their budget. PETA praised this measure(somewhat predictably), designating the Baltimore City Schools the "Most Progressive Public School District of 2009". On the other hand, Glenn Beck of FOX called this a political indoctrination rather than a health-conscious move: "Americans love our steaks, we love our chops, we love our burgers, and you'll throw me in jail, my last meal will be a giant steak. "

I am not sure about adopting Meatless Mondays in public schools. The overall public movement seems harmless enough, but to adopt this in public schools and leaving kids no option but to meatless meals sounds like a violation of food freedom. I doubt the 2rd graders would appreciate this measure when it is forced on them. 

For those older than 8, the website also has meatless recipes, nutritional guidelines and toolkits to begin this movement in your own community.


Some vegetarian dishes I'd eat (and happily eaten):

But today's definitely not a meatless Monday for me! I don't think I can miss out on Umma's home cooking.

mother of all golden hamsters.

While reading "The Seven Daughters of Eve" by Brian Sykes, I came upon this interesting fact about Syrian hamsters, otherwise known as golden hamsters: they are descended from one mother hamster found in the Syrian desert in the 1930's. It had been assumed/presumed, but Dr. Sykes was able to prove it based on conservation of the sequence in the control region of mitochondrial DNA. 

Unlike nuclear DNA, Mitochondrial DNA is only inherited from mother to child, and difference in DNA sequence of the control region suggests length of deviation among ancestors/previous generations. Using DNA from the droppings of hamsters of different breeds, Sykes found that all the 35 different hamsters' mitochondrial DNA were identical, implying his hypothesis was indeed correct, and that the hamsters from all over the world were indeed descended from one single female hamster, the Mitochondrial Eve of Syrian hamsters.

look at that face. link

This prepared him to apply this theory to humans, which brings us to the thesis of this book, where he classifies modern Europeans into seven groups each based on characteristical mutations in mitochondrial DNA, each descended from a daughter of Mitochondrial Eve.


The book is intended for the general audience, and explains scientific concepts thoroughly as they come up. He peppers the book with personal anecdotes and fun observations, which keeps the reading interesting and personal.