savior siblings...

In immunology, we learned about MHC molecules and how they are inherited. Since the three classes of MHC molecules are found in a block, they are often inherited as a unit, a haplotype, which rarely crosses over. Therefore, there are four possible combinations of MHC combinations in a given mating, which gives a sibling one in four chance of matching another sibling.

Immediately I thought of "My Sister's Keeper", which I had read about online. I have neither seen the movie nor read the book. In the book, the couple has another girl after their first is born with leukemia. The sibling who is born to provide an organ to be transplanted is called a "savior sibling"(There IS a term for it!). 

A savior sibling is selected to be genetically compatible. A couple may choose to terminate the pregnancy if the child is healthy but not a match for the sibling in need.

As in Jodi Picoult's novel, the sibling may not be happy about being a savior. Kant would argue that in this case, the savior sibling is being used as a means, and therefore this is immoral... but from a utilitarian point of view, a child is born and with minimal "harm" to the child herself, saves another's life. That's good, right?

Would I want to be a savior sibling? Would I want a savior sibling?

you made a mistake.... doctor.

I went to a Scientia lecture by Dr. Vimla Patel this afternoon. The talk was titled: "Failure to Detect Medical Error: Debunking the myth of the Infallible Expert". Dr. Patel is a biomedical informaticist at UTHSC who studies medical errors.

While the talk was fascinating (an hour went by so fast!), certain points Dr. Patel made really captured my attention. While we accept mistakes as normal and human, when experts make such errors, we may not be as forgiving. Especially in this case, when the expert is a physician whose mistake may affect someone's health/body/life, mistakes are considered an anomaly never to be repeated.

She spoke about the different studies conducted to observe mistakes, detection and correction, and her approach to studying this was fascinating. She had a graph starting with on-paper experiments where residents/students are asked to evaluate a case, then "in vivo" studies where a team having a dialogue was observed, unaware that it was a simulated experiment. Then, of course, there were in situ studies where specific doctors were followed and recorded to detect their mistakes. She mentioned that they are developing virtual experiments to fill in the gaps between the different "realistic" experiments.

She also mentioned that mistakes may not be mistakes, something I took further as an advice on life than on this limited topic alone: there are always uncertainties and unknowns in a situation, and we may do the best we can, but the environment we were in may not have been complete. 

eat less. live longer.

I've always envied people with high metabolism because, well, who wouldn't? I would looove to be able to eat all the pastries I ever want and simply burn it off. For example, I would be able to eat dessert with my regular food instead of eating cake for dinner. I'm only half kidding.

TURNS OUT:

If you would like to live long, having a slow metabolism is better for you. (Meaning, eat less, burn slower, have a lower happiness factor but multiply by longer life span and voila! You'll be less happy but for longer).

In a wide range of organisms including yeast, flies, mice, and primates, calorie restriction has been found to increase life span by up to ~50%. 50%! This process may have been conserved across species because the ability to adapt to environmental stress such as lack of food may be useful. Organisms can then delaying development until the conditions become favorable.

Artificial "starving" situations can be created by restricting calories, and the body WILL respond. Dr. Walford participated in Biosphere 2, an enclosed biosphere project, where the members unable to sustain normal amounts of food, naturally had a restriced diet. The crew members emerging out of the biosphere after 2 years showed improvements in health such as lower blood pressure and cholesterol. He developed the CRON-diet, which recommends consumption of lower calories to maintain a weight about 10~15% lower than their stable "set point" weight.

www.walford.com

The effects of CR diets in humans remain controversial as it has been shown to have mixed effects. CR dieters show improved memory, lower blood pressure, lower triglyceride levels, but may develop eating disorders because well, they're literally being starved.

(Read the NY magazine article of a reporter's attempt at CR diet here).

So what is the actual mechanism behind longevity through CR? In rodents, yeast and company, SIR2, a histone deacetylase has been suggested to mediate this life extension. SIR2 may control further endocrine signaling and DNA repair mechanisms such as p53 and FOXO which increase stress resistance and promote longevity. (Read all about it in this Cell review).

It's definitely not for me. The world is full of too many delicious things for me to give them up. Besides, CR hasn't been proven to completely to have only positive effects, right? So... until then, I'm going to eat my foods, like this from Koriente in Austin:

Mmmmmmm, as I'm sipping my black coffee. It's National Coffee Day today!

bag of worms(literally).

I'm taking Advanced Genetics this semester& so far we have been learning all about Ras. Oncogenic Ras has been found in many different types of cancer, leading to scientists studying this particular protein in relation to cell division and proliferation. 

We have been going through different papers and discussing the specific discoveries throughout the years while learning the techniques used and the questions asked. To set the tone for a specific paper we are reading, we needed to learn about C. elegans.

Specifically, we are learning about vulva development in C. elegans, which is necessary for the eggs to be expelled. In a phenotype appropriately labeled "bag of worms", failure of the vulva to develop causes the eggs to actually hatch inside the hermaphrodite parent worm. The parent essentially becomes "a bag of worms", and the worms eat the parent's tissues from inside out, then burst out of the parent.

Isn't this the craziest thing ever? It's like combining the "Men in Black"'s alien-inside-human's-head plus Michael Crichton's Prey and every parasite nightmare you've ever had. I began laughing in class as my professor began to describe this.

Photograph courtesy of Paul Sternberg

From this website on development of vulva in C. elegans by NCBI.

A-wildtype, B-vulvaless, C-multiple vulvas.

Well, he described it like: "and these baby worms burst out, then... they become bags of worms themselves later". What a vicious life cycle.

Now I'm going to have a very vivid picture anytime someone uses this idiom:

"bag" of worms!

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.