Tuesday, February 12, 2013

the nitty gritty

Hey guys,

First THANK YOU to the two comments!! You give me hope people read the nonsense I type... granted I'm pretty sure I know who you are but I don't care. I'll pretend that you are a random person from cross country who stumbled on my blog and were truly interested...

So in the last post, I was questioning the science on CNN's article (see last blog for link) and whether or not it was blown out of proportion/misleading by the author, Aarathi Prasad, of "Like a Virgin: How Science if Redesigning the Rules of Sex". I found the paper regarding the experiment of the mouse that was born from two female eggs, and also have the supplemental data due to the nice anonymous guy/girl who left it in the comments.

Let's get down to the science:

Just from the abstract I already found a flaw in Prasad's description (at least through the video, I don't know how detailed she is in her book). She had said that it was an immature egg used to fertilize the other egg. That is correct, but she fails to mention that this was not a normal immature egg, it was a mutant egg that had been engineered to knock out 13,000 base pairs in a gene known as the H19 gene. Now, some may say what's the big deal? It's still immature! ... Yes, you're right but the fact at the end of the video how she said that "...our genes, our biology has ways to circumvent things the ought to be impossible..." I hate to break it to you , but our biology naturally can't circumvent the impossible unless we fool around with genes like they did in this paper. In the end she speaks of how more investigation needs to occur but I get the impression, and you may disagree, that this is all right around the corner. Judging by the paper I read, she's so way out field it's not even funny. Not to mention this paper is almost a decade old -it was published in 2004. I know personally if references are earlier than 2008 I can't even use them in some course assignments, never mind go off and write a book about it.

I guess that's one of the major points I'm trying to get across with this topic as well as this blog, that in order for the general audience to give a shit, you make it sound more appealing by not giving detail, which is wrong to do. We need to recognize that leaving out information and emphasizing other points is unethical in the eyes of science (okay my high mighty speech is over, thank you for bearing through it).

If you didn't know this, us geneticists do this in order to genetically engineer... not test tubes & flasks

Kono et al's work is pretty neat I have to say, but the supplemental data is necessary to understand everything that was accomplished and even then some data is just not given. Also to get a full idea of what's being looked at and why, I had to go back in time to when I would have been 5 years old and Kono et al. 1996, "Epigenetic modifications during oocyte growth  correlates with extended parthenogenetic development of the mouse" was published (freaky huh?). Of course, even with UNH's subscriptions I couldn't access the full paper; however, the gist of the 1996 research was that imprinted genes are necessary for fetal growth in mammal reproduction. Imprinted genes are the "expression or repression of genes solely on the basis of the parent from which they were inherited". The imprinted genes from our moms are regulated by a process known as methylation, which occurs during oogenesis. So Prasad was correct in the sense that one egg is immature, or a better way of putting it, lacks of methylation of imprinted loci during the oocyte's (egg's) growth.

What was first done was that Kono et al. took wild type oocytes (oocytes that contain the predominant genotype in a natural population) that were non-growing (ng; lacking the methylation/immature) and fully grown (fg). These fetuses developed to 13.5 days before dying.

Next approach was that they deleted 3,000bp of the gene, H19, at the transcription unit in mutant mice. Their non-growing oocytes were combined with wild type fully grown oocytes. These fetuses developed to 17.5 days but had no further development after that.

H19 and Igf2 are coordinately regulated by cis-acting elements. These in turn are regulated by how methylated the H19 gene is in a region known as the "deferentially methylated region" (DMR) as well as how methylated endoderm-specific enhancers are. H19 encodes for a long noncoding RNA and Igf2 encodes for a growth-promoting factor (IGF-II), a major fetal growth regulator.

Now here comes the good stuff... 13,000bp were deleted from the same H19 rather than 3000bp. So same thing, the mutant mice lacking this section of the gene gave their non-growing oocytes and were combined with wild type fully grown oocytes.

There were 598 oocytes constructed.
457 eggs were cultured.
371 morula/blastocysts were derived and transferred to 26 recipient mothers
24 of these mothers became pregnant
10 pups lived to 19.5 days of gestation when autopsied ... 18 were dead
Of the 10, 2 were successfully restored, having normal morphology
1 of the two was given a foster mother and grew to adulthood

Her name is Kaguya:

                                                            Kaguya w/ pups of her own

We went from 598 to 1. Think about that, and now rewatch that CNN video to see if you can take her seriously.

Now, what they did... was incredible. I do not want to take away the spotlight on their accomplishments. I'm just saying that it's always good to go back to the original source before you believe the media (if you didn't know that already by now).

The rest of the paper goes on about comparing parthernotes vs. the control and then goes on to discuss features in global gene expression among the parthernotes. It's mainly results and if you want me to discuss it further make a comment and I'll be sure to break down the genetics. I'm just afraid of boring you guys to be honest, so fill me in if you want the true nerdy me to start explaining stuff. It's actually really cool with the genes they looked at further and I recommend you look at the data yourself as well (I mean tech you can't believe me either since a blog is a form of media...)

Recipes and music!

Thank you if you have gotten through my first attempt to break down a paper all on my own (I'm actually amazed if you read through the whole thing, you have the patience of a saint). Your reward is my favorite apple pie recipe. I was in charge of the Christmas Eve dinner this past year (after some begging that I wanted to prove I could cook for the family). For dinner I attempted chicken cordon bleu, sauteed asparagus with garlic, and fingerling potato & vidalia onion lyonnaise. Then for dessert I whipped out my apple pie and pumpkin walnut pie. Not to brush my own shoulders, but it all came out wonderfully and my only complaint was that I didn't get to put the sauce on the chicken 5 min before it had to be taken out of the oven (I think it unfortunately took away from the moisture). Anyway, I've been making this pie now for two years and it's a big hit with the friends up at school (my friend Colin has already asked that I need to make it one more time before graduation). I found it at my go-to website, allrecipes.com (love this site!) and took a couple modifications from some commentors (always makes a difference). To summarize how amazing this thing is, basically the last time I made it at school one of my roommates was brought to tears of joy after a long day in classes with one bite (classic college student mental break down- true story). If you want the recipes to the other stuff I made by all means ask! You can write as "anonymous" if you scroll down the options of how you want to leave a comment (yes, I'm bribing you with food to comment... this tactic works with boyfriends, I'm hoping it will work with you... and I mean that in the most loving way possible).

Then for music I have decided to post some tunes in honor of one of our roommates, Mary, who left us this semester to study abroad in London (we miss you terribly!). Please also check out her blog about her adventures in London :)

Also some topics I can write about in the following weeks: 
-Science of Kissing (based on the book as well as a New York Times article)
-biofuel topics
-find a journal article on how art and science relate
-no science anything next time, just some random stories from Boston (aka: my life is a joke series)
-combos? any ideas? (engineering, physics, etc)
Please tell me what you want to read, your wish is my command.


First Aid Kit: Wolf
Lone Bellow: Tree to Grow
Anais Mitchell: Young Man in America

Butter Crust: 1 cup of sea salted butter (melted) , 4 tbl water, 2 1/2 cups of flour
Combine and knead until fully mixed. Lay out evenly in a 9 inch pie plate leaving about a 1/4 of the dough left over for the lattice structure.

Apple Pie: 5-6 (maybe 7) mixed apples, 1 tbl vanilla, 1/2 tbl cinnamon, 1/2 tbl nutmeg, 1/2 cup sea salted butter, 1/2 cup sugar, 1/2 cup brown sugar, 3 tbl all purpose flour, 1/4 cup water
Peel apples and slice thinly. Mix in bowl the apples, vanilla, cinnamon, and nutmeg. Put the apples in the pie dish you had made prior and form lattice structure of pie with remaining crust. In a sauce pan, add butter and melt before adding flour. Make it into a paste and then add remaining ingredients (sugar, brown sugar, and water). Bring to a boil and then let it simmer for 5 minutes. Using a brush or spoon, pour mixture over the lattice structure covering all areas of the pie (try not to spill - I always leak over the pie so I find a brush is really helpful). Put in the oven at 400 degrees F for 15 minutes and then 35-45 minutes at 350 degrees F (I find if your apples are hard go for the full 45 minutes).

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