Sunday, December 12, 2010

Metrodome roof collapses due to blizzard



Minnesota, I miss you. 

There was so much snow and such high winds that plows were taken off the road; something that hasn't happened in years.

In Boston, it's raining.  What baloney.

Monday, December 6, 2010

December 2010

 my very own Charlie Brown Christmas tree


Inspiration:


From Design Sponge, one of my favorite blogs to read, comes the best hack of I have ever seen to make use of the 1990s TV cabinet thing.  Brilliant.   Mom, can I make ours into a kitchen for me?




Pom-pom animals---wonderful!  (via Design for Mankind)




Iceland, Eyjafjallajökull - May 1st and 2nd, 2010 from Sean Stiegemeier on Vimeo.
Beautiful.  Still jealous of Kempt's trip to Iceland.  One day I'll get there. 


Super Grandma (via Dudecraft)


An incredible map of the countries of the world that rearranges countries based on their size and population...very cool. (via Strange Maps)


The Ikea version of the Large Hadron Collider.  Watch out for the black hole, it's vicious.



Really cool statistics of life expectancy and earnings since the 1860s by geography.  Very cool.  [via]



Why Working at Work Doesn't Work (via)


An incredible podcast from NPR's Science Friday that goes back in time to their broadcast in 1993 talking about the internet.  I was in second grade.  I don't remember the internet being a real thing until at least sixth grade in the library, but then in seventh grade, oh man, I was all about making Geocities websites.  Thanks, science club. 


The Empire Strikes Christmas (via)


Things to look forward to:

--I know this isn't typically a thing to look forward to, but I finally have enough money in the bank to start allocating funds to specific actual big-kid mutual funds.  Pa would be so proud! 

--Home.  Soon.  11 days.  Not that I'm counting, oh no. With this comes friends, family, babies, ice skating, Christmas trees, all sorts of wonderful things. 

--Getting my life back to normal.  Or something resembling normal.  This semester?  Not my favorite.

--Snow!  There was Lisa-Frank glitter snow for about ten minutes earlier today, but I'll hold out for the real snowflakes in Minnesota.  I can't wait to see the cabin decked out in fluffy white.

thesis proposal: check!


 
Four days after my thesis proposal, I'm ready to do some science.  Or, rather, get lots of science prepared before I go home...either way, I'm certain that the new year will start off with a bang.  (fingers crossed)

Monday, November 29, 2010

foiled!

...by the wonderful birth of a healthy baby boy to my advisor and his wife.  My thesis proposal talk has been postponed til Thursday, so now I have a talk on Thursday and another the next day.  Let's just say without the hour-long elliptical sessions I've been putting in every morning this week, I'm pretty sure my heart would have exploded from the pressure and stress.  Just keep swimming, it's almost December 17th...

In other news, I just found out three minutes ago in my word-a-day post about the word beaucoup.  Beaucoup, in French, sounds just like boo-coo.  I said the words outloud, and there goes another vestige of my dyslexic childhood, joining the ranks of paradigm (para-dig-um) and inventory (inn-vent-tory vs. in-ven-tory).  I've spelled it booku in my head for, oh, years.  "Booku bucks" was a favorite phrase of someone in my family, maybe dad?  Now looking back, I can't imagine that particular phrase in his vocabulary.  Come to think of it--it's the same beaucoup in "merci beaucoup!"  This inability to spell things and make phonetic connections, wow, it's really quite a talent of mine. 

But--there is sun streaming into my office today (it's been awhile, sun...stay and hang out, will you?)...and I have pumpkin-italian sausage pasta for lunch.  Then tonight, some reading, delivering muffins, and maybe even putting up the Christmas tree.  You never know...

Thursday, November 25, 2010

thankful...

--family.  I wish I could be sitting down to Confirmation potatoes and turkey with them right now, but I'll be home in less than a month to celebrate my brother's graduation from college, and eat lots of Tea House, play in the snow, and watch "The Nanny" late at night with Hillary on my lap.  Sounds like the perfect break to me...

--friends, scattered across the globe.  From Chicago to Minneapolis, from St. Louis to Vienna, from China to Nova Scotia, you are all constantly in my thoughts.

--turkey, gravy, mashed potatoes, stuffing, and Chinese dumplings for Thanksgiving!  Gotta love the potluck Thanksgiving at McCormick--truly delicious and full of surprises. 

--that this semester is coming to a close.  There, I said it.  I will discontinue whining posthaste, because no one likes whiner, least of all me.  But this semester, wow.  It needs to end.

 
Also---to my youngest yet now-sixteen year old brother---you're pretty cool. I'm looking forward to our Star Wars marathon: t minus 22 days!

Friday, November 19, 2010

Thursday, November 18, 2010

because it made me laugh.

I'm sitting here, at 10:49 pm, with a deadline staring me right in the face (not good, guys...not good) ---still feeling slightly ill from this past weekend, and what paper comes up but this one:

Maybe this is a sign that I need to get out more, but wow.  Hilarious. 

Okay...back to work.  See you when I'm done...

Saturday, November 13, 2010

a miserable and feverish Saturday

...made only slightly tolerable by the fact that there was legitimate progress on my thesis proposal.  Now back to the 85 tabs open on my browser, to a life clogged up by science, to bibliography entries swimming in my head.  Delightful Saturday night, to be sure. 

Wednesday, November 10, 2010

Research


Story of my life (thanks, PhD Comics).  After a presentation that ended up being THREE HOURS and 15 minutes last night, I feel exhausted. 

Quote from my labmate:  "well, you know, it wouldn't be worth doing if it was easy.  It's supposed to be hard."

...that doesn't really make me feel better.  But onward ho, right?

Sunday, November 7, 2010

November 2010

 (a few days late)

Inspiration


Ok Go, you are my FAVORITE.  Will you marry me?  You made today so much better than it was.  Thank you.  (and of course, they're in Boston December 5th!?  I am seriously considering springing for tickets)

Citizen Scientists - regular people helping study fireflies, owl behavior, and ecology...very cool.


Blood Sweat and T-shirts, a look at the process of making clothing in India, from cotton to the sweatshops.



 Land Carpet from Florian Pucher...love.


Happy fall!  (illustration by Marguerite Davis, via Sally Jane Vintage)


 
Going West, via Dudecraft



Things to look forward to:

--Being done with my thesis proposal!  I'll be more absent than usual in an effort to prepare my manuscript and my presentation (the practice talk is Tuesday, the paper draft is due next Friday, my actual proposal is November 29th, and I am far from ready)


--Watching North and South with one of the girls on my floor.  She found my weakness in period dramas, so we'll be watching a bit now and then when she has a break in her studying. 

--Thanksgiving and turkey!  Yum.  The housemasters hold a Thanksgiving dinner for all the students staying here over the long weekend, and there is always quite a lot of delicious food.

--I have four of thirty-nine packages sent.  But gosh darn it, more are coming, I promise! 

Monday, November 1, 2010

happy birthday, Grandpa!

My grandparents went to Hawaii for about a month every year for as long as I can remember, staying on different military bases, soaking in the sun and just plain visiting with people and enjoying the weather.  One year, when I was about nine, they took our entire family, quite the incredible gift.  And while I remember some things, memory lane has been aided by the new Hawaii 5-0 series.  Too bad smell-o-vision doesn't exist, because that's one of the most stuck memories in my mind to this day; sticking your face into a plumeria tree, and just inhaling.  I remember a few years later, probably about age 12, when Bath and Body Works became this big thing that all girls were supposed to like...and I saw the plumeria flavor and I was SO EXCITED.  Literally...I was so excited I could barely open the cap!  But when I did, I breathed deeply and was surprised by the most noxious awful fake smell.  And that's when I started avoiding Bath and Body Works.  They ruined me, at such a young age.  If you want to smell plumeria, you gotta go yourself.  And it's worth it.

And Pa?  This reminded me of you and grandma...and yes, made me cry.


from Story Corps, a nonprofit dedicated to helping Americans tell and preserve their stories.

This is something my grandfather championed, the idea of taking care of people, places, and history...the story of this country.  As a veteran and a patriot, he spoke out when an American flag went unlit at night.  As a dedicated outdoorsman, he spoke out when people decided to be rude and trash places in the community, especially campsites and parks.  And as himself, a storyteller and conversationalist, he'd be able to find some connection between himself and another person in less than five minutes, a feat I've never seen anyone replicate.

So, in honor of his 87th birthday, I gave a donation to the Trust for the National Mall in Washington, DC, recently home to the Rally to Restore Sanity.   I often wonder what my grandfather would have thought of Jon Stewart.  But I know that he would have agreed with the idea that shouting gets nothing done.  Listening, learning, helping out--those get things done.  Happy birthday, Pa!

Sunday, October 31, 2010

Happy Halloween!

[watching my daddy carve a pumpkin]

Saturday, October 30, 2010

Saturday

[Halloween pumpkin carved by a friend of mine on the MIT homepage this morning]

Saturday business:
--take home exam
--really honestly totally getting packages ready to send
--outline of my thesis proposal

The carrot?  A night of not-so-scary movies with a friend to celebrate not going out for Halloween.  It's gonna be great.

Friday, October 29, 2010

Beautiful day.






72 and sunny yesterday...see you in April!

Wednesday, October 27, 2010

exciting news!

The PI of my lab was recently awarded an NIH New Innovator Grant to the tune of 1.5 million AFTER overhead (so, 2.6 million total.  Insane...the extra 1.1 million pays for MIT space, janitors, supplies like paper towels, etc...).  This is a very exciting thing for our lab and for our team.


that's my PI!

read more here


And since the abstract has been published, I thought I'd do a bit of translating, given how, um, dense it is.  (abstract will be in blue, explanation will be in black)

Transcript localization shapes many fundamental processes including cell polarity, migration and neuronal activity, and impacts diverse biological processes such as development, memory and learning.

Transcript refers to an RNA message.  When you think of how your DNA influences your cells, imagine DNA as a book.  A really, really, long book.  Now, to get information out of this book and doing something in the body, you have to open the book to a specific page and copy a passage to something called RNA.  Since DNA is a paired script in the book, it only copies half of it to the RNA---the molecules look like this:  DNA is on the left and a helix, RNA is on the right and is kind of half of a helix. 


All of those shape things are the letters by which the book of your genes and DNA are read:  A, T, G, C and U--it always astonishes me that with 26 letters and different combinations, we can end up with Shakespeare, but our bodies make us with just 5.

Cell polarity refers to the orientation of cells.  Since you have a head and feet, you are polar.  So are plants with flowers and roots.  On the other hand, a soccer ball has no polarity; it's the same on all sides.

Migration - just like Canada geese in the fall, both cells and things inside of cells move from place to place.

Neuronal activity is a fancypants way of saying "things in your brain working."

Development in biology refers to the period of time before you have gained some particular level of maturity.  This could mean development as a fetus, or it could mean development as you transition from a child to an adult. 

Although attention has been focused on localization of a few selected transcripts, recent global analyses indicate that the phenomenon is extremely common. 

A "few selected transcripts" are those that are studied first and found to be really important.  In this case, the abstract is saying a few important things have been studied, but it looks like we should study rarer transcripts in order to find more things out. 

In many cases, different transcripts are observed to have distinct sub-cellular spatial localization patterns. 

Sub-cellular means within the cell.  This is a cell:


There are lots of these cells in your body, and they all have a different purpose (help with muscle contraction, transmit nerve impulses, absorb digested food).  The cell above is just a generalized cell.

The word sub-cellular recognizes the space anywhere inside that cell. Spatial localization patterns is a fancy way of saying that these transcripts (RNA) sometimes end up congregating in different parts of the cell, just like hipsters with their PBR at a seedy neighborhood bar, students hanging out in the library, or people like me trawling the thrift store.  It's the same thing---these are different transcripts in different places.  It doesn't meant that I don't got to library, but it means there is a pattern where I go to the thrift store more often than the library.

Several prominent examples of specific transcript localization shaping processes such as body axis polarity in Drosophila and synaptic plasticity in neurons suggest the potential for there being direct functional significance of transcript localization, now recognized to be a commonly observed phenomenon. 

The concept of transcript localization shaping processes isn't as complicated as it sounds.  If we continue with the thoughts of Boston as a cell, and all the different buildings around it were locations that people could be, these people in different places affect how Boston functions.  For example, construction workers in South Boston help to build a new high rise; this changes how Boston is.

In the same way, when you have RNA transcripts spread over an entire cell, you cause different things to happen in different places.  So---if you have a certain transcript in a certain place, you can change what direction the cell moves.  The example above is "body axis polarity" in Drosophila (fruit fly) - in this case, talking about changing the intended head/thorax/abdomen orientation of a fly 90 degrees during development.  That's kind of insane.  But you can do it!  Simply by putting RNA transcripts in one place and moving them to another, you can completely change how the cell looks.  Similarly, you take all the construction workers from South Boston and put them in Somerville along with all the other construction workers in Somerville, you end up with---a lot of construction in Somerville.  It's the same in a cell, believe it or not!

And it's funny--plastic to me means very hard and rigid, which is why it's so ironic that in a scientific sense, plastic means able to adapt. These fly cells are able to adapt depending on where the RNA goes, which is a little bit crazy. But true.  You do reach a certain point at which things are "decided" - but early enough in development, you can definitely change the outcome. 

Plasticity in neurons refers to the idea that although it's a bit trickier to come up with new neurons than it is new skin cells, neurons make new connections all the time, and these influence memory and how your brain works.  If you didn't have plastic neurons, you wouldn't be able to learn!
 
Unfortunately, we have very limited understanding of the protein factors required for achieving specific transcript localization patterns. 

If DNA is the book of life, and RNA is a copied page from that book, a protein is what happens when that page is read aloud; imagine that you were in the world of the Pagemaster... (come on, I know you've seen the movie.  Me at age 8 had a completely helpless crush on Macauly Culkin/the boy in the actual book.  I was big into realism, knowing that I'd probably end up dating an incredibly dorky boy someday and love it).   Anyway, whatever is said aloud comes true, which while very cool is a bit daunting in the story.  But in this case, the proteins become everything that makes up the cell, or help create things that make the cell (example: plant cell walls are all made of starch; but this starch is processed by proteins).   

Anywho, this particular sentence brings up that the RNA must have some way to get to the places it goes, and these probably involve proteins; in Boston, you could walk, you could take the T, you could bike...similarly, science expects RNA to have a whole slew of ways to get to these different places, but doesn't have a really good idea of what they actually are (I vote hovercar).

Moreover, we lack strategies for selectively perturbing transcript spatial distribution in a manner compatible with understanding the associated functional consequences.

Gosh.  We don't have a good idea of what they are, and we don't know how to figure out what they are.  Oh science.  Thanks for your clarity.  But, basically we're stuck.  And that's what this proposal is trying to address.

This proposal addresses these needs by introducing a method permitting regulated targeting of a given transcript to a sub-cellular location, the latter being driven by known or putative localization factors under evaluation. 

So...what we need is something that will allow us to tag along with a transcript of our choice and try and see what's along for the ride.  Or, in plainer terms, a GPS with a video camera attached to a person to show where they go, how they get there, and who they go with.  We're basically super-spies.  Putative is a fancy word for suspected, and in this case we have some clues, but we don't know for sure.  So we need to do a bit of stalking and investigation.

In this approach, transcript localization is entirely experimentally controlled, and is conditional upon either small molecule or peptide signals applied to target cells using high-resolution chemical gradients and post-translational protein localizing modifications, respectively. 

And as super-spies, we control the RNA movement by adding a small molecule or a peptide. 

In science, a small molecule is something little that can get into a cell.  Some recognizable ones are sugars like glucose, or an antibiotic like tetracycline.  We would add these to cells very precisely, and see what happens.  A "high resolution chemical gradient" means that adding this molecule would be very accurate (high res, just like an LCD tv). 

On the other hand, the peptide would be a programmable "PS" put in the DNA book and therefore also in the copied RNA message.  So, if the RNA words on the copied page from the DNA book read something originally like "Help move sugar," we could add a specific PS that says "Actually, help move only fructose."  (something we can do by cloning).  This PS message is called a "post-translational protein localizing modification."

This broadly applicable method has the potential to advance our basic knowledge of the cellular mechanisms underlying transcript localization, and to probe the associated functional implications at both the cellular and organism levels. 

This will help us figure stuff out!

Public Health Relevance: Sub-cellular RNA localization into discrete, transcript-dependent patterns is now recognized to be a widespread phenomenon in many cell types and organisms, including humans.

This is something every researcher has to add to a grant for the National Institutes of Health.  Specifically, what does this project do to positively impact human health?  The argument here is that, even though there is no mention of any disease at all in this proposal, knowing more about the basics can be really helpful.  You know the people who won the 2009 Nobel Prize in Medicine?  Their work was very basic research on things called telomeres...which, as it turns out, are really important in cancer.  They didn't set out to revolutionize how we think about cancer.  But they did. 

Also, the abstract and this last bit is to inform a generalized public what the research is all about, which kind of cracks me up.  I'm a graduate student in this field, and it was impossible to wade through this without copying it into Word, bumping it up to a size 16 font, and reading it aloud in my head, pausing after each sentence.  Meaning?  The whole way we go about "informing the public" is oftentimes a complete joke.  And that's the basics of what I want to do when I grow up; make this sort of thing interesting to learn instead of impossible.

In several well-studied cases, transcript localization is required for establishing proper cellular function, and defects in this process contribute to developmental, cognitive and other neurological problems in humans. 

Aha---here's the public health; there are definite diseases, especially in the brain, that happen simply because there is RNA in places it's not supposed to be.  Or, there are escaped convicts from jail robbing a bank; not quite a good thing for Boston, and it's the same for the cell.

The proposed research will introduce new methods for understanding and manipulating the mechanisms underlying RNA sub-cellular localization, and has the potential to improve both our understanding and treatment of disease processes associated with RNA localization defects.

This research will look into new methods for learning why RNA goes where it goes, who it goes with, and how it gets there. 

We're the superspy tagging different suspects and following their every move to see what happens. And as soon as we know these particular things ---the whos, the wheres, the whats---we can begin to address catching these suspects...or figuring out how to correct a disease in the brain caused by this sort of problem.  But first--you've gotta do your homework and reconnaissance.


Phew.  That was a lot of science.  Time for a porcupine that thinks it's a dog:

Tuesday, October 26, 2010

In the Pantry: organization!

The one benefit of flour beetles is an amazingly clean pantry.  Lemons-->lemonade always wins over being a sourpuss. 

 

Chicago friends, stay safe!


Yikes. Good luck staying cozy and safe today!


Monday, October 25, 2010

Saturday, October 23, 2010

not what I planned on today.

But it did include a hard cider and Stargate, even if these things were by my lonesome.  But I also shouldn't fail to note that I have a roof over my head, people who care about me, fresh rosemary from my garden, carrot cake muffins to bake tomorrow, friends who come to my orchestra concerts and today was a beautiful day.  No, it wasn't a beautiful day on the Cape.  But it was a beautiful day. 

 


So go suck an elf, flour beetles and thirty yeast minipreps-turned Mach1 transformations.  You are so not worth my time.

Now---I'm going to going to put on my homemade skanky dirdl and beat the crap out of Barbie Peep.  Or read some Jane Austen, do the dishes, and go to bed.  Because that's how I roll.

oh goodness.

After a morning (and half my afternoon) spent cleaning out my pantry and throwing out a bunch of food (thanks flour beetles that mysteriously appeared) ---and then dealing with the aftermath of dishes and such that followed...I needed this:



Can I take a nap now?

Thursday, October 21, 2010

Wednesday, October 20, 2010

blinding light.



At just the right moment in spring and fall afternoons, my apartment is suddenly lit by the blinding reflection of the sun setting...a suprised moment of clarity, of eyes blinking, mind confused. 

My world needs more of this brightness, more of this smile-creating light.  I'm no Frodo in the lair of Shelob, but that light is still most welcome in my life.

Tuesday, October 19, 2010

Monday, October 18, 2010

gaaahhhh

Email from my professor this morning at 10 am:

The assignment in Golan for this lecture is Chapter 5, but that is a little thin for my lectures, so I have added (and uploaded) 2 papers that are essential reading assignments. I have also uploaded today's slides.

Really?  Two papers, by 1:30 pm today?  Really?

Add that to the fact that I didn't get paid this September, jeez. Thank goodness for MIT's payroll employees that are on the ball and figured it out for me.

Now to try and figure out when to squeeze in a trip to the Verizon store at Cambridgeside Mall (oh the horror!  I bet they already have Christmas stuff up) --- my phone can last about five minutes on full battery, which is why there has been a distinct lack of long-walk-based phone calls recently, a real shame.

Oh.  And take around muffins, figure out why Netflix thinks I've already opened an account with them (?), plan meals for the next couple of days, do my laundry, make dinner, collapse.

And my thesis proposal is November 29th.  Commence studying. 

(fact of the day: there's a gene called hERG that stands for "human ether a-go-go" after the dancin' legs of flies with a mutation in this gene when they are put under with ether-based anesthetic.  Thanks, William D. Kaplan.  I wish there was a video, but no luck) 

Saturday, October 16, 2010

fall Saturday

Things I did today:


I biked the mile to Trader Joes, my skirt flying up here and there, because I made the stupid decision to look at the pretty fall colors on Memorial Drive.  Instead, I frantically tried to pedal and not flash anyone at the same time, which was a losing battle because of the wind advisory today (really Boston?  Thanks). 

I worked in our freezing cold lab, a miserable experience because they did an unannounced steam shut-off this morning.  Brr.  BRR. 


I dressed in red, orange and green today.  Yes, I've noticed.  I'm kind of a kindergarten teacher in disguise.

I bought bread ends at Flour, the world's best deal for $1.50 - I expected them to be stale and perfect for crouton-making, but not so!  They were beautifully soft and fluffy.  Perfect for a dinner of bread and cheddar broccoli chowder.

I made apple butter!  So delicious, oh my.  Along with the maple cream I purchased, the crepes study break later in the year is going to be so tasty.


I watched Cloudy with a Chance of Meatballs with my apple-butter-making-GRT-partner-in-crime.  Started out very cool and mad sciencey---ended really, really odd (let's just say Owen Wilson voiced the part of a guy that ended up inside a radioactive half sentient chicken carcass)

I went to bed before midnight.  Always a winning time in my book!


PS  Making the Hippo Dance is a fascinating look at how the folks at Radiolab make the hippo---hard-to-understand scientific concepts ---dance and come alive.  That's exactly what I want to do...Jad Abumrad and Robert Krulwich, do you need a science intern in Boston?