Of mice, men, and microRNAs.

   Although RNA is most famous for acting as an intermediate between DNA and Protein, we've come to understand that RNA's role in the cell goes far further in recent years. Some kinds of RNA, like miRNAs, actually change the balances of proteins made, leading to a wide variety of effects.
  What exactly is a miRNA? miRNAs or microRNAs are tiny segments of RNA. Where most RNA segments are about 1,400 nucleotides long, miRNAs are typically only about 22 nucleotides long. While miRNAs are sometimes written out by themselves on DNA (as in the video above), it's more common to see miRNAs created as a byproduct of the creation of other kinds of RNA. Unlike many other types of RNA, miRNAs don't encode for proteins or assist in their transcription of RNAs to protein. Instead, miRNAs prevent proteins from being made from mRNAs by latching onto them before they can be transcribed. In the past few years, miRNAs have been implicated in certain types of cancer, and been used as biomarkers to help detect and diagnose diseases.
   All of this is very exciting on its own, but more exciting still is a paper recently published in Nature Cell Research which suggests that miRNAs can actually travel from material in the digestive system of an organisms you eat into its bloodstream. Scientists at Nanjing University, China found a certain miRNA from rice, called MIR168a, in the bloodstreams of both humans and mice. By varying the diets of lab mice, they were subsequently able to show that the miRNAs found in mouse blood were being ingested.
   This alone is an important discovery, but the researchers further "hypothesized that [plant miRNAs] may play a role in regulating the functions of mammalian cells and organs". Looking through the known sequences of mouse and human mRNAs, they identified about 50 proteins which MIR168a was likely to interfere with, including LDLRAP1, a gene that codes for a liver protein in both humans and mice. By exposing a certain type of liver cell (HepG2) to increased miRNAs, they determined that "Plant MIR168a...significantly decreased the LDLRAP1 protein level in the recipient HepG2 cells" while LDLRAP1 mRNA levels remained unaffected. In other words, the miRNA was preventing the transcription of the LDLRAP1 mRNA, as expected.
   Why care about this result? It further clouds the waters regarding the role environment plays gene expression, an area of much of interest in biology right now. In addition, if miRNA uptake turns out to be common (or at least easy to induce) in humans then it could lead to whole new classes of oral drugs that target the expression of specific proteins.



   If there's one result worth posting about from this week, it is the now famous (and in some circles infamous) exchange of neutrinos between CERN and OPERA, two European physics laboratories. Neutrinos are pretty cool as is, but what's really of interest here is what the neutrinos (muon-neutrinos, to be exact) appear to be doing on their trip from their creation at CERN to their detection at OPERA. They're arriving ever so slightly early: 60 nanoseconds early to be precise. For reference, quick calculation shows that light only travels 24 meters (just under 80 feet) in that time.
   How fast light travels is actually exactly what's at issue here; the neutrinos seem to be arriving at OPERA before light traveling along the same path would. If it is true this is the most significant find in physics for a century at least. For all practical purposes though, getting a result like this is a really good reason to check your equipment for obvious problems.


What is about to happen.

Starting next week (and possibly this week for practice) you can expect to see two new articles per week (posted on Saturdays?)on current events in science along with some reasons you should care.
As part of my first semester at MIT, I'm taking a Science Journalism class. Part of this class is the creation (and weekly updating) of a blog on science, medicine, technology, and related topics.


Living in Simmons

My sketching is still awful, but at least I'm getting the hang of cleaning it up in gimp... More after the jump.

The Hough Transform: New and Improved!

  Ok, well it's still not better than a kerneled transform, but I am getting pretty pictures without the use of any trig! To sum up what I'm doing, I'm trying to use python's lambda expressions to generate a function in Cartesian space from the given points. Then I want to run BFGS over that function to find local maxima. By multiplying r = x_0 cos( theta ) + y_0 sin( theta ) through by r and rewriting as x^2 + y^2 = x_0 x + y_0 y , it's easy enough to see that the hough transform of a given point is actually a circle with one point at the origin and centered at \left( \frac{x_0}{2},\frac{y_0}{2}\right).
  This has the nice property that it's easy to calculate the distance between a given line ( point in hough space ) and the nearest point on the circle as a single square root.


An awful haiku.

Deathcube, what great mass!
Rubber over the solid heart
of a neutron star.


A quick sketch from last night's "Welcome to Simmons" talk

Done in the corner of some scrap paper. I've played around with some post editing in Gimp. Best part was the "Fire Alarm Prevention/ Popcorn Cooking 101" bit. Wish I could have sketched that instead, but I was out of paper space.


A Native Google Talk Client for Linux(Sort of)

I've been using Google Talk more frequently as of late, but upon investigation, I was disappointed to learn that Google hasn't released a Linux client for Google Talk. I did, however, notice a reference to a "native" (whatever that's supposed to mean) ChromeOS client. Since I knew that ChromeOS is running Linux under the hood, I decided to check it out. Amazingly, despite wads of yellow tape warning me that it would wreak havoc on my computer and slay my firstborn, it seems to work seamlessly as a Linux client for Talk in Ubuntu 11.04! Video chatting between two semi-native clients doesn't always work, and using both the client and, say, gmail chat at the same time has it's rough edges, but it's fine.