1-18-08 Project Cloverfield - Warning! Spoilers

Experince a day in the life of a YMR scientist

Hello! In the morning I wake up and I go to work!

At work, samples excavated from the ocean floor are brought back to the lab and spread out on a Petri dish containing some 'media': Nutrients for growth that are combined with agar to form a solid surface! Bacteria that were present in the samples will then grow on the dish, forming a 'colony': Generally a small circle of billions of cells that all started from a single cell/spore in the sample! Each individual colony is then transferred to its own plate and grown so that you have a pure isolate: A pure strain of one bacterial type! Once we have those, they are transferred to a liquid media (also contains nutrients, but no agar, so it stays liquid) and grown in an incubator (keeps bacteria warm and shakes them to aerate the media).

This is called liquid fermentation! Whatever chemical compounds the bacteria might produce are often secreted from the inside of the cells into the surrounding liquid media. Afterwards we extract these compounds from the liquid media using a resin that broadly absorbs most compounds that would be interesting! This resin is then washed with organic solvents which transfers all these interesting compounds from the resin into the organic solvents. Organic solvents are things like ethanol, or acetone (in nail polish remover), dichloromethane (in paint thinner), etc.! These solvent washes, which now contain the compounds produced by the bacteria during fermentation, can then be concentrated and this produces a "crude extract": It contains a whole lot of compounds that were either produced by the bacteria or were present in the liquid media to begin with!

This crude extract (we generate thousands of extracts each year) is then tested in a screen to see if it has any interesting bioactivity! For example, somebody might develop a screen to see if a compound kills cancer cells. A simplified method might involve something like putting cancer cells into a dish, adding this crude extract, and then observing whether or not the cancer cells survive. In a real setting this would be very high throughput...each "dish" would be a tiny 'well' (about the volume of a few drops of water) arrayed in a 'plate'...a rectangular piece of plastic that contains a grid of these wells (usually plates contain 96, 384, or 1536 wells). So then each well of each plate would contain a few drops of a suspension of cancer cells. We add a different extract to each well and see if cancer cells live or die! This way you can screen thousands of compounds very quickly.

You could also do this to look for new antibiotics! Instead of putting cancer cells into each well, you'd put some sort of pathogenic bacteria that you want a new antibiotic against. In reality these screens often end up being a lot more complicated because people don't just want to kill cancer or bacteria cells outright (often these compounds would be toxic to regular human cells too), so they develop a screen that targets something really specific, like a particular protein involved in cancer pathways or something!

If one of these crude extracts turns up as a 'hit' on a screen, we then go about finding out what the specific compound is in the extract that's responsible for this interesting bioactivity! Remember that the crude extract contained everything the bacteria made, which can be hundreds to thousands of compounds. To do this, we perform a fractionation of the crude extract, in which these hundreds of compounds in a single extract are separated based on their chemical properties. This generates a series of fractions, so let’s say I had an extract with a thousand compounds that I separated into 100 fractions.

Now each fraction contains maybe 10 compounds. Each of these fractions is then rescreened, and hopefully we find that the bioactivity is in a particular fraction. Now we know the active compound is one of 10! We then repeat this fractionation process on these 10 compounds, rescreen them and find the active one, and then identify what that compound is. If it's a new compound, somebody would go about studying whether or not it could be a useful drug. So for example, using the screen, we might know that the compound kills pathogenic bacteria, but it wouldn't be a useful drug if it's too toxic to people, or gets broken down in the body too quickly, things like that! This might involve a “clinical trial”: Trying the drug on real people after it's been through plenty of tests and development!

After work, I go home and dine with my wife Akemi! Then I go to bed!

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(via Wired.com) Japanese magazine Shonen Ace posted the first installment of a manga based on J.J. Abrams' new monster flick, Cloverfield, to its website last week. The tie-in manga, titled Cloverfield/Kishin, follows the story of a Japanese boy named Kishin whose fate is somehow tied into the apocalyptic events taking place in New York City. Artist Yoshiki Togawa will draw three more installments of the manga, with the next one slated for online release in late February. There aren’t any English translations available yet, so for those who are curious, here’s a brief synopsis:

The first chapter opens with Kishin helplessly being picked on at school. The bullies tease him about his mom being a weirdo (we find out she is dead in a flashback sequence). Just as a pretty classmate helps Kishin out, giving him back his stolen pants and untying his arms from behind his back, the school emergency alarm goes off. But that doesn’t mean he's off the hook yet –- the bullies decide to lock him in the gym storage space, snickering: "Isn't that what you're supposed to do in an emergency? Go somewhere safe when you're in danger? It's dangerous outside, with us here."

While this is going on in Japan, a cargo shipper at sea is anxiously waiting to dock. He has a baby on the way and can't wait to get home to his wife. Just as he's being reassured that they're not far from shore, a mysterious set of eyes starts to emerge from the sea. The last sentence reveals that Kishin and this monster are somehow tied together.

Check back to Underwire for a synopsis of Chapter Two.

"At the end of Cloverfield you can see something. Many believe that the origin of the Cloverfield monster is from space, and that might be true considering at the end of the movie something falls from the sky.

I still believe that the Targruto company was responsible b/c of their deep sea drilling, but maybe we'll find that out in the next movie.....i hope. The video isn't all that good and you might have to watch it in full screen, but i've seen the movie 3 times already and something does fall from the sky into the water....it happens on the horizon kinda near the boat."

"To understand just how fervent the buzz has been about the movie, you kind of have to look at how Paramount sold the movie in two completely different ways to two completely different audiences. Or, as I call it: The Tale of Two Cloverfield Campaigns"

An Open Letter from Ganu Yoshida

"Dear Friends, Supporters, Investors, and Members of the Tagruato Family,

Ever since I was a very small boy, I have had the dream of owning a company similar to this one. A company where the workers work hard and love each other. A company dedicated to making good change to our world. A company that would bring prosper to Japan and extend that wealth and knowledge into the universe.

Unfortunately, last week was a dark time for Tagruato, this company I love so dearly. I tried to contain the event for the sake of police investigation but now it is the time to come clean and tell our story to the world.

Our newest and brightest oil rigging development, Chuai Station, was attacked by a terrorist environment group called Tidowave. They released a series of explosions on the station, causing the loss of life and bringing the rig down into its knees. Tagruato has faced threats from this group for many years and has, with the help of our friends in the police forces, fought off many prior attacks. This blow, however, was too strong to miss us. The Chuai Station was damaged.

We are working tirelessly to contain environmental damage from the explosions and are already experimenting in the Atlantic for a new Chuai Station rebuilding location while our work is being continued at a temporary facility. We have also opened the Chuai Station Funds, which has currently raised over 300 million yen for the families of Chuai victims.

On behalf of everyone at Tagruato, I would extend my thanks for the overwhelming wave of support we have been receiving from our business partners, friends, and colleagues. We will not rest until these criminals are taken off of the streets and made to answer to the families of those lost at their hands. I know that, with your help, Tagruato will not falter before zealots, but will remain the company I pictured as a boy, dedicated to exploring the magic of our world and controlling the future of us all."

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