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plasmid

Member Since --
Offline Last Active Apr 19 2015 05:15 PM
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Topics I've Started

I'm not a skier

25 December 2014 - 04:50 PM

At sides of my cap
A duo of flaps
They certainly won't stop the winds

And firmly in place
Are goggles on face
The mask to my curvature bends

The skis on my feet
Are nice and are neat
But sliding's a skill that they lack

I've poles in my hand
So balance I can
With arm tethered fast behind back

Edit: changed def'nitely to certainly, to improve poetic meter

Genetic engineering

20 December 2014 - 12:38 AM

Suppose you have a bacterial strain growing in a flask where nutrients are not limiting. The bacteria will grow and divide after replicating their genomes, but cell division isn't perfect so their progeny will be viable and reproductive 99% of the time. You engineer a substrain of the bacteria by adding a gene to its genome that improves its probability of replicating to form viable offspring, but that adds to the size of the bacterial genome so it takes longer to replicate. Will the engineered bacteria outgrow the original strain? How much of an improvement in offspring viability would be needed to do so?
 
Some numbers that might be needed (or might be red herrings):
Let's say you're working with E. coli with a genome size of about 5,000,000 base pairs, and the gene you're introducing is on the small side at 1,000 base pairs. The typical doubling time for E. coli in optimal laboratory culture conditions is about 20 minutes, and let's assume that the doubling time is proportional to the genome size. You're growing them in a flask with 50 ml of media and starting with an inoculum of 1,000 cells of each bacterial strain in the flask, and assume growth will be exponential until they reach a concentration of 5 x 108 cells/ml.
 
Would the answer change if, instead of working with a bacteria, you're working with a virus? Say the virus infects a host cell and utilizes all of the nutrients in the cell to make new virions before killing it and releasing its progeny, and the number of progeny made is inversely proportional to the viral genome size but the time until the cell dies is not affected. If you're working with an adenovirus, its genome size is 36,000 base pairs and let's say it can normally produce 500 virions from one of the host cells you're working with after three days. You start with a petri dish with 107 host cells and infect it with 100 infectious viral particles.
 
Suppose the gene doesn't improve the efficiency of viral replication, but instead reduces its propensity to infect a cell as it floats by? The starting viral strain has a 10% probability of infecting each cell it passes over (note to any biologists out there: that number is completely made up), cells are distributed uniformly on the dish (call it a hexagonal tiling if that will make the math easier), and a virion will travel in a straight line until it infects a cell since it doesn't have to contend with an immune system. Assume that a cell that's infected with one virion will make just as many progeny as a cell that's infected with multiple virions, and the time spent floating is negligible compared to the duration of infection.

I'm not Jonah

23 November 2014 - 06:14 PM

Still loyal to my mother's tribe
By father I'm forsaken
My independent life imbibed
In massive gullet taken

Within the beast who on me fed
The rank miasma burns
My flattened face belies my dread
Beneath, my stomach churns

I plot revenge with failing brain
Concoct a poison dire
If threatened, shall I loose the bane
Beware this man of fire

How would you cross Puzzle Land, part VI or so

20 July 2014 - 03:46 AM

I don't remember where the last Puzzle Land left off, so I'll pretend that you were stuck in jail with a warden who used to be a villain in a James Bond movie. He gives each prisoner a black or white hat and forbids anyone to communicate by any means other than his pet homing pigeon, which is trained to fly around the prison counterclockwise while counting each cell that it encounters and stopping whenever it reaches a prime number. After reading the remainder of the rules and leaving everyone in their cells to work out their hat color with the pigeon, you're the first to get the pigeon.

 

Realizing that the warden never specifically forbade taking off your own hat and looking at it, you do so. You let the pigeon loose so that any other prisoners who have enough sense to look at their own hats will go free, and good riddance to those who would depend on some cockamamie bird-brained scheme to escape.

 

After being released from prison, you then visit the castle of Puzzle Land and are called in service to the king. One of his knights takes you to a room with a pile of 27 coins, and explains that they are all gold and of equal weight except for one counterfeit that is slightly heavier (with the difference in weight between the counterfeit and a real coin being much smaller than the weight of a real coin). Your job, using only three weighings with the Royal Balance, is to identify the counterfeit and throw it away so the knight can bring the real coins to the king.

 

Knowing full well how to handle this, you place nine coins on one pan and nine on the other. Seeing that one of the pans is heavier, you say "All right, looks like the counterfeit is among these nine."

 

The knight, sounding as though something is amiss, says “Uh, you do know that's the Royal Balance, right?"

You: Yes, what of it?

Knight: Don't be too sure that the counterfeit is among those nine.

You: What? Why not? They were in the heavier pan compared to another with an equal number of coins, so the counterfeit must be in there.

Knight: Like I said, this is the Royal Balance. The one we use to trade with merchants. The pan that was lowest is the one that always weighs one coin heavier than the other.

You: ...

Knight: Well how do you think the king built such an empire? Magical royal elves?

You: ...

Knight: That counts as one of your three weighings, by the way.

You: ... now you know there's no way for me to identify the counterfeit in two more weighings, right?

Knight: Well then just find as many as you can that are genuine. As long as we don't give him a fake, maybe he won't bother to count them and figure out that you screwed up.

You: …

Knight: Look, I'll even make it easy for you by de-rigging the balance so it works like normal.

 

As the knight finishes messing with the balance and you're about to get started, the royal kitteh comes along, hops up onto one pan of the balance, and (because it's a kitteh) promptly falls asleep. The knight warns you that aggravating the royal kitteh in an attempt to get it to move is punishable by instant slaying, so the cat will stay where it lays. But he tells you that the kitteh weighs exactly the same as N real gold coins. Using that fact, and the fact that the kitteh is not completely blocking you from putting some coins on the same pan with it, with two more weighings you get the worst possible luck as far as narrowing down where the counterfeit lies, but you toss out N+1 coins and give the rest to the king without being beheaded for giving him a counterfeit. As it turns out, if the kitteh were any heavier, you would have ended up tossing out N or fewer coins instead of N+1.

 

To clarify that last bit, if the kitteh did not weigh N coins but instead weighed M = N+X coins for any positive integer X, then you would have tossed out M or fewer coins rather than M+1 coins in the worst case scenario.

 

How much does the kitteh weigh?


I'm not a rebellious missionary

16 July 2014 - 06:14 AM

Heaven sent with company
Clad in cloaks of four or three
Straight and narrow I'll not be
Thus my fate is cast

Sawn asunder as you're fain
In coffin uninterred lie slain
'neath ice with blood-stained ball and chain
Gouged until the last