microbiology - Salvaging a plasmid from a cell culture stored at the incorrect temperature

I would rinse the cells off the agar using a small volume of LB or similar rich medium. Then use a small aliquot (10 μl) to inoculate a 5 ml culture under selection to see if anything will grow. Meanwhile the remainder of the cell suspension from the vial can be used as input for your favourite miniprep procedure.

If necessary, the DNA that you recover should then be used to transform a suitable E. coli strain. Don't bother trying to analyse the rescued DNA first since polysaccharide contaminants from the agar will probably inhibit any restriction enzyme that you might use.

Good luck!

experimental - What does "delineate" mean in this context?

I think this would me more on topic at English.SE, but (from Merriam-Webster):

Delineate:

1 a : to indicate or represent by drawn or painted lines
    b : to mark the outline of

2 : to describe, portray, or set forth with accuracy or in detail — de·lin·ea·tor noun

In this case, it could be either meaning that is used. Either 2, as Richard Smith said in his answer, to define the experiment's parameters in general, or 1b, to mark, limit a specific area of the ocean in which the experiment will be done. Obviously, delimiting an area in a body of liquid is not very easy.

pharmacology - Do drugs always degrade after they have passed their expiration date?

Drugs do not have to degrade after their expiration date and passing the expiration date has more than one possible meaning.

First of all chemical compounds vary in their susceptibility to breakdown over time. If they are kept away from oxygen, high temperatures (or kept in very low temperatures), and they are of a robust chemical nature, they might be stored for much longer than their expiration date and remain just as strong.

Over time, pharma compounds will chemically break down and lose their potency. In many cases, you will find that they simply don't do anything when you take them. This link cites a study that many drugs can retain their potency 15 years after they are made.

There are important exceptions. Two examples are tetracycline and acetaminophen (tylenol) whose breakdown products can increase the tendency for these drugs to induce liver damage.

neuroscience - Do effects of caffeine on human body change with habitual use?

I've been reading about homeostatic nature of a lot of neurobiological processes - the brain is trying to maintain a balance by desensitizing receptors, re-uptaking and breaking down neurotransmitters.

With this in mind, I'm interested in what happens to the receptors in the brain with chronic use of caffeinated beverages. Let's say an occasional caffeine drinker likes the cognitive boost of caffeine and starts to consume it habitually/chronically - every day. Will the caffeine drinker experience the same effects day after day, or will the effect change over time?

If there is a change in how the body responds to caffeine, are there any time frames that can be used to estimate when the change takes place - is it X days/weeks of habitual use?

Thank you for your input!

zoology - When do most mammals mate?

Why would it evolve?

No research (that I can find) is consistent with specific time of day mating across many species. I can't think of any reason why even just a few quite different mammals (e.g. mice, bats, lions, whales, and humans) would all find a fitness benefit of mating at the same specific time of day and therefore it is highly unlikely to evolve. I would suggest that if there are consistent patterns they are no reason other than coincidence (correlation over causality).

For example, dawn and dusk peaks in activity...

I have no references to back this idea up but lets see how this goes. The majority of mammals will be awake around dawn and dusk because there is likely an over lap between nocturnal and diurnal species at these times. Given that mating (normally) requires the participants to be awake then this would be a time when more animals are awake it is therefore a more likely time for mating to occur. But, as I already mentioned it would purely be because of the increased numbers awake.

Simple statistical illustration of the dawn & dusk idea...

Imagine a raffle with 2000 winning tickets. You buy 1000 and put 500 hundred of these in a box called nocturnal and the other 500 go in a box called diurnal. The raffle is drawn 24 times (perhaps every hour). The first 14 times it is drawn you can win if the ticket is from the nocturnal box, the latter 14 times you can instead check the diurnal box. This means during the first 10 draws you have a 25% chance of winning, and likewise in the latter 10 hours, but in the middle 4 hours there is a 50% chance every draw.

This comes down to a simple statistical phenomenon, if you don't buy a ticket you can't win the raffle.

physiology - How much gas is exchanged in one human breath?

According to Wikipedia

"In a healthy, young adult, tidal volume is approximately 500 ml per inspiration..."

(tidal volume is the volume inspired/expired)

Using this figure, together with values for gas composition also taken from Wikipedia, I estimate that in each breath we take in 18 mg O₂ (1.1 mmol) and we release 36 mg of CO₂ (1.2 mmol) plus 20 mg H₂O (1.1 mmol). These are, as you say, ballpark figures.

Sample calculation:

O₂ inspired = 21% by volume; O₂ expired = 16% by volume

O₂ change = 5% by volume = 5*500/100 = 25 mL

1 mole gas = 22.4 L; 1 mmol gas = 22.4 mL

O₂ change = 25/22.4 mmol = 1.1 mmol

MW O₂ = 16

O₂ change = 17.6 mg

The relative values are reassuringly close to what you might predict from the textbook equation for oxidation of carbohydrate: C₆H₁₂O₆ + 6O₂ -> 6CO₂ + 6H₂O

molecular biology - Is there a Reverse Transcription optimization for long, 9kb, transcripts?

Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep. It will be trivial to make internal primers sets for the PCR that are specific as long as there are no chimeric sequences. If there are, they will probably get primed also. If anyone knows of an optimization and/or other potential pitfalls, I would love to hear them.