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What Makes A Pet Hypoallergenic
I know you can purchase dog and cat breeds that are hypoallergenic so those who are prone to pet allergies will have reduced allergies or none at all. These breeds are specifically bred for that trait, and as a result are typically pricey compared to another breed. These breeds are not necessarily hairless or short-haired, so I do not think it has to do with the amount of fur shed.

What makes these animals different from other breeds in their inability to cause allergies?

Pet allergy is an allergic reaction to proteins found not only in the
  animals' fur or hair but also in saliva, urine, mucous, and hair roots
  and in the dander sloughed from the animals' skin. Thus, the
  widespread idea that "hypoallergenic pets" are those that have less
  hair or shed less is a myth.
Most often, pet allergy is triggered by exposure to the dead flakes of
  skin (dander) a pet sheds. Any animal with fur can be a source of pet
  allergy, but pet allergies are most commonly associated with cats,
  dogs, rodents and horses.
Some dog breeds have been promoted as hypoallergenic because they do
  not shed their hair, shed very little, or have the same pH as human
  hair. However, no canine is known to be completely non-allergenic.
Some cat breeds, especially females are likely to have low levels of
  Fel d 1, the main allergenic protein.
There is only one known hypoallergenic horse breed. The Bashkir Curly
  horse has a uniquely textured coat that lacks the protein (present in
  all other horse fur) believed to be the source of allergic reactions
  to equines.

via

Quotes should be clearly indicated using the quotation formatting and should support your answer rather than form it


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By what mechanism does penicillin resistance usually develop in Streptococcus pneumoniae?
There are three mechanisms:

prevention of the interaction between antibiotic and the target PBP;
modification of the binding of the antibiotic to the PBP;
hydrolysis of the antibiotic by a beta-lactamase.

Medical Microbiology, 6e, p. 200, Murray

PBP: penicillin-binding protein
It may be the case that the most common mechanism is not known.
It is just one of these three depending on the situation.
What is the most common mechanism by which penicillin resistance develops in S. pneumoniae?

I think your guess is quite spot-on. According to this scientific article I found online, They did a whole genome sequencing on penicillin-resistant Streptococcus pneumoniae and their conclusion was

....is mediated by a mosaic of genes encoding altered
  penicillin-binding proteins (PBPs). Nonetheless, S. pneumoniae has
  also developed non-PBP mechanisms implicated in penicillin resistance.

In clinical medical laboratory point of view, S. pneumoniae's AST is done with oxacillin instead of Penicillin because OXA gives better cut-off between Susceptible, Intermediate and Resistance. You may see a big zone of inhibition when you used PEN disk but that doesn't mean the isolate is susceptible to PEN. This may suggests that "hydrolysis of the antibiotic by a beta-lactamase" is less likely to be the main mechanism?

Very good answer!

Maybe you are asking where these genes came from and how they became so common?
It turns out that antibiotics are very common - many free living plants and microorganisms make antibiotics.  Penicillin, the first beta lactam antibiotic found is synthesized by a fairly common mold, they kill bacteria by inhibiting the synthesis of the cell wall.
All three of these classes of defense have evolved over the hundreds of millions of years of evolution since antibiotics like penicillin started showing up (probably more like billions of years).  They have all probably been with us for quite a long time.
Beta-lactamases, which enzymatically neutralized the beta lactam ring of penicillins and related compounds seem to have evolved three times and its not hard to imagine why the genes have stuck around for so long.
dd-transpeptidase, the 'penicillin binding protein' is actually an enzyme that helps to synthesize the peptidoglycan of the cell wall.  It can also mutate such that it tends not to bind penicillin so well, creating a second sort of penicillin resistant bacterium.
Other genes such as ABC drug transporters can kick out strange molecules before they can cause any damage.
These and all other sorts of mutants and genes that convey resistance, once created through selection are around in the huge bacterial gene pool.  Bacteria can pick them up through lateral gene transfer, plasmids (sex), phages and by taking in DNA from the environment.  Most of these genes and traits were sitting around for millions of years, but the increased use of antibiotics has increased the selection pressure to retain these traits in many more bacteria.  That's really where bacterial antibiotic resistance comes from.

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Exercise causes number of cell divisions to approach Hayflick limit faster? And hence shorten life expectancy?
A world class athlete spends a lot of time performing intense exercises.  Correct me if I'm wrong, but I assume that these intense exercises causes significant damage to the athlete's cells, but with proper nutrition, they are able replenish these cells with stronger ones.   This process of destroying and re-creating cells causes cell divisions to approach the Hayflick limit faster, and hence shorten the athlete's life expectancy.
I also heard that caloric intake causes the number of cell divisions to approach the Hayflick limit faster.  World class athletes generally consume substantially more calories than the average individual, which also contributes to a shorter life expectancy.
So for this reason, is the life expectancy of world class athletes generally shorter than the average individual? And what about casual athletes?
Edit
If world class athletes live longer lives than the average individual, why is this so despite performing activities that expedite the deterioration of telemeres, and hence, approach the Hayflick limit faster?

I don't know about the Hayflick limit in humans, but Olympic-class athletes tend to live longer than average, as long as it wasn't a contact sport: http://well.blogs.nytimes.com/2012/12/19/live-as-long-as-an-olympian/

Ok, then i guess i should revise my question to ask why despite doing things that expedite the deterioration of telemeres, they live longer lives?

not sure that exercise causes most cells to divide more - myocytes dont i think...  I think excessive exercise can shorten life due to stress and wear and tear.

As I know there are not many people can live as long to reach Hayflick limit - most of them are dying earlier as a result of heart diseases, cancer, or accidents. A world class athletes have a healthier way of life then odinary people: they have more physical activity, better food and have a visit to docter more frequent.  So I think it is a reason of their longer life.

Athletes who work too hard can actually shorten their lives, but for the most part exercise does prolong one's life.  Neither of these effects probably have to do with the Hayflick limit tho.

Following damage to muscle (e.g., as a result of strenuous activity) the injured fibers are removed (by immune cells) and then replaced by new myofibers (individual muscle cells that join to create new muscle tissue). This is why for a few days after exercise your muscles can be sore - it is the tissues being initially cleared of damaged cells and repaired.
Muscles, like other tissues, have resident stem cell populations ("satellite cells") that are used to replace damaged cells.
Stem cells have potentially indefinite replicative potential, as they express telomerase and thus do not have a traditional Hayflick limit.

Volonte D, Liu Y, Galbiati F. The modulation of caveolin-1 expression controls satellite cell activation during muscle repair. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2005 Feb;19(2):237–9.

I think there's another point here that the cells repaired do not divide and so the tissue in general does not have cell division as a result of exercise.  Even healing from injury probably has a minimal impact in this regard as well.

@shigeta the injured fibres (fused myogenic cells) are removed prior to "healing" (replacement with new fibres), or so I understand it. There may be degrees on damage that can be repaired without total removal, but generally I think the old is cleared to make room for new, stronger fibres (hence muscle being stronger after training (i.e. damage following exercise))

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Formation of ammonia from air and moisture
On extended bicycle trips I sometimes slept under a plastic sheet, which helped with mosquitoes on hot nights. But there was a noticeable build-up of ammonia which made this almost impossible for more than an hour or so at a time.
Air is mostly nitrogen $(N_2)$ and there is always water (containing hydrogen) on a humid day. But I wonder about the mechanism for the formation of ammonia under these circumstances? There are (according to Wiki) trace amounts of methane and $H_2$ in the air. But methane and hydrogen (g) are I think pretty stable.
I wonder if the presence of exhaled air (containing $CO_2)$ could be a factor?
Thanks for any ideas.

If you're absolutely sure it's Ammonia ($NH_3$) you're smelling, it's probably from you.
Ammonia will not spontaneously form at any significant rate from the air. Molecular Nitrogen ($N_2$) is extremely stable.
What can happen is that during marathon-type activities, muscles turn from carbohydrates (which are later converted into glucose and enter into the Krebs Cycle) as an energy source to proteins themselves.
One of the waste products of protein catabolism is Ammonia, which is excreted in your sweat if the body can't convert it into Urea ($CH_4N_2O$) quickly enough:

Ammonia forms with the oxidation of amino groups (-NH2), which are removed from the proteins when they convert into carbohydrates. It is a very toxic substance and only one nitrogen atom is removed with it. A lot of water is needed for the ammonia excretion.

Yes, no mistake about the ammonia. This makes perfect sense. Long distance cycling with little to eat, intense humidity and heat. Thanks.


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How can I resuspend a cell pellet without harming the bacteria?
When using a preculture with Ampicillin in my protein expression, I have to get rid of the preculture medium to avoid carrying over too much beta-lactamases that will destroy the ampicillin in the main culture. To do this I pellet the cells and resuspend.
Which methods of resuspension are best suited if you need the bacteria alive afterwards? I'm not sure how much force I can apply without harming the bacteria, and resuspending very gently takes a very, very long time.
Which methods can be used to resuspend bacteria alive, and which ones are the fastest?

I wonder how many cells are even killed in a pellet?  It seems they always come back into log phase growth in a short time.

Assuming that you are talking about E. coli: As long as you are resuspending the cells in a suitable liquid, e.g. fresh medium or buffer, then from my experience you don't have much to worry about - the cells are very robust. I've found that different strains and growth conditions give pellets with very different qualities - some will resuspend quite well with vortexing. If the pellet seems clumpy then trituration is something that I always found to work - pipette up and down until the pellet breaks up.
If you were going to do some kind of physiological measurement with the resuspended cells then it might require some checking, but if you only intend to regrow and induce expression I would say that giving the cells some time to recover in the new medium (check that absorbance is increasing) before inducing expression should be enough.

Using a pipette is what I'm doing now, though I usually cut off the tip a bit to reduce the force when pipetting.

Pipetting up and down GENTLY, the slower you pipet and the thicker the tip the more gentle it is, or vortexing SLOWLY, high vortexing speeds result in shear stress on the wall, just like fast pipetting with small tips
Bacterias can take a lot, take more care with yeast and even more care with mammalian cells


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Is it possible to do chip-seq on a specfic region?
Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.

Are you interested in doing this in vivo or in vitro (by in vitro I mean adding the factor to naked dna and then crosslinking)? In what species?

If the question here is to perform an assay that only sequences from a specific set of segments of the genome, you probably could, but it would be a lot of work and you'd need a good reason to want to go through that trouble.
Not sure how you would limit the nucleotides you get back to a specific region of the genome say.  The entire point of a CHP-Seq experiment is to get as unbiased a set of nucleotides read and so using specific primers designed against only a specific set of the genome would be hard.
Usually CHP experiments focus the readout they are getting by only focusing on a specific transcription factor for instance.  The number of variants of short binding sequences that usually come out will easily be read by a sequencing lane.  You'd have to have a strong reason not to take all the data genome wide.  Generally the results for many such pulldown sequences are pretty short and frequently can't be found uniquely on the genome, esp if there are lots of binding sites for the protein to be found.
I could speculate that you might synthesize labelled primers from random segments of a cut up library coming from a chromosomal segment you cloned somehow.  That again that seems like a lot of work to cut back on the data you get from the experiment without a big reason for doing this.
Using a CHP-CHP experiment that only has specific regions tiled can make do something like this - this makes the chip itself more economical, making the experiment more accessible.
Hope this helps...

One way to increase power (if that is your goal) is to limit your mapping step: you only seek to map to a subset of the genome, e.g. promoters or transcribed regions.
I'll post a link later, but the reference is Leuleu et al. 2010 doi: 10.1093/bfgp/elq022


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Serotonin - Does being aroused make you sleepy?
My Psychology text book says Serotonin causes "Sleep, arousal levels and emotion"
Does this really mean that when you are being aroused, Serotonin is released, which in turn makes you sleepy? If so, what evolutionary benefit would that have??

This can be answered by reading the Wikipedia article on serotonin, which has a nice list of functions.

I've always wondered whether heightened serotonin was responsible for socially accepted phenomena such as post-coital tiredness and "morning glory"...

You do realize that Arousal does not have anything to do with sex unless you expressly use the adjective Sexual to modify arousal From Medical Dictionary Arousal 1. a state of responsiveness to sensory stimulation or excitability.
2. the act or state of waking from or as if from sleep.
3. the act of stimulating to readiness or to action.

According to this article [1], serotonin (5HT) inhibits sexual arousal:

Dopamine is generally facilitative to male sexual
behavior; however, 5-HT is regarded as inhibitory.
Antidepressants of the selective serotonin reuptake
inhibitor class (SSRIs, including Prozac and Zoloft)
impair ejaculatory/orgasmic function and frequently
inhibit erectile function and sexual interest as well.

However, serotonin can also facilitate erections:

Systemic administration of the 5-HT1B receptor agonist
anpirtoline impaired ejaculation in male rats. On the
other hand, stimulation of 5-HT2C receptors with mCPP
impaired ejaculation but facilitated erections in male
monkeys, suggesting an increase in parasympathetic
influence.

Serotonin release also causes sleepiness after ejaculation in males (source):

5-HT is released in the LHA at the
time of ejaculation and promotes sexual quiescence during
the postejaculatory interval

There are many signalling molecules used by the human body that have a different effect depending on the cell type they are detected by and the receptor type they activate.
I would also like to touch on your question about evolutionary benefit. Evolution does not care about you after you have reproduced. As long as an individual reproduces, evolution is "happy". For example, you think falling asleep after sex is counterproductive on the evolutionary scale? What about Mantises where the female will sometimes eat the male during or immediately after copulation. Falling asleep seems like a pretty small thing compared to that (source):

Although the praying mantis is known for its cannibalistic mating process in actuality it only occurs 5-31% of the time. Especially in laboratory conditions of bright lights and confinement, the female is more likely to eat the male as means of survival. "In nature, mating usually takes place under cover, so rather than leaning over the tank studying their every move, we left them alone and videotaped what happened. We were amazed at what we saw. Out of thirty matings, we didn't record one instance of cannibalism, and instead we saw an elaborate courtship display, with both sexes performing a ritual dance, stroking each other with their antennae before finally mating. It really was a lovely display". (7) There is one species, however, the Mantis religiosa, in which it is necessary that the head be removed for the mating to take effect properly. (5) Sexual cannibalism occurs most often if the female is hungry. But eating the head does causes the body to ejaculate faster. (3)

Anything that makes an individual less likely to reproduce will be selected against. Things that happen after reproduction do not affect the survival of the species and will not be subject to selective pressures.
References

E. M. Hull, J. W. Muschamp, S. Sato, Physiology & Behavior 83 (2004) 291 – 307

Arousal does not have anything to do with sex unless you expressly use the adjective Sexual to modify arousal From Medical Dictionary Arousal 1. a state of responsiveness to sensory stimulation or excitability. 2. the act or state of waking from or as if from sleep. 3. the act of stimulating to readiness or to action.

@AMR if you don't know what a word means, look it up in a regular dictionary, not a medical one. Here are a few: 1, 2, 3, 4, 5. Note that every one of them includes sexual arousal as the primary or secondary meaning of the word. In English, with no other context, arousal will always be taken to mean sexual arousal.

@AMR still, your rather aggressive comment urged me to check my guess and change my answer to be based on fact, rather than guessing. Happily, my guess wasn't far off the mark. Thanks.

It is a very small aspect of what neuroscience terms arousal. The use of the word in the context of the quote cited by the OP has nothing to do with arousal in the sense of sex and is used to describe activity during a wakeful state. You are sophisticated enough of a member to know the distinction and instead of pandering to the question you should have correctly described the use of the broader use of the term in a scientific sense and as it was likely used in the context of the textbook.


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Does one neurotransmitter travel all the way through the nervous system?
Nerve impulses of course go really fast, but the neurotransmitters have to travel through millions of nerves, so how can it go that fast?
Is it a sort of relay with lots of neurotransmitters taking over at each nerve cell, or do the neurotransmitters go all the way from A to B?

What sparked your question? Were you reading something? Watching a movie? If so, what? A little background might help me answer it in a way that fills the gap you want to fill. The reason I ask is that your question seems to hint at a subtle misunderstanding about what a neurotransmitter is. Have you read this?

It's beginners level Psychology. I guess they're more like chemicals that aid passing of electrical signals?

You've got a few things mixed up here:
A signal may travel down a pathway, passing through several neurons (e.g. around 4-8). However, this signal is not always in the same form: From one end of a neuron to the other, it is merely an electric potential which travels down the neuron's cell membrane (from the dendrite to the axon hillock, where the cell decides whether to carry the signal on; if yes, a new potential is sparked to travel down the axon).
When the potential reaches the end of a neuron, i.e. an axon terminal, it causes exocytosis of neurotransmitter. The signal has become chemical now. This diffuses through the synaptic cleft to the next neuron, where it acts on ion channels in the membrane to cause a new electric potential.
So the actual distance a neurotransmitter travels is only the distance between the two membranes at the synapse, i.e. the synaptic cleft. This is only about 20-40 nm wide, so it's fairly rapid :)

Huh, thanks! You mention it only being 4-8 neurons. I can't imagine there being so few between, say, the fingers and the spine? How long are these things?

@DarkLightA some are pretty long. In a human body, they can be more than a meter in length.

Wow! I read there are several billion of them? Is this because every nerve ending has its own connection to the spinal chord?

@DarkLightA Yes, that's probably around the number of neurons you have in total in your body. The actual pathway that a single signal will follow doesn't usually comprise that many cells though. Example: pain (e.g. papercut) -> cell 1: sensory neuron from periphery (e.g. finger) towards spinal chord -> cell 2: afferent neuron from spinal chord towards the thalamus in the brain -> cell 3: thalamic neuron into various brain regions (exact number of cells here varies as far as I know) -> result: you feel pain. Could be I forgot the odd neuron here or there in this pathway but that's the gist.

The bit inside the brain could be quite a lot I think, hundreds or thousands even. Plus, a single stimulus doesn't activate just a single sensory neuron, and there are also cross-interactions of adjacent pathways.


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What chemicals can be detected in sweat?
This question came to mind after reading this article. The article speaks of inducing sweating to determine, by a roundabout fashion, the amount of salt therein. I'm no medic but I find myself wondering whether sweat may be used directly to measure any other chemicals secreted by the body.
For instance:
If one's kidney/liver were to suffer some malady would the body attempt to discharge some additional waste through one's sweat
What chemicals may be detected by analysing sweat?

I recently watched a documentary in which a team demonstrated a type of sensor that would compute blood sugar levels from sweat, which was pretty neat. I guess a lot of stuff is leaked out that way.

@Polynomial: Just the kind of answer I hoped to have. If you would post it as an answer I can atleast acknowledge the effort.

Cystic fibrosis diagnosis. Here is a link to a paper describing the use of β-adrenergic sweat secretion as a diagnostic test for cystic fibrosis.
Anti-cancer therapy and its effectiveness. This report seeks to determine the levels of the anti-cancer drug sunitinib and its active metabolite N-desethylsunitinib in sweat.
I'll add others later.
Here's a 2004 study looking at a particularly unpleasant sulfury compound produced by bacteria in contact with sweat. It's interesting that the enantiomer of the malodorous compound had a grapefruit-like smell.
This paper puts forth the idea that sweat, which contains lactate, lactic acid, urea (of course) and amino acids, can be used in forensics.

I can't provide any real technical details, but I recently watched a documentary in which a team demonstrated a new type of blood sugar sensor that could be simply swabbed against sweat. They were trialling it as a non-invasive option that paramedics could carry, for use on unconscious patients as a means of checking for signs of diabetic shock. They mentioned that it only required a minimal sample; a swab of the palm of the hand was sufficient to gain a decent reading.
I'm unsure as to the mechanism of the device - it could well have been direct measurements of sugars or sugar by-products in the sweat, or it could have been looking for other chemicals associated with abnormal blood sugar levels.

What was the documentary called?

I honestly can't remember. I believe it was a BBC Horizon episode, but I may be wrong.


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What causes random long white body hairs?
I'm sure many of you have experienced this - you scratch your back or brush your hand over your arm and find a ridiculously long thin white hair, sometimes as long as 3 or 4 inches. I know a few people who get these quite frequently, and anecdotal evidence seems to suggest they almost grow almost overnight. A quick Google search for "single long white hair" throws up plenty of references to them, and various beauty advice, but I'd like to know the biology behind them.

What triggers abnormal body hair growth?
What causes these hairs to grow so much longer than other "normal" body hairs in physical proximity?
Why are they so thin and white compared to other body hair?

My primary hypothesis is that the hair cell grows rapidly in an uncontrolled manner, similar to how cancer might, and that the unusual appearance is due to the cells being starved of nutrients. I may be completely wrong, though.
I'm mainly interested in humans here, but if more in-depth research is available on animals that'd be interesting too.

I can add that this has happened to me.  I actually hadn't ever heard of it happening to someone, and I thought maybe somehow someone else's hair became embedded in my skin!  I seem to recall it being very long as well--three or four inches in my arm that just showed up one day.

Would this need to be because of "damaged" DNA or could it just be a repressed gene like the "one white tulip in a field of red" phenomenon? I apologize ahead for terminology error.

I beg your pardon for being skeptic, but apparent overnight growth may also be explained by just being unnoticed for weeks or moths. They only seem evident after being noticed, but before that long hairs are not so conspicuous. I can remember finding a long hair, forgetting about it and finding it some days later.

Since it's been so long, I guess a rushed speculative answer might be at least an idea.
DNA gets damaged randomly all the time, and repair mechanisms are in place to fix it. When the damage is too large or of a very complex kind, permanent mutations can develop, and cause disorders such as cells proliferating without control - i.e. tumours.
I could imagine that the same mechanism could result in cells which overproduce keratin (hair) without melanin (pigment), if the associated genes are affected. Considering that trichocytes and melanocytes, the two cell populations at the base of the hair responsible for production, are among the most rapidly proliferating cell types in humans, an increased risk for mutation would not surprise me. I was able to find a few papers on keratin-associated gene clusters by a quick search, but they all seemed to be related to production of fragile hair rather than excessive length.

Melanoma is not the most common type of skin cancer.  Squamous cell carcinoma and basal cell carcinoma are much more common, though with a much better prognosis.

Silly me, thanks for the hint, goes to show the frequency with which a condition is mentioned (or seems to be) doesn't always correlate with its importance.


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Is there a strong reason to be sceptical about the "cured HIV patient" being reported by mainstream media?
There's a story going round the news about a baby that was, apparently, cured of HIV using a cocktail of drugs at an early age. The story piqued my interest, but details seem scarce. One of the main things I've seen being refuted about it is the difficulty in proving that (a) the child actually had HIV in the first place, and (b) that the child is really fully cured.
I've seen the following arguments:

Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.
Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is "cured".

Are these arguments valid? Are there any other reasons to be sceptical about the claims? Any other information that might be useful in understanding the case?

Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.

The mother's T-cells are in the fetus anyways (15/18 Fetal lymph nodes contained T-reg cells). If the mother is infected and left untreated (as was the case with the Mississippi child), then the viral load is going to be high. The chances of it passing to the fetus are going to be high as a result.

Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is "cured".

"Flawed" is the wrong word. The argument is built into the tests. The child was functionally cured - which means below detectable levels instead of "completely nonexistent within the body." Yes, it's entirely possible that the HIV is hiding somewhere in the body and could make a reappearance, but at the moment it's not showing any significant titer in the blood.
I don't think there's been a test developed that can assess the entire body to find the lone viral capsid left.
However - that isn't to say that the "cure" has been found. So far it's a single person cured this way. One. That makes it a case study, not a therapy, treatment, vaccine, or even reasonable assessment that it's possible to do again.

The one that actually makes me skeptical of the use of this is that this "cure" was primarily a massive dose of antiretrovirals used as catchup therapy because the infant's mother didn't have access to prophylactic treatments while she was pregnant and delivering.
Basically, it's a cure that requires you to have access to antivirals very, very near the beginning of infection, and is largely a solution to a problem that is "solved" in the developed world (maternal transmission of HIV is very rare).
It's not a cure that can be extended to the settings where a cure is most desperately needed. So while an excellent proof-of-concept, and a safety net for when someone is poorly served by the medical system? Sure, this is amazing. As some watershed moment in HIV research? Less convinced.


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Are there any neurotransmitters that trigger all neurons?
I'm reading into the basics of the nervous system, and am intrigued by neurotransmitters. I understand that certain neurotransmitters can trigger more than one neuron type, and may be used as inhibitors or regulators (antagonists). Conversely, are there any types of agonists that trigger excitation in all neurons, regardless of type? If so, what functions do these play?

There is no such  promiscuous neurotransmitter. There is always some difference between central and peripheral nervous system w.r.t neurotransmitter usage.
Glutamate is one neurotransmitter which acts as an excitatory agonist in most neurons (but still.. not ALL neurons)


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How does a thymidine block halt DNA synthesis?
The best I've been able to find is that there's a feedback mechanism, but what is this feedback, and how does the mechanism work? If it's just that the concentration of thymidine is too high, why won't excess quantities of other nucleotides do the same thing? (Or do they, and I don't know about it?)

Excess thymidine in a mitotic cell generates negative feedback on the production of deoxycytidine triphosphate from cytidine-5'-phosphate. Excess quantities of deoxyadenosine and deoxyguanosine also block progression through S-phase. However, as a reagent for the control of replication timing, thymidine has been found to work best as its blocking activity can be applied and reversed more consistently.
Xeros N. (1962) Deoxyriboside Control and Synchronization of Mitosis. Nature 194: 682-683.


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Perception of artificial light - flickering
I noticed something strange a couple of years ago. I was walking down the street at night, when it struck me that the street lights were flickering. But, when I turned to take a direct look at the light source it did not flicker any more. In other words, when the light is not the main focus of your eye, it can flicker.
From then on, I started to focus on these flickerings and they are everywhere. Street lights, lights in a house, but also computer monitors or even projections on a screen. Again, the flickering only happens when you do not look directly at the source.
Does anyone have an explanation for that? Is it the brain's fault, or the eye's?

It's difficult to give an exact answer without actually observing the light and performing measurements. I have a theory, though.
Your peripheral vision is hyper-sensitive to changes in light - an evolutionary trait that provided quicker reactions to predators sneaking up on you. As such, even the tiniest fluctuations in light can be registered with your peripheral vision; much more so than your primary field of vision. In this case, it may well have been that the light was flickering very subtly, or at a very high frequency, which your primary field of vision could not pick up. When your peripheral vision was in play, it immediately spotted the flicker.
This is reliant on a principle called the flicker fusion threshold, which essentially states that there is a threshold of various light properties (including flicker frequency, colour, intensity, etc.) at which an eye begins to distinguish a steady light from a flickering one. Research has demonstrated that species who have high rod density are good at picking up flickering, whereas species with low rod densities have a much poorer threshold. Cone density doesn't seem to factor in very much, since flickering is primarily a change of intensity rather than hue.
This transfers into the human eye, since we have a high rod density (and low cone density) at the edges of our retinas, i.e. in our peripheral vision. If you had the eyes of another species (as creepy as that would be) with a high rod density, you may well have been able to detect the flicker quite easily with your primary field of vision.
To directly answer your question - yes, I believe this is primarily the "fault" of the eye, rather than the brain. The brain has a role in identifying the flicker at a subconscious level, in terms of fight or flight response, but the eye is responsible for providing the elevated sensitivity at the peripheral.

Thank you for your answer! I figured the same: the peripherals of your eye is more sensitive. But it's so strange that you cannot see it when you look directly at it. Thank you for your answer +1. Will see what others have to say about it!

I believe this answer is correct; but I think it's worth emphasising that these things are actually flickering. It's not an illusion; if anything the absence of flicker when directly observing is the illusion.


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Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?
Agar is a relatively cheap substance from red algae.  And it contains a saccharide agarose as well as a small amount of pectin.
Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed.  What happens when a gel is run in agar?  i.e. why remove the pectin?
If you can guess, how is the pectin removed?  I know there are enzymes that might do it, but not sure what's really used.

@dd3 has put down a great answer - esp with the figures in the answer!  Would love to see an answer to what the industrial process is like.

The answer to the first part of your question can be found on Wikipedia:

Agar is a heterogeneous mixture of two classes of polysaccharide:
  agaropectin and agarose. Although both polysaccharide classes
  share the same galactose-based backbone, agaropectin is heavily
  modified with acidic side-groups, such as sulfate and pyruvate. The
  neutral charge and lower degree of chemical complexity of agarose make
  it less likely to interact with biomolecules, and, therefore, agarose
  has become the preferred matrix for work with proteins and nucleic
  acids.

This page compares the result of using agar gels to that of using agarose:

The second part of your question: here's a patent, although I have no idea whether this method of agarose purification is widespread.  Propylene glycol purification of agarose does seem to pop up a lot.  I think people who  purify their own agarose use that method, but I am not sure if biotech companies have other methods.
EDIT: it's propylene glycol, followed by ethylene glycol, that is commonly used, but PEG has been used at least once.

thanks for doing this answer!  I looked at similar patents after looking at the one you are pointing to and as late as 1987 they are precipitating agarose with glycols or PEGs... looks good!

You're welcome. It was a good question, and I enjoyed finding an answer.

Using DMSO (dimethyl sulfoxide), agarose can be separated. After heating and stirring around 2 hrs you will get a yellow stiff gel of agarose by filtering.

this is cool! have a recipe?  I'd like to try this!

@shigeta: here is a paper


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What controls leaf senescence in deciduous tree species, and how can I predict it?
If I want to predict litterfall, what data do I need to collect, and what statistical model might I use?
For example, I might use the following coding to record phenological stage every other day, or perhaps once per week:
|value| description
|-----|--------------
| 0   | all leaves fallen
| 0.5 | most leaves fallen
| 1   | no more green in canopy half of leaves have fallen
| 2   | most leaves yellow or red few leaves have fallen
| 3   | noticeable reddening or yellowing, green still present
| 4   | summer condition

Once I have these data, I can also collect weather data. Now, say I want to predict the day on which each of the transitions ($4\rightarrow 3$, $3\rightarrow 2$, etc) occur.
Many studies use a temperature metric of growing degree days $GDD = (T_{max}+T_{min})/2-T_{base}$, but I have also seen chiling days and photoperiod used to predict changes in phenological stage. I would like to develop a function (statistical model) $f$ that would allow me to predict a date of state change from environemental variables, such as $$D_{4\rightarrow 3} = f(GDD)$$
My questions:

what controls litterfall? Is it photoperiod, temperature, other?
do the controls vary by species?
is there a "standard" approach to modelling senescence?

there was a related question on stats.SE (about modeling bud burst) http://stats.stackexchange.com/q/9797/1381

You might check out the R package chillR by Eike Luedeling, and his various papers documenting its use .

One can sometimes notice street lights delaying the annual shedding of leaves in some species (a well-lit branch will be mostly green while the rest of the tree is turning). So at least part of it would be day/night length in at least some species.
I would expect, however, that the answer varies based on species, genus, and/or family, and that there are probably multiple causes at work (one obvious alternate cause being temperature). Just going from memory of my personal observations, years when autumn weather patterns start earlier do tend to have trees turn and lose leaves earlier, so it's not all day/night length.
Drought is also a factor. I live in a seasonal-rainfall part of the world (US Pacific Northwest), and if summer is drier than normal (and normal is pretty dry), by mid-August many of the native deciduous trees will be starting to drop leaves. (Not all of them, but some of them, definitely more than just a few, will be turning and dropping.)

Can you provide some details with references (at least for some species). It looks more like a long comment as it is now.


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Is there any evolutionary/physiological advantage to multi-lateral symmetry?
Just wondering ; I get the impression a large number of multicellular organisms are multi-lateral in their physical structure. Why would evolution/mutation have retained multi-lateral symmetry in an organism? What advantage/s does symmetry provide an organism?
EDIT:
By multi-lateral symmetry I mean at-least bi-lateral symmetry (as in the case of many beings such as elephants, crabs and fishes), but perhaps more than bi-lateral too (starfish come to mind)
END EDIT:

Could you explain what you mean by multi-lateral symmetry or give examples?

Similar to: http://biology.stackexchange.com/questions/5588/why-is-most-life-symmetrical-externally-but-not-internally

@Kevin: Thank you. The question you found is very similar; it didn't appear in my search for 'symmetry' 'physiology' when i looked - hence this question posted.

Signs of symmetry are determined by the environment. Completely isotropic ecological niche corresponds to the maximum degree of symmetry of organisms (spherical symmetry). Asymmetrization on the axis "up-down" took place under the influence of gravity field and lead to radial symmetry. Bilateral symmetry of the multicellular animals arose with movement.

Bilateral symmetry of the multicellular animals arose with movement is there any place where I could read more on that matter?

Evolution works by tinkering, not engineering.  Gaining an evolutionary advantage in a simple way is rewarded, as is simplicity generally.  Symmetry allows for relatively greater simplicity at the genetic information level (modular body parts driven by repeated application of same genetic instructions).  Without symmetry, more genetic information would be needed to construct a similarly complex organism (symmetric like), with the concomitant exposure to increased genetic degradation.


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Number of reading frames in nucleotide sequence
In class of molecular biology was posed this question:
"How many reading frames start in sequence of nucleotides 5' ... ATATGAATGATGACAT... 3' ?"

Please edit your post to 1) reflect your question (I assume it is "How many reading frames begin in the following sequence?") and 2) show what work you have done so far, or your thoughts on the topic.

Every nucleotide sequence has six possible reading frames, because each codon (determining one amino acid) consists of a base triplet (3 frames), and there is a complementary strand which could be coding (3 reverse frames).
To find the possible open reading frames contained in your sequence, you have to look for start codons. That is: ATG. But, as said the complementary strand could be coding. So if your known sequence contains CAT, that would be ATG on the opposite strand and might also be an open reading frame.
Count them now and then read on to compare answers.

Your specific sequence contains four start codons (3x ATG and 1x CAT, which makes ATG on the complementary reverse).
5' ... AT ATG A ATG ATG A CAT ... 3'
3' ... TA TAC T TAC TAC T GTA ... 5'


text:
Can plants get cancer?
I can't think of any reason why plants wouldn't be able to get cancer, but I've never heard of a plant growing a tumor. I've also never seen a plant with a noticeable abnormal growth. Can plants get cancer?

This is touched upon in this answer

This is a similar post.

Yes, plants of all sizes can have cancerous growths.
Agrobacterium tumifaciens, the causative agent of crown gall disease, produces what is called a tumor. See this link for detailed information on these growths. Alternatively, use a plant physiology textbook to look up the above terms. (Here, is where a textbook is better than a single abstract in PubMed.)
I am certain that you have seen such growths on trees, such as this. Other smaller versions can occur on smaller plants - on stems and leaves, for example. The plant builds up tissue around the A. tumifaciens infection in an effort to isolate and contain the infection and its effects.

Are there any examples of cancerous growths without infection, however?

the link is dead.

incidentally, a tumor is just a growth, or even, classically, a swelling (as in calor, dolor, rubor, tumor) . Tumors are not necessarily cancer.

Burls/Burrs are often defined as tree tumours, and as analogous to cancer in animals. There seems to be numerous reasons why burls are formed (more research is needed on the topic), which include wounds, insects, fungi, DNA changes, environmental stress and viruses. However, burls are localized and often relatively benign, and since plant cells do not move around they cannot metastasize (see e.g. "Can Plants Get Cancer?" from the New York Times). Since burls have multipe causes the 'Cancer/tumour' label might not fit very well to all types of burls, and in some cases normal shoots can sprout from burls that have been removed from the tree (indicating that the burl was not caused by damaged DNA).
Galls are related tumorous growths that are usually caused by parasites (insects, virus, bacteria, fungi), and are often induced by plant hormones (at least from insects/mites, see Insect and mite galls). However, in the case of crown gall caused by the bacteria Agrobacterium tumifaciens the tumorous growth is due to a DNA transfer, which will permanently modify the infected cells (Gheysen et al 1987).
As you can see, the answer to your question depends on if you are interested in tumorous growths in general (where many types of burls and galls should qualify) or cancer in particular (if defined as unregulated cell growth caused by permanent DNA damage).

Could not fit in a comment. The following is purely intuitive, I have not much knowledge in this field and no reference. I am just guessing and I'd welcome some corrections. I was thinking about three points which effect opposite each other.
1) In plants, there are no cells specialized in transporting stuff throughout the body (I think!) while there are many cells that travels a lot in animals. Therefore, I0d guess that plants cancer are much more likely to only remain localized while animal cancer are more likely to create metastasis. As a consequence, I'd expect that cancer would be more lethal in animals than plants.
2) The number of mitosis occurring in the lifetime of an individual is probably positively correlated with the occurrence of cancers. Because plants tend to be bigger than animals, I would expect more mitosis in plants and therefore, I would expect that cancer are more common in plants than in animals.
3) According to life history theory, the intensity of selection on a gene decreases as the ratio of the fitness pre- and post- expression of the gene. Because plants never really age and stop reproducing, I would expect that selection against cancer would be stronger in plants than in animals resulting in a less cancer in plants than in animals.


text:
How is instinctual information encoded?
If instincts are passed on through genetics, how is that information encoded in DNA?
For example, spiders instinctively know how to spin webs. Does that imply that the algorithm for web spinning is directly encoded in spider DNA?

related: http://www.physicsforums.com/showthread.php?t=280432

Web spinning in spiders is a complex behavior and probably involves a number of different factors, genetic and environmental. Genetically there are surely many different genomic regions underlying the development and expression of the behavior.
Is the algorithm for web spinning directly encoded in the DNA? Not directly. There is not a single region of contiguous DNA sequence that codes for all the steps involved in building a web. Instead, there is a sequential and parallel developmental process beginning at fertilization (earlier if you include parental epigenetic modifications) - encoded and regulated by the genome and its products - that, without too many errors, generates a viable and fertile web-spinning organism. But the DNA sequence involved in that algorithm is spread all over the genome and includes coding genes, non-coding (ncRNA) genes, and regulatory regions. And the genome alone will not carry out an effective algorithm without proper environmental inputs like nutrition and parental provisions.
The act of constructing a web, when and where, and the design of the web is likely carried out via brain architecture and neuronal patterning, but of course these structures are built based on the DNA-based, developmental algorithm. In that sense, there are many nested levels of algorithms.
One of the best models used for studying behavioral genetics is the fruit fly Drosophila. Many different behaviors have been studied at the genetic and molecular level in Drosophila including courtship, foraging, sleeping, and memory-related tasks. A popular science book on behavioral genetics worth checking out is Time, Love, and Memory by Jonathan Weiner. It details the work of Seymour Benzer and provides a lot of background and easily understood explanations of how genes and their products can work together to exhibit complex phenotypes like sleeping patterns. It includes a detailed (though not up-to-date) description of circadian gene circuitry and how it develops.
At the moment, the best that I can think of for an algorithm directly encoded for by DNA is the sequential activation of HOX genes for animal body plans. But even in this case DNA code does not progress through correct development without other factors.

+1 sound good, do you have any primary references?

Thanks, Abe. If you're looking for some hardcore data, the most interesting paper I've read recently, and that I enjoyed, investigated how innate courtship behavior is modified by learning. Besides characterizing the changes in behavior based on experience, it described the genetics and cell biology that regulates the behavior. http://www.nature.com/nature/journal/v489/n7414/full/nature11345.html

Regarding web-spinning: after a quick search through pubmed, there really isn't much literature on the behavior. The genetics and transgenics of silk production is heavily studied (you may have heard about silk-producing goats), but nothing detailed about web construction. There have been studies on web making by intoxicated spiders. You can find some primary sources from the wikipedia references. http://en.wikipedia.org/wiki/Effect_of_psychoactive_drugs_on_animals


text:
Antibody-antigen database
Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ?
Input : antibody + antigen sequence
Output : quantitative binding/affinity estimate
Many thanks.

great question.. I am also looking for something similar.. actually looking for "Input : quantitative binding/affinity estimate  + antigen sequence Output : antibody"

The binding constant of an antibody-antigen complex remains an empirical measurement.
There have been many efforts to solve this problem quantitatively and qualitatively over the years since the original crystal structures of an lysozyme-Fab complex there are over 400 structures at the www.rcsb.org in a search for antibody antigen complexes.
At this point the general methodology is to model the structure of the antibody-antigen complex.  Then from the complex a free energy of binding is estimated, or more reliably, variants which might bind more tightly can be modelled.
There are tools available to do this work, but they are still far from perfect.  This 2012 paper compares a new antibody-antigen crystal structure against the results of several modeling suites.  In Table 4 the authors show that the invariant parts of the structure as well as some of the hypervariable loops are really precisely modelled, but hypervariable region 3 was way off in this case (rms error of about 2 Angstroms).  Which is not precise enough to calculate actual free energy of binding.
Currently while free energies of binding and therefore estimates of binding constants are not reliably calculated from protein complex structures.  Such software is in practice used to rather compute the relative binding strength of two models (see this 2012 example).
This 2010 paper which describes SnugDock, a newer suite of software, outlines a state of the art antibody-antigen design process (emphasis added).

One could envision a complete computational antibody engineering pipeline starting from the antibody sequence and ending with accurate predictions for optimized antibody-antigen interactions. In this paper we have been successful in reaching the second step by computational docking using computational models of the monomer antibody. The next stages may be additionally challenging. High-resolution complex structures might next be used for computational alanine scanning, computational affinity maturation or alteration of binding specificity. For antibody therapeutics, structures will help define drug mechanisms for regulatory approval, enable epitope mapping and humanize constructs. These applications require varying amounts of resolution and further testing will reveal the full utility of the SnugDock predictions.

As you can see, the method recommended is to create a series of models to try to create tighter relative binding.

Thanks a lot! Do you know any database displaying the empirical measurements you mention at the beginning of you answer ?

Good question - this reference might be a good one for you http://nar.oxfordjournals.org/content/40/D1/D1230.short. Not sure if its still around.


text:
Does the Enzyme Monoamine Oxidase, Isoenzyme A have an allosteric modulatory site?
Does the Enzyme Monoamine Oxidase, Isoenzyme A (MAO-A) have an allosteric modulatory site? I ask because I would like to know if it is possible, in theory at least, for a positive allosteric modulator of MAO-A to be developed.

I think an allosteric modulatory site has already been found, but it's not specific to Isoenzyme A, if that's what you were looking for.
See these papers:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564771/
http://www.jbc.org/content/270/17/9856.full


text:
Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?
I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.
I've found a huge amount of extremely interesting papers about how biological network data is accumulated and how it can be studied.
However, what I haven't found is any examples where the network data was used to make a novel prediction which was later experimentally shown to actually exist.  What are some of the cases where this has happened?

There is very interesting work in this regard done by Ed Marcotte. An overview of the "machine" and its conservation across species is here. The point here is the machine or network is conserved, but used in different ways in different organisms. Hence, the phenotypes of mutants might be different, but they'd be consistent across many variants in the components of the machine.
One paper of his describes a tool, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. This is available at www.functionalnet.org/RIDDLE.
Look at their approach to prioritizing candidate disease genes by network-based boosting of genome-wide association data.
Some specific examples of the conserved "machine" are given in this elegant PNAS paper. It is nice how they tested the genes in Xenopus embryos.

Eric Davidson should be your first port of call for GRN related work!
He published a great paper not so long ago demonstrating exactly what you're talking about. By including spatio-temporal dynamics of gene expression (e.g. differential equations modelling the time scale of gene expression) they constructed a boolean logic based predictive model for gene expression in early sea urchin development. Their results were not only accurate, but actually made predictions about genes that they hadn't experimentally tested...
Check it out:
http://www.caltech.edu/content/modeling-genes-development
and paper:
http://www.pnas.org/content/early/2012/08/22/1207852109.abstract


text:
What in soy are people allergic to and will these allergens be passed along if an animal that has eaten soy is consumed?
I have two related questions about soy allergies and possible reactions.

What is it that are humans who have soy allergies actually allergic to? What is the allergen?
If an animal eats soy, are those allergens broken down or retained? Can the consumption of that animal cause an allergic reaction similar to direct soy consumption?

I think this is a worthy and interesting question. I've rewritten it to try and make to not personally medically related.

There are multiple soy protein allergens.  This has a pretty good review in the introduction.  Here is a list of some of the allergens (same paper).
Chickens on soy diets do lay eggs with higher concentrations of soy isoflavones than chicken on non-soy diets. (Edit: higher concentrations of soy isoflavones are also found in chicken tissues -- see ref 4 below.) References (originally found here) are:

Saitoh, S.; Sato, T.; Harada, H.; Takita, T. Transfer of soy isoflavone into the egg yolk of chickens. Biosci. Biotechnol. , Biochem. 2001, 65, 2220-2225.
Saitoh, S.; Sato, T.; Harada, H.; Matsuda, T. Biotransformation of soy isoflavone-glycosides in laying hens: intestinal absorption and preferential accumulation into egg yolk of equol, a more estrogenic metabolite of daidzein. Biochim. Biophys. Acta 2004, 1674 (2) 122-130.
Lin, F.; Wu, J.; Abdelnabi, M.; Ottinger, M.; Giusti M.M. Effects of dose and glycosylation on the transfer of genistein into the eggs of the japanese quail (Coturnix japonica). J. Agric. Food Chem. 2004, 52, 2397-2403.
Vargas Galdos, Dante Miguel Marcial. Quantification of Soy Isoflavones in commercial eggs and their transfer from poultry feed into eggs and tissues. Thesis. Ohio State University, Food Science and Technology Graduate Program, 2009; http://etd.ohiolink.edu/send-pdf.cgi/Vargas%20Galdos%20Dante%20Miguel%20Marcial.pdf?osu1236706764.

However, I do not know whether this is enough to cause an allergic reaction if consumed. (There's plenty of anecdotal evidence, but no clinical studies that I know of.)

Are soy isoflavones among the allergens listed, though?

@octern: they're not listed, but that table references only the major allergens (as per the authors of that paper, there are around 20, although only 7 are in the table). Hence, my last statement - anything I can find regarding this is anecdotal evidence from not necessarily reputable sources.


text:
Combining gene expression data from two species
I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest associated with each of those genes in the other (the important part is that the genes are identified by the CG number). The second dataset is this study from multiple species where genes are identified by "GLEANR" ID's like this one: "dsim_GLEANR_10060".
I would like to extract all of the values from this study for the D.melanogaster and D.simulans data, then link that to the Annotation ID's in the first dataset (to connect my variable of interest to the sex bias in expression for each species). The trouble I am having is connecting the orthologous genes within the second study to each other, and then connecting them to the CG identifiers in the first study.
Does anyone have any suggestions on resources which can be used to get this all to link up?

This is the FlyBase page for the example gene: Dsim\GD10095. There, you have a section "orthologs", linking to OrthoDB. So my suggestion is: Find the list of synonyms for D. simulans on FlyBase (perhaps here?), download the Drosophila section of OrthoDB, and finally find the 1:1 orthologs.

Thanks, I am looking at this now - I assume each gene has a unique FBgn and their orthologs are identified by the ODB6_OG_ID (?) and the species identified by DROME, DROSI, DROSE... taking just those three variables I can create a data frame of each ODB6_OG_ID in the first column and columns for each species giving its orthologous FBgn ID for each species of interest? But how do I "Find the 1:1 orthologs"?

Sometimes you have a strain-specific gene duplication, which you probably want to exclude to keep things simple. So you can check for each species if there's more than one gene associated with an ODB6_OG_ID, and remove those.

I got this all working after a good ol' fashioned wrestle with R today - thanks a lot for the help!

You could also use biomart for this purposes.
Click on the "ID Converter" tab in the "Tools" section (on the left).


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Can IVF decrease the probability of trisomy in the fetuses of older mothers?
Is trisomy mostly due to complications with fertilization?
If so, does in vitro fertilization reduce the probability of trisomy for the fetuses of older mothers?
If not, can zygotes be screened before in vitro fertilization?

Trisomy is due to non-disjunction in meiosis (the process in which eggs and sperm are created). This happens before fertilization.
Trisomies are more frequently seen in children of older women.  It's not fully understood why this happens, but it is likely related to the fact that the oocytes do not complete meiosis (and become eggs) until ovulation.  Here's an interesting paper that examines the physical causes of non-disjunction, but you might want to read up a bit more on meiosis (depending on your background) before tackling it.
You might screen for nondisjunction, but I don't think it's possible without killing the cells.  See the Wikipedia page on karyotyping, which explains how an amniocentesis might be used for a prenatal genetic diagnosis.  I don't know the regenerative capabilities of the human blastocyst, but if you had enough cells for a test, I don't think the blastocyst would develop normally.


text:
What exothermic reaction distinguishes warm blooded animals?
I would appreciate an answer specifically in the form of an exothermic chemical reaction. Namely, the one primarily responsible for generating heat in warm blooded animals that does not take place in cold blooded animals.

Don't have time for an answer, but see here, where someone asked a similar question: http://en.m.wikipedia.org/wiki/Wikipedia:Reference_desk/Archives/Science/2011_October_2#section_13. If it's not complete, it should at least get you started.

The first link on that page takes you to an explanation.  One reason is that shivering produces heat in warm blooded animals.  In mammals, which have brown adipose tissue, uncoupling protein 1 disrupts the protein gradient in the mitochondria, leading to release of some energy as heat rather than ATP.

Related: https://biology.stackexchange.com/questions/2503/is-there-a-relationship-between-efficiency-of-cellular-metabolism-and-warm-blood

Brown adipose tissue or brown fat is one of the primary ways of generating body heat, and it is only found in warm-blooded animals. It is brown due to the high numbers of mitochondria, and heat is generated by uncoupling the electron transport chain from ATP synthesis by oxidative phosphorylation.
In the typical (ATP-producing) mitochondria, an energy gradient is formed by storing protons within the inter-membrane space, and these then flow through the ATP synthase to power the generation of ATP from ADP and phosphate. In brown fat mitochondria, Uncoupling Protein 1 (UCP1 or thermogenin) forms a pore in the inner membrane, allowing the proton/electron ratio to reach equilibrium and robbing ATP synthase of its motive power. This is what generates the heat.

From Wikipedia

The heat comes from the release of the proton gradient - it's just being changed from electrical energy to heat energy. I don't know if there's a specific chemical reaction going on...

Kind of like why resistors get hot (though with them, it's electron traffic)?

@Pete - Exactly.

While all animals and even plants generate heat from chemical reactions or mechanical motion of their tissues (like muscle tissues), warm blooded animals have brown fat which has the unusual ability to generate heat directly from metabolic energy.
The particular chemical process you are looking for is performed by uncoupling proteins (UCPs).  They reside in the mitochondria and rather than use the proton gradient in the mitochondria to generate ATP, UCPs pass protons through the membrane and generate heat.
Brown fat is brown because of a relatively large iron content associated with many extra mitochondria (brown adipose tissue appears to be derived from muscle cells and not white adipose tissue).  Its a heat generating organ in humans, particularly infants.


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What is the appropriate blender speed to maximize nutrition and digestion of fruits and vegetables?
Blender companies state that a blender for smoothies should have speeds of at least 30000 rpm. They argue that only at 30000 rpm are cells of fruits and vegetables sheared enough to maximize nutrition and ease of digestion.
Would blending at lower speeds, such as 20000 rpm, be sufficient?

Could you explain what chlorophyll has to do with your question?

Sounds very much like a marketing ploy...

You might start by asking the company where they got their numbers and if they have published citations or data to back up their claims. They're making two claims, first that 30k rpm is necessary to shear cells, and second that shearing cells is desirable and improves the nutritional properties of the food.

Related: http://cooking.stackexchange.com/questions/22639/how-important-is-rpm-in-a-blender

@dd3 thanks for editing. Chlorophyll has nothing to do with it

This is better suited for [cooking.se]

I'm guessing that what they mean by 'maximize nutrition' for digestion is that they are assuming that the cells are broken open.  This would make the co-factors we call vitamins, protein and sugars freely available to the digestive system and more easily absorbed.
I think it is a marketing literature claim, though the blender may have some valid advantages... details below.
Stainless steel waring blenders used to be typical pieces of lab equipment which could be used to homogenize tissue to extract proteins or DNA from tissue.  These blenders would typically run from 10k-30k rpm.  The web search for 'cell lysis blender' gives lots of examples of prepping DNA from plants at these speeds, but they don't complain for speeds towards the lower end of the range.  A reputable looking example in my short search: This paper for tomato fruit cell wall preparations doesn't even give a speed the blender might have run at.
Cell lysis in the literature is not precise - the cell toughness, the strength of the tissue around it and other such factors all come into play.  Putting woody stems into your blender and those cells won't really get opened up at all.  Also in the cell literature cell lysis buffers may have detergents or other chemicals (the reference above is done in 50% ethanol) to weaken the cell walls.  Not exactly what you'd want to use if you were making a health drink.
In experiments they have to contend with oxidation that happens when the cells are broken open with all the air whipping through the mixture.  This is one reason you don't see blenders in labs to much anymore - hydraulic presses, sonicators, and bead beaters have taken their place - they have less aeration in the mixture and also deliver more power so that they can break open yeast and bacteria, which blenders really can't.
So there will be some vegetables where the cell walls won't break open and all the nutrients won't be so easily accessible.  It must help to be running at the top end of the range, but there will always be some vegetables which won't be broken open.  For most things like bananas and apples it sounds like you'll get similar benefit with other blenders too.  Just have to think about how much more are you paying for that extra 10k of rpm I guess.
Is there a benefit to breaking open the cells and letting all the nutrients (as well as cell waste) break out into solution?  It might give you a quick pulse of nutrition when you drink, but I'm pretty sure all the cells of a piece of fruit or vegetable will be pretty much broken down and extracted by the end.  On the other hand, it sounds like it will save the digestive system some work...  So there's that question too.

Very nice but... how does all of that compare to the effects of HCl in the stomach? If HCl breaks apart food anyway (which it does...) the advantage of a >30K rpm blender are small or non-existent at all.

you are correct I think. I've read that you actually don't need to chew your food.  Including the action in the intestines, the conventional answer is that the digestive system does eventually break down all the nutrients you take in.    Still, its not completely equivalent - it must be less work for the digestive tract if all the nutrients are in a juice than if you swallowed a bunch of cherry tomatos in their skin.

sure I agree with that, but I was more puzzled by the fact that a 20K rpm blender would be worst then a 30K rpm one...

Probably not a lot worse.  I should have said that I think the differences are marginal, though its reasonable to assume that 30k will get a bit more than 20k. When I say a bit, it might be 80% vs 70% of cells.  Not a big difference with many fruits and veggies.  Most tissue will be liquified nicely at 20k if not completely. Running longer will lyse more cells, but will also heat the sample as well as oxygenate it, which can oxidize the contents.


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Can a sound frequency 'not' within human hearing (20 Hz - 20 kHz) damage hearing when it is of high volume?
We can't hear sounds outside the range of  20 Hz - 20 kHz. However, if an inaudible sound is played at high volume, will one's hearing be affected?

i think i found an interesting reference here... see the linked question


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Chemical structure prediction
I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure with optimal geometry of random small chemicals (say 30 atoms)? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a command line UNIX program which computes mols from formulas.

Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction.
http://www.mti.univ-paris-diderot.fr/fr/downloads.html

Am I reading this right, you have chemical formulas and want to get a set of 3D coordinates (of the energy-minimized conformation)?

@MadScientist yes that's correct but its not possible for all molecules just some

Did you try to use Bioclipse:

Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations.

For the reference, there is also USPEX, which works for a wide variety of molecular and continuous structures (mostly inorganic, though).

USPEX can be used to predict stable crystal structures at given P-T conditions, knowing only the chemical composition (or to predict both the stable compositions and structures, given the element types). USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties.


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Speciation by polyploidy
Speciation can occur by polyploidy. My understanding of the process is as follows:
'polyploidy is when the number of chromosomes in an organism's cell doubles. This means that the organism has more chromosomes than other individuals of the same species, meaning it cannot mate with other individuals. The polyploidy organism then evolves, eventually leading to it becoming a separate species'.
I realise this may not be exactly correct. Is someone able to provide a better description of speciation by polyploidy?

By definition, polyploidy just means that a cell or organism contains more than 2 pairs of homologous chromosomes (or is more than 2n). This is more common in plants than it is in animals. The plant, as shown below, undergoes failed meiosis, which means that the diploid (2n) cells never become haploid (n). As a result, a plant ends up with more than 2n when it self-polinates. The shown result is tetraploidy (4n), but there are other possible results (3n, 5n, etc).

Multiple plants within a population can end up with the same polyploidy number. They can then reproduce with each other but not with the original plants or any other plants. As a result, they become biologically isolated from the original group of plants and are considered a different species. It is a type of sympatric speciation, which means that it occurs without geographic isolation.

In the genus Rhododendron polyploid species are common especially in deciduous azaleas and lepidotes. Yet complete reproductive isolation of the poylpoid species from the closely related diploid species is the exception rather than the rule.
Closely related diploid and tetraploid species interact in natural contact zones to create triploids and some triploids are able to reproduce with both populations.
Hybrid triploid lepidotes seem to freely set small amounts of viable open pollinated seed.
Tetraploid and hexaploid species and hybrids appear to interact even more freely than diploids and tetraploids. Pentaploids are often semi-fertile.
For Rhododendron, ploidy level creates a barrier to sexual interaction but that barrier is not absolute and is sometimes surprising porous. In fact the triploids may act as a pathway in the transition from diploid to tetraploid in that 2x (reduced) X 2x (unreduced) can create 3x and 2x (reduced) X 3x (unreduced) can create 4x. Moreover, C D Darlington established that triploids can throw 1x and 2x gametes so 3x (reduced to 2x) X 3x (reduced to 2x) can produce 4x or 3x (reduced to 1x) X 3x (unreduced) can produce 4x. Darlington documents the historical development of garden hyacinths from diploid species to triploid and then to tetraploids using a triploid pathway.
The development of tetraploid hybrid elepidote Rhododendron 'Countess of Derby' also illustrates a triploid pathway.
One cannot rule out the possibility that the ability of the diploid species to interact with newly created polyploids actually contributes to the creation of the tetraploid species.
The diagram below illustrates how the triploid 'Pink Pearl' has produced diploid, triploid, and tetraploid offspring when interacting with diploids and has produced a tetraploid offspring by interacting with another triploid.

The flow cytometry for this research on the genus Rhododendon was performed by Dr. João Loureiro, Dr. Silvia Castro, José Cerca, and Mariana Castro Plant Ecology and Evolution Group, Centre for Functional Ecology, Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Portugal.
References
Meiosis in Polyploids
by W. C. F. Newton and C. D. Darlington
in Journal of Genetics 1929
The history of the garden hyacinths
by C D Darlington, J B Hair and R Hurcombe
in Heredity 1951
Ploidy level estimations in deciduous and elepidote hybrids of Rhododendron
by José Cerca de Oliveira, Mariana Castro, Francisco J. do Nascimento, Sílvia Castro, John Perkins,Sally Perkins, João Loureiro in Jornadas Portuguesas de Genética, Coimbra, Portugal; 05/2011
Weighing in: Discovering the ploidy of hybrid elepidote rhododendrons
by Sally Perkins, John Perkins, José Monteiro de Oliveira, Mariana Castro, Sílvia Castro,  João Loureiro in Rhododendrons, Camellias and Magnolias, Royal Horticultural Society, Editors: Simon Maughan, pp.34-48 2012
Untersuchung des Ploidiegrades elepidoter Rhododendron-Hybriden by Sally Perkins, John Perkins, Mariana Castro, José Cerca De Oliveira, Silvia Castro, João Loureiro in Rhododendron und Immergrüne , Deutsche Rhododendron-Gesellschaft e.V. , Seite 21: pages 21-42; 11/2013

Can you add the reference (at least) for this figure?


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What is the difference between a circular and a cat's-eye (slit) pupil?
I've been to local zoo the other day and one lizard caught my attention: its pupils are circular, which, I thought, is not usual for reptiles. Turns out it is, but now I can't find any explanation on why some animals have one kind of pupil and others have the other. Lizards can have both, and so can snakes. The only difference I have found is that circular pupil can't shrink quite as much as a cat's-eye pupil, but that hardly explains why circular pupil even evolved in the first place as I don't see any advantage to it.
Ideas?
P. S. Fish only have circular pupils so that shape is older, right?..

Slit-pupil vertebrates are mostly nocturnal. Isn't? may be that allow to pass more light into retina at night?

Circular pupils are always functionally superior to vertical pupils; a slit does not correctly focus light from all directions whereas a circular pupil does. If you observe cats when they're hunting at dawn and dusk*, they have big, circular pupils; it's only when they're in bright light that the pupil shrinks to a slit. So why have vertical pupils at all? Because, as you mention they're capable of letting a more controlled range of light into the eye.
Thus vertical slits let you be active in a wider range of light conditions at the cost of poorer vision in bright light; whilst circular pupils continue to function well in brighter light but at the cost of not allowing such a large range of control over the amount of light entering the eye.
It is then easy to see why you get both kinds of pupil: circular pupils are favoured by animals that are typically active in bright light and need good vision under these circumstances; vertical pupils are favoured by animals that are primarily active in low light but need some ability to see in bright light.
*- it's often stated that cats are nocturnal, this is untrue; cats are crepuscular - that is they are most active at dawn and dusk.

I have thought about it, but don't understand how exactly non-circular hole negatively affects vision. For example: a heavily used сamera  lens can often have a broken iris, which takes irregular shape. The only clearly visible effect of this is the shape of unfocused background lights and other bright points. it doesn't worsen the sharp part of image in any immediately visible way. That's why I've discarded this reason when thinking of pupils.

Your mention of cats hinted that vertical pupils have to do with night vision, and indeed they do.
The retinas of cats and other nocturnal animals are very sensitive to even the tiniest amount of light. This can make their eyes hurt when exposed to bright sunlight. So their pupils have to shrink as much as possible in the sunlight, and, as you pointed out, vertical pupils can shrink more than circular ones.
EDIT: People pointed out in the comments that cats have vertical eye pupils only in bright sunlight. In low-light conditions, the pupils expand to a circle.

It was my first (and only) idea that nocturnal animals have vertical pupils. It didn't confirm, though, there are lots of nocturnal animals with circular pupils. So, not all nocturnal animals have vertical pupils. I didn't think of it the other way, though - all animals with vertical pupils might be nocturnal. Have to check it, thanks. P. S. I am somewhat familiar with photography and the second theory doesn't make sense to me. Depth of field (DOF) is something you only need to be concerned with at short distance.

Why can vertical pupils shrink more than circular ones? Isn't the lower limit on pupil size always 0?

@Kevin: how do you imagine a circular pupil shrinking to 0? Where will pupil tissue go?

The pupil is an opening in the iris, not tissue: http://en.wikipedia.org/wiki/Pupil

@Kevin: I didn't realize... Still, muscular system for circular pupil seems less trivial and more restricting

Your alternative explanation makes no sense: animals with vertical pupils have these pupils expand to circles in low light conditions so the slit is not used during night vision.

I will remove the alternative explanation (which is not mine but a research study I linked to), people come up with many arguments against it.

@VioletGiraffe "Still, muscular system for circular pupil seems less trivial and more restricting." I think you might be forgetting that animals also have sphincter muscles that can pretty much close completely.

In bright light, a cat can also squint, thus approximating a circle with a square-like aperture. So a vertical pupil is not that much of a liability to focusing. The same cannot be said of a horizontal pupil (unless the eyelids are vertical). Additionally, a vertical pupil might optimize detection of horizontal movement, which is likely an advantage in hunting prey on the savannah.

How does a vertical pupil help to detect horizontal movement?

I think I'm in error there. It would be a horizontal slit according to wikipedia on pupil. If someone can confirm, I'll fix my response, or else delete that point.

With more digging, I found contradictory evidence. http://www.graphic-fusion.com/beyondbokeh.htm - so I don't know the correct answer. I am inclined to believe the photography based info more strongly.

@SmokeyVW thanks for the link to the bokeh examples pages. I had the question of how a cat (or a vertical line pupil animal in general) would see and that link showed exactly what I was looking for.

There was a study published this last year (2015) that suggests that the pupil style of an animal is related to its strategy for predation. This means that land animal pupils evolved as adaptations to the niche that they filled.
The study distinguishes between herbivorous, active, and ambush foraging behaviors. Ambush predators tend towards vertical pupils, where as active predators (those that chase down and kill their prey) tend more towards circular. The pupils of herbivorous foragers tended to be mostly horizontally-elongated as is the case with goats. Eyes also tend to be forward set in predatory animals and more at the side of the head in prey animals.
In Why do animal eyes have pupils of different shapes? Banks, et. al. Science Advances
07 Aug 2015: Vol. 1, no. 7, e1500391 DOI: 10.1126/sciadv.1500391 It is suggested that

AbstractThere is a striking correlation between terrestrial species’ pupil shape and ecological niche (that is, foraging mode and time of day they are active). Species with vertically elongated pupils are very likely to be ambush predators and active day and night. Species with horizontally elongated pupils are very likely to be prey and to have laterally placed eyes. Vertically elongated pupils create astigmatic depth of field such that images of vertical contours nearer or farther than the distance to which the eye is focused are sharp, whereas images of horizontal contours at different distances are blurred. This is advantageous for ambush predators to use stereopsis to estimate distances of vertical contours and defocus blur to estimate distances of horizontal contours. Horizontally elongated pupils create sharp images of horizontal contours ahead and behind, creating a horizontally panoramic view that facilitates detection of predators from various directions and forward locomotion across uneven terrain.

Figure 1. Why do animal eyes have pupils of different shapes? Banks, et. al. Science Advances
07 Aug 2015: Vol. 1, no. 7, e1500391 DOI: 10.1126/sciadv.1500391

I see one possible advantage to round pupils. A slit pupil gives higher visual acuity vertically than horizontally because of diffraction and when a slit pupil is very nearly shut, there's high diffraction in the horizontal direction giving poor horizontal visual acuity. A round pupil on the other hand gives a creature the highest visual acuity in all directions for a given area of pupil. A smaller pupil is better for reducing chromatic aberration but chromatic aberration can be pretty much neglected because for any creature with evolutionary pressure for sharp vision in all directions, good accomodation will ensure at least one wavelength of light focuses onto the retina forming a sharp image because the sun emits a continuous range of wavelengths.


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How many nucleotide pairs code one gene?
As I know three nucleotide pairs (triplus) code one gene.  But I have found next information in  the "Molecular biology of the cell" by Bruce Alberts:

Mycoplasma genitalium:  it has only about 480 genes in its genome of 580 070 nucleotide pairs.

But 480 genes * 3 ~ 1500 nucleotide pairs.
Where I have made mistake ?

you said 480 multiplied by 3 equals to 1,500 but it actually equals to 1,440...

Please quote a source for your statements in a question. If you had done so you would have realized that your statement about nucleotide pairs and genes was incorrect nonsense.

You seem to have some confusion, so let's clear things up.
A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.
Each gene consists of nucleotides bound together, which are interpreted by the cellular machinery in groups of three, called triplets.
DNA is first transcribed into messenger RNA (mRNA), which is then translated into proteins.
Each triplet codes for one aminoacid not one gene! In fact genes are not "coded" by anything, they are the code!
Now, what I just wrote is extremely simplified, there are other important details that I omitted, but hopefully it cleared your doubt.
To give you some further detail: not every single nucleotide in a gene will code for an aminoacid. There are regulatory elements such as the promoter of the gene, which allows the enzymes that transcribe the DNA to attach to the gene (essentialy it says: "hey, start transcription right here!"). Similarly, enhancers and silencers can tune up or down transcription of the gene.
In eukaryotes there are big stretches of DNA called introns that are not coding for anything but have big importance for regulating transcription. In fact a single mRNA can be used to code more than one protein, using a process called alternative splicing.
There are also regions of DNA that code for RNA sequences not translated into proteins at all, but which have all sorts of regulatory functions in the cell.

In addition to the above answers, one needs to first understand the difference/relationship between a Gene and the genetic code. The genetic code is written in triplets (3 nucleotides) and one triplet of nucleotides codes for one amino acid (a.a) except the Stop "triplets" or codons(UAA, UAG, UGA in nuclear DNA)
Now since one protein/polypeptide is made up of more than one amino acid and that one gene codes for a specific protein, the gene will be a set of triplets
SUMMARY
Gene = Protein
Protein = a.a + a.a + a.a......
a.a coded for by 3 nucleotides(triplet)
Thus Gene will have many triplets
You can Calculate again now
Knowledge about the process of transcription (formation of mRNA from DNA) to translation gives a better and deeper insight.
Hope that was helpful?
Regards
Lubega Jason (Biomedical scientist; Molecular & Cell biologist)
Makerere University - Uganda

Why are you multiplying 480 * 3?  Do you think every gene is only 3 bases long?
If the average protein length as 500 amino acids, every gene would have on average 1500 nucleotides.  480 genes 1500 bases long = 720,000.  So the proteins of m.genitalium  must be smaller than that on average, but that's realistic.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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What is a "tool strain"?
When a biologist is talking about a genetically engineered mouse strain which is a "tool strain", what does that mean? What is the exact definition of a tool strain? What is the difference between a tool strain and any other mouse strain?
Also, how are tool strains connected to recombinase techniques? Does using a recombinase automatically create a tool strain? Or are the properties "tool strain" and "recombinase containing strain" independent from each other?
If it is important, the context is mouse (and possibly other animal) strains used in cancer research.
It would help if you could keep the explanation high-level. I only have high-school biology knowledge and I am trying to make sense of the requirements for a software application for use by biologists.

It would be helpful if you could quote a section from the instructions to that software because such terms tend to depend on context.

There are no instructions. I am trying to elicit requirements from a single key user who doesn't "get" set theory. She is talking about several types of tumor models and animal strains, and when she tells me of model types A and B, she is not capable of telling me whether A is a subtype of B, B a subtype of A, both are synonyms, or unrelated. Because she is always thinking in terms of concrete data, she cannot generalize it. And when I try to pry it out with focused questions, she starts contradicting herself. Googling has helped a lot, but with the tool strains, I hit a wall.

For what it is worth, she convinced me that "tool strains" and "recombinase strains" are synonyms, and that there are other, unrelated types of strains, like "reporter strains", GE-strains without recombinase, and non-GE strains which may have spontaneous diseases like A/J, or be healthy like FVB/N. Then I found examples of reporter strains having recombinase and concluded that my understanding is wrong. Still don't know whether a strain is considered a "tool strain" in the context of a certain experiment, or whether it is a property of the strain itself.

Is there anyone else you can talk to? :) In my mind, recombinase strains could be a subset of tool strains, as a recombinase like Cre mentioned below is certainly a tool for genetic engineering, there are other "tools" that can also be used.

In extension to shigeta's answer, I could well imagine "tool strains" and "recombinase strains" to be equivalent in the sense that they mean strains of mice whose genome you can easily manipulate.
Cre recombinase is an enzyme which can recombine (effectively insert) genes from a plasmid (which you somehow delivered to the cell) into the cell's genome, if Lox-sites are present (Cre-Lox recombination). This is a very common method of integrating genes into eukaryotic model organisms (i.e. mice).
By tool/recombinase strains they could simply mean mice which express recombinase already, so that you can readily insert your genes into specific cells by delivering a plasmid with the genes on it, and then triggering Cre recombinase in the cells you want to modify in order to integrate the genes into those cells' genome.

Until a better answer shows up...
A tool strain appears to be a mouse strain that is useful for making recombinant mice.  It has genes inserted into its genome to make detection of your manipulations easier.  In this case several phenotypes (luciferase, human SMN) can be observed as well as a tetracenomycin resistance marker is in place so that offspring with the gene can be easily estimated.

These Tg(SMN2)89; Smn1+/-; Tg(SMNΔ7)4299; ROSA26rtTA; "old" Luci-TRE-SMN mice allow high levels of both luciferase and full-length human SMN expression to be regulated by the addition/removal of doxycycline. These may be useful as a fluorescent reporter and/or Tet-On/Tet-Off tool strain for doxycycline-inducible rescue of Type II (moderate) proximal spinal muscular atrophy (SMA).

I have always called those reporter mice...

its a new term to me as well.  Its a big time saver though because you never know when a recombinant mouse gene has bred into a new generation - you'd otherwise have to do a PCR and sequence from each mouse you get.  Now you only need to validate a few likely candidates.


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Batch convert miRNA names to Accession IDs?
Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.
EDIT: both @rg255 and @shigeta have provided solutions to the underlying issue, but I am curious to know if something exists for miRNAs that is similar to a site like this.
EDIT 2: miRNA names are of the form 'hsa-let-7a' and Accession IDs are of the form 'MI0000060'

in what species? this website looks like it will have them http://www.mirbase.org/cgi-bin/browse.pl?org=hsa If you are trying to connect them to data I'd suggest you find the table you want, save it in to a .txt file and use R to match them up.

Somehow, I completely missed that page. Thanks! (If you wanted to post that as an answer, I'd accept it.)

in what species? this website looks like it will have them mirbase.org/cgi-bin/browse.pl?org=hsa If you are trying to connect them to data I'd suggest you find the table you want, save it in to a .txt file and use R (using the merge() function - df=merge(df1,mirbase,by="miR_names") would be a rough guide) to match them up.
Here is a batch converter - http://atlas.dmi.unict.it/mirandola/tools.php - add the text list to box on the right and it produces a table.

Thanks, especially, for pointing out the merge function; I hadn't considered a solution in R.  (The only issue I see is that this particular table doesn't include mature miRNA IDs, but it's a useful list for other reasons.)

@dd3 see added batch converter tool - but could you post an examples of what "miR name" and "miRBase Accesion ID" typically look like so I can tell when I find the right thing. I.e. are you expecting a sequence of numbers, letters, alphanumeric sequence, symbols, a word, a sentence, or (albeit unlikely) an extract from a Shakespeare text... thanks

This is what I meant. I know this wasn't part of my question, but do you have any idea whether something like this exists for mice?

no idea I'm afraid

Well, thanks for all of your work on this question, especially with the repeated edits. (I'll work on making future questions clearer from the start.)

If you want it all, download the mirRNA.xls.zip file from mirbase here:
ftp://mirbase.org/pub/mirbase/CURRENT/
its a spreadsheet that includes these data as columns and also more information besides - for the entire database.

bulk downloads in columnar format are always the way to go :)

That, and Python. I think I make dictionaries for everything.