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What causes the tonotopic organization of the inner ear?
I'm trying to understand why tones are registered in the way that they are in the inner ear, i.e., why are high pitched sounds sensed at the base of the cochlea and low frequencies in the apex? I've been unable to find out the specifics of this tonotopy, but as far as I can gather this is due to the physical properties of the basilar membrane.
But what exactly are those physical properties? Does the basilar membrane vary in size and stiffness along its length, so that each bit has its own resonant frequency, or is there something else going on?

The frequency tuning in the cochlea is due to a number of factors.

The primary factors of cochlear frequency tuning are generally ascribed to the passive physical characteristics of the basilar membrane (BM), which OP already identified in the question - The BM is wider and more flexible at the apical end (low-frequency region) and narrower and stiffer at the basal end (high-frequency region). Like the strings on a guitar, stiff and thin cords produce high-pitched sounds, while loose and thick cords produce low-frequency sounds. The stiffness of the BM gradually decreases from base to apex, while its width gradually increases along that length, thereby creating the gradient of characteristic frequencies of the basilar membrane (Purves et al., 2001) (Fig. 1).
Another factor that may play a role is the length of the stereocilia. Stereocilia are the mechanotransductive hairs that give the hair cells their name. In the inner hair cells (IHCs) the stereocilia are mechanically deflected when a sound wave eneters the cochlea. That in turn leads to neurotransmitter release from the IHC and that in turn stimulates the auditory nerve. The stereocilia increase in length towards the base of the cochlea. Longer stereocilia respond most optimally to longer wavelengths (lower frequencies). Hence, stereocilia length also provides another mechanical gradient that facilitates frequency decomposition in the cochlea (Snow & Wyckam, 2009).
A last factor is more physiological in nature; the frequency tuning of the cochlea is much sharper than can be explained on the basis of the passive membrane properties of the BM. For example, studies in dead cochleas show a shallow tuning of the BM, while the tuning in alive cochleas is much sharper. Hence, it is thought that an active mechanism has to be at play. Generally, the outer hair cells (OHCs) are attributed this function. OHCs start to increase and decrease in length when the BM moves in response to sound. They are thought to amplify the BM response to sound. If these OHCs only amplify a very narrow set of frequencies and not others, they may indeed be capable of sharpening the tuning curve of the associated nerve fibers, but the exact mechanism behind this is unknown (Purves et al., 2001).

Fig. 1. Frequency tuning along the basilar membrane. source: Purves et al., 2001
References
- Purves et al. (eds.) Neuroscience 2nd ed. Sunderland (MA): Sinauer Associates (2001)
- Snow & Wyckam, Ballenger's Otorhinolaryngology: Head and Neck Surgery, John Jacob Ballenger (2009)

To add to Christiaan's answer, the length of the hair cells also changes along the basilar membrane. They are longer and floppier near the apex. There are many levels of mechanical interaction occurring--the basilar membrane vibrates, the outer hair cells change length and articulate with the tectorial membrane which is also moving, the displacement of the fluid beneath the tectorial membrane causes inner hair cells to depolarize, etc.
Also, if you're asking for an ultimate 'why,' high frequencies are more quickly attenuated so it would make sense for them to be represented at the base, right at the point of transduction from the middle ear. Interestingly, I believe the cochlea grows out from that point during development (e.g. the apex moves out/up/around) but low frequency hearing is the first to mature.
Edited to add sources:
Change in length of hair cells, see table 2: http://upcommons.upc.edu/bitstream/handle/2117/26076/MorellUltrastructure2014_final+proof.pdf;jsessionid=82346B40F24139DA94D7217DCA227C18?sequence=9
Discussion of attenuation by frequency: https://physics.stackexchange.com/questions/87751/do-low-frequency-sounds-really-carry-longer-distances
Cochlear growth: http://onlinelibrary.wiley.com/doi/10.1002/dvdy.10500/pdf


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Neuron activity on body parts measurable?
Is it possible to measure the neuron activity on body parts like the back or the arm? Or is this done already?
Of course neuron activity can be measured on the scalp using an EEG. I wonder if similar technology could be used to do the same on other parts of the body.
I know there is EMG which measures muscle activity and  that's also easier to measure as the voltages are multiple orders of magnitude higher. But I imagine that one could get much richer data by directly sampling neuron activity.

To meausure single-unit neuron activity you need to use a microelectrode system, but it is very invasive. How useful the information collected depends on what you searching for. If you interest in neurophysilogy its the way to go, if you interested actual outcomes then the average neural response to stimulus is actually more useful

@SciEnt OK, for single neurons one needs (very) invasive sensors. Can you get any statistically stable measurements when you just attach a bunch of sensors and measure all neurons there at once, non-invasively?

(When measuring EEG you don't measure single neurons either, however with multiple sensors one could measure location based somehow, as far as I understood)

yes, after processing you do get a good stable signal. Computational work uses these neural averages as 'the' signal. In the end synchonicity of neurons working together is what really matters. I have found " Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems " really useful

@SciEnt Thanks a lot, this very much answers my question! I guess I have an interesting read now ;) (If you like to make an 'official' answer out of it, I would mark it as answered...)

To measure single-unit neuron activity you need to use a microelectrode system, but it is very invasive. How useful the information collected depends on what you searching for. If you interest in studying the neurophysiology of neurons its good way to go. If on the other hand, you are interested actual outcomes stimulation then the average neural response is actually more useful.
Computational work often uses these neural averages as 'the' signal. In the end synchronicity of neurons working together is what really matters in achieving higher order functions.
A good book I have found  " Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems " by Dayan P., Abbott, LF., (2005)
really insightful into how brain activity is measured and analyzed. Prior knowledge in Calculus and Statistics will greatly help make sense of the math, but even without it is enlightening.

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Questions about Genetic algorithm paper of Gilman and Ross
I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion  of a regulatory structure that directs flux in a simple metabolic model."  ( The following link leeds to the paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236362/)
I know this is an old paper, but maybe someone here remembers it. I really need the answers of the following questions because the enzymatic model explained in the paper is very important for my master thesis.
First:
The author defines a system of two ODEs but the initial conditions of these ODEs are not printed in the paper. The author just writes: "Initial conditions for the integration are determined by letting the network relax to steady state. " (see p. 1324 on the lower right) . But how is this meant? In this paper the author wants to optimize the mentioned ODEs , so how can I find initial conditions, when there are not all parameters of the ODEs given?
Second:
On the top of page 1324 are two needstate functions defined, called xi_T and xi_F. When I plot xi(F), the plot looks completely different from the one depicted in figure 3b in the paper. So the function defined in figure 3b) must be wrong. Did anyone realize that error and has a workaround for that? Of course I could define my own functions but I want to stay as close to the model in the paper as possible.
Thank you very much for your help.

The first thing, before asking on a random website, would be to see if you can track down the original authors and ask them. It was only published 20 years ago, so there's a good chance they're still alive. First try searching the website of their university, then expand from there. Look up other papers, find old postdocs, see if they know where to find them. Biology is a small world, and people have connections everywhere. With a little earnest work on your part you ought to be able to track them down. Hell, the contact info for Ross is given in the paper, shoot him an email.

@MattDMo Do you really think I didn't already do that?

no offense to you, but given the usual quality of 1-rep "Please do all of my research for me" questions we get, my answer would be yes. If you already have, then congratulations!

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Are any species of life now increasing besides humans?
I see how many species are growing extinct, but what species (excluding humans) are increasing in number?

Chickens. Dogs probably. Lots of others. Even some populations of Tigers are increasing in number thanks to conservation efforts. The question is too big to answer completely. If you have a species in mind then I'd as about that instead.

Yes, many are, especially ones associated with humans and human-generated structures and conditions (e.g., trash, global warming, water nitrification). Some hitchike on subjects of human commerce (e.g., potted plants, tires) and we tend to call them called "invasive species."
Some prominent examples in North America are the European starling, rock dove, house sparrow, domesticated cat, wild horse (mustang), tumbleweed, kudzu, many eucalyptus species, purple loosestrife, garlic mustard, zebra mussel, Argentine ant, fire ant, Japanese beetle, Asian long-horn beetle, Phytophora infestans, etc. One of my favorite examples, and a rather odd one, is the nine-banded armadillo.

(source: sfsu.edu)
Some of these species are increasing in abundance at the cost of other species, increasing the pace of extinction.
http://www.nature.nps.gov/biology/invasivespecies/

You might want to find a slightly more updated graphic, seeing as the 1982 territories are projected. Try Wikipedia.

Sure, but I will not find one this beautiful. Also, the projections held very well.

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Are there known functions of AST, ALT, and amylase in the blood?
A number of enzymes can be measured in the blood or plasma that aid in the diagnosis of certain diseases. For example, patients with particular liver diseases may have elevated aspartate aminotransferase (AST) and/or alanine aminotransferase (ALT) levels in the blood. These enzymes are normally involved in biochemical reactions of metabolism that interconvert amino acids with other metabolic intermediates - that is, biochemical reactions that are common within the liver cell. Also, patients with pancreatitis frequently have elevated amylase and lipase levels, which are digestive enzymes normally secreted into the gastrointestinal tract. During pancreatitis these enzymes are released into the blood, rising and falling with the resolution of pancreatic damage/inflammation.
Pathologically, the tissues that are damaged in these diseases (liver and pancreas, respectively) are the source of the elevated enzymes. In healthy individuals, however, these same enzymes are still found in low concentrations in the circulating blood. What is the source of these enzymes that are found in low circulating concentrations? Is it still those same tissues (e.g. AST/ALT from the liver)? Is this secondary to "normal turnover" of cells within those tissues? Or, alternatively, are these enzymes secreted into the blood to serve a particular function?

For example... There is a freely available manuscript by Arnold and Rutter published in the Journal of Biological Chemistry (1963) that discusses experimental evidence for active amylase secretion from the liver during an isolated liver perfusion experiment. Amylase continues to be secreted, even in the absence of other enzymes that would otherwise indicate liver damage (suggesting that the amylase is intentionally being secreted for some unknown purpose). This is an paper from almost 60 years ago - do we know what some of these enzymes like AST/ALT and amylase do in the plasma? Or are those functions still unknown?

These enzymes, while useful markers of disease, are not only produced during the disease state, and are not only produced in one organ. It is therefore not surprising that there are always low levels released into the biochemical milieu that is the blood. If there are not even low levels of the enzymes then that might indicate that the organ is not doing it's job properly.
I'll approach this from a veterinary viewpoint but I imagine it is much the same in humans. My preferred source for information about veterinary clinical pathology is Cornell's EClinpath site.
The major tissue sources of AST are liver, skeletal muscle, and cardiac muscle. A small amount is produced by erythrocytes. In lesser concentrations it is also found in renal epithelial cells and brain tissue. It therefore should be no surprise that low levels are found in blood. It is not difficult to picture a small amount of leakage from erythrocytes in the normal state, even without pathologic haemolysis, given the regular turnover of cells and permeability of erythrocytes – although I suspect this is a minor source. Just due to the fact that the liver's normal function is to deal with many cytotoxic compounds, even in the completely healthy patient there always is going to be some low level of hepatocellular damage. As a result, a very low serum level of AST might be indicative of a poorly functioning liver (e.g. with a chronic hepatitis).
Among veterinary species there is considerable variation in the clinical usefulness of ALT. For example, it is a very useful indicator of liver disease in dogs and cats, much less so in horses. Much like AST, ALT is also produced in liver, muscle, kidney, and erythrocytes.
Amylase is known to be produced by cells in the pancreas, salivary gland, duodenum, ileum, ovary, and testes. Of course, the pancreas produces the most of this enzyme, which is why it is somewhat clinically useful (though I can't say I like it much at least for veterinary species).
The bottom line is that these enzymes play an important role in biochemical reactions of many different tissues. While the enzymes may be produced in predominance in one tissue, they have the same function (at a biochemical level) in all these tissues (i.e. they convert the same reactions). I view it more as a difference of the tissue need for these enzymes rather than a difference in function between tissues.

Harry - I guess my question bluntly is "is there any evidence that these enzymes (like AST, ALT, amylase) are intentionally secreted from healthy, non-damaged tissues? This is what is alluded to in the JBC article, but I've never heard any evidence for this in my experience.

@Vance I'm not sure, and I couldn't find any studies that specifically track these enzymes from their source in healthy patients. But I guess the point of my answer is that, for example, healthy functioning liver tissue might by definition of its function lead to mild hepatocellular damage and thus AST/ALT leakage. I understand this isn't a completely satisfactory answer so I hope that someone can come up with some numbers for us.


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How does the human stomach handle a mix of digested and undigested food?
As I understand it, the stomach digests the bolus into chyme and then passes the latter on to the small intestine. This process takes between 40 minutes and a few hours.
However, what happens when the processing of the bolus is not completely finished and new food arrives in the stomach?
Will the stomach pass on all the food, including the only partially digested "new food" to the small intestine when the time for digesting the first load is up? Or will it keep all of the food until all of it is completely processed? Or does it have some way of allowing only the processed parts to pass on and keeping the unfinished parts behind, like a gate control?

Stomach has gates- an entry gate (GI sphincter) & exit gate (pyloric sphincter). Stomach keeps on passing some amount of chyme continuously as it gets digested. The new bolus mixes in with food in stomach, until stomach reaches its max (thats when you vomit) ;)

Thank you, @user19099, does that mean that the small size of the sphincter-opening makes is possible for (finer) chime to exit while it keeps the (larger) bolus in? Or how does the stomach "know" what to pass on and what to retain?

Well I'm not expert in this field, but it is related to the small size of the pyloric sphincter due to which bigger particles retain inside while the semi-liquid chyme passes on.

The regulation of emptying of food from the stomach to the duodenum takes place with the help of feedback mechanisms involving the duodenum and stomach.
Nature of the chyme which inhibits stomach emptying by the duodenum:

Excessive acidic chyme.
Chyme contains too much undigested or unprocessed proteins and fats due to which its tonicity and irritability changes.

Regulation by the duodenum:

Nervous regulation:
The enteric nervous system,the vagus and the prevertebral sympathetic ganglia play the key roles in nervous regulation of this feedback mechanism because when food enters the duodenum they provide stimuli that activates them which inturn inhibits pyloric pump.
Hormonal regulation:
Cholecystokinin, secretin and gastric inhibitory peptide inhibits pyloric pump,gastric motility,gastrin effect on stomach emptying respectively.

Thus,when much undigested chyme passes to the duodenum,duodenum regulates if the digestion process should be prolonged or not in the stomach.
Factors promoting emptying of stomach:
Gastric food volume and gastrin hormone promotes emptying by stimulating the enteric nervous system for emptying and enhancing pyloric pump respectively.
Thus, the distinguish between a digested or undigested chyme to be passed to the duodenum or the time for which the food must stay in the stomach for digestion is entirely under the regulation of these factors.
References:
https://www.ncbi.nlm.nih.gov/pubmed/1126597
https://www.ncbi.nlm.nih.gov/pubmed/7943335
https://en.m.wikipedia.org/wiki/Gastrin


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Do clients of cleaner fish queue up?
I can't remember if I saw it in a cartoon, a documentary, or both, but the notion is that the clients of cleaner fish wait in line to be cleaned. "Clients" means the fish (or other aquatic animals) who are cleaned by cleaner fish.
I tried to find a study whose sole purpose is to confirm that client fish wait their turn to be cleaned by cleaner fish, but I only found articles that seem to refer to this while studying other cleaner fish behaviour.
Statements I came across that support the notion:

Most photographs of fish in coral reef are at cleaner stations because the fish are waiting there which allows photographers time to photograph.
Cleaner fish "have a positive impact on local reef fish diversity", which could imply many different fish come and may not attack each other to benefit from the cleaner fish. This one's more of a stretch.
"Others wait no longer than 30 seconds before searching for cleaners elsewhere." The source is German, so I can't go deeper.

Do fish wait in line to be cleaned by cleaner fish?
Side question: Is this an example of reciprocal altruism?


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Identify tropical flower
Can anyone identify this tropical flower? It was found on a vine(?) in a garden adjacent to a rainforest in tropical north east Australia, however it may not be indigenous.

It is a passion flower (Passiflora) Here's a similar one: http://www.kew.org/science-conservation/plants-fungi/passiflora-racemosa-red-passion-flower , but if I am not mistaken there are a lot of species.

Some sort of passionflower (genus Passiflora). They have very distinctive flowers.
Could possibly be Passiflora miniata.


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Making a hole in a tree is okay? Or does it damages the tree?
I am watching a TV series named "Treehouse Masters." What they do is make houses on trees or around it getting physical support from a big strong tree, like this:

But to make the support strong, they make a big hole in the trunk of a tree

Then they put a steel beam into it, like this:

In some cases, they make more than one hole. So, does this affect the tree in any way?
If anyone makes a hole that big or even bigger but doesn't fill it with any other thing(like the beam), will the tree heal itself?
I have heard that trunk is the most important part of a tree. So I am curious to know if this act is cruel towards the trees or not.

Trees don't have nerves or brains, so anthropomorphizing the effects of an action upon them as "cruel" is misguided. Yes, trees can be damaged by injuries that are too many or two large. However, they can also heal quite well if they are healthy overall. While the trunk is extremely important for holding up the tree, the bark and the layers just under it are the most important for delivering nutrients in between the leaves and roots. The inside wood of a tree is avascular, and essentially "dead", so the difference between a 5 cm deep hole and a 30 cm deep hole of the same diameter is small.

It can have a negative effect if parasites are able to take advantage of the holes in the tree.The bark is the first line of defense against parasites and making holes without covering them tend to have a negative effect.Furthermore, the bark also protects the plants against adverse weather conditions.


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Can someone identify this bird? It looks like it has a few deformities

All pictures taken at Lake Roberta in Tampa, FL.
All pictures depict the same bird.
(The wing deformities can be explained by the lake water being slightly highly toxic, but the neck I can only assume to be caused by the Muscovy ducks that live in the lake.)

What does "slightly highly toxic" mean? Just a little bit highly toxic? Sort of toxic? Mildly polluted?

How can ducks make it have an odd neck? What's odd about it?

It's an anhinga, as@kmm commented. There's nothing wrong with it; it's not deformed in any visible (to me) way. They spread their wings to dry, as they are darting birds that do not float on the surface of the water, but beneath it.
Here's one drying itself on a turtle.


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What is the molecule responsible of the yellow color of the Agave americana?
Does anybody know what is the molecule responsible of the yellow color at the edges of this plant?
I noticed also that the new forming yellow part at the begging stage is soft green until it is exposed to light. After the exposition to sun light it change from soft green to yellow(like that of the image bellow).
Does anybody have any explanation?

Xanthophylls, I would guess. These are leaves and all leaves do contain Xanthophylls but the green colour due to chlorophyll dominates. These parts of leaves do not produce chlorophyll.

I think that your explanation is good. But I do not know why this type of  evolutionary adaptation...If there is no chlorophyll but only
Xanthophylls all the yellow parts are useless in therm of photosynthesis, I guess.

Yes. These parts are non-photosynthetic.


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Is there a law that defines an upper bound for the speed of growth of an organism?
I was wondering if there is some biological law (or chemical/physical law for that matter) that limits how fast an organism can grow.
I know that the growth of a plant is often restricted by the deficit of some nutrient (e.g. phosphorous). Phosphorous fertiliser over comes this. However, if one were to give a plant its optimal ratio of nutrient, sunlight, CO2, etc... we could probably not increase its growth speed by a factor of 1000, by increasing the dose.
Why is this?
Is it because of the speed at which cells can replicate? or the speed at which light can be converted into chemical energy? or the speed at which minerals can be absorbed by the plant? or is it just a habit rather than a law?
Is it possible to calculate the upper bound of growth for an organism (or specifically any given plant)?
Please excuse if my terminology is rudimentary.

yes there are growth models but growth process is incredibly complex and there is no single law/model that would universally apply to all organisms. Logistic growth models are used for modelling most populations but they are very simplistic.


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When did death due to aging first appear?
As I understand it, single-celled organisms that reproduce via mitosis essentially live forever. When a cell divides, one cannot say that either one of the new cells "is" the parent and the other the child, neither is older than the other, and we might say that the original cell is still alive as long as either of the cells resulting from the division is. With humans the pictures is very different, of course: we have no trouble telling parents and children apart and no one lives longer than about 120-something years.
When in evolutionary history did organisms stop living forever? Was it with the advent of multicellular life with differentiated cells? Sexual reproduction?

This is a similar question where the asker is confused about the difference between aging in yeast and in multicellular organisms. The comments back and forth got out of hand.

Whilst both a single-cellular and a multicellular both appear to age, this is only a rhetorical similarity. You are defining single-cellular organisms as immortal because the lineage doesn't die; this process occurs for the cells in multi-cellular organisms (we are all directly related to the ancestral cell -the lineage of cells is immortal) but the organism dies. I'm voting to close this question because it's unclear what you're asking given that there has never been an instance where an organism was immortal that mortal creatures evolved from (except that one damn jellyfish).

For the record, this is a good question in the sense that it highlights a common and easy to misunderstanding use of terminology since the media band around "immortal cells" a lot. However the SE Q&A isn't a good forum for ironing out the misunderstanding without a very specific question.

I think both @Roland and James are telling me that when a cell divides, we should consider the two resulting cells to have age zero rather than age equal to that of the original cell. Under this definition the question is, at best, poorly phrased. I suppose one way we might think about the daughter cells' age is by considering whether they inherit any age-related wear and tear from their parent.

(Not an evolutionary biologist, but I couldn't resist :)
I don't think your premise is correct. In (symmetric) cell division, we should consider that the old cell "disappears" and two new cells appear; neither of the two daughter cells is the parent cell, they are both descendants of it (hence the term "daughter cells"). The parent cell is gone. Therefore, at least for symmetric cell division, the lifetime of a cell equals the length of a cell cycle. So cells are not immortal --- only the cell lineage is.
Asymmetric cell division (as in stem cell division, not budding) is more tricky. Here it might seem as if there really is an immortal cell (the "stem cell") generating "mortal" offspring. But I think the situation is really the same as in symmetric cell division: most of the cell cycle mechanisms are identical, and again two new daughter cells are generated, and the parent cells disappears. The asymmetric part is that only one of the two daughter cells are "permitted" to continue the line. Again, the cell line is immortal, the cell is not.
But this is still true in higher organisms: the germline is an immortal line, while the somatic cells are not. So the key difference between higher organisms that have a clear life span and unicellular organisms is the appearance of cells that do not generate offspring, but instead support the cells that do.
I'm not sure there is a sharp transition from single cells to the germline/somatic cell situation. Intermediate cases are found in all sorts of single-celled organisms where certain cells "decide" that it's better to support their (genetically identical) neighbor in some way to rather than divide themselves; these are a form of "somatic" cells. All sorts of community behavior in bacteria and other microorganisms could be viewed in this way. During evolution this behavior has gradually got encoded into the DNA itself, with more and more sophisticated "support systems". Higher animals are really just the latest version of this, where the entire body is really just a support system to ensure survival of the germline.
I would suggest reading Richard Dawkin's books on this subject, especially The selfish gene. They are well written and quite accessible.

I too am not a specialist, but The Selfish Gene is pretty old fashioned and outdated often being referred to as one of the "blunders of biology". Eo Wilson who was amongst the developers of that theory and many others are outspoken on the issue of the "the selfish gene" mistake.

@James Say what? Who refers to The Selfish Gene as a blunder? Creationists?

@Alex I thought this was old news no? There is a large movement of evolutionary biologists, and I'm sure even Dawkins has different views based on new observations. ...also, for different reasons, creationists! From io9 article "To be clear, biologists like West-Eberhard and others are not saying genes and their selfishness aren't important. But they are merely one part of a much larger and more complicated mechanism, which involves inputs from the environment which affect how genes express themselves."

... From the mouth of the horse: https://twitter.com/RichardDawkins/status/408142568468119552?ref_src=twsrc%5Etfw I have read the book cover to cover and there are indeed holes and examples that contradict the model. Paper from the journal of physiology expands on this more than I can!

@James That a model does not explain every single part of reality does not at all invalidate it. I've read the book cover to cover as well, and it's a fantastic book for anyone wanting to learn the core concepts of evolution, even disregarding the selfish gene theory. If you want to call it outdated, a blunder and a mistake, be aware of many bs-filters engaging.

@Alex I used these words because that's what it has been described as by others who are paying closer attention than me. It's a fun book that did exceptionally well, but there is so much we have learned since then. 40 years in genetics is a long time! I wouldn't recommend it as a place to start learning about evolution. Just because it's written by Dawkins does not excuse it from scepticism. Furthermore, being sceptical of Dawkins et al 40 year old model does not make me a bs religious nutter, which could possibly be an accusation inferred from your previous comments :/

Well, regardless of controversy about how "selfish" genes may be, I think Dawkin's book presents the basic concepts in a good way, and in particular explains what "immortality" means in the context of this question. But please feel free to add a more recent reference!


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calculate elimination rate constant
A patient diagnosed with cancer takes antiproliferative drugs. Suppose the intake of drug(dose) is 250mg and excreted amount 125 mg. Amount of excreted drug as metabolites 1 and 2 are 75mg and 50mg. T1/2 is 4 hours. Calculate its elimination rate constant (K).
My idea is : amount actually used from the body is 250(dose) - 125mg amount excreted= 125mg. Which means that we are at steady state. Steady state is reached after 4 half lives (t1/2). Taking this into consideration we calculate 4 k respectively: K=0.693/4 ; K=0.693/8 ; K=0.693/12 ; K=0.693/16

Just posting the exact same question again just because the previous/first one was closed and downvoted, isn't going to help.

You can use this equation to very generally describe the one-compartment pharmacokinetics of a drug:
Cplasma = (Dose*F/Vd)e^(-kt)
Where F is the fraction that is bioavailable and Vd is the volume of distribution of the drug.  These values can be obtained from the Lexi-comp monograph.  If a drug is administered i.v., F = 1.  k in this equation is your elimination rate constant.

Your description of steady state is not correct.  Steady state is reached with multiple administrations of the drug after 3-5 half lives.  We usually assume steady state is reached in 5 half lives.  Here you are only dealing with one administration of the drug and a steady state is never reached.  The drug will be continuously cleared from plasma until Cplasma = 0.  The time that this takes is usually 5 half lives (50% of initial plasma concentration excreted after 1 half life, 75% after 2 half lives, 87.5% after 3 half lives, 93.75% after 4 half lives and 96.875% after 5 half lives).

Without any plasma concentration data, a route of administration, volume of distribution and bioavailability, a proper elimination rate constant cannot be calculated.  Consider the case where an oral drug is only 75% bioavailable.  This means that 75% of the administered dose reaches the plasma and systemic circulation while 25% is cleared initially by stomach acid, digestion, poor absorption from the GI tract, etc.  The elimination rate constant for this drug will be different than for one that is 100% orally bioavailable.


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What type of Gorgonzola cheese fungus/bacteria is this?
I have purchased a gorgonzola cheese and it came with some orange/yellow fungus/bacteria in the cheese's surface. Anyone know what kind of fungus/bacteria it is, and if it's safe to eat?

I highly doubt if the nature of type of fungi can be identified just by looking at it.


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Evolution of the common honey bee's stinger
Has the common Honey Bee evolved a stinger designed for penetrating human skin so it will cause as much damage possible even if it means death? A honey bee can sting other insects and mammals more than just once, but that is not the case when inserted in the skin of a human it will be the bee's first and last sting. http://www.todayifoundout.com/index.php/2014/04/differences-bees-wasps-hornets/
The current form of the honey bee's stinger has evolved barbs. These barbs will cause the bee to lose its stinger in human skin giving the stinger more time to eject the apitoxin and apis virus into the nervous system causing extreme pain and for some anaphylaxis a severe allergic reaction.
Question- With the information and references I have provided, is there evidence that the Honey Bee's stinger has evolved specifically to be more effective against humans?

[citation needed] what is your evidence that a honeybee's stinger is most efficient in penetrating human skin? Also remember that evolution works both ways; human skin may not have great evolutionary pressure to ward off bee stings, whereas something like bear's fur may be under a stronger pressure

Bees sting all sorts of animals to defend their hive/territory - birds, dogs, rodents, bears, moose, etc.

@MattDMo-can you name a animal allergic to bee stings?

I thought they were really awful at stinging us, no? Their stinger get's lodged in our gooey skin and they rip their guts out trying to escape! I imagine they're more aimed at damaging insects and just so happens that a swarm can even deter larger animals if needs bee. tehe!

@user5434678 - a five second google search shows that dogs can be allergic to bee stings.  Your premise seems flawed.

@User- can is a another word for possibility.Your google link is eralevent to my question.

Anaphylaxis isn't really that relevant for dissuading a predator; they could do a lot of damage before it kicked in. It's the pain of the sting that drives them off. Presumably we can agree that bee stings are painful for animals other than humans?

The answer to the question "has evolution designed the common Honey Bee's stinger solely for stinging man-kind?" is no.
A honey bee's barbed stinger remains in the skin of any mammal afterwards due to its elasticity (skin closes back around the base after penetration) but can be retracted after stinging another insect. It isn't a human-specific thing. Presumably this is because it takes more toxin to dissuade a mammalian predator than an insect given their size. A little dose of toxin is released straight away but in order to deliver a dose large enough to irritate a large predator the venom sac needs to remain attached. The resultant damage kills a sterile worker bee but removes an attacking predator that could do much more damage; it is a strategy that confers a selective advantage.
The reference you cited  doesn't appear to say anything about other mammals, just other animals, so this doesn't actually contradict your other source. Insects are animals too!

"Stingers in bees evolved from ovipositors", here is a good reference of how bee stinger have evolved.
http://www.askabiologist.org.uk/answers/viewtopic.php?id=4021

The defense of the honey bee, having a barbed stinger which continues to pump venom even after the bee is swatted away by the intruder, (be it a human or a bear or other animal), is called "sting autonomy." When defending against a large mammal, the more stings the more likely to have an impact.
The reason the honey bee colony can afford to lose many guard bees in this manner is that they are a highly social species, called eusocial, or truly social (the highest level of social structure). The colony typically has 10s of thousands of members, and the queen is constantly laying eggs to replace lost workers, which usually only live 4-6 weeks, in normal summer activity.
Only the social bees are likely to sting you. Most bees are not social. The honey bee is the exception, so most bees will not sting you (if you can even find them). There are 3600 other species in the US besides honey bees, (which represent one, single species). And furthermore, honey bees will not sting you unless you approach or open their nest, (or grab one in your hand, or crush one) which is unlikely to happen accidentally. They will not attack you unless they are defending their nest- never at a flower! I doubt you have ever been stung by a honey bee, as most people confuse them with yellow jackets, which are not bees, but social wasps. The yellow jacket also has a barbed stinger but much smaller barb (and a much more defensive temperament), so it may or may not get stuck in your skin.
You can read all about stinging insects in the wonderful book, The Sting of the Wild, by Justin O. Schmidt.
Bee Well! - Carl the Beekeeper (Cornell University Master Beekeeper)

Welcome to Biology.SE! We could certainly use expert help with answering questions about insects, but please note that answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). That allows non-expert users to learn more and to verify your answer — also, since we have no way to verify your identity this is important for distinguishing truth from opinion. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site and then [edit] your answer. Thank you!


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What is a cognate enhancer sequence?
What is a cognate enhancer sequence?
While reading a paper (1) presented at a journal class in graduate school, I encountered this sentence:

HIF-1 binds to its cognate enhancer sequence, the hypoxia-responsive
  element (HRE), and induces the expression of various genes related to the adaptation of cellular metabolism to hypoxia (the switch from oxidative to anoxic respiration),16 escaping from hypoxia (invasion and metastasis of cancer cells),17,18 improvements in hypoxia (angiogenesis)19,20 and the resistance
  of malignant tumors to chemo as well as radiation therapy.

(1) Is Wikipedia's definition of an enhancer correct for this case? Then does 'cognate' mean "related to, tending to be found together", whereas "sequence" means there's a chain reaction that occurs?
Y Zhu et al, "Involvement of decreased hypoxia-inducible factor 1 activity and resultant G1–S cell cycle transition in radioresistance of perinecrotic tumor cells" Oncogene (2013) 32, 2058–2068

Cognate means of common origin.
In molecular biology, cognate is used to refer to known interacting pairs of functional entities. For example, cognate receptor of a ligand means the primary (default) receptor with which this ligand interacts. Similarly, cognate sites (which also includes enhancer) of a transcription factor (TF) refers to the well known and validated binding sites of the TF.
Also see this post.

I disagree. Cognate, as used in biological science, does not mean "of common origin", it just means related. See my answer to a later question.


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How to feed bacteria out of lab
I want to take a sample of skin infection bacteria (I suppose combination of staphylococus, strep, etc) and give it to the doctor for analysis but the appointment is in two weeks. The bacteria will be dead by then, right? Is there any home-made nurturing solution that I can put them in to preserve them until then?

Depends on the bacteria. You can inoculate the bacterial cells in a sterile isotonic solution like saline and store the sample in the fridge (4⁰C). The cells will survive for 2 weeks.

Do you have sterile swabs with which to take the sample? Just a regular cotton swab won't work.

The problem that stands out the most is will a clinical lab even bother running tests on a patient-procured sample, and second to that, would the results be valid?

Thank you everybody for your answers. Then I can give it a try by extracting the crust that contains liquid on the inside with sterilized tweezers and try to preserve it in saline in the fridge. I hope that the lab will accept it cause the alternative is no sample or me going to the emergency for a pimple since I will never manage to synchronize the doctors appointment with the random moment that it decides to re-appear every time :P

In a lab there are so many ways of doing this. However, at home is a little tricky. This is what I would do:
Keep your bacteria in a liquid media.
Liquid Media: make the media out of NaCl and AS CLEAN AS POSSIBLE (distilled if possible) water (concentration 18g NaCl / L). Place a sample of the bacteria into the solution. Freeze solution with bacteria (-20 degrees C if possible). Take out when wanted.


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clades on a tree - biopython
Suppose we have an alignment. When a phylogeny tool (PhyML in this case) is used on this alignment, a tree consisting of 5 clades is returned.
The thing is: suppose we have this alignment on a web site, and some user uploads a new sequence to add to this alignment. After realign with the new sequence, phylogeny inference is applied, and then, a tree visualizer.
I'd like to know which one of the 5 clades contains the new sequence (if any), without the need of looking at the tree.
How should I approach this issue? I think that first of all, I should define my clades (how to?), and then, measure distances from my new sequence, to all clades, and keep the one with the shortest distance...But I'm not sure if this is a good strategy (not to say I'm not sure how to accomplish this..)
This is maybe more of a concept question...
I'm working with biopython.

Welcome to BiologySE... thanks for your question. Do you think this is more of a programming question? If so, you may want to ask it on another SE site. Also, check out the help page for tips on how to ask a good question - you may want to edit and/or revise what you have to improve it. See this link: http://biology.stackexchange.com/help/how-to-ask

You could decide to just insert the new clade next to some "closest" one ("closest" being defined in a clever way that remains to be devised), but it is possible that the result will be different from what you would obtain by reconstructing the phylogeny from scratch. The reason is that the information that the character combination in the new clade brings may alter the relationships between the other groups present in the data in a newly optimized phylogeny.
An example of application is that one typically wants to add more taxa in a phylogeny in oder to prevent long branch attraction.
As an aside remark: When one speaks of a "clade", one usually thinks of a bunch of terminal taxa (leafs of the tree): do you want to insert an whole bunch of taxa forming a monophyletic group, whose internal topology is already known, or just one terminal taxon?


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Enzootic vs Epizootic?
I'm studying microbiology and I see these words - epizootic and enzootic, often but there are no clear explanations for them online. Can someone help please?

Analogous to endemic and epidemic.

I can't believe I didn't see that before! Could you please put that as an answer so I can credit you?

Enzootic and epizootic are analogous to endemic and epidemic, respectively.
Enzootic means something that affects a population of non-human animals  in a limited spatio-temporal region whereas epizootic is relatively more widespread.
Endemic and epidemic are more general terms and do not, technically, apply to only humans.


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How does sodium ion increase blood pressure?
So I have been reading about the RAAS system and I was wondering how  natrium (sodium ) ions increase blood pressure.I have been looking up on the internet and have yet to find an answer.Help

Sodium acts on the juxtaglomerular cells of the kidney, which are then activated to produce and secrete renin. Renin hydrolyses angiotensinogen into angiotensin I. Next angiotensin converting enzyme (ACE) converts angiotensin I to angiotensin II.
Angiotensin II is the product that causes the increase in blood pressure, because it is a potent vasoconstrictor. With peripheral vasocontriction the heart has more resistance to pump blood against, thus higher blood pressure. Additionally, angiotensin II stimulates secretion of aldosterone from the adrenal glands, which acts on the distal tubules and collecting ducts in the kidney to retain sodium and water, thereby increasing blood volume and thus blood pressure.

Image: RVC 2008
This pathway is one reason why ACE-inhibitors, such as benazepril, enalapril, lisinopril, or perindopril, are used to treat hypertension (high blood pressure). With less activity of ACE, there is less angiotensin II, and blood pressure goes down. Hypertensive patients are told to consume a lower sodium diet because that will lead to less activation of the JG cells in the kidney, which will eventually result in less angiotensin II, and thus lower blood pressure.

This is a thorough answer, and I like the graphic. However it's a DROP in sodium that is detected by the macula densa that ticks up RAAS. That's the whole point of the system: since water follows salt the two parameters usually have a high degree of correlation and a drop in sodium suggests a drop in blood volume. Thus the need to kick up AT2 to keep the blood pressure up when volume is low.

The increasing of the concentration of sodium ions in blood would attract water from the surrounding tissues, because of the osmotic pressure.
The increasing of the total volume of blood(it has adsorbed water) makes the blood pressure higher.
That is why in summer the blood [pressure decreases]. In  fact, sweating makes us lose body salts, so the volume of blood decrease and so the pressure.
http://www.bloodpressureuk.org/BloodPressureandyou/Yourlifestyle/Eatingwell/Salt
http://www.medscape.com/viewarticle/489515

"I guess" is not an acceptable supporting citation for an answer. Please support your claims with links to the relevant primary literature, or at the very least from secondary sources that cite primary ones, such as Wikipedia. I'm very interested in particular to see supporting evidence for your claim that blood pressure decreases in summer.

Please add a reference that can be accessed (ideally through PubMed). The one from Medscape cannot be accessed.

This answer was expected at our high-school chemistry exams.

Your body removes unwanted fluid by filtering your blood throught your kidneys, the extra fluid is eliminated in urine. Basically the kidneys uses osmosis to draw the extra water out of your blood, using a delicate balance process of sodium and potassium. When you eat too much salt it increases the sodium in your bloodstream than wrecks the delicate balance, reducing the ability of your kidneys to remove the water. So the blood preassure gets higher due to the extra fluid and extra strain on the delicate blood vessels leading to the kidneys.
Here´s a link to help more : http://www.bloodpressureuk.org/microsites/salt/Home/Whysaltisbad/Saltseffects


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map list of proteins into an already built network
I have a built reliable network which can be downloaded from here
http://www.filedropper.com/mynetwork
This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example
set1: Q9Y4Y9, P62310, Q9Y4Z0
set2: Q9Y333 ,P62312, O15116
set3: Q9Y4Y9, P62310
set4: Q9Y4Z0, Q9Y333, O95777, P62312
set5: O14497, P51532, Q8TAQ2, Q92922, P60709, O96019

I want to know if it is possible to map the above IDs to the built network? I don't mind using another algorithm, or software , only the result is important
Thanks

There are markup languages used for describing the network. They have the mapping and the network viewer loads the network file written in the markup language. You have to add more details; as it stands the exact question is a bit unclear.


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How common is it for environmentally occurring bacillus strain to contain some sort of plasmid?
I am designing a method for testing whether two new bacillus isolates, that are ionic silver resistant, store the silver resistance mechanism on a plasmid or on the chromosome of the bacteria.
In my method, after I do a plasmid extraction on the bacteria, I want to use nanodrop to see if plasmids are even present in the bacteria (if no plasmids are found, then the silver resistance mechanism must be stored chromosomally). After this, I want to use heat shock or electroporation to place the plasmid in a silver sensitive bacteria, and see if the newly transformed bacteria is ionic silver resistant (this would suggest the resistance mechanism is stored on the plasmid)
I have been looking at how other people have tested for this, and I have found that the nanodrop part is not done. I thought the nanodrop would be a good control to make sure the plasmid extraction went well, and if plasmid DNA was not found, it would save me from doing the rest of the experiment.
One reason why I thought they didn't do nanodrop was that perhaps most environmentally occurring bacillus contain plasmids, and thus nanodrop would be unnecessary step.
So my question becomes how common is it for environmentally occurring bacillus strain to contain some sort of plasmid? Also, if anybody has any suggestions for improvment of my method, please let me know.


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What's this insect?
Found on my indoor egg plant. I also have aphids, spider mites, and psyllids on it, and am hoping it's a predator like a ladybug larva but the colours are wrong. It's about 6 mm long. Found in New Zealand.

We can't identify anything if you don't give us your exact location. "China" is not specific enough, "southern Beijing city" is fine.

The photo isn't very good, but I'm almost sure that's a hemipteran (a planthopper, leafhoppter, depends on the type of hemipteran, I can't say). And it seems to be a nymph (a imature individual).

As Lfppfs said it seems to be a nymph of planthopper, Dictyonissus griphus.

This website has more pictures. If you are interested you can find fully formed (matured) Dictyonissus griphus.

Nice picture, looks very much like mine.

It usually has a long fibrous white tail, as you might have seen from the rest of the pictures I linked. I wonder what might have happened to its tail.


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What chemicals/substances exist in green capsicum (peppers) that do not exist in red capsicum?
I have known 3 people in my life that have incredibly adverse reactions (one called it an "allergy" and his symptoms did resemble such) to consuming any form of green pepper (capsicum) but have no problems with red peppers (also capsicum). Besides the obvious chlorophyll -- which I rule out since none of these friends had issues with green vegetables -- what else is unique to the green peppers that could possibly cause such reactions?
My limited understanding is that green and red peppers (at least with bell peppers) are actually the same peppers at different stages of maturity. If that is true what changes within the plant during the maturation process?

You mean chilli peppers, right? Peppers are actually a totally different species.

Thanks for asking, I will clarify the question. Capsicum includes both chilis and bells, as did/do my friends' problems.

@VanceLAlbaugh if you will note, in the question I wrote "red peppers (also capsicum)"

Why all the down votes on this question? What is wrong with it?

There are no down votes.

@WYSIWYG. My alerts are showing a -40 points for this question with no explanation. If there are no downvotes then what caused the -40 points?

There cannot be -40; that would require 20 downvotes!! or reversal of 8 upvotes. Neither of which seems to be the case. You have given a bounty of 50 points. Those 50 points get deducted from your rep. You got 2 upvotes i.e. 10 points. So the net rep change on this question is -40.

@WYSIWYG -- Doh! Of course it was the bounty. Sorry but it just didn't click. Of course you can see why I was so concerned about what I thought was 20 downvotes. :P

Your limited understanding is indeed correct - the different colours indicate different stages of maturation, even though different colour cultivars exist (e.g. some that remain green even if fully ripe).
It is known that the different maturation states have different vitamin and/or mineral concentrations (see here or here). This indicates that different biochemical pathways are active and that therefore the enzymatic set-up is variable during pepper maturation (which could have an effect on tolerability as it might also affect other plant components).
Moreover, you are right that the green colour is - at least partially - caused by chlorophyll but also non-green bell peppers often have chlorophyll (Lancaster et al., 1997) but that probably is not the cause of your friend's responses.
More likely the cause is 3-isobutyl-2-methoxypyrazine (IBMP) which gives the characteristic (green) pepper smell and has highest concentrations in green peppers (that's why it is called green pepper smell). It has one of the most intense odours that can be detected at very low concentrations, even within the complex odours of wine (Pickering et al., 2007), according to Roth, 2014 perhaps even below PPT concentrations.
So how does this fit together? Pickering et al., 2007 also suggest that one should determine 'consumer rejection thresholds' for methoxypyrazines, indicating that it might be repellent to some people even in low concentrations of 1-2 ng per litre. This could explain your friend's aversion but evidence for the allergy component is dubious.
I did find one paper (Jensen-Jarolim et al., 1998)  about allergen expression in peppers (birch allergy like). However, no green-specific allergens are reported, and it even seems like green peppers would be a better choice to avoid these allergens.

Thank you. Very interesting about the odors. I am reluctant/cautious to use the term "allergy" myself, just passing on what one of my friends called it. His reaction to an accidental ingestion of a tiny amount (undisclosed odd ingredient in a potluck dish at a social event) was rapid onset of significant respiratory distress and intense nausea to the point of needing emergency medical intervention. I only observed one such incident but he advised there had been a few prior incidents over approx 50 years.

@O.M.Y: That sounds quite weird, yes. But well, there are rare or unheard/unthought of allergies and now you know that there are green pepper-specific (or at least enriched) substances. So who knows ... Maybe your friend should have that checked.

It actually is 3 friends/aquaintances I've known through the years who have had this problem so it is not unique. All of them have consulted doctors, one has consulted an allergy specialist and had the whole "grid-of-pins-on-the-back" test. They tested positive on a whole range of usual's like shellfish and strawberries but also on odd items like vinegar, nutmeg, olives, and alcohol. Another friend (not one of the 3) has a weird allergy to real gold, makes their skin inflame soon after contact (but no reaction to other metals). Yes, they have been tested by a doctor also.


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Reason behind using inducible promoter for heterologous expression
Protocols often seem to use regulatable promoters when expressing a heterologous gene in a host like yeast where they add something like IPTG to induce expression from (say) the lac promoter.
Is there a reason to do this as opposed to using a constitutive promoter? i.e. Is there reason to think that regulatable (inducible) promoters have higher expression levels than constitutive promoters?
In other words, what utility is there in having an external "switch", i.e. the IPTG to turn on expression on-demand rather than just boost the default expression level using a promoter not requiring induction?
The goal here is small biomolecule synthesis by industrial fermentation of a transgenic yeast.
Example Protocol:
L21 Star™ (DE3) E. coli cells (Invitrogen) were co-transformed with the plasmids pACYCDuet-4506 and Ct94-pETDuet and transformed cells were selected on carbenicillin (50 μg/ml) chloramphenicol (34 μg/ml) LB-agarose plates. Single colonies were used to inoculate 5 mL LB medium with 50 μg/ml carbenicilin and 34 μg/ml chloramphenicol. The culture was incubated overnight at 37° C. The next day 2 mL of TB medium supplemented with the same antibiotics were inoculated with 0.2 mL of the overnight culture. After 6 hours incubation at 37° C., the culture was cooled down to 28° C. and 1 mM IPTG, 2 mg/mL mevalonate (prepared by dissolving mevalonolactone (Sigma) in 0.5N NaOH at a concentration of 1 g/mL and incubating the solution for 30 minutes at 37° C.) and 0.2 mL decane were added to each tube. The cultures were incubated for 48 hours at 28° C. The cultures were then extracted twice with 2 volumes of ethyl acetate, the organic phase was concentrated to 500 μL and analyzed by GC-MS as described above in Example 3. In these conditions sesquiterpene production above 200 mg/L was routinely achieved. Beta-santalene was produced.

This sounds an awful lot like a homework or quiz question. As such you need to show your effort to answer the question. Please refer to Biology S.E help center for information and policies on asking questions on the site. These links, http://biology.stackexchange.com/help/how-to-ask , http://biology.stackexchange.com/help/on-topic , and http://biology.stackexchange.com/help/dont-ask are particularly helpful.

@AMR I'm not sure why you think this is a Homework question & I'm also not sure how to convince you that it is not. In any case, if it helps I am working on a feasibility study to industrially manufacture a 250 MW secondary metabolite which is currently only available as a plant extract. The wild type gene responsible has been sequenced. The native expression is low, <50 mg/L mostly because of bottlenecks in making FPP the precursor & FPP-sinks via Squalene.

Inducible promotors are a useful tool especially in experiments where the inserted/altered gene may needs to be suppressed at first. Consider an experiment where one wishes to investigate a putative Alzheimer-inducing gene in a model of old age. When you insert the exogeneous/altered gene, you may wish to suppress expression up until the point where your animals reach a sufficiently old age to mimick geriatric patients developing Alzheimer symptoms. Another example is where one uses genes that are lethal or induce gross developmental changes in utero when expressed during development.

@Christiaan Makes sense. I was just wondering about my industrial fermentation use-case where all I want to do is maximize the yield of a secondary metabolite.

Heterologous promoters often express genes that are toxic to the organism when expressed in too high quantities. When the genes are expressed constitutively, the organism will either grow slowly or die before they reach a high density suitable for production of the protein.
As such, it is not about expressing the genes all the time, but expressing the maximum amount of gene product over the shortest period of time. It doesn't make sense for the cells to express the gene product all the time, if they can't reach sufficient densities first. More product will be made if the cells are allowed to grow to a relatively high density, then inducing expression on all of them. This would allow relatively large production levels in a short period of time.

Perfect! This explanation makes a lot of sense. This is exactly the part I was missing in my understanding. This totally justifies using induction.


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what do I need to use for protein protein interaction network
I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with another protein and a relationship
YAL011W YBR231C 0.804967
YAL011W YDR190C 0.790977
YAL011W YDR334W 0.840367
YAL011W YDR485C 0.815874
YAL011W YJL081C 0.574536

or sometimes I only see this
YAL011W YBR231C
YAL011W YDR190C
YAL011W YDR334W
YAL011W YDR485C
YAL011W YJL081C

what do I need to make a network ? and which structures normally used for making these networks.

What does PPI Stand for? Google UK suggests Payment Protection Insurance.  Please avoid abbreviations in titles and define them in questions.

@David sorry david , it stand for protein protein interaction

If you are asking solely about data structure, the two data formats that you have given are essentially the same. Each row represents a PPI, so in a network a line (edge) will link the proteins (nodes) given in columns one and two. Column three is an edge score, but it can indicate a few things,  confidence in the interaction or strength of the interaction. Your network will for a single central node with 5 nodes linked to it in a wheel shape.
PPI networks may also be represented in Proteomics Standards Initiative Molecular Interaction XML Format. This provides a controlled vocabulary for programmatic access to data.
The choice of data structure, there are many, is yours but simple formats (as above) are often sufficient. It is important to be mindful of the meaning of the network, are the PPIs directional? Do you have estimates of interaction (edge) confidence? Do you have estimates of interaction (edge) strength?
Cytoscape will allow you to visualise a protein-protein interaction network (PPI) such as the two that you have given. The Bioconductor project provides a number of options for the visualisation and analysis of PPI networks in R.
If you want to create or build a PPI network from a single protein or list of proteins then Cytoscape, and possibly plugins such as Genemania, can also do that.
String is also useful for building PPI networks. The developers have focussed on a wide-range of species and their data export options will allow you to see the same network in a variety of data formats.

your answer was great , I really appreciate it, Let me ask you a question, I have identified a list of proteins lets say 100, then if i go the String , it gives me a network, but I have no idea how it is built. Lets put it in this way, would you mind to give me a small example of if one has (as an example) 10 proteins ID, how he can reach to a network ? I already liked your answer , thanks

It's somewhat complicated but the creators of String have published a number of papers which describe how the  database was assembled. If you want to know about individual interactions clicking on an edge provides that information.

I have read many of them, I think it is like a black box, they normally work with physical interaction but not easy to understand :-) . can you give me an example using Cytoscape then ? do you know what I want to know? I want to know how to make the structure ready to be used for PPI network . this is all what I want to know .

If you are viewing a network on the string webpage clicking on the evidence pane below the network window provides a basic description of each evidence type. If you want a file of interactions to work with; Tables/Exports > "as simple tabular text." will provide a file that can be imported into Cytoscape, the first two columns are your interactions, import those first. Cytoscape provide good tutorials. Have a try and maybe ask another specific question if you get stuck? Goodluck.

ok thanks, I asked as a second question http://biology.stackexchange.com/questions/48624/how-to-make-many-cluster-in-one-figure


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Is there a difference in the energy produced from the hydrolysis of GTP and ATP?
Is the energy produced from the hydrolysis of GTP greater than/less than or the same. I know that GTP can be converted to ATP through a pathway and so my thinking was that GTP would be less.

The base attached to ribose has, I guess, negligible effect on the stability of the third phosphate. So, I guess the energy released should be the same. Still looking for valid references.

As @WYSIWYG said in comments, there is no effect of change in nitrogenous base on the third phosphate. Why? Simple, they are too far to directly influence each other's stability. See the diagram (of ATP) below from wikipedia:

and of GTP from here:

What one can clearly interpret from these diagrams is that there would be no effect on the energy released by hydrolysis of the third phosphate by the nitogenous base present. It will remain -30.5 kJ/mol(1) in both cases.

You are almost certainly correct, but you do not cite an experimental value of the free energy of hydrolysis of GTP to support your statement, which I think is required. (And not so easy to find.)

You are correct, there is (probably) no citation for it. I'll  search for it tomorrow when I'll  be free :)


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Can a cleaved plasmid "close" without exact matching "sticky ends"?
Say if you have a multiple restriction site and use two restriction enzymes on it to cleave a plasmid, can it recombine with ligase?
My concern is that without the small sequence of nucleotides that were in between the two restriction sites, the two ends of the plasmid won't stick and anneal. Would it work if the two sticky ends are almost the same in sequence – two bp off instead of all five?

The plasmid won't religate efficiently if the ends are not compatible.  However, it's possible that very rarely your plasmids may re-ligate, perhaps because of a tiny level of contamination with exonuclease that trims back the ends to be blunt.  Or there may be spontaneous blunt breaks or other strange events.  This may happen in a tiny fraction of the plasmids, one in millions, but since your transformation step selects for circularized plasmid very efficiently you may end up detecting it.
Note that these rescued plasmids are often aberrant since they are unpredictably trimmed at the ends or otherwise followed a non-designed path to circularize; this is not something you want to count on for your cloning, it's an annoying byproduct that you want to avoid.

As I expected and much appreciated


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What is the evolutionary advantage of having pubic hair?
Only humans have pubic hair. What is the evolutionary advantage in having it?

Not true. As far as I know marsupials have pubic hair. (e.g. Macropus eugenii)

I have no evidence, but it would provide a visual cue about maturity and fitness to potential mates.

Many consider pubic hair to be a sort of protection or warmth, however this can only hold true for the vagina, since pubic hair doesn't offer any additional protective advantages to the male urethra. The most prevailing theory is that simply it is one of the odor producing parts of the body and humans (like most life forms in general) are simply aroused by strong smells. Also most odour producing parts are usually accompanied by hair in order to "catch" pheromones. It is notable that those odours are not the direct product of glandular secretions, as those secrations are in fact odorless. It is their combination with bacteria that gives every person a unique smell. This unique smell gives a lot of important information to the canditate sexual partner. Here is an interesting study about odour importance in sexual reproduction as well as the role of MHC(Major Histocompatibility Complex)
If you are interested you can read further for for the Importance of smell in sexual production

So in short the pubic hairs catch pheromones that combine with bacteria to give potential sexual partners information. But what is the evolutionary advantage? Are you saying that this applies to other mammals too, but since they tend to have a lot of hair all over their bodies they don't need special hairs by their genitals as humans have got?

There isn't a definite theory as to why pubic hair exists.The evolutionary advantage -if any-is exchanging information. The study explains this very thing. Individuals strongly prefer a partner with smell different than theirs.This leads to MHC-heterozygous offspring, which in turn means they are better protected against a wider range of parasites. Still, like no one is completely sure what is the significance of pubic hair. Most likely it is simply catching pheromones.

And as to why swe are the only animals having pubic hair, we are one of the few hairless mammals, so we need some areas covered with hair. Most probably this area was selected because it was warm and close to the genitals (so strongly linked to sexual activity).


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Can anyone identify this dragonfly spotted outside of Boston, MA?
Can somebody identify this dragonfly please? It was seen about 15 miles west of Boston.

This dragonfly? I see two of them, one eating the other.

Yes...I interrupted lunch for the greed darner. Not sure what the other one is, you really can't see it.

It is a male Green Darner.
Pretty common in general, especially in the US.


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Can RNA be extracted from tissue suspended in formalin?
There are two tumor samples floating in a 10% formaldehyde solution (i.e formalin). Is there a protocol for RNA extraction under these circumstances? I am concerned that using the protocol for Formalin Fixed Paraffin Embedded (FFPE) tissue will damage the RNA, since there is no paraffin for the xylene to remove.
If I were to use the FFPE protocol without xylene, should I homogenize the tissue before removing the formalin, or after?

Can you please link to or describe in detail this FFPE protocol that you're referring to?

@MattDMo It is the RNeasy FFPE Kit mentioned in WYSIWYG's answer.

Formaldehyde forms adducts with RNA and can also make it more susceptible to degradation. It can also cause crosslinks to form between RNA and proteins (or possibly other RNAs). For all these reasons extraction of high quality RNA from formaldehyde fixed samples is very difficult and the yields are low (Howat and Wilson, 2014).
Have a look at this article by Evers et al. (2011) which explores optimal conditions for removal of the formaldehyde adducts. However, this study does not involve actual RNA extraction from fixed tissues, which would be even more difficult.
RNeasy FFPE Kit from Qiagen claims to be specially designed for RNA extraction from formaldehyde fixed samples. The product description says that the lysis buffer contains substances that reverse the modifications formed because of formaldehyde. There is a similar kit from Thermo-Fisher. Russel et al. (2013), report that the RNA yield was similar between fixed (using Qiagen RNeasy FFPE kit) and unfixed samples (using Qiagen RNeasy Plus mini Total RNA extraction kit).

should I homogenize the tissue before removing the formalin, or after?

Homogenize after removing formalin. Since the tissues are already brittle because of formaldehyde fixation, you need not use harsh homogenization procedures. Pipette gently. You can use proteinase-K and DNAse to remove proteins and DNA respectively (RNeasy kit involves these steps).
For future experiments, you can store the tissues in RNAlater solution (Thermo-Fisher; or similar formulations from other vendors/lab). Store one part of tissue in formaldehyde for IHC/ISH and the other in RNAlater for RNA/DNA extraction.

If I recall correctly, the RNeasy FFPE kit is designed for extracting RNA from formalin-fixed, paraffin-embedded tissues; however, I've heard that it works fine for just formalin-fixed tissues, skipping the deparaffinization step.  I haven't tried it myself, though


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Are there diseases for which a placebo treatment is state of the art?
I was reading about the placebo effect, and I wondered if there exists or ever existed a disease with the following properties:

There are no known treatments for the disease that perform better than a placebo.
The placebo has a positive effect on patient outcomes.

If there is a disease like this, what do doctors do? Do they give out prescriptions for sugar pills because the pills will do better than nothing?

The ethics of knowingly providing a placebo are iffy.  There was a study once of placebos for asthma, or something like it.  Some patients reported feeling better, but objective measurements of lung function showed they were not.  That misconception could have been dangerous for the patients.

psychosomatic or imaginary ones. comes to mind.

I'm voting to close this question as off-topic because it is not about biology in terms of SE Biology but about medicine or medical ethics.

I agree this can be moved to Medical Sciences SE.

I'm voting to close this question as off-topic because this is not a question about biology in terms of SE Biology but a question about medical practice.

Doctors sometimes use "open-label placebos" - substances that have no known physiological effect on the treated disease, but have been associated with symptoms improvement in some studies. Open-label means doctors openly tell people it's placebo. The example is treatment of irritable bowel syndrome.
Doctors use not only fake drugs, but also real drugs as placebos. There are some doctors who don't have a courage to say they don't know how to help, so they just prescribe "something" (a real but ineffective drug) in the hope they will convince someone that they provided some help.
Prescribing "placebo treatments": results of national survey of US internists and rheumatologists (BMJ, 2008)

Prescribing placebo treatments seems to be common and is viewed as
  ethically permissible among the surveyed US internists and
  rheumatologists. Vitamins and over the counter analgesics are the most
  commonly used treatments. Physicians might not be fully transparent
  with their patients about the use of placebos and might have mixed
  motivations for recommending such treatments.

There is a common practice to prescribe:

Vitamins or antibiotics for common cold, flu and other viral infections (Montana DPHHS ; JRSM Open)
Antipsychotics, antidepressants and sedatives for personal problems that can't really help to solve those problems
Various drugs for fibromyalgia

The seeming effect of placebo can discourage a person to seek for the real treatment.

This may be a valid comment on the “common” behaviour of some doctors but does not answer the quite specific question regarding specific diseases and “state of the art” which I assume means recommended treatment in this context.

Treatment of depression, fibromyalgia and irritable bowel syndrome is typically treated with various drugs, even when there is insufficient evidence about their effectiveness, so they are placebos in this regard - even if doctors who prescribe them disagree. So, for the mentioned conditions using placebos is the state of the art.


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Is every protein encoded by just one gene?
Beadle and Tatum proposed the “one gene, one enzyme” hypothesis in the 1940s, and this was later modified to “one gene, one protein”, i.e. that one gene codes for one protein.
Have any exceptions to this emerged subsequently? Are there single proteins, parts of which are encoded by separate genes?

don't forget that one gene can can code for multiple proteins... splice variants https://en.wikipedia.org/wiki/Alternative_splicing

@VanceLAlbaugh But are there proteins that emerge from more than one gene instead of parts of one?

@VanceLAlbaugh Is it possible that two adjacent genes melt together and are expressed if as they are óne gene?

The short answer to your initial question is yes. There are many examples of proteins that are the result of the expression of multiple genes. Hemoglobin, immunoglobulins, microtubules made of different tubulin subunits, etc. As for the other question, that is less prevalent in eukaryotes. It is not unheard of for bacteria to express operons as a single RNA, though ribosomes usually translate individual proteins. Viruses are known to do this. HIV's genome is translated from a long RNA that contains multiple genes into a single polypeptide which is then cleaved post-translationally.

@AMR There is a single gene that codes for a polyprotein, not multiple genes. After proteolytic cleavage multiple proteins arise. This is an example of one gene, many proteins and not the vice-versa.

@WYSIWYG "During viral maturation, the virally encoded protease cleaves the Pol polypeptide away from Gag and further digests it to separate the protease (p10), RT (p50), RNase H (p15), and integrase (p31) activities. These cleavages do not all occur efficiently, for example, roughly 50% of the RT protein remains linked to RNase H as a single polypeptide (p65)." http://hivinsite.ucsf.edu/InSite?page=kb-02-01-02#S2.1.2X

@AMR I didn't deny. But this essentially means that they are encoded by a single gene. There is no dispute there, I believe.

@WYSIWYG  you are mistaken. gag and pol are considered to be distinct and independent genes from one another. Both are genes that encode for polyprotiens. They are expressed together as they are transcribed in a single RNA, are translated as a single polypeptide chain, and then are post-translation ally cleaved by HIV proteases. Not my definition, just what virologists and geneticist shave characterized.

@AMR that's what I said. gag is a gene that codes for a polyprotein that gives rise to multiple proteins. That is one gene many proteins. Are you saying that gag and pol are transcribed together as a single RNA and so they should be considered one gene? That's more like a polycistronic RNA. BTW, gag-pol is also a gene in itself and there is a gag-pol polyprotein. I haven't yet read HIV gene expression in detail but I know it is a bit complex.

@WYSIWYG it was only addressing the question in the third comment "@VanceLAlbaugh Is it possible that two adjacent genes melt together and are expressed if as they are óne gene?" And I answered initial that you would not find it in Eukaryotes, but can see it in viruses. I am not saying they are one gene, but would fit the description of two genes being expressed as if they were one gene and then the translated product of those to genes, itself a single polypeptide chain is posttranslationally cleaved into the relevant gene products.

As this has come up again I have edited the question and provided an original reference to the idea.

You may be interested in trans-splicing.

There are proteins encoded by more than one gene.
It would be a heterodimer protein of quaternary structure. One famous example would be haemaglobin, which is assembled from alpha and beta sub-units.
Also, one gene is capable of coding for multiple proteins!
https://en.wikipedia.org/wiki/Protein_dimer
https://en.wikipedia.org/wiki/Protein_quaternary_structure
https://en.wikipedia.org/wiki/Hemoglobin

Though hemoglobin is not a dimer as your answer seems to imply.

As I had modified the question I had to clarify the "yes" in your answer.

I'm surprised that one gene is capable of coding multiple genes, which brings to mind a question I'm gonna ask now.

Generally speaking the answer would seem to be:

“No, a single polypeptide chain is encoded by a single mRNA from a
  single transcript of a single gene.”

Obviously if one uses the epithet, protein, for a hetero-multimer like haemoglobin, one could say yes instead.
So far, nothing new since the question was posed two years ago. But, at the risk of being shot down in flames, let me suggest two possibilities.
1. Immunoglobulins
The vast diversity of antibodies arises not from the fact that there are a vast number of immunoglobulin genes in the genome, but that there is a repertoire corresponding to different sections of each antibodody chain, the recombination of which in individual B-cells gives rise to different genes. See, for example, this section of Alberts et al. As far as the precursor cell is concerned, the mature immunoglobulin chains are the products of different genes. As far as the mature individual B cells are concerned, each chain of their gene products arise from a single recombined gene.
You pays your money and you takes your choice.
2. Metalloproteins
Let us consider the metalloprotein like urease. This enzyme, which breaks down urea to ammonia and carbon dioxide, requires Nickel to function. One can adopt the standpoint that the protein is not complete without the metal cofactor. The genetics of urease has been well studied in certain pathogentic bacteria like Helicobacter pylori, where it is part of a gene cluster. Other components of this gene cluster encode proteins required to deliver nickel ions to the inactive enzyme.
One could argue that without Nickel the protein is incomplete, so that functional urease is encoded by multiple genes of that cluster.
Depends what rules we are playing.

There are protein complexes which are made up of multiple subunits.  Whether you call that one protein or a multi-protein complex might depend on whether you have a gene-centric or protein-centric point of view.

Not really. A protein is a single polypeptide chain. There are many proteins that exist (sometimes solely) as a part of multi-member complexes, but those complexes are never referred to as proteins. They're called protein complexes, even by very "protein-centric" (your phrase) biochemists.

Now, there have been cases where a complex was initially thought to be a single protein, and named as such, but further research showed it contained multiple subunits. But after the new knowledge is disseminated, one wouldn't keep referring to the complex as a protein.

@MattDMo What is meant by subunits? Doesn´t every protein contain them?

@descheleschilder - ask a question as a question post, not a comment.

@MattDMo You are kidding, right? from Lehninger Principles of Biochemistry; protein: A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by polypeptide bonds. quaternary  structure: The three-dimensional structure of a multisubunit protein, particularly in the manner in which the subunits fit together. Hemoglobin is a protein... and its subunits come from distinctly different genes that encode the polypeptides that make up the subunits of the protein.

I would say the distinction is functional and structural. A polymerase holoenzyme has subunits that perform different functions and could be considered a protein complex. A nuclear pore complex is structural and provides a substrate for interactions with other proteins that creates a selective barrier into and out of the nucleus as well as creating directionality in nuclear transport. The subunits of hemoglobin or the light and heavy chains of immunoglobulins work together to produce a particular function so those would be considered more proteins than true protein complexes.

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


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Damselfly identification
Can somebody identify this damselfly? Found near a stream about 15 miles west of Boston.

I would have called that a Blue Darner, but apparently that's been a local Missouri name and not a real name this whole time, so I don't know what the real name would be. It was even called Blue Darner on the official FFA entomology exams.

It be an Argia anceps, but the shade of blue is a little off. The pattern of black marks looks close though. Wikipedia points out that many damselfly species have very similar appearances.

@user137 is it September 19th already?

@arboviral What does September 19 have to do with it?

@user137 https://en.wikipedia.org/wiki/International_Talk_Like_a_Pirate_Day ("It be [...]"). :)

@arboviral You mean you don't talk like that every day?

Just got word from a biologist from State of Mass......“Violet Dancer” (Argia fumipennis)

It looks to me like a male Argia fumipennis violacea

Some additional details, reason(s) for why you think it's a male, and an embedded image would be good to see in your answer. +1 if you can do this. Thanks.

The damselfly in question belongs to the subspecies Argia fumipennis violacea. The species as a whole are referred to as variable dancers, however, this subspecies most commonly goes by "violet dancer".
As mentioned in another answer, this is in fact a male, which is most easily observed by the overall purple body color, as well as the blue accenting on the end segments of the abdomen. In contrast, a female will have a brown body color; both male & female have wild black markings throughout the abdomen, and transparent wings. Consider the following for comparison.

Female on left; male on right.
And then, a general image to match the one you provided:

Found near a stream about 15 miles west of Boston.

Differing from most other genera within the family Coenagrionidae, dancers are generally found along moving water, so this sounds spot on. They seem to live quite comfortably around your area, however, according to this illustration, they aren't well documented within MA itself.

(Source)


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Do any non-human species have packed abs?
The classic "six-pack abs" in humans is due to tendons stretched across the abdominal muscles and low body fat. Do any other animals have a similar arrangement of tendons that could result in visible "n-pack abs" for a sufficiently low body fat individual?

Most animals are quadripedal and therefore their abdomens are generally not exposed. Perhaps the tendinous intersections required for the abdominal flexibility required for a bipedal posture. See here.


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Can ants survive a plane ride?
I just came back home a few hours ago from the airport and my aunt had peaches in her car full of ants. This made me wonder if the ants had joined us from the plane?
This leads to the question can ants can survive at high altitude?

mind that your title question differs from the final question. Surviving at high altitudes is not the same as surviving a plane trip. Conditions are very different.

It depends on the altitude of the plane, species of ant, flight length, location in hold, and more, but generally yes, they should be able to survive. At such locations that a plane flies at, the temperatures range from 0 to -50 degrees Centigrade. At such extreme temperatures the ant's entire body system is brought to an almost complete stop, where their heart is barely beating, and nervous system barely functioning other than to tell the heart to beat, and other normal involuntary actions. This means they won't need to consume as much oxygen (because their slowed brain won't need as much) allowing them to survive with the minimal oxygen in the atmosphere.

But only jet planes fly in that altitude. Propeller planes fly low. Considering that the plane was transporting fruits, I don't think it would have allowed the temperature to drop to such low levels (that would have ruined the fruits). Regarding oxygen: I guess, since ants thrive in deep underground holes, they can tolerate low oxygen levels.

You have a point, but the same would apply on a smaller scale in a prop. plane, correct? @WYSIWYG

Isn't the pressure and temperature in the cabin controlled to some extent?

There are several problems with the question, which prevent a clear answer. For example, the ants were perhaps most likely colonizers from the vicinity of the car and not plane. Specifically, it's unlikely that you transported a whole colony in a single peach (even if you got a queen, it would be a fairly slow process). Next, it's unclear if you mean crevice/outside of the plane, or inside the cabin (see comments above). It would also be helpful to tell which flight locations and species (roughly) were involved, in the case of cabin transport.

Yes @Luigi But they were in the hold, not the cabin


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Why are bald heads so "shiny"?
Why do males with baldness have  shiny skin on their head, whereas we don't experience such "shiny skin" in other parts of body without hair.

There are products to put on your head to make it more shiny.

I always thought that bald people put some clear polish on there heads

Think of what happens when you don't wash your hair for days. It gets oily and greasy. This oil-like substance on your hair is called sebum and mainly works as a lubricant . The Sebaceous glands responsible for excreting sebum don't stop working when the hair follicles attached to them do. The result is a "shiny" head.

Actually people "shine" there heads on purpose. There are products sold for this.

Some do. Their bodies either doesn't produce enough sebum or they want a more "shiny" look. A slight shiness is natural in any bald head though.

Do bald people not wash their heads frequently?  And why is my chin not shiny if I shave regularly?

@jamesqf Well you have made an excellent point and it has really made me reopen this question. This sebum theory is good but incompletely explains the question.

I have seen many people who keep washing their head as well but still have "shiny" head. It doesn't explain it fully I am afraid.

Washing your head every single day dries it out, hence triggering the excessive production of sebum instead of hindering it.

It’s due to fibrosis. Men with androgenic allopecia suffer from chronic inflammation of the scalp. Male pattern baldness is a poorly understood disease, but what most people don’t know is that it’s an auto immune skin condition. The hormone DHT appears to trigger a cascade of events leading to inflammation and fibrosis This results in a build up of scar tissue, I.e. fibrosis that gives a swollen and shiny look to the scalp. Scalp fibrosis results in reduced blood flow and hair follicles shrinkage and eventual death.  https://perfecthairhealth.com/the-ultimate-hair-loss-flowchart-why-we-lose-our-hair/
You may not realize it, but claims that bald men’s heads are shiny due to sweat and grease is quite insulting to people suffering from an embarassing and irritating auto immune disease. It’s just an uneducated guess in the truest sense. An attempt to explain something without having done any research into the subject. Armpits are usually sweaty and produce oils but are never shiny.

Interesting answer. Can you please add some references to it?

Welcome. Please refrain from shooting at other answers and focus on writing a good answer by providing sources to your claims.  I've toned down your answer a bit.

Skin produces a material called Sebum which is naturally shiny, on skin with hair much of this is absorbed by the hair. In addition the skin over the top of the head is very smooth and fairly taunt because the skin does not undergo much flexion. Smooth surfaces are shiny, skin on a bald head is often smooth and taught (which makes it smoother) which makes reflectivity more even which makes it shinier (glossier) . Smooth taught skin and sebum oils and waxes contribute to being shiny, so even if say your face is not normally shiny the above combination makes the skin on the head shiny. Drying of the skin can also contribute.
Note how people in with uncommonly smooth and hairless skin any large smooth taunt patch (like the thigh or cheek) will also often be shiny (glossy) unless they use makeup.


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Calling Alterations in Exome Data
What are the main technical differences between accurately calling somatic point mutations vs copy number variation (CNV) in exome data? Side note: would you need other -omic data to accurately infer CNV (exome data isn't enough)?

Exome data can be used to determine both somatic point mutations and copy number variations.  The limiting element for the power of detection for both is read count (how many reads per gene).
Exome data:  Exome data uses a reference (for a trio, that would be parents; for cancer, that would be a paired normal sample from blood or non-invasive tissue) in order to determine if a certain point is mutated or not.  Next-generation sequencing is prone to sequencing errors, so having a high enough read count is essential to properly calling a somatic mutation.  Even so, issues with highly repetitive sites can make this difficult.
Using exome data for copy number is happening a lot nowadays.  The number of reads is used as a proxy for how many copies exist, and the balance of alleles at any given gene tells you whether there has been loss of heterozygosity.  Of course, with exome data, you aren't getting truly genomic data.  But there is enough coverage using the exome to pick up the big events.
CNV data: Copy number analysis is now conventionally done using a high density SNP (single nucleotide polymorphism) array.  These are designed to be biallelic, and come in two types.  First are the copy number SNPs, which are designed to give the best information about copy number.  Then there are the genotyping SNPs, which give information about loss of heterozygosity.  Often, SNP array data is higher quality, but this is determined by your platform.  Newer platforms have extremely high coverage of the genome and can allow you to really pick out focal changes.
These arrays, based on manufacturer's recommendations, are not meant to be used for somatic mutation calling.

As far as bioinformatic pipelines, you can use similar tools for each.  For example, the Aroma package in R has pipelines for both Exome & SNP array data.  GISTIC 2.0 from Broad can be used to find focal copy number changes.
A word of caution: It is always best to validate what you find in one platform with another.  I recently worked on a paper that used both Exome sequencing and SNP array data to determine copy number.  Using GISTIC, there were no focal peaks that matched.  The broad chromosomal trends were the same, and that's what the group reported.

Thank you, really nicely worded and clear. As a follow up, would RNA seq data help clear up some of the confusion associated with highly repetitive exomic data, potentially by comparing matched normal and tumor transcriptomic data? Would using DNA microarray data help you infer copy number variation also?

Expression data only tells you about expression (transcription) levels, not necessarily inherent copy number.  However, there is a relationship.  It depends on the scientific question.  RNA data is VERY useful additional data, because it allows you to connect gains or losses with transcription level changes (which may arguably be more biologically interesting)!

My understanding is that DNA microarrays (such as those used in CGH) give copy number information but not LOH information, and therefore don't give a full picture of what's going on.  For example, you can have 2 copies, but have lost one parental allele (and thus duplicated the other parental allele).  This wouldn't show up in CGH, but does using SNP array data.

Right - it sounds like you would need to combine the DNA microarray data with whole exome or genome data to get that connection. 2) Thank you so much!! Would you mind upvoting?


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mtDNA sequencing error rates
What is the method to estimate the error rate in mtDNA sequencing?
E.g. we are given a profile like this:
16069T 16126C 73G 152C
Is there a method, a table of known values, or any other way to say that there is an x% chance of 16069T being incorrect?
I'm asking because I would like to have a method to estimate the probability of the profile being incorrect. Something like:
Perr = Perr(16069T) X Perr(16126C) X Perr(73G) X Perr(152C)


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"Genotype structure"?
What does a geneticist mean when they write "genotype structure", e.g. the sentence "...represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal."
Citation: http://bioinformatics.oxfordjournals.org/content/28/14/1811.long

Please [edit] your post and add a citation to where you read this. Context is very important.

Sorry about that @MattDMo

The line can be found in the Results subsection of the Abstract in the second sentence @MattDMo