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What is the IC50 exactly?
I am reading the paper "Activity of the bcr-abl kinase inhibitor PD180970" but I don't understand how IC50 works on table 1. Can you tell with simple words and give me an easy example?

The IC50 is the concentration of an inhibitor at which you observe the half maximal inhibition. See the figure from the Wikipedia:

The IC50 can be seen as a way to measure the effectiveness of an inhibitor on a biological function as an enzyme. In the case of PD180970 you have an inhibitor which inhibits the p210 Bcr-Abl tyrosine kinase. The IC50 is the concentration at which 50% of the kinase is inhibited.
In table 1 different mutations of the tyrosine kinase are tested against the inhibitor to see, if the mutations have an influence on the IC50. This is important as PD180970 is considered as an anti-cancer drug and possible mutations would make it less effective here.

Thank u Chris. I have also some questions about this paper. 1)Do you know the weakness of the kinase assay and mtt assay. Maybe there was another experiment which they could do?

also why in the table 1 the use two assays for check the ic50? it's complicated!! and why the results are different in one mutation?

They test the activity on the "naked" kinase in vitro and then also the effect of the inhibitor in a cell based assay (MTT assay, in vivo). That the inhibitor works on the kinase alone doesn't necessarily mean it works also very well in the cell. The T315I mutation most likely affects binding of the inhibitor. If this happens not as good, it will dissociate easier and you need a much higher concentration of your inhibitor to show an effect.

ok!!! can you suggest me another experiment, which there is not in this paper, to check their results of imatinib and pd180970? (how about to transfer this cells in mouse?) maybe there is a better method in your opinion?

No, sorry. For that I am not really deep enough in the field.

ok chris!! thank u very much!! i will try later to find if there is another method, searching in this blog :) if you can think anything let me know!! thanks!!

The IC50 is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of EC50. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).


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What triggers the migration of robins?
I live in central Massachusetts, and have begun seeing robins, as we generally do in early March. The temperature is well below normal, though, and three feet of snow are covering the still-frozen ground from which they usually feed. We were expecting them to arrive late, when conditions would seem more conducive to survival.
What triggers their migration process?

I don't know about the specific cues that American robins use for migration. This species is also both a short range (e.g. between states or to lower altitudes) and long range migrant (e.g. Florida & Mexico), so the cues that they use can probably differ between overwintering populations. There are also year-round populations of robins in the US, but probably not many (if any) in Massachusetts. There are however at least two papers that show that American robins are arriving earlier and earlier, at least in Wisconsin and Colorado (Inouye et al, 2000 and Jones et al, 2012). The studies find that arrivals dates have shifted ~13 days earlier between 1990 and 2010 in Wisconsin and 14 days earlier between 1981 and 2000 in Colorado. The study from Colorado also shows that the first date of bare ground has not changed, so snow melt has not changed over the time period. As a consequence, the interval between arrival and bare ground has grown by 18 days. This could indicate a phenological mismatch between spring arrival and the resources used by robins, and your observations seems to agree with this pattern.
This are at least some comments and a couple of papers that could be useful for your question. Sorry I cannot say more about the actual cues used for their migration.

I'm not a specialist in this area, but I would guess that the length of day-light periods compared to night time could be a good trigger. This is quite independent of the weather, is quite constant (even though length of days is known to have changed through over the millions of years past since the formation of earth).

I live in Boston, Massachusetts. At the Back Bay Fens, a couple of miles from downtown, the Muddy River is partly bordered with dense stands of Phragmites reeds. Back in the 1990s I discovered that robins nest among these reeds in spring. According to Cornell University's Laboratory of Ornithology, this is the only place in North America where robins are known to do this. (Phragmites are loathed by conservationists and wildlife officials because they are supposedly worthless as habitat.) In late autumn large flocks of robins roost in those same reeds at night, flying out and dispersing to feed every morning. On a number of occasions I made careful counts of the robin flocks leaving the reeds during November and December. The count was well up in the thousands of birds on several December mornings. On calm sunny mild winter days a few robins can be heard singing very softly---the so-called whisper song---at the Fens and elsewhere in Boston.

Please add some references to your answer.

Thank you for these answers. My robin sightings decreased over the first few weeks since I wrote this, however they're back in full force now. This made me curious enough to do further research, and I happened upon two fact sheets about American Robins, whose scientific name is Turdis Migratorius, meaning Migrating Thrush.
I've extrapolated data from a series published by Learner.org entitled Journey North, and will be referring to and quoting sections of this and this.
As indicated by the thorough sources referenced in @fileunderwater's excellent answer, it's clear that not all robins migrate, and among those that do, there are a number of variables, many of which are not fully understood. Robins are considered nomadic, meaning they travel in many different directions, and, unlike other species, they don't necessarily come and go from the same location, further complicating the study of migration.
In general, food supply is the robin's most important consideration, and weather controls the availability of that food, so a complex combination of the two appears to be the main migration trigger.

Migrators rely heavily on earthworms, caterpillars and other insects for the bulk of their diet.
In the fall, they fly south because the ground freezes, locking them out from their favorite food, earthworms, and because winter weather makes it impossible to find juicy caterpillars and other insect food.
The same theory applies in their motivation to return from the south. Soils in the south can get so warm and dry that worms retreat deeper into their burrows during hot, dry spells, making them harder for robins to find.
Robins are easily overheated, so they become stressed and restless when the southern temperatures remain high for an extended period of time.

The south to north migrators are programmed to follow something called a 37-degree isotope. They move ahead of warm fronts, the intention being to settle down where the temperature averages 37 degrees or more. That weather pattern also brings spring rains, causing the ground thaw that triggers the end of earthworm hibernation.
The male robin migrates first. He bulks up by eating more than usual to sustain him through the arduous journey, which is why the first robins we see are generally chubby! (The male also has a much darker head than the female.) As @fileunderwater pointed out, in some areas robins have begun to arrive significantly earlier, while the ground is still frozen, so that extra preparation helps them survive for a time by eating berries and insects found in trees. If all else fails, some will re-join a flock and fly to a warmer area for a few days or weeks, which supports my recent observation.
Upon arrival, the male's job is to stake out a territory conducive to good breeding conditions. Once he finds an area that has a good feeding source, a safe place for breeding, and the right materials for the female to create a nest, he spends most of his time in a nearby tree singing. It's a unique sound rarely used at any other time, and it lets other males in the area know to stay away.
A few weeks later, the female arrives. Her trigger seems to be related to  ideal nesting conditions.

She has no urgent need to return early, since there is nothing important for her to do until there is a good mud supply for building her nest. As a matter of fact, if she builds too early, hard frosts at night can weaken her nest. And if she runs out of food too soon before the nesting season, it can make it hard for her body to produce eggs. So she waits until conditions are more favorable and she can continue to get a reliable winter diet as long as necessary.

A few other fun facts about migration:

Robins migrate mostly at night.

They fly at speeds of 30-36 mph, traveling between 100 and 200 miles per day.

To keep from getting lost, they figure out their location on the planet in much the way sailors on the high seas once did--using the angle of the sun in relation to the time of day. If blown off course, they fly to where the sun will be at the proper angle.

Flock sizes during migration vary greatly. Although groups of 10-50 are the most commonly seen, they'll fly in groups as few as three or four, and I (the author of one of these articles) once counted 60,000 robins flying along Lake Superior in just 5 hours!

For various reasons, many robins don't survive migration. Scientists estimate that only 25% of fledglings born in the summer survive until November, and even many experienced adults die during migration.

source: Stack Exchange

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Atelectasis due to decreased surfactant in lungs
Surfactant is a protein lipid mixture produced by alveolar pneumocytes composed of Dipalmitoyl Phosphatidyl Choline lipid, apoproteins and calcium ions.
This surface lines the alveolar epithelium thereby reducing surface tension preventing lungs from collapse.
Atelectasis is collapse of lung mainly due to lack of surfactant.
Moreover it may also be due to obstruction of the airway tract.
My question is why is this surfactant found to be lowered in patients who have undergone cardiac surgery under pump oxygentor? Why does long term exposure to 100% Oxygen affect the surfactant.
Is it due to its chemical composition or is it something to do with pulmonary circulation?
This Wikipedia article states alveolar collapse due to Oxygen Toxicity
http://en.m.wikipedia.org/wiki/Oxygen_toxicity

Long-term exposure to excessive oxygen will lead to damage in pulmonary tissue. This damage resembles the same damage which is seen in patients with Acute Respiratory Distress Syndrome (ARDS). In these patients surfactant specific proteins are damaged by proteolysis. This proteolysis is caused by the neutrophil elastase enzyme, after a massive influx of activated neutrophils.
The damage done by exposure to excessive oxygen is thought to be done by Reactive Oxygen Species (ROS).

Reactive oxygen species (ROS) are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. ROS are formed as a natural byproduct of the normal metabolism of oxygen...

These ROS can cause oxidative damage to DNA, RNA and proteins. They can form covalent bonds between molecules in the surfactant, thus inactivating them. Damaging of molecules can lead to cellular damage, causing ROS-mediated necrosis or apoptosis. Therefore there will be less surfactant production possible.
Also interestingly:

An important feature of pulmonary oxygen toxicity is that it is almost impossible to distinguish from damage caused by other lung injury processes. Consequently, it is unclear whether deterioration of lung function during high concentration oxygen therapy is due to worsening of the primary disease process or to oxygen-free radical-induced damage; the administration of high concentration oxygen may be perpetuating lung injury in some patients.

So in patients who undergo long-term 100% oxygen exposure, for example due to lung problems, the problems could be perpetuated or even worsened due to oxygen therapy and the oxidative stress caused by it.

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Is consuming proteins different vs. consuming amino-acids and how?
Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that statement, but I lacked arguments... As far as I know, amino-acids are part of proteins. So, when proteins go to our body with food, we digest it and make amino-acids. Then they can form any kind of proteins we need. The same would happen when consuming amino-acids directly, not in protein form. Maybe then the process would be faster. But from my point of view, there is no much of a difference. Could anyone please give me a more sound opinion on why is consuming proteins and amino-acids different, if it is?

I am not an anabolic expert, but I bet that for growing muscle specific aminoacids are needed more than others. Hence, consuming aminoacids may give the body builder the opportunity to provide targeted supplements?

Essential amino acids are important for muscle synthesis. The only benefit I could draw from consuming amino acids is that there's some time-dependent benefit vs digestion time of whole protein. On the flip side, however, you find that amino acid supplements can require half the bottle to get the same output as, for example, a whey powder. Some of these pills are sometimes simply whole protein anyways. Consuming essential amino acids should be the goal, and how to time this for best performance could be a legitimate literature search.

What bodybuilders usually consume are not pure amino acids (which would usually be too expensive) but protein powders prepared from various sources - wheat, soy bean and so on. It helps building up muscle mass when training accodingly.

To put it shortly:

Proteins have properties that individual amino acids that make up the protein does not have.
Similarly the individual amino acids have properties that the protein does not have.

This is analogous to elements vs compounds.
The site referenced below quotes 3 experiments done to examine this phenomena.
All experiments compared effectiveness of whey protein with that of essential amino acid (EAA) supplements. Experiments 1 and 2 involved old people while experiment 3 involved young people.
Conclusion of experiments is as follows:

Both EAA and whey protein (15 g of EAA and 15 g whey was taken by the respective groups) induced muscle growth, however EAA had better anabolic effect as compared to whey.
In this 3 groups were compared. 15 g of whey vs 6.72 g of EAA vs. 7.57 g of non-essential amino acids. Whey had higher anabolic effect as compared to EAA while the third group showed no improvement. This additional anabolic effect is attributed to unknown mechanisms. The anabolic effect was measured using a different method add compared to the first experiment. So results may not be comparable.
In this 3 groups of young men were compared. The first group was given carbohydrate (30 g) and EAA (15 g) drink, the second group liquid meal containing same quantity of EAA and total 850 calories while the third group was given both. The conclusion:

The third group, as expected had the highest anabolic rate
The first group (protein and carbohydrate drink) had better anabolic rate when compared with the liquid meal group though they both took the same amount of EAA. The difference was in carbohydrate content. The liquid meal had higher carbohydrates content when compared with the first group.

Whey has insulinogenic effect invitro. Whey also has the same effect whether taken before or after exercise while the protein drink has better effect when taken before exercise.
Among amino acids leucine, when taken alone has anabolic effect comparable to a mixture of EAA.
In conclusion:

However, whey contains various bioactive peptides that act to enhance recovery and potentially in other ways that positively effect the adaptive process to exercise (12). These bioactive peptides are not found in EAA, BCAA, or Leucine, and appear to be a unique quality to dairy proteins. So what we can't say is that these aminos are the deciding factor in whey's effects...or that we can use one in place of the other (interchangeably) in all cases.

http://www.vpxsports.com/article-detail/supplements/whey-protein-versus-amino-acids-whats-the-difference
Please read the article which has more details and graphs and references for further study.

I have only quickly skimmed this article, but I would be very cautious about  relying on it. It is full of claims without supporting references, and it's written by the company that sells these supplements. The studies cited are small, short-term and measure wildly different things.


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Incubation time of Antarctic Phosphatase in lab
Antarctic Phosphatase is used to catalyze the removal of 5' phosphate from DNA. If I'm using it in the lab on a sample of 1-5 micrograms of digested DNA, how would I figure out how long to incubate the sample at 37 degrees Celsius?

I typically just react it for an hour, that amount of DNA doesn't seem excessive.

This set of protocols was really helpful for me when I got started cloning.

VTC because not looking up the manufacturer protocol counts in my opinion as an unresearched homework question.

For 5' extensions or blunt ends, incubate the sample for 15 minutes at 37 degrees Celsius.
For 3' extensions, incubate the sample for an hour.
https://www.neb.com/protocols/1/01/01/vector-dephosphorylation-protocol

Depends on amount of enzyme added.


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Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor
Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) and $O^{c}$(mutation in the operator, the site where the repressor binds).
$I^{c}$ mutants are usually recessive: the Lac Repressor cannot bind to the operator, however, if a wild-copy of the gene is present in a merodiploid, the inducible pattern of expression is restored, because the Lac Repressor acts in trans (that is, it will inhibit expression of both operons when lactose is not present).
However, I've read that there's a strain ($lacI^{d}$) which is dominant, so the expression is constitutive even in the presence of the normal repressor. According to the article linked, abnormal subunits may mix with normal subunits, resulting in a disfunctional tetramer, even if a wild type lacI is also present.
In terms of protein structure, why some mutations may have this effect and be dominant while other mutations do not interfere with normal copies of the protein and are recessive?

They explain in the paper you linked to that these muteins affect tetramerisation of the repressor. This means weaker binding of the repressor and no DNA looping. Does that explain it for you?

@canadianer partially. Why some mutations may lead to incorporation of abnormal subunits to normal subunits and in other mutations this doesn't happen?

The lac repressor act as a tetramere molecule and requires all 4 of the subunit to be able to bind DNA to act on the operon and repress β-galactosidase expression.
The "all 4" is the key here, if any of the 4 subunits is unable to bind DNA then the whole complex cannot attach to the operon. The lacId mutation produces a repressor subunit that cannot attach DNA, yet can tetramerize with other lac repressor subunits, therefore impeding WT subunits to bind the operon.
For your question on the protein structure. Mutations can occur at different locations in a gene and therefore impact different proteins domains. Proteins contain different type of domains, such as an active site for an enzyme or a binding sites for attaching to the DNA. A mutation might act on one of the domain while leaving others fully functional.
In your case this is exactly what happens, the mutation is in the protein region involved in binding DNA but does not affect the region involved in the protein-protein binding with other subunits.

Concerning the difference between dominant vs. recessive mutations, in general, recessive, or loss-of-function mutations, are much more frequent than dominant, or gain-of-function, mutations, because there are many different ways to "break" or inactivate a protein.  For example, not every amino acid site has the potential to mutate to a residue with dominant phenotype, but most sites can mutate to a side chain that might destabilize, disrupt, etc.
The lacId allele is a dominant loss-of-function (and so somewhat more complex than the simple explanation I just gave). It makes a so-called "poison product"

lacID is an example of a dominant-negative allele (or mutation) so the phenotype is visible in m/+ (the bacterial merodiploids are the prokaryotic version of heterozygotes), and therefore, by definition, dominant, however the phenotype (in this case constitutive expression of the lac operon) is the same as the loss-of-function phenotype (a complete knock-out, or deletion of the lac Repressor gene).
If m/+ has the same phenotype as m/m it could be dose-sensitive, or the protein could be a multimer, or the mutant protein could titrate (or sequester) an interacting protein.


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How would you effect bulk DNA gene therapy for a human?
Let's imagine  that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to make our genome do what we want, but it's a major refactor.  We're going to have adjust 10-15% of our DNA. (Note this is just a contrived example to suggest why we would want to make such a drastic change - our ability to actually know what changes to make is unimportant for the question.)
How would we replace/or modify this much of our DNA?  It seems the problem is very similar to gene therapy, but on a larger scale.
A few possibilities come to mind.  We could make a virus that would modify our DNA.  Or perhaps we could generate the new genome and inject it into some cells which would then just outlive the others (eg because these cells won't have a Hayflick limit) or will be able to generate lots of new adult stems cells with the "refactored" DNA?

I don't think replacing that much DNA would be possible in anything larger than a zygote.

Why is this opinion based?  It's not a question like "what is your favorite codon".  I'm asking a serious question about the ability to replace DNA in a complex organism.

Any statement of the form "Is X possible" where X is a completely speculative and untested concept is opinion-based here.

@MarchHo - I reworded the question. I fully expect that an approach is possible, eventually.  I just don't know what approach would work.  I suggest two.  Perhaps the virus approach is untenable because virii are small and replacing that much DNA would not be possible even with a complex DNA.  http://en.wikipedia.org/wiki/Gene_therapy is basically this same concept at a much smaller level.

I think the bigger problem is replacing the DNA in every cell of an adult. Gene therapy will probably be most successful in cases were you only need to deliver a small amount of DNA to a certain set of cells. There are enough problems getting a 5000 bp plasmid into tissues, trying to get entire chromosomes into cells would be much harder.

"cells which would then just outlive the others (eg because these cells won't have a Hayflick limit or will be able to generate lots of new adult stems cells"
You're describing cancer cells, unfortunately. A major challenge is that all cells accumulate mutations with time, and with rounds of cell division - so a major "upgrade" would be improved genome maintenance. This would be a challenging thing - the machinery and systems maintaining our genomes are complex!

The replacement of whole chromosomes with ones designed de novo is possible now: http://www.sciencemag.org/content/344/6179/55

@Yehosef I like your question, and think of similar things, in the context of doing business in the intersection of tech and genomics. Have you any thoughts on that? Would love to Skype, if you are interested.

@tyrex - I've thought about it.  You can contact me at gmail.com

@Yehosef Thanks, I wrote an email. If it didnt reach you, let me know, and I will give an email address here.

Let's imagine that we understood DNA programming and our genome very well and >realized that there were some significant flaws (we die, we need sleep, etc.) And >let's imagine that we understand how to make our genome do what we want, but it's a >major refactor. We're going to have adjust 10-15% of our DNA.

I think we both recognise that this is a very naive view of biology and the nature of how organismal properties emerge (through multiple levels of systems) ultimately from the genetic code, the information in the genome, and the developmental process.
It is more pertinent and promising to think about treating genetic diseases.
Some genetic diseases are caused by mutations to single basepairs (e.g. the HgbS variant of the haemoglobin beta chain, which causes sickle-cell anaemia).
Other genetic diseases are caused by rearrangements of large segments of chromosomes, and the gene dosage imbalances that arise from this (e.g. Charcot-Marie-Tooth syndrome 1A). Finally, some genetic diseases are caused by a major gene-dosage imbalance caused by having an unusual set of chromosomes, "aneuploidy" (e.g. down syndrome, where chromosome 21 is present in 3 copies).
'Large-scale' gene therapy could be something useful for aneuploidy. Recently, the mechanism for inactivating one X-chromosome in female somatic cells has been applied to silencing the surplus chromosome 21 of Down Syndrome.
In yeast, a 'designer chromosome' has been chemically synthesised, and has been used to replace the corresponding native chromosome in yeast cells.
So although I think the premise of your question is basically science-fiction and naive, it is becoming possible to silence or replace whole chromosomes. More realistically than making our species immortal and ever-awake, this technology could possibly translate to therapies for some genetic diseases. But of course, the problem of retrospectively getting your therapy in to many somatic cells is still there. Engineering zygotes is feasible but has ethical problems - also, where pre-implantation screening is permitted, IVF can simply include genetic selection rather than genetic engineering!

Thanks for the answer!  I don't recognize it as a naive view of biology b/c I really know very little about biology.  But I understand computers and programming and my understanding of DNA/biology is that they are very complex biological machines/computers.  Even though our understanding of these mechanisms is only in its infancy, I don't see any reason we won't eventually understand it at a level that we can program whatever we want (see http://en.wikipedia.org/wiki/Synthetic_biology)  Maybe that's naive - but I'm not convinced.

The problem is that the kinds of properties of living things you can readily see and care about (you list needing to sleep, mortality - these are especially tough cookies!) are emergent, and very far abstracted from the genetic information. Abstracted through multiple layers of extremely complex non-linear dynamic systems, such as genetic regulation, patterning in development, tissue interactions.
Also, these properties have emerged from evolution by natural selection, and this 'blind' optimisation process often leads species down dead-ends, often compensating its past wild excursions...

Evolution by natural selection doesn't have foresight, and so while it is busy selecting 'fit' individuals under the circumstances du jour, over long time-spans it can be raising dependencies and fragilities. The panda bear is a great example, along with the swathes of extinct forms.
Maybe for a computer scientist you could think about digging down into treacherous local minima...?
But your question is a super-interesting one, and it turns out people are working both on replacing large chunks, and replacing all instances of a short 'word'.

I understand that it's not always as simple as finding the "need sleep" gene. Genes cause proteins which cause lots of interesting thing. But I expect that within the next few hundred years (at least) the growth of our understanding of biology combined with growth in computer simulations/modeling will provide us with tools far beyond our ability to even grasp them today.  We have computers today which are creating simulation of the formation of the universe - how many more years before we have reasonably accurate models of human biological systems?  I don't expect that many.

Yeah the future is exciting, let's hope we live long enough to see some interesting stuff. We're currently at the stage where (rather) small proteins and some solvent can be simulated as a system of atoms under relevant physical forces, for long enough for the protein to fold up in to a reasonable structure. But this is the top of the top and isn't really giving an insight in to biology yet (it will!!)
Meanwhile we're trying to predict folded protein structures from sequence data as a short-cut. It's slow progress....

A major drawback and problem with your idea is that some genetic problems are developmental and have no effect if applied on adults. For example, a gene known to cause crooked teeth would have to be fixed before permanent teeth grow in - no point in patching it after that, except if you also want to patch in infinite tooth replacement.
Retroactively fixing developmental problems through DNA is a pain. In the worst case, you have to clear out the defective piece, then regenerate it after the patch. Bioactive machine parts or cybernetics might be preferable. If you have the tech to fix DNA like that, you probably have the means to produce the needed machine parts.
"Modifying the DNA" isn't a magic solution either. There are all sorts of ways that genes can be deactivated or suppressed - and there's a field of study around such mechanisms known as epigenetics. You could waste billions on patching a gene only to find that your patch has no effect because you failed to consider these.
The most promising applications of gene treatments for adults are mainly in cases where a faulty gene generates a malfunctioning product that is normally constantly needed. An example is genetic insulin deficiency (where a person is unable to produce insulin, effectively causing diabetes.) If the gene is corrected, insulin can be properly produced.


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How long the homologous arms of the "repair" sequence must be to do homologous recombination?
I am trying to figure out the details of the homolougous recombination in order to be able to insert a certain piece of DNA in the host genome after double strand break.. Does anybody know how long the homology arms of the repair template must be ? Can the left arm be longer than the right one? I have read several papers which have different sizes 90 bp vs kb..
In my case, i am not so much preoccupied by off target but the insertion should occur also on the desired site possibly at high frequency and as fast as possible.
Thank you,
Paola

As little as 14bp of homology can work. See this reference.
I would recommend at least a length of 90bp but 1kb is probably overkilled. Yes both arms can have different length (staying in the same order of magnitude).


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Is there a DNA analogue to ribozymes?
If not, is it impossible for DNA to have enzymatic activity?

Not very common, and not found so far in nature, but they exist and are called deoxyribozymes.
Additional information:
Deoxyribozymes are the equivalent of ribozymes in the DNA world and can function as catalysts for different biochemical reactions, such as DNA cleavage. While DNAzymes (short name) were synthesized in a laboratory context (In-vitro) and proved to be active, no observations were made of DNA molecules having an enzymatic activity In-vivo which is of course not a definitive proof they don't exist in nature.
The latter point is a major difference compared to ribozymes which were proved to be active and functional in living cells.

How did I miss the analogous name? :P

@TheObscureQuestion Thought the same when I saw you question :D. By the way excellent question, I actually knew about them because I looked that up recently while asking myself the exact same question.

Can you at least give a short summary of the Wikipedia article? Dropping a link (and this is more or less it) is usually not appreciated.

@Karolas I thought about doing that but they are just exactly the same as ribozymes but DNA-based instead of RNA-based. Anyway you are right I will add some more information.


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Is there a specific mechanism for the delivery of pain medication?
For example, when one takes aspirin or ibuprofen does the chemical get dispersed to all pain receptor? My question really is, how does the chemical know where to target in the body? I figure wherever there is pain in the body that a certain signal is being produced; which possibly acts as a chaperone to direct the medication chemical where to bind and inhibit.

Short answer
No, orally taken painkillers act systemically.
Background
Taking a painkiller orally results in the drug being taken up into the bloodstream by the digestive system. From there it can potentially reach all tissues.
In other words, a pain response does not act as a chaperone. A hypothetical drug that would home in on tissues with a pain response, while avoiding unaffected tissues would be the ultimate painkiller, if it existed.
EDIT: To emphasize that painkillers act systemically I will elaborate on aspirine's pharmacokinetics. Notably, aspirine's actions are not restricted to the pain centers in the brain, and I quote the following excerpt from Wiley's interactive Concepts in Biochemistry]1:

Aspirin's analgesic and anti-inflammatory effects are due to the drug's ability to stop the production of prostaglandins that cause tissue swelling and pain.

Aspirin's antipyretic (fever-reducing) effect is due to its direct action on the hypothalamus gland, which results in vasodilation of peripheral blood vessels and sweating.
Prostaglandins are also the key mediators of platelet aggregation. By modifying the COX enzymes within platelets, aspirin causes platelets to lose the "stickiness" that is needed to stimulate blood clotting.
Hence, by these examples it can be seen that aspirine works in the periphery (wound swelling and pain), centrally (brain's hypothalamus) as well as in the bloodstream. Hence, aspirine (and other orally administered painkillers) do not target specific areas in the body, and most certainly not only the brain.
There are such targeted drugs, however. An interesting one is carbamezipine, an anti-epileptic that blocks Na+ channels. It blocks Na+ channels only when they are in an active conformation, however (i.e., engaged in action potential firing). Epileptic activity is basically paroxysmal (massive), synchronous over-activity in the brain that is accompanied by massive Na+ channel activity. Hence, epileptic activity will in effect trigger the drug into action.

Though these drugs enter systemic circulation, the pharmacokinetics for different body parts may be different.

Thanks for explaining. I always thought that it works by blocking the signals in brain i.e. at one place.

@WYSIWYG - agreed, but see edited answer. It is a systemic drug.

@jnovacho - no, your assumption is incorrect, I stressed that in the edited answer. If you ask a question in order to get your presumption verified just to dispute alternative (and in this case correct) answers, don't ask the question :)

See for a verification of a systemic mechanism of action @Corvus 'answer

Everything in the answer above is correct, but I think the OP wants to know about aspirin's action against pain specifically. Aspirin's action against inflammation is distributed throughout the body whereas its action again pain is distributed more locality (spinal nerves + perhaps brain). Even in the latter case I know of no evidence that it is targeted to specific neurons or brain regions; I believe the antipyretic effect on the hypothalamus is not to due to targeting but a consequence of whatever reduction in prostaglandins has occurred system-wide.

@Corvus, I doubt. OP is talking chaperones as if molecules are guided by something. They are not.

Most NSAIDs derive their analgesic effects from inhibit the cyclooxygenase (COX) enzymes that produce the prostaglandin-H2 precursor to the prostaglandins that sensitize neurons to pain.
Edit: With respect to where this takes place, the COX enzymes are expressed in inflamed tissues as well as constitutively in the stomach and kidney. The prostaglandins whose production they block act on the spinal nerves and can diffuse across the blood-brain barrier.

Can you add more information on distribution of COX2 in the body and if possible pharmacokinetics of any of these drugs to explain how they may affect different body parts differently.


text:
What causes the line patterns in the palm of the hand?
The line patterns on the hand are unique to each individual, but what causes these lines and re they advantageous in anyway?

Is this a homework question?

The lines on the hand are known as flexion creases, and they exist because in their absence, the skin will stretch outwards when the palm is closed due to the decreased surface area of the closed palm, causing problems with gripping.
Developmental disorders such as Down Syndrome often cause there to be only one palm line, known as the simian crease, as shown on the left.

I don't think this answers the entire question that was posed by the OP.


text:
How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action?
The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli.
Apparently, it always binds in sites that are away from -10 and -35 elements of the promoter by multiples of 10 base pairs (-70 or -60, for example). How could this be related to its mechanism of action?
I've searched about this particular activator and I found that it acts mainly by recruiting RNAP to weak promoters, although it does alter the architecture of the DNA, introducing an abrupt bend (for some CAP-dependent genes, this favours conformational changes in RNAP involved in the initialization of transcription): here's the crystallographic data.
However, I did not find anything conclusive about the pattern of binding to distances which are usually multiple of 10 base pairs (which is close to the number of base pair in a complete turn of the double helix).

The spacing between TF binding sites is often important as it directly relates to their relative orientation. If two binding sites were, say, 15 bp apart, the TFs would actually be on opposite sides of the DNA helix. This is why the spacing between -10 and -35 is so critical for efficient initiation. I don't know if this effect applies to the spacing you mentioned (60 to 70 bp); at first thought, it seems like it would be less relevant as there is greater flexibility over such a distance.

I found a great article that might help. To summarize the contents of the article, there are two classes of CAP dependent promoters/genes, and the distance of the CAP bindings site in these classes are different. Also the actions in which CAP is involved are different in the two classes of promoters. In the first class it does not overlap with the promoter region and is only involved in RNAP recruitment. In the second class it overlaps with -35 element of the core promoter and is involved in multiple interactions.
So the binding distance of the CAP is determines what interactions is it involved.
You can see the difference between the two classes on the picture below (taken from the article i linked). And I think this answers your question on why the patterns are multiples of ten - because this is the space needed for alpha-CTD to make a bridge between the protein complexes, or the CAP to interact with the RANP complex.

I only took a glance at the paper I linked and quickly extracted the info, but I hope it still helps


text:
Why is E.coli used as a model?
Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?

Short answer. It was discovered pretty early (late 1800's). It is easy to get (you probably know where it comes from), purify, grow and is not virulent. E.coli spreads very rapidly (30 minutes division rate).
Why this one in particular and not another similar bacteria? Well you have to choose something at some stage and usually the more an organism is used the most valuable it becomes which means that more and more scientists will start to use it creating a loop which favors certain organisms, like it happened with E.coli.
E.coli started to be studied because Theodor Escherich wanted to prove the "germ theory of disease" which led him and later other scientists to work with E.coli and everybody uses it today.
By the way, the mouse model is actually quite interesting. Started by breeding huge amount of mice for selling them as pets.

Not virulent? It's a pretty nasty bug

@AliceD The E.coli strain used routinely in laboratories is part of the group A and is a non virulent one.

That's interesting. +1


text:
What is the explanation for the smaller number of tRNA than codons?

Translation, or decoding, of the four-nucleotide language of DNA and
  mRNA into the 20–amino acid language of proteins requires tRNAs and
  enzymes called aminoacyl-tRNA synthetases. To participate in protein
  synthesis, a tRNA molecule must become chemically linked to a
  particular amino acid via a high-energy bond, forming an
  aminoacyl-tRNA; the anticodon in the tRNA then base-pairs with a codon
  in mRNA so that the activated amino acid can be added to the growing
  polypeptide chain.
Some 30–40 different tRNAs have been identified in bacterial cells
  and as many as 50–100 in animal and plant cells. Thus the number of
  tRNAs in most cells is more than the number of amino acids used in
  protein synthesis (20) and also differs from the number of amino acid
  codons in the genetic code (61). Consequently, many amino acids have
  more than one tRNA to which they can attach ; in addition, many tRNAs
  can pair with more than one codon.

If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would have to contain exactly 61 different tRNA species, one for each codon that specifies an amino acid. As noted above, however, many cells contain fewer than 61 tRNAs.
What is the explanation for the smaller number of tRNA than  codons codons?

Th reason for this is that for the third base of the tRNA non-Watson-Crick pairing is allowed. This phenomenon is called "Wobble base pairing". See the figure (from here) for illustration (from here):

If you have a look at the codon table for amino acids, than the variation in the code for one amino acid mostly happens on the third position (from here):

This allows a smaller number of tRNA than 64, as there is some flexibility. The third base can be represented like this (taken from this answer):

In the table Cricks predictions are compared to the pairings found in experiments.

Mostly this, but there's also post-transcriptional tRNA modification so instead of U you can have e.g. cmo5U in the wobble position to pair with all 4 canonical bases..

I would add that the genetic code is degenerate, which in this context means that there is more than one way to "spell" some of the "words" in the "message." Since there are only 20 different words (the amino acids), and since the "alphabet" for this code only contains 4 different letters (the nucleotide bases), if we add the limitation that all of the words in our message are the same length, then 3 bases per a.a. is the most efficient or economical code (4 x 4 x 4 = 64 possible combinations). By removing the 3 termination codons in the code there are 61 codons that need to spell 20 a.a.

The table shown is that of Crick’s original wobble predictions. These did not all turn out to be correct, specifically that U in the anticodon only pairs with A or G in the codon. An updated table can be found in the answer to another question.

@David Good point, thanks. I updated the answer.

Watson-Crick base pairing can be violated by wobble base pairing.
The 5' of the anticodon has more freedom in binding, that is why, for many amino acids, the last part of the codon has more possible characters.

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


text:
What happens during kefir fermentation process?
I’ve found many sources about the positive effects of kefir for the digestive system. However I haven’t found any information about the fermenting process.
What is the exact biology (chemistry?) behind the process of milk becoming kefir?
What do the kefir grains exactly consume from the milk? And what do they defecate?  What happens inside the microbes?

I think this can be answered to some degree with links to some deeper references. In my opinion no need to close it.

The fermentation is relatively complex, as quite a number of different bacterial species and yeast live in the Kefir grains. These are made of of the polysaccheride kefiran which immobilizes the bacteria (in contrast for example to yoghurt). The microbes live symbiotic on this matrix.
According to the references a number of different microorganisms has been found, these include mainly Lactic acid bacteria, followed by yeasts and acetic acid bacteria. The species include: Lactobacillus paracasei, Lactobacillus parabuchneri, Lactobacillus casei, Lactobacillus kefiri, Lactococcus lactis, Acetobacter lovaniensis, Kluyveromyces lactis, Kazachstania aerobia, Saccharomyces cerevisiae and Lachancea meyersii.
In brief the lactobacilli break down lactose to produce lactic acid, while the yeasts make alcohol and carbon dioxide while the acetobacter species make acetic acid. This consumes the lactose and the fat content of the milk making it suitable for lactose intollerant people. It also lowers the pH of the kefir. The exact mixture is hard to identify as this contains strongly on the exact composition of the kefir grains.
If you are interested further, I recommend you have a look into the references, I find both articles relatively good to understand.
References:

Brazilian kefir: structure, microbial communities and chemical
composition.
Microbiological, technological and therapeutic properties of kefir: a
natural probiotic beverage.

Well essentially the added Lactobacillus species ferment lactose and other sugars to lactic acid, thus lowering the pH of the product (they take up lactose use it as an energy source under anaerobic conditions and secrete lactic acid). This gives the kefir and other fermented milk products their sourness. Also the lower pH prevents many other bacteria from growing in the product so this is also serves as a natural preservation method. Further more the low pH can denature some of the protein in the milk/kefir resulting in a more solid form. Many of these Lactobacillus species or their relatives are natural part of our gut flora.


text:
Help with STRING database data
I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions.
My idea is to compare the topology of connections of the same protein on different organisms.
However, I noticed that the same protein can receive different ID on each organism.
So I would like to know if there is any way to convert all ID's into just one pattern.
Thanks.

Proteins evolve and have different sequences between species, so you would have to define what you mean with "same protein". One option would be to use an orthology database like eggNOG. (eggNOG has the same protein identifiers as STRING.) Then you could figure out 1:1 correspondences between proteins.
You probably also want to read up on Roded Sharan's work, e.g. Global alignment of protein-protein interaction networks.

Hello @Michael this was exactly what I was searching for. Thanks for your help and for the reading suggestion.

If I understand it correctly you have downloaded for example 1000 protein sequences with 1000 IDs, but there are duplicates in sequences so in reality it is like having 600 unique sequences with 1000 ID's? If so it should be fairly easy to write a script which would create a set of unique sequences with all corresponding IDs so you could choose which one to use.
In python it could be done using the sequence as dictionary key with the ID as a value. While looping over each sequence check if the sequence is already in dictionary. If yes, append the new ID as a value.
Finally you would get
seqs = {
'DFABIODFAFDIOAF....':['ID001', 'ID007'],
'ANOTHERUNIQUESEQUENCE':['ID50'],
...
}

from which it should be easy to choose
TBH not sure about efficiency of this but this depends on the size of dataset? How large is it? Just give me a sample dataset and I can write it.

Hello @Pocin thanks for your help and for your answer, but my problem was how to convert the protein ID used on STRING to a different database ID (e. g. Uniprot). Using solution provided by Michael I 'll be able to make this correspondence.


text:
What sample sizes are ideal for carrying out Bayesian Skyline Plots?
I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 polymorphic sites within each population and one dominating haplotype that comprises almost 90% of the population (the rest being rare haplotypes). Because, BSP uses Coalescent processes for the calculations, the sample sizes would have a effect on the results. I wanted to know if sample sizes of around 30 (for DNA alignments of 700bp) would be ideal for carrying out the analysis and expect reasonably good results ?

What software are you using?

Note that any plot is just a visualization method. You should be asking about sample sizes for reliable analysis. I am not an expert at this but according to wikipedia, Coalescence time and heterozygosity are dependent on population size. You have to clarify what you mean by "results".

I found a PLOS one article that might help. In this they used similar numbers you're planning to use (if i get your question and the article's data right).

The influence of the sampling scheme was investigated by drawing 40 samples in three different ways: 1) all 40 samples from a single deme, 2) 4 samples from each of 10 demes and 3) one sample from each of the 40 demes in the structured population. These correspond respectively to the local, pooled and scattered

(taken from the above linked article)
So depending on your sampling scenario your 30 samples seems to okay.
Also this is a link for the BEAST FAQ that might be helpful.


text:
How did bullying arise evolutionarily?
By bullying, I mean individuals harassing others with name-calling or violence but not for the purpose of gaining resources such as with extortion or theft. The only explanation I've thought of is that bullying offers practice for types of extortion that do result in increased resources.

What you might find interesting is now many domains of study can contribute to your answer. For example economics and culture might play a part in the onset of behaviors deemed oppressive or intimidating.

Having an ennemi is the best way to have friends. bullying is a group activity and would possibly be performed so to increase the level of trust within a group of friends.

@AliceD please never ever suggest cross-posting. We try very hard to avoid duplicating questions on multiple SE sites. If a question can fit on both sites, it should be tweaked to ask for different aspects of the issue based on each site's scope, not repeated.

Asking for examples of bullying in species other than humans, and reasons/context for these behaviours will probably be more fruitful and easier to answer. This can hint at the evolutionary context for bullying in humans as well. Evolutionary “how” questions are usually extremely hard to answer.

@fileunderwater Well, the OP did mention namecalling, which implies interest in the evolution of human bullying. So a "human-centric" answer seems appropriate. Also bear in mind that any given trait can provide multiple benefits, and as such can arise for different reasons in different situations. Basically, bullying may have evolved in our species for slightly different reasons compared to why it did so in other species. Convergent evolution may favor bullying for many reasons, and so focusing on human bullying again, would not seem inappropriate.

I think bullying is really more of an emergent behavior that manifests itself because of natural aggression built in for survival, as well as our complex social-based psychology leading to insecurity when dealing with other:

People who are highly aggressive, and or apathetic to the suffering of others are more likely to control a majority of resources if they don't face significant opposition. This leads to their favored propagation obviously. Then, in their free-time, with all resources under control, they simply continue to do what comes naturally to them: dominating others. It can also work even in those without the ability to actually control resources, due to lack of intelligence for instance. I have met far more non-intelligent bullies than the reverse. The reason for their behavior is still explained by an attempt to control their territory and social status, however ineffective.
Again, due to our complex psychology centered around social interaction, we can develop insecurities about our self-perceived 'fitness', and therefore acceptance by mates and peers. This low self-esteem can lead to bullying others to boost one's ego. Chemically, this can result in a release of endorphins because they feel they have achieved something, which supports bullying behavior as an emergent behavior. Also, those with lower intelligence are likely to have trouble with reasoning skills, and therefore find it difficult to self-analyze and realize their behavior is negative. This leads to bad interactions with others, which can make those individuals feel even more insecure, which in turn fuels their drive to assert themselves through bullying.

Many studies have been conducted on sociopaths/psychopaths. Just like any other evolved trait, whether or not their "personality disorder" is beneficial to the propagation of their genes depends on environmental factors. If they face only opposition from entities that are relatively weak, physically and mentally, then they have an advantage over those peers. But if their peers are sufficiently strong and organized, then the personality disorder becomes a disadvantage if they can't adapt, because they will be attacked by those seeking cooperation from others when they misbehave. Obviously, when our species' numbers were few, high-aggression and a willingness to kill for resources needed for survival aided in survival. In these modern times, its less acceptable for socio/psychopaths to display their innate behavior, due to modern laws, but obviously society can take turns that allow them to express themselves without worry...see the holocaust or any other genocide for an example.
https://link.springer.com/article/10.1007/s40806-017-0097-5
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=2ahUKEwj5vKjk88bjAhUfJTQIHaFDA9wQFjABegQIARAC&url=https%3A%2F%2Fwww.apa.org%2Fpubs%2Fjournals%2Freleases%2Famp-a0038929.pdf&usg=AOvVaw1fUJiPHl8rSKMm6Gc9VEeA

Can you provide some references.

While I do not have references of studies on this exact focus, I will post references tomorrow concerning the genetic propagation of genes leading to aggression, as well as references concerning the link between aggressive social behavior and genes, with aggression serving as a means of increasing genetic propagation.

Next time onwards please try to include references for your answers. Also feel free to use help centre for any assistance that you need in order to create a proper answer or a question. Your answer may be down voted if you are not providing any references for them, and it will affect your reputation(if you cares). :)

It is extremely hard to prove a negative.

I find this answer very human-centric and it seems to be framing bullying a priori as “bad”. See e.g. statements on social insecurity and sociopaths. Given how common bullying is in human societies, across time, in different contexts and levels, I don’t think that is the most fruitful way to speculate on the evolutionary background. I doubt that bullying should be seen as an unfortunate side-effect, given how common similar behaviours are in other group-living/social animals, from apes to wolves and birds (e.g. poultry).


text:
Questions on DNA damage
I'm not strong in biology, so bear with me on this:
I've been reading that as we age, our DNA is damaged by internal (e.g. errors during replication) and external (e.g. sun damage or radiation) factors.

If you take, say, an 80 year old, can you find DNA in their body that's the same as when they were a newborn? What kind of cells would have undamaged DNA?
Is DNA damage distributed evenly across the body or will some parts have more damage than others?
Is there any published data on how much DNA damage an average person accumulates over their lifetime? I'm not sure how this can be quantified, but I'm wondering if there has been any study on gauging damage.

Since errors frequently occur during cell division, I guess cells that divide less frequently (e.g. mature neurons do not divide at all) will probably have less damage. Some cells not only divide fast, but also become polypoloid (e.g. liver cells), so these cells probably can tolerate a lot of mutations.

Also, this new article may be of interest DNA mutation clock proves tough to set. Apparently, rates with which mutations accumulate over human generations may be fluctuating!

Excellent question!

You would definitely be able to find quite a few sequences of DNA that are undamaged (in fact most of them would be undamaged), but it is very unlikely that any cells in his/her body would have a perfect copy of the entire original genome.
I'm sure that cells closer to the skin (exposed to more radiation) would have more mutations, but beyond that most everything depends on where you live, your habits, etc. (if you're a smoker you will obviously have more mutations in your lung cells).
Under regular circumstances (low levels of mutagens), about 3 nucleotide mutations occur in the human genome per cell per division (DNA replication) (from http://www.ncbi.nlm.nih.gov/books/NBK26881/). The rest of the math would be a very rough estimate, seeing as you'd need to make a lot of assumptions (cell division rate average, other mutagens an organism may encounter, life span, the list goes on), but however you want to do it, there's the number you need to start with.

I hope this helps.
CDB

Hi. Thanks for your answer. Regarding the first question, is it possible to use multiple DNA samples and compare them to one another to derive the entire original genome? The goal would be to identify damaged sequences and replace them with the undamaged ones from other samples since I assume a single block of DNA is unlikely to be corrupt in every single sample. I think a similar concept is implemented in cryptography and data storage in computers to achieve integrity.

@Mark13426 Sure. See e.g. this PLoS Computational Biology paper and references therein. Often the aim in these studies is to map cell lineages rather than infer the genotype of the fertilized egg, but the information is there if you wanted to do it.

I'm not sure how you would identify which sequences were the original, undamaged sequences unless you had a reference (such as a map of the organism's genome when it was an embryo), but it would be very possible to retrieve an entire complete and undamaged genome from perhaps only a few hundred cells if you could identify the original DNA. May I ask what your project is regarding? It sounds very fascinating!

@CDB It's not generally true that cells closer to the skin have more mutations; what matters more than e.g. UV exposure is the number of cell generations that a cell goes through. Intestinal epithelium turns over rapidly and can have up to an order of magnitude greater number of cell generations than other tissues, resulting in a higher number of accumulated mutations over the lifetime.

Very true, however skin cells would be much more prone to mutations from radiation and radiation is a much more deadly mutagen than just mistakes made inside the cell itself seeing as radiation actually destroys the nucleotide.

@Mark13426 I apologize, I just realized something that you said in your comment. Comparing the cell genomes themselves to find the original genome without a map of it would be possible. It would just be very extremely difficult.

@CDB Regarding radiation leading to higher rates of mutation in epidermis than in more rapidly proliferating tissues: is do you have evidence for that, or is that just a hunch? Because in mouse, it goes in the opposite direction. And liver tissue, with its high exposure to mutagens, accumulates vastly more mutations than epidermis.

Thanks both of you. I'm not involved in any project. Over the last year, I've been interested in the study of aging. The older I get, the more I think about death, so I have a personal interest in why we age and whether it's preventable. With regards to genome preservation, I've been asking myself whether it makes sense to get my genome sequenced (not sure if this is commercially possible) and use the data in the future if future medicine can take advantage of it. Sounds like genome reconstruction is difficult, so why not map out whatever I have now while I'm healthy? Sorry, if I sound silly.

You've asked a number of questions here, but yes -- mutation rates have been studied extensively in humans as well as in model organisms. And as you suggest, they vary substantially across tissues. One starting point to read about how mutation rates are measured and how they vary across species, tissues, etc., is a 2010 Trends in Genetics review by Mike Lynch. See particularly Table 1.


text:
books for beginners in research in mathematical biology
I am a M.SC(mathematics) student. I have no subject like mathematically modelling.But  i'm interesting in research in mathematical biology.Initially which book i should study.
Please guide me.THANKS...

This is far too broad to answer effectively.  We don't know anything about which specific areas you are interested in or what your level of ability is, aside from that you haven't had any mathematical modeling coursework.  Most books would probably be accessible for someone with a background in ODEs, and I'm sure you've had experience with those.

additional info is needed for sure. Everything can be mathematically modeled.

Beside the Otto & Day book, also consider Murray's Mathematical Biology: I. An Introduction (also Mathematical Biology II: Spatial and Biomedical Applications). It covers different applications and is written for people coming from a math background.

Probably the best contemporary book taking a broad view of mathematical biology modeling is Otto and Day's 2007 book A Biologist's Guide to Mathematical Modeling in Ecology and Evolution published by Princeton University Press.
There are also a number of books that focus on more specific areas e.g. mathematical population genetics, ecological modeling, infectious disease epidemiology, etc. But without knowing which areas of modeling interest you it is difficult to recommend at this level.

sorry for too late comment ...i'm interesting in mathematical population genetics

The post is too broad. Mathematics is used in tons of different fields of biology.
Population genetics is one of the main field of biology that is contains quite a lot of mathematical formulations. This post gives a list of references for books in population genetics.

was this perhaps intended to be a comment?

You are right. It should have been a comment. Too late to add comments though.


text:
What physiological processes within a muscle cause the latent period in a muscle fiber?
This is a lab question I cant find the answer in the lab manual or in the text book.
What physiological processes in a muscle cause the latent period in a muscle fiber?
Please help.
Edit:
The latent period is the short delay between the muscle action potential and the beginning of muscle tension development. This is what I'm talking about. I'm sorry I didn't make that clear.

The action potential causes Ca2+ ions to be released in the cells, that is needed for muscle fiber contraction. There is a small time delay from the arrival of the action-potential until the Ca-ions are released and reach the required concentration in the cell for contraction. On the molecular level there is a protein called troponin (this is bacically located on the actin filament along with tropomyosin and obscures the myosin binding site(s)), that bind calcium and then undergoes conformational change - this also adds up to the delay. After this - the conformational change of troponin - myosin and actin can bind together and contraction can occur through conformational changes. All these binding and conformation changes take a small time to be completed, and thus causes a small delay. Below is a picture about the molecular mechanism ofof muscle contraction taken from this wiki page. The linked wiki page has real good detailed information.

I found this article and where they exactly measured things. To clarify my answer (taken from the linked article):

Electromechanical delay (EMD) was described as a time elapse between the onset of muscle electrical activation and onset of force production, reflecting both electrochemical processes [i.e., synaptic transmission, propagation of the action potential, excitation-contraction (EC) coupling] and mechanical processes [i.e., force transmission along the active and passive parts of the series elastic components (SECs)]

So as for the whole muscle, not for just one cell the delay is caused by the things listed in the above quote - although excitation-contraction (EC) coupling and force transmission (things I have described earlier) take place in every single muscle cell that is in a specific muscle fiber.
Edit 2: I found a good and simple ppt/pdf about AP propagation and muscle contraction here.

I think this pretty much sums up the steps necessary from neuro-muscular junction until contraction, but what is the rate-limiting step? Your answer is basically a summing up of events, and not a dedicated answer to the question from m y understanding of PO's intentions. I mean, a chemical synapse is pretty much a 10-ms event if I am not mistaken, so that's not the bottleneck. What is?

The Latent period is caused by:

Time taken for the stimulus to travel along the nerve to the neuromuscular junction
Time taken for the impulse to cross the neuromuscular junction and to stimulate the muscle
Time taken for the excitation-contraction coupling to occur
Time taken by the lever to overcome the inertia of rest
Time taken to overcome the vicous resistance of the muscle.

The latent period is usually about 10 ms.

Taken from Textbook of Practical Physiology Edition 2, by GK Pal & Pravati Pal


text:
"Enhancers" of enhancers?
I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to make a Russian doll analogy. I know about epigenetic markings but I am really looking at an example of a DNA region directly acting on a enhancer similar to an enhancer acting directly onto a promoter.
I am asking that because I couldn't find any examples and was wondering if I missed such a report/paper.

Do you care if it's from a viral genome?

@AtlLED If it is a DNA virus then that works. I am interested in DNA secondary and tertiary structures.

It could be possible that certain enhancer regions can bind the regulatory proteins with higher affinity than other enhancer regions, thus surpressing the amount of activation of the genes regulated by the 'lower affinity enhancer region'.

@Wolgast Interesting idea. This would be some kind of gene regulation via competition. I don't know if this actually happens in the cell (i.e. if some TF are in concentration ranges which would provoke such effect) but in any case it is worth looking into this. Thanks.

Yes indeed. I'm am interested where this will lead you. Let me know if you find anything! :-)

@Wolgast Will definitely do!

If you're looking for a strictly and directly DNA-DNA mediated effect (no histones, no transcription involved) I'd look for sequence effects on chromatin remodelling, modulating access of transcription factors (TFs) to their elements. Something about this might be in this paper:
Szerlong, H. J., & Hansen, J. C. (2011). Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochemistry and Cell Biology = Biochimie et Biologie Cellulaire, 89(1), 24–34. doi:10.1139/O10-139


text:
Do DNA repressors exist?
I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am looking for some kind of anti(or reversed)-enhancer equivalent in the genome which would act like an enhancer but reduce gene expression.
I am aware of repressed/poised enhancers which would kind of be that process, even if not really a pure repression of the target gene but rather a "non-overexpression". I also know about insulators but again this would be a different mechanism.
Some intergenic region binding protein repressors which by a folding mechanism similar to enhancers would repress a gene perhaps?

To my best knowledge DNA enhancers are bound by proteins, thus enhancing activity is actually carried out by the activator proteins not the DNA itself. If I get your question well you're asking if similar sequences exist but with inverse effect? Am I right?

@poka.nandor You are exactly right.

OK, thx I just wanted to make sure I do not misinterpret your question and end up having a bad, irrelevant answer. I'll look into it:)

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen.
In the "classical" way the silencer is bound by a  transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the assembly of the general transcription factors. See the figure from paper 1:

Additionally there are non-classical negative regulatory element (NRE), which are usually elements upstream of the promoter which inhibit the binding regulatory proteins. NRE can also be enhancers depending on the proteins bound on them. Some NRE can induce a bend of the DNA, inhibiting the access to enhancer or promoter elements.
References:

Transcriptional control and the role of silencers in transcriptional
regulation in eukaryotes.
Transcriptional Regulatory Elements in the Human Genome

Thanks! How did I forgot about them I don't know :)


text:
Do transcription factors bind to both strands of DNA?
Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. Any reference books, papers or links will be helpful.

possible duplicate of On which strand does the promoter sit?

I don't think this is a duplicate, in fact I might vote to close the other question and link to this one, as the accepted answer is much clearer and nicely illustrated, with links to sources. However, both questions are fundamentally different, and neither necessarily needs to be closed. Yes, they are about similar things, but are not identical.

The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding proteins obviously bind one strand but they do this in a non-specific manner.
RNA-binding proteins recognise the sequence on a single strand by inserting intercalating planar residues between bases! All of this binding is non-covalent.
Transcription factors recognise sites in dsDNA, with DNA-binding domains. The rest of the protein might surround (partially, to varying degree) the negative outer surface of the dsDNA double helix with positively-charged surface, in order to hold it on to DNA as it scans (perhaps) along its length.
DNA-binding domains: major groove

The following domains are found in many transcription factors, and they all recognise both strands. More correctly, they recognise basepairs and their orientation. The first 5 pages of this lecture slideshow demonstrate that the chemical groups on the side of basepairs, accessible in the major groove, allow proteins to distinguish A:T, T:A, C:G & G:C by the order of hydrogen-bond donors, acceptors, and a methyl group.
Hence, TFs recognise a sequence of basepairs - oriented such that one strand is (e.g.) pTpCpApG, and the complementary strand is pCpTpGpA; and the bulk of the protein may 'sit' on one strand or the other - or a nearby gene may locally define one strand or the other as the coding strand but this does not mean that this one strand is read.

Zinc fingers probe the major groove with reading helices.
Helix-turn-helix motifs do much the same.
Leucine zippers also do much the same.

These are common domains that all recognise basepairs in the major groove by interactions with residues on a probing aplha-helix.
TATA-binding protein: minor groove
TATA-binding protein (TBP) is a different, interesting case. It binds the 'TATA-box' via the minor groove, where the exposed chemical groups only distinguish [A/T] from [C/G], but not their orientation. This means that the sequences on each strand cannot be easily read from the minor groove. TBP instead recognises the shape and flexibility of the double-helix at the TATA-box, 'grips' it by the minor groove and bends the DNA, which aids the melting of the strands to the transcription 'bubble'.

The TATA-box sequence is usually pTpApTpApApA on the coding strand upstream of the transcriptional start. This is the convention when giving the sequence of a TF-binding site, but you couldn't say that TBP actually reads TATAAA - it doesn't!
Here is another, similar set of lecture slides.
Even better, here is the same material covered in a popular textbook.

@Teige : Comprehensive answer

Addition to the answer provided by Teige.
Transcription factors bind to both the strands however your question also included proteins in general.
DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) and Rad52 bind to ssDNA during replication and recombination respectively (there are more examples). These are not transcription factors though.


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What are genome wide functional linkages?
There are two types of interaction classifications used to describe Protein-protein interactions, namely physical and functional. Whilst physical interactions are obvious in nature and methodological determination, I was wondering what a functional interaction/linkage refers to, such as the one cited in the below paper, and is it purely inferred from genomic data?
"Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps."

did it!!!!!!!!!

It would be great if you show some of your workings! A simple google search would have provided you with your answer! I don't think the question should have been closed so once it opens I will answer it but please show what information you have found so far!

okay this is what I got to know, multiple proteins working together to attain a particular function can be termed as protein functional linkages. Am I correct?

Genome wide functional linkages refers to protein in a biochemical or signalling pathway. Inferences of functional interactions can be obtained from methods such as coexpression data from microarray analysis. Since experimental detection of genome-wide protein–protein interactions is costly and time-consuming a computational scope for essentially predictive genome-wide protein–protein interactions is created  [1], which is what the above paper is referring to. As obvious from the abstract of the paper, there are many ways of obtaining the linkages, which are often inferred by the Rosetta Stone, Phylogenetic Profile, Operon and Conserved Gene Neighbor computational methods [2].
Algorithms that identify genome-wide interactions between proteins mainly focus on coregulation of interacting proteins. These methods assume that the genes that are coregulated often occur close to each other on the genomes and show conserved gene order. Thus the genes, which are part of an operon, could be functionally linked.


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How can (or did) Deinococcus radiodurans continue to evolve after developing resistance to mutation?
Deinococcus radiodurans has a remarkable ability to resist damage to its DNA due to radiation, dehydration or (to my knowledge) any other source. It keeps multiple copies of its genome and has a repair mechanism as well.
My question is: how could this thing evolve to be so sophisticated at preventing the processes behind evolution? It seems that a mechanism to prevent errors would also prevent changes, so that as soon as the organism got OK at preventing changes it wouldn't be able to evolve to get better at it. Were genes for these processes borrowed from other extremophiles? Is the assumption that it was in such extreme environments that the damaging influences were keeping up with the repair mechanisms? That's my guess, but I'd love to hear from others with more knowledge of evolutionary processes.

According to the "Functional adaptation" section of this webpage, Deinococcus radiodurans uses repair proteins to stitch up DNA after radiation damage. Meaning, after a burst of radiation, the DNA will be in pieces and the repair proteins put it back together. It seems like this mechanism would not come into play during other forms of DNA mutation that happen during replication, such as point mutations or inversions.

Deinococcus radiodurans did not "develop resistance to mutations".
It is able to repair its chromosome when scatered in pieces by radiations or desiccation, while other bacteria would die in such conditions.
So this is adaptive in extreme environments, such as deserts (where it has evolved) or canned corned beef (where it was discovered).


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Yeast absorption of different spectra of light
I'd like to monitor the growth of a yeast population by shining light through it and monitoring the change in light that gets through as it grows. I'm not sure if I should use IR, or any particular colour of light.
Are there any charts that show the light absorption of brewers yeast to different spectra of light?

Usually the growth of microorganisms is monitored at 600nm.

Why not just run a spectrum of a yeast suspension and zero it to blank growth media?

You can also use a plate reader and 96 well plates it its feasible for your experiment.

Thanks for the comments. I am going to use Chris's information and try with a 600nm LED.

Here I have "Kilju" made with two different yeast. On is a blend of wild yeast and d47 I made wine with last year, and the other is bread yeast. One (the bread yeast) has additive light reflection (as in it appears to be brighter) while the other is subtractive and looks as if it absorbs light. https://i.stack.imgur.com/Ffp5I.jpg

Most of the loss of light being transmitted through individual cells is not absorbed, rather it is scattered (redirected from its original direction to a new one without loss of energy).  There is actually not very much in cells that can absorb visible light, and virtually nothing at all that can absorb many red or near-infrared wavelengths.
Scattering does depend on wavelength, but the relationship is very complex.  For scattering from small cellular components (mitochondria for example), Rayleigh scattering dominates, which will decrease with the 4th power of wavelength, so that green light will scatter much more strongly than red.  For larger components that are comparable or larger than a wavelength (nuclei or whole cells), scattering will increase much more slowly.  The relationship between the direction of scattering and the size/wavelength is even more complex, but is very useful in applications like label-free cytometry where cells can be sorted based on scattered light.
600-800 nm light is a reasonable choice because it will not damage the cells unless the power level is very high, although using shorter wavelengths may give you more sensitive measurements.


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Is hands-only CPR as effective as traditional CPR?
Is hands-only CPR as effective as traditional CPR ? Wouldn't 30 chest compressions + 2 rescue breaths be more effective if the person doesn't have a pulse AND not breathing?
From my understanding (correct me if I'm wrong) by doing chest compression you manually make the blood continue to circulate the body in order to deliver oxygen to the organs (and most importantly, to the brain), but after some time (several minutes?) all the oxygen from the blood will be used up, and if the person is not breathing, that means that no new oxygen is entering the bloodstream, so that would mean that chest compressions alone won't provide oxygen to the brain anymore, so they would be useless... am I wrong?

During CPR, you should push on the chest at a rate of at least 100
compressions
per minute

@MuditKapil I don't think that is what is being asked here. What's being asked is, if you are doing hands only CPR as opposed to CPR + rescue breathing aren't you just circulating the same O2 depleted blood?

I taught CPR for 4 years for the Canadian Red Cross. In a very practical sense good quality hand-only CPR is what every lay person should be doing. Call 9-1-1 as fast as possible. Push hard, push fast and don't stop for interruptions. Either you caught the person in the 10 minute window where they are still oxygenated and medics/physicians can save them in which case breathes are not useful (blood ox is still high) or they're blood ox has dropped and likely noone can save them. Keep in mind a barely alive person has very little oxygen demands.

The wikipedia page for CPR actually goes into some detail on this, going to block quote the section here for ease of access,

Compression-only (hands-only or cardiocerebral resuscitation) CPR is a technique that involves chest compressions without artificial respiration. It is recommended as the method of choice for the untrained rescuer or those who are not proficient because it is easier to perform and instructions are easier to give over a phone. In adults with out-of-hospital cardiac arrest, compression-only CPR by the lay public has a higher success rate than standard CPR. The exceptions are cases of drownings, drug overdose and arrest in children. Children who receive compression-only CPR have the same outcomes as those having received no CPR. The method of delivering chest compressions remains the same, as does the rate (at least 100 per minute). It is hoped that the use of compression-only delivery will increase the chances of the lay public delivering CPR. As per the American Heart Association, the beat of the Bee Gees song "Stayin' Alive" provides an ideal rhythm in terms of beats per minute to use for hands-only CPR. One can also hum Queen's "Another One Bites The Dust", which is exactly 100 beats-per-minute and contains a memorable repeating drum pattern. For those with non cardiac arrest and people less than 20 years of age, standard CPR is superior to compression-only CPR.

The American Heart Association has assembled some efficacy testing studies in the following review article, Hands-Only (Compression-Only) Cardiopulmonary Resuscitation: A Call to Action for Bystander Response to Adults Who Experience Out-of-Hospital Sudden Cardiac Arrest. Importantly, the human clinical studies reported no significant difference between those who received conventional cpr and those who received compression-only CPR. Some animal efficacy studies are noted, and with respect conventional CPR, the animals that didn't receive "rescue breaths" experienced a lower survival rate. In the end they note some limitations to hands-only CPR:

"...raised concerns about the possibility that recommending hands-only CPR for witnessed sudden cardiac arrest will, in fact, increase the complexity of decision-making for bystanders or that unresponsive victims of noncardiac medical emergencies (eg, drowning, drug overdose) will not receive rescue breathing."
"There may be situations in which ventilation alone could be life-saving but is not provided. There may be an interval after cardiac arrest when ventilations become absolutely critical for survival."

And as to the content in the second paragraph of the original post,

"It is important to acknowledge that during cardiac arrest without lung inflation and ventilation, there is a continuous decrement of blood oxygen saturation. At some point in time, the possible hemodynamic advantage conferred by continuous chest compressions (without ventilations) will be offset by this reduction in oxygen saturation, and the ultimate result will be a compromise in oxygen delivery. One porcine cardiac arrest study (3 minutes of untreated ventricular fibrillation, then 12 minutes of CPR) suggests that after 4 minutes of continuous chest compressions without rescue breathing, the delivery of 2 rescue breaths every 100 compressions provides a survival advantage over chest compressions alone."

The paradigm, again, is that hand-only CPR provides opportunity to get some help, other than no help at all, but the review also notes that more clinical data is needed on all fronts.

I might add that not doing un-protected rescue breathing is being recommended as a way to prevent infection (same reason we wear disposable gloves when handling bodily fluids).

Thanks for your response, but it doesn't answer the 2nd paragraph of my question, which is what I'm interested in knowing.

I can get how "Stayin' Alive" will keep you in rhythm, but I am not sure if humming "Another One Bites The Dust" won't scare the daylights out of any bystander/helper who is not familiar with this exact recommendation.

Sorry, i wasn't available to edit in more information due to some time constraints, but I've begun updating the answer to something acceptable.

I will address your second paragraph. When you compress the chest, you are also compressing the lungs and some of the air in the lungs leaves. This air is them replaced when you come off the chest. And the lungs naturally reinflate. The mechanism alone in higher quality cpr helps circulate the blood and it is oxygenated with the air that is moving through the lungs from the compressions.
When I was working in the ER in Arizona, Tucson was one of the city's that did a pilot program using hands only cpr in it's ambulances. This was prior to making the changes in 2010 and the survival rates were much higher. Of course they did obtain an advanced airway when there were respiratory issues and once they arrived at the hospital. This allowed the second rescuer to start a line, place the patient on the monitor and AED etc.
Hope this helps!

Welcome to Bio and thanks for your compelling answer. However, we urge users to add sources to their material such that others can background read on your material.


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When is the second polar body extruded from the egg nucleus?
When does the second polar body gets expelled from the egg nucleus during oogenesis ? I know that it occurs after the entry of the sperm into the secondary oocyte but does it occur before the fertilization or in the period between the entry of the sperm and fertilization ?

As stated in the answer by @CDB, these polar bodies don't last too long, and the second polar body which forms as the result of meiosis II, extrude only after fertilisation. The secondary oocyte is arrested in metaphase II until it becomes fertilised, so meiosis II can only by completed after ovulation and fertilisation (see e.g. UNSW Embryology: Meiosis at https://embryology.med.unsw.edu.au). This means that meiosis II, which actually forms the second polar body, occurs as a result of fertilisation. The secondary oocyte becomes a mature oocyte (ovum) by the expulsion of second polar body into perivitelline space.
The metaphase arrest is caused by the presence of two types of cytoplasmic activity
1. MPF - maturation promoting factor
2. CSF - Cytostatic factor that inhibits APC/C

Only when MPF is present, stabilized by CSF, and active will the M phase persist. However, this complex is very sensitive to calcium, such that a rise in calcium tilts the equilibrium away from complex synthesis towards destruction.

Capcitated spermatozoa that have undergone an acrosome reaction is capable of fusion and Calcium mediated calmodulin is required for this process. When fusion happens spermatozoon ceases to move and the nuclear with parts of mid piece and tail passes to the ooplasm. So sperm initiate Calcium release at fertilisation this helps in the completion of the 2nd meiotic division.
For further detail on these processes you could read the article Penetration, Adhesion, and Fusion in Mammalian Sperm-Egg Interaction
Increased Calcium activated Calpain (calcium dependent cysteine protease which causes CSF to disappear thereby activating APC/C which in turn causes dissociation of MPF. This results in completion of 2nd meiotic division.
For further details I recommend you to read Johnson and Everitts Essential Reproduction (6th edition), cell cycle chapter in The cell by Bruce Albert (5th edition)

During oocyte–sperm fusion and second polar body expulsion, the cytoplasmic contents of the sperm cell membrane (now fused with the oocyte membrane) pass into the oocyte cytoplasm. Between 4 and 7h after fusion, the two sets of haploid chromosomes each become surrounded by distinct mem- branes and are now known as pronuclei (see Fig. d). The male is usually the larger of the two. Both pronuclei contain several nucleoli. During the next few hours, each pronucleus gradually moves from its subcortical position to a more central and adjacent cytoplasmic position. During this period, the haploid chromosomes synthesize DNA in preparation for the first mitotic division, which occursabout 18–24h after gamete fusion. The pronuclear membranes around the reduplicated sets of parental chromo- somes break down (see Fig. e), the mitotic metaphase spindle forms and the chromosomes assume their positions at its equator. The final phase of fertilization has been achieved: syngamy (or coming together of the gametic chromosomes) has occurred. Immediately the first mitotic anaphase and telophase are completed, the cleavage furrow forms, and the one-cell zygote becomes a two-cell conceptus.

Polar bodies will usually undergo apoptosis in about 17 to 24 hours after the egg forms (the final stages of telophase II (cytokinesis)) because they have relatively little cytoplasm and shunted organelle development (Schmerler & Wessel, 2011).

A secondary oocyte contains n/2C genome and a sperm fuses with a cell with n/C genome (matured ovum). Therefore a secondary oocyte must divide and eject a polar body and that happens due to fertilisation.
so the answer is after fertilisation and before entry of sperm.

Hi Shoaib. Welcome to [biology.se]. Can you please add a reference to support your answer? Good references include books, peer-reviewed articles and verified websites of academic/scientific organizations.


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What type of flask should I use to culture NTERA2 embryonic cancer stem cells?
I'm just starting my MSc research and I am in the process of making a list of equipments/consumables to order. Is there a specific flask in which I can culture NTERA2 (NTERA2/D1) cell line?

I just use regular TC-treated Petri dishes and flasks - nothing special.

I found a protocol by ATCC for NTERM2 cells, and it didn't mention any specific flask, so any cell culture flask would do. Since ATCC is basically a cell culture bank I trust that their protocol is valid.


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Is (are) there any crucial gene(s) for the formation of flower in flowering plants?
I am interested in qualitative (flowers of some plants have petal or sepal, but some plants have not) and quantitative (number of flowers of plants) differences between flowers of different plants.
Formation of flower in flowering plants is under control of which genes?
Which genes are the most important ones in flower development, for example which gene tell the flower that you should have for example 2 stigmas. or which genes tell the plant that you should have 4 flowers or your flowers will not have sepal...
Thank you

I think this is far too broad (all flowering plants, different features, both initiation and development). You are asking for a textbook. Can you narrow this down?

I am looking for a brief description

I think you are looking for the ABC model of flower development


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Do butterflies see behind?
Butterflies, like many other insects, understand that I am getting near from behind. How do they feel this - through vision, hearing, or some other sense?

Short answer
Butterflies can see behind them.
Background
Merry et al. (2006) have estimated the field of view of the butterfly, by investigating the Orange Sulphur butterfly (Colias eurytheme):

Colias eurytheme. Source: Massachusetts Butterfly Club
The authors found that this butterfly has a very large visual field, encompassing
93% of the spherical space around the animal. There was a small blind spot behind the head not seen by either eye. Another study by the same group showed similar results in another species of butterfly, the Empress Leilia (Asterocampa leilia). Here is a picture of the estimated binocular field of view of the Orange Sulphur, revealing that the animals' vision is virtually spherical, with only a small blind spot at the back (the white area):

Source: Merry et al., 2006. Grey is the field of view, white the blind spot posteriorly. Cardinal directions are indicated (Dorsal, Ventral, Posterior, Left and Right).
Here are a few pictures of other species of butterfly that show the protruding compound eyes covering a large field of view:

Sources: Alex Sukonkin and PhotographersDirect
The feature of large visual fields in insects is, however, not restricted to butterflies (Lutowski & Warrant, 2002). Another insect I often try sneak upon to take pictures are dragon flies, and more often than not they fly away regardless of the angle I approach them. They too have these large compound eyes with a field of view extending to the back:

Source: Nature North

References
- Lutowski & Warrant, J Comp Physiol 2002;188:1-12
- Merry et al., J Insect Physiol 2006;52:240–8

Butterflies have nearly 360 degree field of vision (see e.g. Belth. Butterflies of Indiana), so they can see you or other predators approaching from behind at the same time as they examine the flower they are feeding from. A large field of vision is common in many animals that are preyed upon, and for instance many birds (e.g. waders) have 360 vision, some even with overlapping, binocular vision behind their heads.

You beat me by 21 seconds! +1 for your evolutionary perspective :)

@AliceD Well, your answer is more complete with better references though.


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What is the role of RAGEs?
According to articles I read, AGEs (advanced glycation end products) activate RAGEs (receptors for AGEs). This activation increases the ROS (reactive oxygen species) levels in the cells.

2003 - Reactive Oxygen Species-Regulated Signaling Pathways in Diabetic Nephropathy

Free radicals can cause damage in cells, which is definitely not good. What do you think, what is the role of RAGEs, which is more important than cellular damage?