text:
Is there any genetic similarity that defy evolution theory?
For example,
say species A is common ancestor of B, and C. Species B is a common ancestor of D and E.
We would expect that there will be more genetic similarity between D and E than D and C. And those genetic similarity must exist in B.
In other word, we won't expect genetic similarity that don't "cross" the common ancestor or the evolutionary tree.
The exception is probably genetically engineered bacteria.
That being said, am I correct?
Some people say that we have similarity with pigs and chimps even though our common ancestors may be to far off. That won't happen right?
To summarize
I expect that evolutionary tree will form a well, tree. Genetic similarity would infect "nearby" trees and can't jump between trees without connectors, such as common ancestors.
Is that what we observe for ALL species?

There's a weird debate going on in the comments of dmm's answer and there were several downvotes that I don't understand on my answer. Do you think my answer answers your question? I thought you were interested in understanding whether or not D might be more genetically similar to C than to E, is it correct? Or were you mostly interested in a debate of what is "believing", or about a science-religion debate? Or something else...

Note: dmm's answer and the debate have been deleted.

A reader might also want to have a look to this post on the same subject

You have an excellent answer from Remi.b already but I just wanted to add/emphasise this (because there is always more than one way of explaining something and IMO the site benefits from having many answers to the questions)...
The tree we construct does not necessarily accurately reflect what happened in evolution. If B & C evolved from A, and D & E came from B, we would create this tree if we measured using the correct indicator. But the methods we have are not perfect. The first evolutionary trees were based on morphological descriptions etc. and clearly some of the classifications were going to be wrong. These days we use molecular methods, which are probably more accurate but could also be wrong some times. For example if we based our phylogeny on one SNP variant we could have some idea about the phylogeny between a few species, but if we based it on millions of SNPs we would have a much better idea - as technology & models improve that is becoming more realistic. The key point here being there is a difference between the trees we can draw from evidence, and the real evolutionary tree.
If, for example, D evolved from B but was more genetically similar to  C it could be due to convergent evolution (if the same mutations are selected for in C and D but neutrally or negatively in B). This is because, if there is a shared standing genetic variation at the point of speciation or the same mutations occur after speciation, and then C & D are imposed under similar selection and B is not, the allele favored in that environment will spread in C & D but not B (it may drift in B).
Imagine this with humans, where populations split off around the globe. Two populations spread from Africa (A) in to Southern Europe (SE) and Western Asia (WA). Population WA then derived two more populations - Central Asian (CA) and Eastern European (EE). If the Eastern European population developed a habit for drinking cow milk, and that information passed to the Southern Europeans, then selection would favor the ability to digest lactose in those two populations. If we then used the lactase persistence SNP (which had standing genetic variation at the time of divergence) to derive a phylogeny the populations SE and EE would appear related because the allele for lactase persistence is common, but in A WA & CA it would be rare (neutrally evolved). In this case the phylogeny we construct would be different to the true phylogenetic tree.
Basically if there is genetic variation at the point of divergence, or convergent selection, or any gene flow occurs after divergence it makes assessing the phylogeny more difficult and prone to error.

+1 Very good clarifications for important concepts I only wrote some lines about.

Very good point in deciding where my simple theory would go wrong.

Your question seems rather confused to me, I don't quite understand it. Below I try to explain some stuff, I am not quite sure it would help you finding the answer to your question. Let me know if it helps you and how I can improve this answer.
While natural selection selects for a given allele (gene variant), mutations create new variation. And because of this process of mutation there is genetic pattern in species D that would cannot be found in species B (assuming that we have the DNA of species D). But what is similar between B and D were probably also present in their common ancestor B. The exceptions are molecular convergent evolution and horizontal gene transfer (natural of artificial).
Because of common ancestry …

Humans have similarities with pigs

Example: endothermic amniotes

Humans have similarities with a bug

Example: bilaterial symmetry

Humans have similarities with jellyfish

Example: Heterotrophy

Humans have similarities with an oak tree

Example: We have mitochondrias

Humans have similarites with any living things on earth!

Example: Genetic information is hold into a DNA/RNA molecule.

If you might observe that D is genetically speaking more similar to C than to E… This can be due to:

Horizontal gene transfer (artifical or natural)
The mutation rate (or ability to fix mutations) in one lineage might be greater than in another lineage.

For example, if lineage E underwent many mutations, they might be genetically speaking have accumulated many difference compare to D, way more than the number of difference that D has with C.

The phylogeny might be wrong
There might have had some convergent evolution.

Think about fishes which opsins in the eyes need to be adapted to the amount of light which depends on the turbidity of the water. After the three lineages splitted, the change of envirronment might have occured the sequence AATGATCCT suddenly became beneficial. Only two lineages had the chance to produce the right mutation. Or maybe lineage E live at low depth and therefore it doesn't need this mutation because there is enough light at low depth anyway.

Therefore, one should not expect a common ancestor to be the arithmetic mean (supposing it means something) of the current species. And one should not expect that two closely related species on the tree of life should necessarily be more genetically similar to each other than any of the two to a third species.
Note that the phylogeny is constructed mostly based on genetic data. Which makes that two closely related species (on our tree which is not necessary the absolute tree of life) are (almost) necessarily more genetically similar (it is kind of a definition then).

I hope you don't mind, I added an image to make it easier to follow the discussion.

Are there genetic similarity between humans and pig that don't exist in chimps?

Yes there are. The reasons are found in the last part of my answer. The most important point concerns the mutation that occurred in the chimps lineage.

Note that if the rates of evolution are considerably different in different branches, taxa from slow-evolving lineages may have smaller genetic distances from each other than to their respective fast-evolving sister groups. Although this is not expected on the level of species.

Someone downvoted my answer. Please let us a comment when doing so.

@har-wradim Yes this is what I meant in the second point of the list of possible reasons. You're welcome to edit if you want to make it more understandable. Thank you.

O, I see. I'm not sure, the way you formulated this point is totally clear for everyone. What about adding another sketch for this case, supplied by a description in terms of distances?

Correct answer otherwise. Down-vote was definitely not from me :)

@har-wradim Ha ha no I didn't think you were the guy who downvoted. I updated my answer hoping to make it more understandable.


text:
Are there genetic similarity between humans and pigs that don't exist in chimps?
Chimps are our closer relative.
Any genetic similarity between humans and chimps must exist on the common ancestor.
Pig branch out sooner. So, any genetic similarity between humans and pigs must be on common ancestor between humans and pigs. That must be on common ancestor between humans and chimps.
But chimps may evolve differently.
Hmmm... I am confused.
Actually is there any?

This is a great question. Looking forward to the answers.

For those wanting to answer: Here is a closely related question that share many similarities ;)

Yes there are!
I think it would make more intuitive sense to you if you would have switched the words chimps and humans in your question:

Are there genetic similarity between chimps and pigs that don't exist in humans?

Then, you would directly answer, of course, there are genes concerning bipedalism, brain (FoxP2 for example), digestive track (adult production of lactase for example) and so, and so… which are different in humans but might not have much reasons to be so different between pigs and chimps. Those mutations occured on the human lineage after the split between human and chimps.
To answer your question:

Are there genetic similarity between humans and pigs that don't exist in chimps?

Yes. Most of these difference are due to mutations that occurred in the chimps lineage after the split of the original lineage into human lineage and chimps lineage.
The following are improbable but would also allow to explain such similarities:

Genetic admixture or introgression between human and pig after humans and chimps lineages splitted.
Convergent evolution.

Maybe pigs and human got the same beneficial mutation that never appeared in the chimps lineages.
Maybe pigs and human, due to the fact that today live in cold climates evolved the sequence ATTCGCTGA which cause them to produce a more efficient shivering!

This question doesn't make a lot of sense.  Humans, chimps and pigs are all eukaryotes, share a lot of sequence similarity due to common ancestry.  We are all vertebrates, we are all placental mammals.  So there is a lot of similar sequence between us, more than we have with lizards.
So humans, chimps and pigs all have a common ancestor. Is it possible that there are some sequences where the human versions have drifted farther from the common ancestor than either chimps and pigs have?  Sure, it's possible but probably not very common.
Here's link to ensembl's page on one random gene, the transferrin receptor.  You can see the % identity between the orthologues of a number of species.  Chimps and humans are 99% identical.  Pigs are 76%.  All the primates whose transferrin sequences are known are in the 90's percentage wise, the other mammals are not nearly so close a match.
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000072274;r=3:195754054-195782085;t=ENST00000360110
Here's another gene, where the gene has changed much less over time, but pigs are still not as similar to human as chimp
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000138379;r=2:190920423-190927455;t=ENST00000260950

Perhaps what Jim Thio is interested in is the xenografts from pigs to humans..

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
What are the visual, behavioral similarities and differences between Yellow Fever Mosquito (Aedes aegypti) and the Tiger Mosquito (Aedes albopictus)?
The Tiger and Yellow Fever Mosquito visually look very similar.
Recognizing the difference is important for tracking and controlling the spread of Yellow Fever, Dengue fever and other diseases. Especially important, now that the range of the two have overlapped in the United States.
I have some questions about the commonalities of these mosquitoes.

Evolutionarily, How can the similarities be explained?
Why do they both have the black body with white stripes?
What is the best way to tell them apart?

A. aegypti, the Yellow Fever Mosquito

A. albopictus, the Tiger Mosquito

Assuming that Aedes is monophyletic, the similarities between them can be explained simply by the fact that they share a very recent common ancestor and are therefore very closely related!

For the best way to tell them apart, see this guide: http://www.cdc.gov/dengue/resources/30Jan2012/comparisondenguevectors.pdf
Specifically, it seems that the silver pattern on the torso is different (lyre-shaped for Yellow Fever Mosquito, more linear for Asian Tiger Mosquito).  Location is probably also an important determinant.

+1; thoracic markings are the way to do it. I'd recommend adding a photo or image comparing the two (e.g. http://www.nzdl.org/gsdl/collect/who/archives/HASH017f.dir/p010a.gif) to your answer..

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Identification - What kind of animal leaves these tracks?
I live in the suburbs of Washington DC where it recently snowed. I was admiring all of the tracks left behind by wildlife of all kinds when I came across these prints, that I was unable to recognize from charts of common animals prints online.

What is unique about them, is that each print, has 3 points, and there is only one straight line of prints, about 2-3 feet apart, where as I would imagine a deer, or other 4 legged animal would leave staggered footprints. We have a lot of deer in these parts but these dont seem to match deer print patterns I've seen online.
Each print is about 5 inches by 4 inches at their widest/longest points (they are longer then they are wider).
Note, the snow has melted somewhat since they were initially made.

The only candidate I could imagine is hare.
Sometimes it leaves a single track from its fore-limbs (from a theoretical point of view, I'd say it happens when the snow is relatively deep.)

I'd say hare too - seen them leaving tracks here!

Excellent, thanks. Upon closer inspection and watching some videos on youtube on how hares move, it seems that the "dot" may be its front paws close together and the 2 longer lines are its hind legs. Seeing them walk its common for them to cross their hind legs in front of their front paws creating this pattern.

O, I wrote "hind-limbs" - now corrected.

@n00b I had the same confusion when I first encountered these tracks, it wasn't until I found some very fresh ones where I could even see the pads of the paws that I worked out what it was.


text:
Can humans be printed?
Is it possible to spray stem cells on fully grown skeleton to get fully grown humans?
Currently, just read about recent advances, and wondered if something like this is possible.

No.
Very early in the development of an organism, it is just a clump of cells.  Then those cells communicate, and determine where they are in the clump, which determines their eventual fate in the full organism.  In mammals, for instance, cells split into three different layers, and the skin and nerve cells develop from cells in the outermost layer...etc.
You can't just dump a bunch of stem cells somewhere and expect them to know where they are and what they should be developing into.

I am tempted to downvote such a strong opinion... what if you replicated the exact configuration of elementary particles of a person?

A skeleton is itself very complicated.  It's not just apatite in the shape of a skeleton.  The bones have structure, and many have bone marrow.  Tiny cells navigate through the bone matrix, keeping it sound.  Those cells, and the ones in the marrow, need a blood supply to keep them alive.  Plus, what swbarnes2 said.

And through these cells our bones are actually alive. The osteoclasts and osteoblasts are in a constant process of building up and breaking down bone mass.

See spryaing stem cells is not that easy as it sounds.The main difficulty working with stem cell is keeping their stem cell characteristics intact till the development actually begins.Stem cell can be amny types such as pluripotent,totipotent,multipotent etc.As you asked bone,bone is also a result of stemcell.So point is first you have to generate bone and bone generation is a massive and intricate process.You need many growth factors for this process and these growth factors are developmental time specific it means it is expressed at only a certain point of time.So I think it's difficult


text:
Why is cyanide poisonous?
I know cyanide inhibits complex IV in the electron transport chain, but I don't understand why this makes it so toxic. If cyanide is bound to the complex, can't the electrons just bypass it   and reduce oxygen directly? That way fewer protons would be pumped out of the matrix, but most still would, and aerobic respiration would just be less efficient, rather than stopping entirely.
Essentially what I'm asking is what causes the electrons to get "stuck"?

Electrons get stuck because they can't be passed to complex IV, and this causes a backup in all the complexes of the electron transport chain. Therefore the cell faces an energy crisis, and eventually causes death.

But that doesn't explain why the electrons have to be passed to complex IV. My question is why can't they bypass that complex if it's deactivated and just go straight to oxygen? From what I understand, premature electron leakage toward oxygen is one of the reasons cells don't produce ATP at the theoretical maximum efficiency.

That leakage is due to the inefficiency of the complex-specificity, i.e. sometimes the highly specific requirement of substrate for these electron-transfer enzymes relaxes and it allows some electrons to leak, forming free ionic oxygen radicals. Otherwise, they are very specific in what they reduce and hence cannot bypass the predetermined chain disabling the effect of cyanide.

all these comments could be incorporated into answers - please don't answer questions in comments!

Cyanide binds cytochrome oxidase so as to prevent the binding of oxygen. Electron transport is reduced to zero, and none of the oxygen breathed in can be used. Cytochrome oxidase is one of a superfamily of proteins which act as the terminal enzymes of respiratory chains, so if the cyanide is binding to the cytochrome then it inhibits the process and making it dangerous. Another example I would give rotenone which binds competitively.

That makes sense; I think for some reason the mental model I  was using involved oxygen just floating around the complexes and magically abducting electrons when they got close enough to one of them, but your answer combined with Satwik Pasani's fixed the blight of stupidity I seemed to be suffering from for a while there. Thanks.

This answer seems to suggest that rotenone inhibits cytochrome oxidase, but it doesn't, it inhibits electron transport at complex I > ubiquinone.


text:
Why do most animals never seem to evolve over millenia?
People often say, including those with extensive knowledge in biology, that a certain species of animal will evolve in one way or another:

From changing environments.
Mutations.
Possibly even genetic engineering from human animals.

My question lies in the fact that, aside from the latter option, why haven't any differences in animals'(except humans) markup, morphology, intelligence, DNA, behavior, or any habits changed over thousands or (possibly millions) of years?
A cockroach has had the same behavior it has today more than 10 million years ago, and there have been no advancements in the species in the slightest bit.
It makes you question evolution, because why don't other animals (like cockroaches) have any changes over 10+ million years, yet humans, like me and you somewhat, have, in a relative period of time similar to the linked geological period above, evolved from spear tossing hominids into someone brilliant enough to even ponder this question.
If modern humans are the result of mutations in genes, why has no one species over the course of hundreds of millions of years been fit enough, or advanced mentally as we have, or even in any slightest bit?

The cockroach hasn't changed because it is perfect as it is :-)  Evolution isn't directed towards advancement (even when said "advancement" isn't a figment of anthropocentrism), it's driven by survival & reproduction.  Cockroaches survive & reproduce quite well as they are.  Absent some major change in the environment, where's the driver for change?

Cockroaches have changed quite a lot, modern cockroaches are very different from cretaceous cockroaches, there is also quite a variety of them (and that's without including termites). saying they are the same is like saying humans and lemurs are identical becasue we are both primates. Your premise is based on your own lack of knowledge about the organisms not a real lack of change.

People with extensive knowledge in evolutionary biology won't say list these three elements as the three ways evolution happen!

Would you notice cockroach evolution if it happened?  In fact, there is a recent example of evolution in common household cockroaches: they've evolved to resist the sugary baits used in traps: https://www.livescience.com/34647-cockroaches-evolved-avoid-baits.html

Just in the last 100 years we've seen peppered moths change color, drug-resistant bacteria, pesticide-resistant bugs, metal-tolerant centipedes, and so much more. Other animals are evolving quite well in fairly obvious ways.

Universal laws of action and reaction put epigenetic pressure causing adaptive diversity of species. Life acts like a liquid, filling the container named: environment. The speed of evolution is direct proportional with epigenetic pressure. Crocodiles or sharks are self sufficient for hundreds of millions of years barely evolving if any at all.
ENVIRONMENT PRESSURE in my opinion it's causing diverse changes. Besides, why fix something if it's not broken or change something when it's not necessary?

How come most animals never seem to evolve over millennia?

The word "seem" in your question should not be disregarded. You seem to assume that cockroaches (or most animals as you say) did not change much the last tens or hundreds of thousands of years. But what do you know about that (no offence here)? Have you actually reviewed many kinds of research that estimate the rate of evolution of different randomly chosen lineages in the past 500,000 years? I think you assume that other species evolved slower than humans rather than know it. And you will certainly put much more importance to the evolution of the gene FoxP2 (involved in language) than to a gene allowing cockroaches to have a better sense of smell. This is a biased view of what is a rate of evolution. It would be much wiser to consider a rate of evolution as something like the number of newly arising mutations that succeeded to get fixed in the population. See Haldane's rate of evolution and the Darwin unit. Please don't make the mistake to think that being smart (or complex) is some kind of the goal of evolution and those that are not smart (or complex) are "less evolved" or that they evolved more slowly.
You also seem to want to point on the evolution of DNA and evolution of habits. I guess you might be appreciative of the evolution of human knowledge and culture. But this is obviously something that does not have to do with genetic evolution but is rather a matter of cognitive capacity. You cannot compare the change of culture and traditions of insects and humans as insects have mostly no traditions.
Now, this is obviously true that different lineages evolve at different rates. Many things influence this rates such as the population size, the mutation rate, the generation time, the selection pressure (which itself might depend on social structure or the rate of environmental change for example). In these terms, I would rather believe of Homo sapiens as a lineage that should have a rather slow evolutionary rate.
Homo sapiens is quite a recent species. And speciation is often linked with phenotypic divergence, with niche competition and niche complementarity and therefore with a high rate of evolution. In these terms, I would believe that humans are a lineage with high evolutionary rate.

This is a tricky question.
First, evolution tend to be slow, although there have been recent examples of very fast evolution as well. So for most evolutionary processes, we are not present long enough to see them either happening or see the outcome. Therefore its also hard to say that no evolution is happening - see your cockroach example. How do you know that these animals are the same as 10 Mio years ago? And even if it is like this, it can also mean that these animals fit their niche so good, that there is not much pressure for further adaption.
This can change pretty fast as examples from mites (here a report in the BBC, this is the original publication). Another example of fast evolution (of bigger animals) are the Cichlids in the Lake Victoria, which developed new after the last time the lake dried up completely something like 12.000 years ago. After that, an estimated 300 endemic species developed (see here) which was then reduced by pollution and other environmental problem. The remaining species are evolving again to occupy the free niches (see here).
In the case of the human, we are pretty lucky, that no other intelligent animal has come up so far. They would have fought for the same biological niche and living space with one species eventually dying out. This has, for example, happened to all the other homo species (habilis, erectus, neanderthalensis). As a species, we are quite young (around 200.000 years), so there is something going on. And there is genetic diversion between humans, but still not as much, that we cannot cross each other anymore. And with 7 billion of us now present, it's not that easy for mutations to come through at our reproduction rate.

aside from the latter option, why haven't any differences in
  animals'(except humans) markup, morphology, intelligence, DNA,
  behavior, or any habits changed over thousands or (possibly millions)
  of years?

What evidence is leading you to that conclusion?  For horses, example.  (From the talkorigins article):

The first equid was Hyracotherium, a small forest animal of the early Eocene. This little animal (10-20" at the shoulder) looked nothing at all like a horse. It had a "doggish" look with an arched back, short neck, short snout, short legs, and long tail. It browsed on fruit and fairly soft foliage, and probably scampered from thicket to thicket like a modern muntjac deer, only stupider, slower, and not as agile. This famous little equid was once known by the lovely name "Eohippus", meaning "dawn horse". Some Hyracotherium traits to notice:Legs were flexible and rotatable with all major bones present and
  unfused. 4 toes on each front foot, 3 on hind feet. Vestiges of 1st (&
  2nd, behind) toes still present. Hyracotherium walked on pads; its
  feet were like a dog's padded feet, except with small "hoofies" on
  each toe instead of claws. Small brain with especially small frontal
  lobes. Low-crowned teeth with 3 incisors, 1 canine, 4 distinct
  premolars and 3 "grinding" molars in each side of each jaw (this is
  the "primitive mammalian formula" of teeth). The cusps of the molars
  were slightly connected in low crests. Typical teeth of an omnivorous
  browser.

So from that, you conclude that the DNA, morphology, and intelligence of horses hasn't changed at all in 50 million years?

In response to this part:

If modern humans are the result of mutations in genes, how come no one species over the course of hundreds of millions of years has been fit enough, or advanced mentally like we have, or even in any slightest bit?

All animals are the result of evolution, which includes mutations.
Now, what you should understand is that evolutionary changes have to be selected for, but also must be immediately useful to the organism if they cost more.
There is a long term tendency in our lineage towards increased brain sizes. Animals -> Mammals -> Primates -> Humans. This long term development need not have happened in the first place. In the Jurassic Period, the most successful group of animals were dinosaurs, who in general had small brains.
In addition, our brains require far more calories than the brain of, say, a chimpanzee. Even if you have a lineage that, over the generations, has a tendency towards larger brain sizes, it would also need to be able to hunt or forage more in compensation for the increased caloric needs. If it were not able to do so, a larger brain would actually be a profoundly negative characteristic, a useless drain of energy.
In addition, the benefits of increased intelligence are highly circumstantial. Consider if you gave a cheetah all the brain power of a human. It might then understand that if it dug a hole and placed fake grass over it, it could catch an antelope for less effort than having to stalk and chase it. Less effort means less calories expended and ultimately most of an organism's fitness has to do with how much energy it expends in trying to procure energy (calories).
But lacking opposable thumbs and hands with digits, it would be unlikely to accomplish such a thing. Also, such tasks are more efficient when done by a group, but many animals do not coordinate group-wise as extensively as humans do. So what we have is at least 3 but probably many more things which all have to come together in the same species for them to rise to the top of the food chain like we did:

Dextrous limbs (i.e. opposable thumbs and seperated digits)
Brains tripled in size (relative to other species of ape)
Behavior of extensive group coordination (tribes)

As you can imagine, a species evolving our intelligence and using it to dominate the local ecosystem as extensively as we do is therefore a rarity.

You have put high effort for an answer, but please consider adding some references to your answer.

Evolution is an ongoing process; it has no predetermined goal or direction; it never stops. Nothing ever stops because everything is ever-moving, ever-changing.
Is man more intelligent now than few thousand years ago? Has mankind a better understanding of the phenomenal and noumenal realms now than the people who composed the Upanishads, the Brahmanas, the Vedas ~2,500 years ago, which was preceded by hundreds if not thousands years of oral transmission (myths) from generation to generation?

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


text:
What is the best way to orally administer a water insoluble powdered drug to macaque monkeys?
They typically need to be given ~150mg, once a day, and it'll last for two weeks. The drug is very water insoluble, becomes almost like a paste, not suitable for tube feeding. And yes, this is for for real lifesaving medical research.
The best we can come up with right now is putting them to sleep, mixing the powder into Nutella, and putting it under their tongue. The idea being they'll wake up and swallow the mixture.

I'd give this a veterinary tag, but it doesn't exist, and I don't have enough points.

So what's it soluble with? Could you dissolve it in oils, like coconut oil? I suppose it tastes too bad to just mix it with mashed bananas?

Can you mix it with food? Especially something what your macaques like?

Could you not suspend it in some liquid?

If it is not water-soluble (lipophobic or hydrophilic), the only other alternative would be that it is fat-soluble (lipophilic or hydrophobic). Consider adding the powder to fatty solids or liquids which can be absorbed from the GI tract into the vascular system, if that is where you'd like the drug to go to be distributed throughout the body. Ideally, you would need to look up the target concentration of the drug within the blood in order to be effective, its volume of distribution, its bioavailability, its half-life, mechanism of metabolism, and calculate from there how much you would really need in order to last the full 2 weeks.

Thing's aren't always water or oil soluble, I've tried to dissolve indigo dye in several organic solvents with no luck. Of course any drug as insoluble as indigo would have terrible pharmacological properties.


text:
How is membrane capacitance related to the increased speed of saltatory conduction?
Here is the original question which inspired my question. As explained by the answers there, the reason saltatory conduction in myelinated neurons is faster than non-myelinated conduction is because the capacitance of the membrane is lowered by reducing the number of channels (Channel density) or equivalently, increasing the spacing between channels. I also did a preliminary study of membrane electrodynamic modelling here and here.
From what I gathered from the linked question, the decreased capacitance overcompensates the effect of absence of channels reinforcing the sodium current, and on the whole, increases the speed of conduction by allowing the depolarizing potential to travel to the adjacent node faster than in case of an unmyelinated fibre. In view of this, I have a question:-

Why does lower capacitance increase "the effectiveness of nearby
  nodes" or allow the depolarizing voltage to "travel not by ion
  diffusion, but as an electric field"? I am comfortable with capacitors
  and related physics, but why would lower capacitance allow propagation
  of the changing voltage as an electric field, is still unclear to me?
  (The links I have placed also help quantify the problem
  mathematically. This allows us to say that $\lambda$, or the rate of spatial
  decay of potential, increases, decreasing the effective
  length of the neuron. Why should its decrease help faster conduction?)
And another question is, how would reduced density of sodium voltage
  gated channels cause a decreased capacitance?

Very nice question! I'll go through your three questions sequentially.
Q1: Why does lower capacitance increase "the effectiveness of nearby nodes" or allow the depolarizing voltage to "travel not by ion diffusion, but as an electric field"?
A: Capacitance basically results in sequestering of charge of opposite polarities along the cell membrane, which basically results in a neutralization of charge differences. The effect of this is explained on the website of Amrita and I quote:

[...] a higher capacitance results in a lower potential difference. In a cellular sense, increased capacitance requires a greater ion concentration difference across the membrane.

What myelin does is insulating the neuron, thereby decreasing its capacitance. You could say that by increasing the thickness of the membrane, the negative insides of the cell do not attract positive charge outside the cell. It's a bit simplified, yet it effectively describes what myelin does (see cambridge web page on capacitance).
So in a myelinated axon, when Na+ enters the cell in a node of Ranvier, the positive charge entering the cell is not counterbalanced by outside negative charge and hence, the charge is not or at least less counterbalanced. This allows for the depolarizing potential to be transmitted by electric charge. If there were no myelin, the depolarizing potential would fade out pretty quickly along the axon by neutralizing charges outside the cell. Without myelin the opening of more sodium channels in the direct vicinity are necessary not only to transmit the action potential across the axon, but it is also necessary to amplify the signal to prevent it from dying out. In a myelinated axon, hence, the depolarizing potential reaches much farther and in answer to your next question:
Q2:This allows us to say that λ, or the rate of spatial decay of potential, increases, decreasing the effective length of the neuron. Why should its decrease help faster conduction?)
One could say that myelination effectively decreases the length of the axon (the lamba parameter) as the depolaring potential reaches further along the axon.
The fact that the depolarizing potential reaches further means that voltage-operated sodium channels can be activated at larger distances from a certain depolaring potential. Hence, adjacent nodes of Ranvier can be spaced by as much as 1.5 mm. Due to the fact that the next node is activated by passive spread of an electric field, which is pretty much instant, it skips the intervening distance with about light speed, greatly enhancing conduction velocity.
Q3: And another question is, how would reduced density of sodium voltage gated channels cause a decreased capacitance?
Basically there are no ion channels below a myelin sheath as they are totally useless there. It is the myelin that decreases capacitance and there happen to be no channels underneath.

Wonderful answer. One follow-up question, though. Is the decrease in capacitance due to myelination a consequence of only the increase in separation of the charges or is there some contribution by the actual material of the myelin?

@SatwikPasani - sorry for this slow response. Capacitance can only be mediated by insulators because charges have to be separated. Conductors will allow charge passage. So yes, myelin should be insulating and therefore a fatty substance like myelin is best. Salinic watery substances should be avoided.

The Hodgkin-Huxley model:
$$I=C_m\frac{dV}{dt} + g_k(V_m - V_k) + g_{Na}(V_m - V_{Na}) + g_l(V_m- V_l)$$
Where $C_m$ is membrane capacitance per unit area and $g_i$ are membrane conductances.
Reducing the number of channels does not affect capacitance; it basically reduces membrane conductance.
Myelination causes reduction of number of channels (concentrating them only at the nodes of Ranivier) and also increases the effective membrane thickness.
Capacitance decreases as an inverse function of "inter-plate distance" (of parallel plates) which is the membrane thickness. This reduces the capacitative current.It also prevents the build up charge and thereby allowing it to propagate forward (Longitudinal current). IMO, the effect of myelination of capacitance would be much less than that of its effect on conductance.

Hi, do you know how myelination causes reduction of number of channels? See my question here.


text:
How much does a biological experiment to validate a gene function cost?
I am computer scientist working on machine learning methods applied to predicting missing Gene Ontology annotations.
In many papers, I wrote that my computational methods are very useful to suggest to the biologists  on which gene functions they should address their research, because my software need less resources (a simple laptop connected to a database) and less time (e.g. with a dataset of all the Homo sapiens Gene Ontology annotations: about 3 hours) than their biological experiments.
Now a reviewer asked me to be more precise. Truly, how much does an in vitro experiment to biologically validate a human Gene Ontology annotation run by biologists cost?
How much money, broadly?
How much time?

Wow that can vary from a couple of months and a few thousand dollars to a lifetime and millions of dollars.  I can give a couple of examples, but this is an extremely broad question.  Wet science is not cheap might be the message here.
Gene Ontology terms are meant to cover all biological roles known for genes.  Terms are added and retire regularly.  They embody thousands of person-years of work to establish the framework of what is going on in cells.  At the same time its a limited vocabulary of gene behavior.  It doesn't represent a complete catalog of all known gene behaviors (e.g. in such detail that it could only be the property of a specific gene) and it is also uneven in the level of its detail of its leaf terms.  Its an ontology that is manually assembled and edited and therefore subjective.
I just did an overview of GO 1.2.  there are 34153 unique GO terms.  That's easily 10s of thousands of separate assays, so picking a group of important ones might be useful. There are also lots of orphan GO terms, where only one gene is currently attached to the term.
For GO annotations, a simple and typical case is a metabolic gene which has a high homology to a known gene and you are only trying to verify that biological role, and you have a functioning biological laboratory.
A breakdown might be:

clone the gene ( \$200 to \$1000 and up): order primers, use PCR to insert the gene into a plasmid or get the gene synthesized if you have to, transform it into bacteria,  ideally sequence it to make sure you have it right.
purify the protein ( \$500 maybe).  Run a check culture to see if the protein is produced, then run a full culture with induction, lyse it and then purify on an affinity chromatography column.  you may need to run a second column to get the protein pure.
do a kinetics study with mass spectroscopic validation of the products (minimally about \$300).  Cost involves reagents - if you have an assay you can use a UV/Vis spectrophotometer this can be simple, if not it can be much more expensive. This part will vary with the enzyme you are looking at.

Hopefully you get all these steps right the first time.  Salaries are not included in this cost.
The more complicated the GO term, the more difficult the work will be - they are not all equal.  If the protein function can't be verified in isolation, but must be in situ (i.e. in the living organism). Then you start to get into time.  What if your gene is involved in protein routing through the golgi apparatus and modulates the function of other proteins for instance?  That's going to require a very specialized and difficult set of experiments that should involve someone with experience in that field.
Finding GO annotations which are not clear from sequence similarity - unknown functions or new genes which reflect previously unestablished GO Terms could cost even more and take a good deal longer.
Still, high throughput studies are being done to find and validate electronic GO annotations.  And with that scale, the cost per experiment will go down.  Take a look at Olga Troyanskaya's research for an example of such an effort.

Can you please escape the $ signs with \$ to prevent SX going into the math mode?

@shigeta Thanks a lot, that is what I was looking for. And for the example you give the $ prices, can you also give a broad time schedule?

Hi David, If you had a well equipped laboratory, but without high throughput scaling, It could take 2-3 weeks per enzyme in the simple case.  Also the costs of the reagents will vary - they can be expensive...


text:
Which restriction enzyme would i use?
Plasmid pBr322 includes two genes that confer antibiotic resistance: a gene for ampicillin and  a gene for tetracycline. The cutting site for the restriction enzyme BamH1 is in the middle pf the tetracycline resistance gene. The cutting site for the restriction enzyme Pvu1 is in the middle of the ampicillin resistance gene.
If you were using a cell culture plate that contained ampicillin, which restriction enzyme (BamH1 or Pvu1) would you use to cut the plasmid and excise the gene you wanted to insert?
Attempt:
I would assume you need to use Pvu1 since the cutting site is in the ampicillin resistance gene, but the correct answer is BamH1. Why?
Any help would be awesome! Thanks!

Remember than Pvu1 cuts in the middle of AmpR, and when you insert your gene you'll be disrupting its function, meaning that any transformed colonies will no longer be able to grow on Amp-containing media. This is why you want to cut with BamH1 - the disruption to the TetR gene is irrelevant, and it leaves Amp resistance in place.
The point of growing on antibiotic-containing media is to select for cells that have taken up your plasmid - cells that haven't can't grow.

I would go with BamH1 enzyme as the cut site in pBr322 is BamHI 375 and ss you are plating  it in a ampicillin plate you need the ampicillin resistant gene to be intact for screening so by using BamHI you will not disrupt the Amp resistant gene


text:
The least complex animals with ability to dream
People can dream, dogs can dream, cats probably too when they are sleeping.
What about other creatures?
Can a bird dream?
Do rats have dreams?
Are there any studies about that kind of thing? What is the most simple organism that have brain structures that allow them dreaming during the sleep?

Why has this question been downvoted ?

Yes why has it been downvoted? at least comment feedback to suggest improvement...

Since mammals all share the same neural structures it is quite likely that most non human species dream, but as yet, the simplest animal I could find that has been scientifically demonstrated to dream is the rat, as proven by Massachusetts Institute of Technology (MIT).
MIT not only established that rat were capable of dreaming about the events they had experienced while awake, but that the content of the dreams could be manipulated with audio cues the rats had been trained to respond with in a specific way.
Sources:
http://en.wikipedia.org/wiki/Brain#Mammals
http://web.mit.edu/newsoffice/2012/neuroscientists-achieve-dream-engineering-0902.html

At least one study from University of Chicago showed that birds dream...about singing.


text:
Why don't we have hair on palms?
We have hair all over the body except palms.
What is the biological reason behind this?

The main functional reason is we need to be able to grip things with our hands (and feet, which are also hairless), and hair would interfere with that. Physiologically, the epidermis in these parts of the body is very thick and highly keratinized, and when combined with the thick underlaying layer of dermis, this results in skin that does not support the growth and maturation of hair follicles.

A support for that is that other hairy animals also don't have hair on their 'gripping surfaces' - palms of other primates and feet of mammals and birds.

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


text:
How are T cells transported?
T cells are formed in bone marrow and mature in Thymus. How are they transported from bone marrow to thymus ? Through the lymph vessels ?

The progenitor cells of T-cells (they do not develop into T-cells and show their characteristics before reaching the thymus) are mobilized into the bloodstream and enter the thymus from it by crossing the endothelial barrier. The figure shows schematically the development of the precursor cells from hematopoietic stem cells (HSC) and the migration of the precursor cells (it is from the paper linked below):

See this review for the details (if you have problems accessing the article, let me know):

The long road to the thymus: the generation, mobilization, and
circulation of T-cell progenitors in mouse and man.

prothymocytes are attracted to the thymus from the Bone Marrow by a chemotaxis , thymotaxin, a factor from thymic epithelial cells.
then it enters into the thymic cortex where Thy-1  and terminal deoxynucleotidyl transferase (TdT) is expressed. During TCR gene rearrangement, TdT increases TCR diversity by inserting nucleotides at the D and J junction sites. IL-2 and IL-2R are expressed leading to autocrine proliferation of T cells.
now the  pre-T cell  rearranges TCR genes (gamma/delta, alpha/beta). At this stage the pre-T cells are CD3+CD4-CD8- or "double-negative" cells. Double-negative cells that productively rearrange gamma and delta chain gene segments develop into CD3+CD4-CD8- gamma/delta T cells that are exported to the periphery in small numbers. Successful rearrangement of a set of TCR genes suppresses further rearrangement of TCR genes on the sister chromatid , thus each cell only expresses TCR with a single specificity.
The majority of double-negative cells will go on to rearrange alpha and beta chain gene segments. The beta chain genes are rearranged and expressed first with a pre-T alpha chain to form the pre-TCR . Once the pre-TCR recognizes some intrathymic ligand , a signal is transmitted through CD3 which:
halts further beta chain gene rearrangement (allelic exclusion)enhances alpha chain gene rearrangement causes CD4 and CD8 to be expressed
The alpha beta T cells now become CD4+CD8+ or "double-positive" cells. T cells which fail to productively rearrange TCR genes die by apoptosis.
At this point the T cells are in the deep cortex which contains epithelial cells expressing both class I and class II MHC molecules. T cells with alpha beta TCR which are capable of binding self-MHC on epithelial cells continue to proliferate and differentiate into CD4+CD8- or CD4-CD8+ T cells. Nonreactive (not self-MHC restricted) T cells die by apoptosis. Thus, T cells are positively selected for self-MHC restriction in the thymus.
T cells that survive positive selection traverse the junction between the cortex and medulla. Some of these T cells have low affinity TCR for self-MHC alone or combined with self-peptide while others have high affinity TCR. The medulla is rich in BM-derived dendritic cells and macrophages which express high levels of class I and class II MHC. T cells with high affinity TCR for self-MHC alone or combined with self-peptide interact with these dendritic cells and macrophages, and are eliminated by apoptosis. Thus, negative selection eliminates self-reactive T cells  in the thymus.

Hi Krushna, I'm not sure this answers the question of how T Cells move from bone marrow to the thymus beyond your very first sentence.


text:
Antigenic and non antigenic
Can any foreign molecule be non- antigenic ? Can any foreign peptide be non-antigenic ? What is the difference between an antigenic and a non-antigenic peptide ?

Molecules are antigenic if they are able to elicit an immune response. Let's incorrectly equate "antigenic" with "elicits antibody response". It's conceivable that a molecule might elicit an immune response, but not generate antibodies - this nuance is not particularly helpful for answering the question.
Antibodies are proteins which recognize antigens. Exactly which antigen they will recognize depends on the exact sequence of the antibody. This sequence is generated by chance, but it is generated by recombining an array of pre-existing sequences: This means that not every conceivable antibody sequence can be generated by the immune system. Moreover, it is also possible that no antibody at all can be generated for a given substance. So, no, it is not guaranteed that you will be able to generate antibodies for every possible substance. In fact, companies which sell monoclonal antibodies for Western blots often find the occasional substance which will not generate antibodies from their animals (rabbits, mice, goats, and so on).
A second complication is that many molecules are very weakly immunogenic and rely on adjuvants.
Lastly, there is a simple counter example to your question: There are many foreign molecules, both LPS and peptide, produced by bacteria which do not trigger the immune system at all. This applies to all the species that make up our gut flora, since it would counter productive for the body to attack its own symbiotes.
Of course, the immune cells at some stage learn which molecules are "own" molecules, so that they do not attack their own body. If the "foreign" molecule is presented to them at that learning stage, they will not recognize it as an antigen in the future.

Something is antigenic because it acts as an antigen - it binds to an antigen receptor in the immune system (antibody, B-cell receptor, T-cell receptor, etc.). While the concept of "foreign" in immunology is often (incorrectly) equated with antigen, that is not the case. For example, there are many chemicals one could think of that are foreign (non-self), but don't usually raise immune responses - nylon, for example.
The difference between an antigenic and non-antigenic peptide is that the antigenic peptide, when presented in the correct circumstances, can raise an immune response. This means that, theoretically, the exact same peptide sequence can be both antigenic and non-antigenic depending on the environment - whether it's being presented in an immune-suppressed environment, for example. However, it's more common to classify antigenic potential based on whether it's possible for the substance to raise a response in an otherwise "normal" immune environment.

What exactly makes a substance antigenic/non antigenic ? I want to know the molecular basis for this/

In principle every molecule above a certain size (single amino acids for example can not) can be immunogenic. A very important function of the immune system is to differentiate between molecules, which are foreign and which should raise an immune response and those, which are not and which therefore have to be tolerated. If this differentiation doesn't work, this lead to autoimmunic diseases.
There are two processes which are important here: self-tolerance and tolerance against foreign (or peripheral) antigens. Basically said for self-tolerance autoreactive lymphocites (B- and T-cells) are eliminated from the pool of developing cells, before they can fully differentiate. Only 1-2% of the cells which start developing go get through this selection process. Peripheral antigens (for example from food) are usually tolerated when there is not other immunologic process in the peripheral lymphoid tissues.
The process looks in principle like this (image taken from the second review listed below):

I will not write the whole process here, but the Wikipedia article on this topic is a good start. What I can also recommend is the Immunology book written by Janeway and colleagues (if you can get it via a library) and you can have a look on this two reviews:

Immunological Tolerance: Mechanisms
Primer: mechanisms of immunologic tolerance.

If you have problems accessing the articles, let me know.


text:
Thymus and maternal microchimerism
I read in Bruce Alberts Molecular Biology of The Cell :

....If,however,cells from one strain of mouse are introduced into a neonatal mouse of another strain , some of these cells survive for most of the recipient animal's life, and the recipient will now accept a graft from the original donor, even though it rejects "third party" grafts.

As far as I understand , in this experiment,they got these results because thymus hadn't yet learned what was "own" and what was "foreign".
Is  the reason for why maternal microchimerism does not invoke immune response related to the above experiment ? Can we apply the same logic here ?

You are on the right track.  This is an example of microchimerism (the maternal part is a bit off), and the key issue at hand is central tolerance.
Background:
A good definition of microchimerism is:

Microchimerism is existence of an allogeneic DNA in a living creature. (1)

Scientist do this on purpose for all kinds of reasons, but mostly to ether is study the immune system directly or to get a near-transgenic model.  It should be noted that this isn't perfect, and that when you try to do this, you often can lead to auto-immune problems and often death of the mouse (30-50% survival in early work).  If you go back to one of (if not the) pioneers of immunology, Peter Medawar, you can see when how this was done:

Mice and chickens never develop, or develop to only a limited degree,
the power to react immunologically against foreign homologous tissue
cells with which they have been inoculated in fetal life. Animals so
treated are tolerant not only of the foreign cells of the original
inoculum, but also of skin grafts freshly transplanted in adult life
from the original donor or from a donor of the same antigenic
constitution. (2)

If you would prefer a visual layout of the experiment, Starlz put together one in his review of transplantation (Pubmed):

After looking over the section you quoted from Alberts, I'm pretty sure he was in fact referring back to these early experiments.  But that was all the way back in the 1950's, what have we learned as the mechanism in 60 years?
Possible Mechanism:
The truth is that we don't have an absolute grasp on how this works when it doesn't cause an autoimmune problem and abort the fetus or even neonate pup.  It's import to note that it probably does cause auto-immune problems and various other side effects (like sex differentiation) in mammals.
But when and how it is tolerated is likely mediated by central tolerance, and the ability to get the foreign MHC molecules tolerated by early lymphocytes.  Essentially, the cells have to get incorporated into the AIRE machinery at an early enough stage that the T-cells are selected against the foreign cells.
There is enough biology here that an in-depth answer could be a dissertation, so I only want to touch on a few more points.  You should note that this was done with relatively genetically similar animals, and most modern researchers use cells modified from genetically pure mouse breeds.   We also know a lot more on how the cells "recognize self" and the HLA types of the population.
You are most likely to succeed when the MHC molecules are very similar (ie from a direct family member).  This happens when the host and foreign cells have an HLA type match.
TLDR:
The lymphocytes, mostly T-cells in this case, of fetal mammals seem to be able to look at very similar MHC molecule on a foreign cell and decide "eh.. close enough," and build negative selection (part of β-selection) against lymphocytes that would kill the foreign cells.  This requires that the cell be in the right place at the right time, and of course, be "close enough."
Do let me know if something is not clear or needs to be expanded upon.  As someone who works in Immunology, I have difficulty determining where the detail line should be.

Thank you so much for such an awesome answer ! I never thought someone would give such a detailed explanation !

Have you come across papers showing evidence that maternal microchimerism in humans is tolerated because thymus of fetus thinks the maternal cells are its own cells ?

@biogirllajja No I don't and that's for a couple of reasons.  Cells going from the mother to the fetus are much more rare in humans than the reverse.  The only times we tend to find out about it tends to be when there is a problem and it isn't tolerated.  Your question would have to answered by a large, costly, study of the healthy population.  There's just not going to be the funding for it.


text:
Immune reaction to "new" protein
I read in Bruce Alberts Molecular Biology of the cell :

Normal mice,for example, cannot make an immune response against one of their own protein components of the complement system called C5.
  Mutant mice, however, lack the gene encoding C5(but are otherwise
  genetically identical to the normal mice) can make a strong immune
  response to this blood protein when immunized with it. Natural
  immunological tolerance for a particular self molecule persists only
  for as long the molecule remains present in the body. If a self
  molecule such as C5 is removed, an animal gains the ability to respond
  to it after a few weeks or months. Thus, the immune system is
  genetically capable of responding to self molecules but learns not to
  do so.

So, why does an immune reaction not happen when a new protein is introduced to patients lacking it ? For example if you give clotting factor to hemophilic patient.

They actually can produce antibodies against the clotting factor (as @Xylo pointed out, many patients do produce the clotting factor that's being replaced, just in insufficient quantity, which lowers a lot the risk of an immune response). The antibodies against the clotting factor are called inhibitors. See here for more info.

Thanks !  In the link you provide, it is written that the reason for this is uncertain. Do you think the reason could be the one I pointed out in the post ?

Yes, and my understanding is that the uncertainty resides in the fact that even some patients which do produce endogenous clotting factor sometimes react, while you'd expect they shouldn't.

Does the endogenous clotting factor reaction classify as autoimmune ?

Sometimes the antibodies are actually the origin of the clotting problem and in that case yes, absolutely. Now when the patient is naturally lacking any production of that factor and the antibodies appear due to therapy, then I guess so but I'm not sure, sorry.

You are absolutely right in that there will be immune reaction against proteins that are not naturally present in the body.
However, hemophilia is not caused by complete lack of protein. It is due to loss of function of the clotting factors due to mutations. The proteins are still present, but they do not have the ability to bind and/or activation of their catalytic function. So, there will be no immune activity against exogenous clotting factors given to hemophiliac patients.

Thanks !   I am not able to recollect any examples but isn't there any disease where a protein is totally not made and then we artificially give that protein ?

When it comes to genetic disorders, you have to remember humans have diploid chromosomes. Most eukaryotes are diploid. So, if there is deletion of a gene on one chromosome its allele would still be present and its gene product will be made in the tissues/cells that they are normally expressed.

ok! SO it is extremely rare that there will be disorder such that no protein is expressed but I think there can be at least one !

I cannot recall any specific disease where both copies are deleted. But, it is possible.  An example of the situation you are describing would be blood determinant antigens, O, A and B. When people with O-type are transfused with A-, B- or AB-donor blood, there will be immune reaction against it.  So, to summarize, if you transfuse with protein  that was not present will definitely generate an immune response.

In hemophilia, it will not as the protein is already present albeit in active state.

This is a concept of the immune system called "Immune tolerance". Basically it makes sure, that you cannot make antibodies against yourself (which would obviously be bad).
New antibodies are "tested" against the body and if there is an autoreactivity, the corresponding B-cells go into apoptosis.
If this self-protection does not work, this leads to autoimmune diseases like SLE.
The Wikipedia article about it is quite nice for the beginning and also has a lot of references for further reading.


text:
Manufacturing toxoids

Toxoids produced by tetanus and diphtheria bacteria are detoxified
  with formaldehyde, yet their antigen properties remain.

Source : Biological Science by Taylor
What does formaldehyde do ?

The toxins of both Clostridium tetani and Corynebacterium diphtheriae are so toxic that you cannot use them for immunization, since the amount needed for proper antibody production would kill the individuals. For that purpose the toxins are "de-toxified" by reacting them with formaldehyde which takes away the toxicity but the resulting toxoids are still immunogenic.
This happens by the reaction of the formaledehyde with the free aminogroups of the sidechains of the amino acids to form azomethin groups. This changes the protein so much, that it cannot bind to glangliosides any more which renders it untoxic. The immune system can still recognize unmodified parts (for this 8-10 amino acids in one stretch are enough) and make antibodies.


text:
Electronic laboratory notebook (ELN)
I have been using old style lab book for some time now but with increasing work on computer and storing sequencing results and gel pictures on computer it would be nice to have everything on computer in a form of labbook.
Does any of you uses a good ELN that would be free as I don't think university will be willing to pay for it :)
Thank you for your answers.

I still prefer the good old[tm] Labnotebook. No dependencies on (proprietary) software or a computer. I generate quite some digital data (blots, sequencing etc.) this is stored on the servers of my university. We looked into this in our lab, but discarded the idea pretty fast. Most solutions are either expensive and/or proprietary. Then a lot of these programs are not bought, but rented for a monthly or yearly fee, so once you are in you basically will not get out there anymore. Or it takes a lot of work.
I found one free (for up to three projects), this is Labguru.
There is an article about this on Bitesizebio, which has a few interesting comments. And there is another blog entry about this worth reading.
One of the problems with ELN is a legal one, since a labbook is a legal document providing evidence a what has been done and the results of it. They can be very important when it comes to patent legal battles.

I do not understand the legal problem here. So if I use it data that I put in my ELN might be partly owned by the company who is providing ELN or what?

No, not that. But your entries have to be safe against manipulations. A bound book has numbered pages to prevent the removal of pages with non-fitting results. And it will probably be pretty difficult to move from one solution to another, when a product gets discontinued.

Although there are some definite advantages to physical labboos, and perhaps some legal obligations, I have been loosely using Synbiota for keeping track of general procedures to be done. It has a long list of interesting features, but I particularly like the integrated DNA editing tool, as well as the ability to share projects and updates with labmates.

I am not sure what you need.
Probably Libre Office (a free MS Office like program, including a rich text editor, with image support) will suffice for you.

This is not a decision you, or even your lab can make on its own.  Notebook policies are almost certainly developed by the lawyers of your university.  It would be up to them to certify any change to those policies, in coordination with IT, who would have to be on board to guarantee the integrity of the electronic data.


text:
Death because of no radio waves
I read somewhere that a man dies if he is isolated from natural electromagnetic fields and waves. (I imply fields of radio frequencies and below.)
Is it true?

note that visible light and infra-red are also EM waves. Humans can survive in total darkness for a while though....it would be pretty cold too!

@Memming: certainly light, UV, and infrared don't count in my question

what frequency of EM wave, then, are you talking about? Without the magnetic field of earth, there would be too much solar wind/cosmic ray as well.

@Memming: I am about radio frequencies and below. I do not ask on indirect effects of EM on survival of human (such as about Earth field protecting from Sun rays), only about direct effect of EM on human body.

I see. So less than GHz range? Could you update your question to clarify this? :)

I never heard of anybody dying in a Faraday cage, so I don't think lack of EM or natural electric field has any effect, at least short term.

This question appears to be off-topic because it is based on an unreferenced claim

@porton I think your right, we all know that every body above absolute zero dissipates energy as em waves, so if a person is isolated from all em waves it implies that there is no em wave coming to him, so the person dies because hi will be at absolute zero temperature at that moment. Hope it answers your question.

I've never heard of such a thing, and a quick Scholar search didn't yield anything significant. In fact, artificial radio waves are used in things that usually save lives, like MRIs.
If we were truly agnostic about this, we could say that it might or might not have an effect on human survival due to the general lack of evidence or even indication of a claim, but like the orbiting teacup, it's safe to assume that given our current extensive set of knowledge of biology, radiowaves do not affect human at all, and that as it has not been observed, the claim doesn't have a scientific basis.


text:
bioinformatics /genomics
i am looking for likely truncation sites to prove recombination in sequences. i have 4 sequences. i believe one to be the "real sequence" and the other 3 to be recombinants caused by cleavage possibly due to Arg c proteinase. I know my sequences overlap due to multiple alignments i have performed using UniProt and i have chosen the enzyme due to carrying out cuts on Expasy cutter. If anyone could point me in the right direction this would be much appreciated.
many thanks in advance

-1 question not currently legible and not clear what you are struggling with. edit the question to make it readable and make the question itself clearer.

thank you i have rephrased the question, i am new to this site i am looking for truncation sites in sequences if you have any information on useful literature it would be greatly appreciated.many thanks

Can you please make this a redable post? Posting a ton of sequences seems not helpful to me at leat unless you re-phrase your question. These are protein sequences, so you will not find any stop codons.

i have specified i am not looking for stop codons but truncation sites the sequences are the ones i am comparing, i am sorry they are not readable as i cannot paste them "in frame".....if you could please direct me towards literature on identifying truncation sites as i believe these sequences to be recombinants of each other due to the alignments i have performed. many thanks

Truncation sites of what? Proteins? Protein translation? Transcription?

my professor said pro peptides.....i believe the 3 of these sequences are recombinations of 1 main sequence i retrieved from UniProt

Then I would recommend using a sequence alignment tool (clustalw should do it) and align the sequences to find out if there are similarities.

i have done this and i have the alignments which shows there are overlaps...i just don't know what to say to prove my observation beyond what i can see....so i was told to look for "likely truncation sites" to back up my observation, hence my post do you possibly have any recommendations of what direction i should be looking in? many thanks

using the "preformatted text" option on the alignment text would help to make it much more readable. And RE your comment on you other post - I am being helpful so there is no need for rude comments, properly written and clear questions get better answers, this is how things are done on the SE sites.

thank you with regards to the pre formatted text option, and it was not a rude comment i am new to the website and everyone has been extremely helpful however if you read the post you would see it is not a duplicate question and an unnecessary response since i am new and trying to navigate my way around the site. many thanks

http://chat.stackexchange.com/rooms/1997/biology this would be agood place to get that sort of help

thank you, do you know anything on sequence recombination due to cleavage and/or truncations?

The sequences you have posted seem to be (protein) amino acid sequences. The stop codon are present in DNA sequences and in mRNA sequences.
In DNA, the bases are A, G, C and T; stop codons are TAG, TGA and TAA.
In RNA, the bases are A, G, C and U; stop codons are UAG, UGA and UAA.
In DNA and RNA, other letters are used to specify degeneracy.
What you have here looks like protein sequences. So, there are no stop codons in sequences you have posted.

thank you this is correct i meant to say i was looking for truncation sites not stop codons.


text:
Erythroblastosis Foetalis
If Rh- mother has Rh+ baby, the mother can become sensitized during first pregnancy and then if subsequent fetuses are also Rh+, there can be eryhtroblastosis foetalis.
I read that if mother is O- and baby is any +ve blood group other than O+ , then mother will not become sensitized during first pregnancy because a and b antibodies present in her blood will attack the antigen present on the fetus RBC and there will be no time for the mother to synthesize antibodies against Rh.
My Question : Can't the same logic be applied to all other blood groups? For example : A- mother and B+ baby.

if mother is O-

That means:

group O in ABO system: anti-A and anti-B antibodies
group Rh- in Rh system: no D antigen and no ant-D antibodies unless previously senzitized

baby is any +ve blood group other than O+

ABO system: A, B or both antigens present
Rh system: D antigen present

So, the mother has anti-A and anti-B antibodies and her immune response will be directed towards the fetal RBCs containing A, B and D antigens. But, in theory, the immune system should also produce anti-D antibodies because of antigen presenting cells which will expose D antigens to T lymphocytes.
What is known is that if the mother already has anti-D antibodies, no other are secreted from fetal D antigens. This is how passive immunization vaccines work:

This is done so that the fetal Rhesus D positive erythrocytes are destroyed before her immune system can discover them. This is passive immunity and the effect of the immunity will wear off after about 4 to 6 weeks (or longer depending on injected dose) as the anti-Rh antibodies gradually decline to zero in the maternal blood [1].

But the mechanism is not clearly understood:

The most fascinating aspect of the story scientifically is that we still do not have a complete, mechanistic understanding of how this therapy works. The original hypothesis that Rh-immune globulin functions by clearing fetal Rh(D)-positive red blood cells from the maternal circulation, thereby hiding this foreign antigen from the maternal immune system, is inconsistent with the fact that passive immunization with Rh-immune globulin guides the fetal red blood cells directly to antigen presenting cells, the same cells responsible for initiating an immune response to foreign antigens [2].

References:

Wikipedia contributors, "Rh disease," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Rh_disease&oldid=615938189 (accessed July 28, 2014).
Eldad Hod. A Treatment for RH Disease. Available from http://pathology.columbia.edu/rh_disease.html (accessed 28.07.2014)

I read about this in nelson pediatrics. Will add that information whenever possible. ..


text:
List of all reported bacteria
I would like to know were to download a table file with all reported bacteria and its corresponding PHYLUM, CLASS, ORDER and FAMILY.
Basically, its the same table than this one from GOLD genomes but containing the non-sequenced bacteria too:
Thanks for you help, Bernardo

I am not sure if such a complete list exists. There are some lists available, which look pretty complete. Have a look at Labrat and Microbexpert. There is also a book available, which contains an approved list of bacterial names, see here. Otherwise you can of course search your way through PubMed and see, what comes out.

Thanks Chris, but I need the list in table format (tab or comma delimited file). I couldn't find this option in the websites you suggested.

Oh, I am not sure if this list exists at all. You could try to contact these websites and ask them if they can provide this data in a different format.


text:
what does sequences overlap indicate
what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other
and how does one go on to prove this
many thanks

At first it only means that these sequences share a similarity (sorry, but its not more). This can mean that they are smaller parts of a bigger protein which has been broken up, it can mean that you aligned different proteins which are only partly similiar and so on. To go over this, you have to provide some more information. And/or show an image of the alignment if possible.

Just curious @user5182 are you currently doing a Bioinformatics MSc at ICL?

@chris yes i think that one of the sequences is the "real sequences" and the other 3 are bits of it rearranged, i am working with toxins specifically if this helps, i tried to post the sequence earlier but unfortunately as it was not in frame people complained about how it was unclear. please let me know if there is anywhere in specific i should be looking. many thanks

@hello_there_andy no im doing an MSc in pharmacy my dissertation is on toxin diversification in a coral reef

Expanding on the comment by @Chris:
Short Answer
Overlapping sequences imply evolutionarily conserved regions, i.e. preserved by evolution through time due to theirs having some important function.
Long Answer
Assuming the sequences are homologous, overlapping regions of similarity reveal "evolutionarily conserved regions".
These are regions in the protein sequence that are shared by the ancestors through ancestral history due to that shared sequence bearing some important function at the phenotypic level. Evolution acts to "preserve" the sequence through natural selection if that function was important for fitness (see Negative selection).
E.g. Perhaps the shared sequence codes for an active site for an enzyme that is shared by all the ancestors you are using in the multiple sequence alignment - natural selection will then prevent changes to that sequence from occurring.
Look at this online lecture for finer detail.

one more little piece of information: with proteins there are always short but good overlaps which in most cases indicates similarity of domains..

it means those region are conserved if you compare two sequence and find similarity one example is the hox coding region which is conserved and it shows similarity

Go on to add information on how one goes on proving this


text:
Looking for raw cell videos from a light microscope
First off, I'm not looking for online lectures.
I am trying to find creative commons licensed videos of live cells moving around without annotation or anything extra. I would prefer a few minutes of video of tumorous somatic cultures of eukaryotes in vitro and at a few different magnifications but it doesn't really matter. I don't have a microscope or I'd just get some pond water and look at multicellular organisms. The license must be creative commons or public domain, the author must be citable, and the subject organism should be known.
Any ideas where to find such video? Thanks!

The website you want is The Cell: An Image Library. They also have movies. A quick search of 'Homo sapiens tumor' revealed several Creative Commons videos of tumor cells moving around in vitro with attribution and no annotation or anything else. Sometimes the site can be a bit buggy, but it's a pretty awesome resource when it works.


text:
DNA degradation rate
Usually DNA sample manipulation is realized with an ice box at hand in order to avoid degradation, and also its storage is set at -20ºC. Nevertheless, DNA has been obtained from really ancient samples that were not in a cold environment and even our DNA is at 36ºC. Furthermore, when performing PCR, samples are put into a massive heat shock and at high temperatures.
Then how needed are those protocols in order to grant correct DNA quality? how much can a sample be left without need to worry? and how does this degradation happen (DNAse free environment)

Really awesome question !

DNA decomposition isn't a phenomenon that is too common.
In nearly all cases, DNA is broken apart to the accidental contamination with nucleases. Long-term storage of DNA in the -20 is also suggested in order to significantly lower the rates of these nuclease enzymes.
Additionally, DNA only truly fragments at very high temperatures (>90-100 degrees Celsius) due to the nature of the covalent chemical bonds that form DNA. Nearly any organic molecule will degrade at very high temperatures, and some will degrade at lower temperatures due to unstable structures or heat-labile bonds.
Of course DNA will deanneal at somewhat-high temperatures due to its double standedness , but allows for reannealing to the initial molecule once the temperature is brought down.
One additional reason for potential DNA degradation is DNA shearing, which will occurs when you tear up your DNA physically due to exposure to rigorous shaking, resuspending or other "violent" techniques.

and how common are nucleases?

Not that common, but just think about how it only takes one enzyme to destroy your entire sample. A "source" of nucleases can be from your fingertips too, which is why its very important to wear gloves when dealing with DNA directly.

DNA is a incredible stable makro molecules. It survives in out cells and we can do things like PCR (which need serial heating and cooling steps) with it without degradation. As long as you work clean, your DNA is not at risk. We usually keep our working stocks of plasmids or primers in the fridge at 4°C to avoid repeated freeze-thaw cycles.

@Chris, exactly. If you treat your DNA well, it would treat you well (experimentally, that is). :)

@JunkDNA One important source of DNAses and RNAses when isolating nucleic acids are the cells/tissues themselves from which the DNA/RNA is isolated. Pure nucleic acids in an appropriate buffer are very stable, in my experience RNA samples can be stable for years at 4°C or even above (small RNAs with stable structures).


text:
How many different smells can a human recognize?
How many different smells can a human recognize?
If the space of smells is not discrete, how many dimensions it has (for example, the space of colors is three-dimensional).

Another way to rephrase your question would be "how many different chemical receptors do we have in the nose?". Is it correct?

@Remi.b no, we have 4 types of photoreceptor cells, but our color space is 3-dimentional.

Here and here are posts on color perception by the way. Note: Your question might be a good fit for cognitive sciences also.

I really don't know much about this subject… Does it really make sense to talk in terms of dimensions? If we talk about color, then it might seem that there is only one dimension as any color can be define with only 1 number. Could you provide an in-depth explanation of how you apply the concept of dimension to visual perception (and other perception)? This might help.

"any color can be define with only 1 number" - this is not true.

@Remi.b http://en.wikipedia.org/wiki/LMS_color_space http://en.wikipedia.org/wiki/Young%E2%80%93Helmholtz_theory

All colors fit on a line from red to violet by decreasing wavelength. We see in three dimensions because we have three types of cones. Intermediate values on several axes allow us to infer the real value of the wavelength. That's why I thought we can reduce your question to the number of chemical receptor we have in the nose. Explain me what you think I am missing.

"All colors fit on a line from red to violet by decreasing wavelength." - no. For example, grey does not fit.

@Remi.b "That's why I thought we can reduce your question to the number of chemical receptor we have in the nose." - I already commented that we have 5 types of photoreceptors in the eye, of whom 4 participate in imaging, of whom only 3 participate in color vision. So the number of receptor types does not indicate the dimentions of the sensual space. For example, rod cells while being different from cone cells, give perception of white color, which also can be obtained with only cone cells.

3 participe in color vision and therefore our vision of color is in "3 dimensions". But anyway. I might not understand, I let other people trying to answer or to make sense of the question.

As nobody is suggesting an answer I'll give my guess that I already discussed in the comments and give some extra details about ongoing debates on the subject.
We'll start with the sense of color sight in order to make easier. One can argue that we see in 3 dimensions because we use three cells which level of activation inform the brain of the color. I guess that the whole 3D space delimited by the maximum level of activation of each three receptors can be used. Therefore, it is nothing else than the number of receptor that determine the number of dimensions in which we can sense. Now it is assuming that each receptor can send signal of different strength information of the intensity of the light or smell.
According to wikipedia. Mammals have about thousands of genes that code for olfactory receptors. Moreover, the question of how these receptors work is still debated

In mammals, each olfactory receptor neuron expresses only one functional odor receptor. Odor receptor nerve cells function like a key-lock system: If the airborne molecules of a certain chemical can fit into the lock, the nerve cell will respond. There are, at present, a number of competing theories regarding the mechanism of odor coding and perception. According to the shape theory, each receptor detects a feature of the odor molecule. Weak-shape theory, known as odotope theory, suggests that different receptors detect only small pieces of molecules, and these minimal inputs are combined to form a larger olfactory perception (similar to the way visual perception is built up of smaller, information-poor sensations, combined and refined to create a detailed overall perception).[citation needed] An alternative theory, the vibration theory proposed by Luca Turin, posits that odor receptors detect the frequencies of vibrations of odor molecules in the infrared range by electron tunnelling. However, the behavioral predictions of this theory have been called into question. There is no theory yet that explains olfactory perception completely.

Note: the two competing theories for color sights: Opponent process and Trichromacy
Hope this helps!
I think this question would also be a good fit for cognitive science beta.

"One color can be describe by one single value (it is unidimensional). This value can be the wavelength for example. " - this is wrong. You cannot describe all possible colors with a wavelength. For example, you cannot describe grey, white or magenta.

@Anixx Yes you're right. I updated my answer.

"Therefore, it is nothing else than the number of receptor" - As I already pointed out we have at least 4 types of receptors with different points of maximum. And to be precise there is also a fifth type. So the number of receptor types does determine the number of dimensions of the color space.

According to this wiki article we have 3 receptors for the color. But anyway, I don't know much, I suggest something as nobody is giving any answer. Sorry, I can't do better. I added, two wikipedia links that are competing theories of color vision.

unless you know beforehand the color space dimensions, you cannot tell which receptors are used for the color just by counting their types. We know that only three types of receptors participate in color vision BECAUSE our color space is 3-dimensional, not the other way around.

authors: Евгений Иванков


text:
How is color information transmitted from the eye to the brain?
Is color information sent from the eye to the brain frequency-modulated, or are different colors transmitted by different axons?
I know that each ganglion cell is connected to multiple photoreceptors. How do ganglion cells tell the brain which photoreceptors were exactly activated and by what color?
Do ganglion cells correspond to particular colors?
Can one ganglion cell transmit different signals to the brain?
How does the brain know which color the light has, if signals of different receptors are mixed in the ganglion?

I believe that some preprocessing takes place in the retinal ganglion cells (see also http://en.wikipedia.org/wiki/Color_vision#Color_in_the_human_brain), so the brain does (probably) not have any information on which types of cones that are activated. I dont know how the colour information is transmitted from ganglion cells to brain though.

possible duplicate of What gives things their colour?

@The Last Word no, that answer deals with the eye.

@fileunderwater I heard somewhere that without preprocessing the optical nerve would have a diameter of several centimeters. :-)

Short answer
Color vision is mediated by spike rate modulation (frequency modulation if you like), as well as ganglion-cell specific stimulation.
Background
Ganglion cells exist that transmit opponent colors. The color opponency model predicts that we cannot perceive a greenish-red or yellowish blue, which is quite right. We can, however, see mixtures of the two channels, such as red and yellow (orange), and red and blue (purple).
Then opponent model predicts the existence of ganglion cells that are sensitive to red/green opponency and blue/yellow opponency (in trichromats like humans):

Indeed, it has been shown that these ganglion cells exist, i.e. cells that increase their firing in response to short-wavelength-sensitive (S+) and decrease their firing to middle-wavelength-sensitive (M-) and vice versa (Yin et al., 2009). Hence, it is not so that the frequency of light is represented in firing rate per se, but the frequencies of light are translated in spike rates, because spike rate is the only means in which neurons can transmit graded responses. In other words, every type of graded information is translated into spike rate eventually, including pressure differences, acoustic loudness etc.
Hence, as ganglion cells are sensitive to opponent pairs of colors, they do respond to particular colors. However, a "purple ganglion cell" does not exist, it is the combination of red and blue activations that lets us see colors due to synthetic processes in higher neural centers.
One ganglion cell can send different signals to the brain as it is basically an analogue converter of the red/green and yellow/blue opponent colors.
These inputs are sent to the thalamus (lateral geniculate nucleus) and higher visual cortices, where color-selective cells pick up the signals and integrate them for further processing. Here color mixtures are made to present the full gamut of colors as we know it:

Source: Dot-Color
Reference
- Yin et al. J Neurosci 2009;29:2706-24
Further reading
- Advantage of opponent color?


text:
Database of Medical Assertions
Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be in some sort of structured format, or be in free text.

What an interesting idea for a database! Do these type of databases exist for other fields? I've never heard of something like that until now. I'd love to browse such a resource. Looking forward to answers!

@A.Kennard: they definitely exist for computationally-driven domains that are narrow in scope! For example, the Neuroinformatics community is actively creating knowledge bases of Neuroscience-related information, and the Bioinformatics community has been active here for some time. I don't know about clinical findings, though, which would be handy for some machine learning experiments I'd like to try!


text:
How much DNA of mitochondrial origin is incorporated in main cell's DNA?
And especially three points :

in which chromosomes is it located (especially for the human case) ?
how do we know about it ?
does the proportion and composition vary a lot from one eukaryot to another ?

We know about nuclear DNA having a mitochondrial origin mainly in two ways: (1) a sequence in the nucleus is found to closely match a sequence found in mitochondria, or (2) mitochondrial proteins are found to be encoded by the nuclear genome but not by the mitochondrial genome, and those proteins seem likely to have been necessary for sustaining life of the mitochondrial free-living ancestor.
The integration of copies of mitochondrial DNA into the nuclear genome is an ongoing process.  Pieces of DNA can float around and occasionally be spliced into a chromosome.  Most such integrated pieces are entirely nonfunctional (the functional version remaining in the mitochondria) and can pretty much be considered junk despite being replicated when the chromosome is replicated.  Useless gene-like pieces are often called nuclear mitochondrial pseudogenes or NUMTs (see, e.g., pseudogene.net).  NUMTs are of technical importance because they interfere with genome studies: the sequences of the NUMTs can easily be mistaken for true mitochondrial DNA leading to false conclusions about mitochondrial genomes.
A more general term is endosymbiotic gene transfer, which can be used to describe nuclear DNA which was derived from DNA originally residing in mitochondria but now is no longer found there.  Some of this is nonfunctional, but much is functional, coding for proteins which after translation are sent to the mitochondria.  In fact, the overwhelming majority of mitochondrial proteins are coded by the nucleus, many of which probably had a mitochondrial origin.
Eukaryotes do vary in how much nuclear DNA is of mitochondrial origin.  A majority of functional genes are probably ancient and so tend not to vary a lot between organisms.  On the other hand, nonfunctional NUMTs are often relatively recently established and so often vary widely between organisms.
Particular nuclear chromosomes are not associated with mitochondrial origins; the integration of free floating DNA pieces is mostly a fairly random process.
For more detail, you might want to see Timmis et al's review, "Endosymbiotic Gene Transfer".

Interesting question. I researched this a bit now and the phenomenon is termed "numt" for  "nuclear mitochondrial DNA". This term descrives the transfer of cytoplasmic mitochondrial DNA sequences into the separate nuclear genome of a eukaryotic organism. It seems that most of these sequences are inactive. This list at pseudogene.net has a large number of sequences in a lot of different organisms, for humans insertion between 0,2 and 14,2 kb are listed. Most of these sequences are detected in the deep sequencing projects underway these days and by comparative sequence analysis. An example is this paper, where they found mtDNA on chromosome 1 of homo sapiens, which was still part of the mitochondria in homo neanderthalensis.
For more information you can go to the list of papers I list below, this should be a good starting point:

http://www.ncbi.nlm.nih.gov/pubmed/11369110
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020273
http://www.ncbi.nlm.nih.gov/pubmed/15014143
http://www.ncbi.nlm.nih.gov/pubmed/18721785

The papers should all be accessible, if not, let me know.

Thanks a lot for these pointers. I had no accessibility troubles.


text:
Ethidium bromide and mutagenesis on cloning
When performing a DNA cloning, sometimes PCR amplicon is run in agarose and it is detected by ethidium bromide marking under UV light. After that, gel is sliced, DNA extracted from gel....... until eventually you have your transgenic organism. The thing is that when doing so, you use the very same DNA sample that was "contaminated" by ethidium bromide, so does this DNA you are using for transformation contain ethidium bromide? if so, how can it affect in numbers to mutation risk?

Purified DNA contains negligible amounts of ethidium bromide. PCR and gel clean-up kits remove it quite well. There is, though, a risk of mutation from the fact that you're visualizing the gel in UV light with ethidium bromide. The risk of mutation from UV is minimized by exposing the gel as little as possible, and by using "preparative" transilluminators that come with a low-light setting for cloning purposes. If you work well and quickly, the chance of mutagenesis isn't higher than the chance of a polymerase incorporating the wrong nucleotide.

The ethidium bromide stays in the solution when the DNA is purified (either with a column or with precipitation).

While it is possible to get mutations from the ethidium bromide, this is hardly the only source of mutations in the process.  Taq itself will introduce mutations fairly frequently, so sequence sensitive procedures typically use a higher accuracy (but slower and more expensive) polymerase, like Pfu.  As stated before, the UV can also cause mutations.  The PCR process iteself can result in primer dimers and other "funky business".  Inappropriate sequences can be picked up from environmental contamination, particularly if you frequently use the same restriction enzymes in the lab, because sequences with appropriate "sticky ends" will be all over the place, no matter how much you clean.  If inserting into a plasmid, multiple inserts can get ligated into the final product, depending on how homologous the sticky ends of the insert are.
The solution is to accurately sequence the final transgenic product before you put it in the transgenic organism.  I usually have the plasmid (I work with plasmid transfections) sequenced, as well as cleaving the plasmid insert from the plasmid and running it on a gel.  The sequencing catches any base swaps/indels and the gel makes sure there is only one copy of the insert in that particular plasmid.
You would be surprised how often you get mutations and other "garbage" in the final product, which is why it's important to make multiple batches together.  I make mine in batches of 8, so that at least a couple will be exactly what I intended to produce.
Reference: My own research/experience with site-directed mutagenesis and construction of plasmid vectors for transfection.