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If you catch COVID-19, do you need to be vaccinated after recovery?
When we catch a cold, influenza, or COVID-19, the body starts to produce antibodies against them, so the body becomes immune for a period of time. That means one should not catch them again whilst there is the presence of immunity. Being vaccinated during this period of time seems to be useless.
Imagine someone caught COVID-19 one month ago, should they get vaccinated later?

I don't think the question is suitable under the community rules. Having said that - indeed, in most affected countries vaccination is recommended only a few months after teh recovery from COVID-19. Moreover, as teh sanitary measures go, the certificate of recovery from COVID-19 is usually accepted as an equivalent of the vaccination certificate.

I’m voting to close this question because it is a medical question, more suitable for SE Medical Sciences.

Yes. Studies on reinfections consistently show that a booster vaccination after an infection further reduces the risk of contracting COVID-19 a second time. The recommended time interval is 6 month after the infection.
A vaccination also can reduce the symptoms of Long Covid although the mechanism of this effect is not yet known.

To which studies do you refer?


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Why do some men have patchy beards?
Why do some men have patchy beards? Or more specifically, why would some hair follicles lack sufficient 5-alpha reductase while others nearby don't when their genetic code is identical and they are both the same type of cell? (See below.)
(Though my actual question is more broad in nature, the answer to this particular example should give me what I'm looking for.)
On this website (http://beardcoach.com/2009/11/why-you-have-a-patchy-beard/) explaining why some men grow patchy beards it says:

"When the dermal papillae of your beard follicles utilize testosterone, they actually metabolize it and create another androgen as a byproduct called dihydrotestosterone...To utilize testosterone and create dihydrotestosterone, your beard follicles need yet another substance, an enzyme called 5-alpha-reductase.  This enzyme is necessary for this conversion, and if you have low levels of it, then you have low levels of dihydrotestosterone.  More importantly to the topic at hand, if you don’t have enough 5-alpha-reductase, the dermal papillae of your beard follicles can’t properly use testosterone to tell your hair matrices to make hair.  And if your beard hair matrices aren’t making hair, you aren’t growing a beard."

What it doesn't explain is why certain hair follicles have sufficient hormone (or enzyme to utilize it) and others don't.

source: Stack Exchange

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sort: votes


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Can other animals see black differently?
I am not sure if this is the right place for this question, but this is a debate that has been going on between two colleagues for days and I need a resolution because it's driving me crazy. So any help would be appreciated.
It is a common philosophical argument that it is impossible for one person to know if another person is at the same place on the colour wheel (e.g. how I see blue and how you see blue could be different, and we will never know). By that reasoning, it is possible that some species see colours differently to us. However, black and white are not the colour wheel because they are not colours. So essentially, the question is, could another species that "sees" by sensing light with their eyes as humans do ever see an "absence of light" as a colour OTHER than black.
I am not quite sure what these two imbeciles are debating, but I believe they are arguing as follows:

Party 1: Black and white are shades not colours, and therefore, even if another species saw colours differently, they would always see black as black, white as white, and all shades of grey relative as usual to the colours they see.
Party 2: Black is only inserted into our vision by our brain to resolve the "problem" of not receiving any light. So, therefore, it is equally possible that another species could deal with this problem" differently, and they will see something other than black.

As to how humans define shades and colors is irrelevant. we can never look into the brains of an animal. We can't even verify if between-human differences exist between black and white. They are perceptual constructs. it's all in your brain. Therefore party 2 is the least incorrect.

Yes, my point exactly. Party 1 is arguing that it is impossible for such between-human differences between black and white to exist, because they simply indicate the "raw amount of light" I guess.

Or are you simply saying we don't know enough about how the brain works to answer that question?

What is incorrect about party 2's argument? Or is that the bit we can't tell? Sorry if I'm going round in circles..

it states "They will see something differently" - we can't tell. what experiment would tell you what an animal sees? we can't even tell apart what two humans perceive.

Yes, animals can see 'black' differently, in terms of different shades, similar to what you stated about humans perceiving different hues of 'blue'. It is all relative to the cones in the eye of the referenced animal. Animals that see in black-and-white see several different hues of both, black and white. Animals that depend on color to judge the ripeness of a food also see in several different hues of black. For example, a parrot differentiating between seeds that humans may perceive as both being 'black'. Here is a color chart showing the colors that bees can perceive in juxtaposition to humans; it indicates high differentiation between hues of black, as opposed to humans' low differentiation.

Hues of black? That is grey shades. I don't see grey shades in the figure. If you are referring to the 340 nm peak in bees, that is ultraviolet... . -1

So, would the statement "Any animal that sees light as we do will see black just as humans do", be incorrect? If so, then in this sense, black is a colour like any other?

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How to compare two RNA transcripts?
In this paper, the cuffcompare RNA package is reported:

Because of the stochastic nature of sequencing, assembly of the same
  transcript in two different samples may result in transfrags of
  slightly different lengths. A Cufflinks transfrag was considered a
  complete match when there was a transcript with an identical chain of
  introns in the combined annotation.

What does this mean in terms of comparing two transcripts to see if they are the same? Does that mean two transcripts are considered equal if they have the same introns, even some exons are missing in one of the transcript? What do they mean by transfrag? Is there an example?

Another way to look at this question is that. What's the precise definition that two transcripts are considered equal and thus my experiment has positively assembled the transcript.

If some exons are missing in one of the samples then the introns will, by definition, be different. What this allows is for the bounds of the outermost exons to vary a bit. This is particularly useful for exon 1, which often has lower coverage.

Thanks for the reply. However, I'm still not very sure how two transcripts are compared as stated in the paper. In this context, what's the precise definition of a match? Does that mean if I have 10 exons in the reference, and I get 8 of those exons (excluding the first and last exon), it's a match?

Forget about exons, you can clearly see that what you posted doesn't mention them.

Yeah, that's my question. What do they really mean in the paper? I tried to digest it but I couldn't understand what they meant.

Draw out a few example isoforms on a piece of paper. Have one skip an exon. Are the introns then the same between them (no). What if the exons are the same except the TSS or TES differs a little, are the introns then the same (yes).


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Average width of the male body
I've been looking for the average width (at widest point) of the average American male body but couldn't find it anywhere so far.
When I say "widest point", I mean that if you draw a rectangle (that gives X for width and Y for height) around the whole body, all of it should fit inside the rectangle, whether the shoulders are wider than the hips or vice-versa. I'm looking for the average value of X (arms against body).
If the hips are the widest point inside the rectangle, the width should contain the width of the hands that are against them.

Do you have (or know where I can find) that information?

I am so wondering now whether in the USA the average widest point would be the shoulder or the belly. Did you mean the point for which the average is the widest or the average widest point (consider the the widest point might be should for one person, belly for another and butt for yet another person)?

@Remi.b i meant at widest point

Let me re-ask my question. Do you mean measuring size at shoulder, belly and butt and then each of them and consider the largest number or do you mean taking for each individual the largest of these three values and then average those max values? Note that even once this is clarified, I am not sure anyone will be willing to really look and analyse such data for you.

why exactly are you asking that? What will you do with that information? If you explain a bit about your real problem, maybe we can help with it. Right now it looks like XY problem http://xyproblem.info/ For example, for health studies people use waist circumference. Caskets come in 28 inch wide or 31 inch wide options (quick google)

In addition to the other comments, I don't see any interesting Biology here as defined for this stack.

Widest as seen from the front, or from the side?  And if from the front, do you measure at the shoulders, or include the arms?  And if the arms, how are they held?  (That is, some people with a good deal of chest muscle have their arms out at an angle.)

hi. thanks for clarification. You might get some answers, but i urge you to describe your problem fully, not just request for X.

@maashatheytaz won't this mostly just covary with weight? More overweight people will have on average wider bodies. This seems a curious variable to attempt to measure.

I think it's a perfectly valid question, but highly doubt that anyone has an empirical answer because the information indeed isn't biologically relevant (and hence nobody has it). I could imagine it being interesting for game or furniture design, or architecture. As @aaaaaa said, it does sound like an XY problem and you should probably go back to the X and figure out which Stack Exchange site can provide you with information that might solve your problem.

@NatWH that's why I am asking for an average. They are anatomy statistics made out there, so if we a range, we can extract an average.

@maasha theytaz: I don't think an average is going to be all that useful, because there are distinct body types (mesomorph, ectomorph, &c).  Add on the effect of either obesity or weight training, and it seems like few people would actually be close to the average.

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How do longleaf pine trees adapt to the florida keys rainforest?
I know that longleaf pine trees can be found in rainforests, but I can't find anything.

This question is way too broad! Can you please let us know what exactly you are interested of? What species? What forest (Canada type of rainforest or Brazil type of rainforest)? What evolutionary event? Are you looking at current rainforest trees that have broad leaves and are evergreen or trees that had broad leaves that have now evolved toward needles or whatever?

I have to whine a bit.  I am sure this question's wording has been changed...as have lots of questions after the fact after answering.  Is there a way to tell?  I surely do not remember pines, I do remember broad leaf plants in the rain forest.

Conifers have evolved to handle cold winters, not rain forests per se.  What the heck does 'long leaved conifers' mean?  White pine with long long needles?  How about Ponderosa or Jeffery Pine?  Conifers aren't meant for tropical or subtropical regions.  Perhaps the monkey puzzle tree might qualify? Conifers evolved to be able to hold onto their 'leaves' by thick epidermis resistant to freezes.  There are even hardier deciduous conifers.  Why would my answer be voted down?

This is sort of a too broad question but here are a few ideas.  The second most fragile part of plants are the leaves. In the latitudes and elevations that experience freezing, plants have learned to abscise their leaves and go dormant for the winter season.  Conifers have thick, waxy, very thin leaves that most conifers do not need to shed.
In a rainforest there is no danger of too cold temperatures.  That is why there is an abundance of broadleaf trees and plants in the rainforest.  Most of our indoor plants are tropical rainforest species.
There is also an awful lot of rain in a rainforest. There is a problem with leaves covered with water, as it inhibits the absorption of CO2.  Beneath the leaf, O2 is released as a by-product of photosynthesis.  Broad leafed plants that have adapted to an environment with lots of rain, little wind, and being crowded together have leaves designed to 'wick' the rain water off the leaf to run down the midrib and off the pointy tip or lobed or curled under leaf margins.  This clears off the water and allows the plant to take up CO2, or it would not be able to do photosynthesis to make its own food for energy.
The other cool thing I can remember, is that broad leafs of plants are able to 'adjust' to the light. Similar to a 'solar sail' in outer space. If in full sun, those leaves get thick and stay smaller.  If in shade, very normal in a rainforest, those leaves can thin and get larger in order to capture as much light as possible.
A better wording for your question would be, 'why is there an abundance of broad leaf species versus conifers in a rainforest'?  If I've been able to translate your question correctly?
Hope this helps.

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Why is the ratio between action potential and threshold value called the 'safety factor'?
"AllorNothing Principle. Once an action potential has been elicited at any point on the membrane of a normal fiber, the depolarization process travels over the entire membrane if conditions are right, but it does not travel at all if conditions are not right. This principle is called the all-or-nothing principle, and it applies to all normal excit- able tissues.
Occasionally, the action potential reaches a point on the membrane at which it does not generate sufficient voltage to stimulate the next area of the mem- brane. When this situation occurs, the spread of depolar- ization stops. Therefore, for continued propagation of an impulse to occur, the ratio of action potential to threshold for excitation must at all times be greater than 1. This “greater than 1” requirement is called the safety factor for propagation."
This might be a more basic, straightforward question but for some reason, there's not much info on it on the web.
I'm guessing its called the 'safety factor' because it means that not any stimulus can cause an action potential and that the cells remain at equilibrium/their un disturbed state for most of the time, but this is only a guess.
Source of Info: Guyton & Hall Medical Physiology textbook

Can you please quote from your book? I think you may be missing some context.

Action potentials propagate by depolarization of one section of the membrane causing depolarization of an adjacent section.
It is necessary that this depolarization be greater than threshold. If the amplitude of the action potential were to drop below threshold, it would fail to propagate. Additionally, it would be quite slow and inefficient.
Therefore, the action potential amplitude is far greater than the threshold. This helps speed and builds in a "safety factor" to ensure the action potential propagates - that's what your book is saying.

Got it, thank you so much but may I ask one last question ? What determines  the maximum potential (the peak) reached in action potential ? I read in some student's notes that the the membrane potential never goes above 0 for small nerve fibres. To specify, he wrote : "Overshooting (meaning that the Inside potential becomes larger than zero)  happens in large nerve fibers but not in smaller fibers and many central nervous system neurons. " Does that mean that the larger the nerve fibre the higher the peak ? I'm also uncertain whether he means nerves of the CNS overshoot or not

@LiaAhmed That should probably be a separate question

Could you please explain why they use the number one? What  is the ratio exactly?


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

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

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

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

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

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

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

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

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

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


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Pavlovian Conditioning And Synesthesia
I have been reading about Pavlovian brain conditioning and it seems that documented cases are mostly limited to motor reflexes (like conditioning an eyelid to close when hearing a tone) or taste aversion . Basically information flowing through Cerebellum and Hippocampus. Are there proofs or scientific studies about the limitations of such conditioning? Or studies about what can be associated and what not?
Let's imagine for example that a subject looks at a black neutral screen and whenever some tone is played, the screen turns bright red. After an intense conditioning would it be possible that this subject, when blindfolded would see some red when hearing that same tone?

Probably more suited to the cogsci SE: http://cogsci.stackexchange.com/


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Is it possible to create DNA of a species that could be any animal
I was thinking about a fiction world in which all animal (at least vertebrate) could crossbred because they share same number and layout of chromosome but differ in hereditary detail (like human skin color) and/or using epigenetic modifications.
Is it actually possible? And how large of DNA it could be to code all vertebrate form and function?
I'm programmer so I just think DNA as a code. And it seem we could refactor and reuse most of DNA code between tetrapod species (also between arthropod-arthropod species)

I don't really understand your question. Are you asking something like "what is the Shanon's entropy of all vertebrates DNA put together?"

I am voting to close as unclear. In addition of the post being unclear to me, my rough understand of the question in the post does not match the one in the title.

The very similarities in number and layout of chromosomes that allows animals to breed with each other are the same similarities that cause them to end up with reasonably similar phenotypes. As soon as the genomes are too different to breed with each other, the phenotypes of the animals are so different that we categorise them as different species (usually). Therefore, I believe the question that you're really asking is, "can epigenetic control alone result in phenotypes so different that they would seem like different species?"

(Because their genetic similarity is what makes them de facto the same species)

@Armatus That's right as my first question. What I meant is not just epigenetic but also hereditary like lactic tolerance. But on wider scale, such as same specie being ruminants herbivore in one area but carnivore in other place but still able to mate if they met. What I want to know is are there any impossible trait that can't be code in the same layout like that in DNA

@AlwaysConfused I press upvote at your right comment. As I was state that I am thinking about fictional alien (parallel) world, I just want it scientifically possible

Suppose genome A generates organism oA and genome B generates organism oB. Their phenotypes pA and pB are quite different from each other.
Because genome A and B are not similar enough, organism oA and oB cannot sexually produce viable offspring.
Your question seems to boil down to: "Would it be possible to generate oA/pA and oB/pB from genome A, or a genome similar enough to genome A such that it can still sexually reproduce with genome A?"
So you basically ask whether any genome A could simultaneously produce pA and pB under different external conditions.
Answer: Possibly? The genes involved in the development of organisms typically don't respond to external stimuli but to genes which were active before them (in time). Various genes produce proteins which sense temperature, osmotic pressure or particular chemical species or ions. If those were factored into very early developmental programs, feeding into transcription factors to modify gene expression according to external factors, the same genome could produce drastically different organisms.
To speculate more about this yourself, it would probably help to go away from a code-based understanding of DNA and think more about what it is physically and biologically. Unlike computer programs, DNA "programs" can modify themselves and other programs or the functions they execute.
Biologically, DNA is an information carrier that is transcribed into RNA, which can have functions of its own and/or be translated into proteins. DNA interacts very tightly (physically) with a lot of RNA and protein components, and most things that happen in cells and tissues around them end up modifying the way DNA is handled in some way. Keywords that you could look up are "gene expression", "gene regulation" and "developmental biology".


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What is the progressive evolutionary advantage that leads to flying?
As far as I understand, all life started as non-flying and flying came about by natural selection. What is the evolutionary advantageous "path" to flying? Or is there something else to explain this?

You mean why animals "started" to fly? Because there was a large uninhabitated niche to live in: The air and the third dimension.

I've heard that insect wings may have developed from some sort of breathing structure. Both would be very thin with large surface areas.

@Chris no, my question is the ability (and organs necessary) evolved.

@Chris I would rather say that it was an escape from land based predators.

@WYSIWYG I would include this in the niche: Escape from predators, other ways to access food and so on.

Which type of flight? flight has evolved several times and not through the same path.

The honest answer to this and many other similar evolutionary questions is that we don't know the answer. We can sample information from many different points along an organism's developmental timeline using the fossil record, genetics, etc. and reconstruct various states of said organism's development. The overwhelming evidence is that evolution is the process that connects these various states, but reconstructing the detailed trajectory that leads from one developmental state (e.g. flightless) to another (e.g. flying) is often formally impossible due to the low time resolution of the information that we have.
That being said, plenty of people have speculated as to the origins of flight, and there's an excellent wikipedia article on the subject. From the article:

Powered flight has evolved only 4 times (birds, bats, pterosaurs, and insects)... Insects were the first to evolve flight, approximately 350 million years ago. The developmental origin of the insect wing remains in dispute, as does the purpose prior to true flight.  One suggestion is that wings initially were used to catch the wind for small insects that live on the surface of the water, while another is that they functioned in parachuting, then gliding, then flight for originally arboreal insects.

i like the parachuting, i think thats a satisfactory answer (although still a theory without evidence)

do you know if theres a good source for these types of explanations? cause i have a whole bunch more paths i would like explained.

@tryingToGetProgrammingStraight Yes I do! BAHFest is truly an authoritative source for such information.

@tryingToGetProgrammingStraight More seriously, it really depends on the organism/system in question. For example, the debate over why humans started walking upright has been a particularly acrimonious and silly one.

@tryingToGetProgrammingStraight If you have a whole laundry list, try posting them here. Just maybe keep it to one a day.


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Expression of an ancestral gene
Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?
Update:
By ancestral gene I mean a gene which was used by an ancestor but than changed slightly through evolution, though it still serves the same purpose. And by the misleading conclusion I mean that using this similarity between the product of the ancestral gene and the modern protein as evidence that the organism is descended from the ancestor.

What context are you working in? What're the misleading conclusions?

Without further information, question is impossible to answer.

specifically, please try to explain what you mean by ancestral gene?

I think that this pretty clear now. The first things that comes to mind is the convergent evolution and hereditary gene transfer.

I still think the question is too vague. Could you make an example with a specific protein and showing what conclusion would be misleading?

Do you mean expressed recombinantly?

Your updated question is still very vague, but I'm going to assume it is basically: "Why would the ancestral version of a gene be mistaken for a more recent version than the modern gene?"
If this is incorrect, please let me know and modify your question to clarify.
The simple answer to that question is that the mutations that occurred after the Ancestral gene resulted in less apparent divergence than the LCA (last common ancestor), which would cause the Ancestral gene to seemingly have more polymorphisms - and the general assumption is that the more polymorphisms (mutations) that a gene has undergone, the more recent it is.
So let's say you have the following DNA sequences:
5' - AAAT - 3' = LCA (Template)
5' - AAAG - 3' = Sample 1 : # Differences = 1 Nucleotide
5' - AACG - 3' = Sample 2 : # Differences = 2 Nucleotides
The general assumption is that the larger the difference from the LCA, the more mutations have occurred over time. So, under the general assumption, Sample 2 is probably the most recent version of the sequence.
However, and this is what I think is the answer to your question, because mutations can occur in any order and at any place in the genome, it is entirely possible for the third (from left) Nucleotide to have followed this mutation path: A -> C -> A
That would make Sample 2 appear to be more recent than it is because it essentially mutated "back" to the LCA version of the gene, despite being a linearly older version than Sample 1. In this way, an Ancestral gene can be mistaken for a more recent evolution of a gene. This is also why genomic data is never as strong as when paired with fossil records or other corroborating data that also aligns with the genomic data's proposed timeline; though the odds of a mistake being made grow exponentially less as more of the genome is compared and analyzed.
With very recent mutations; on the scale of hundreds to thousands of years, it's sometimes necessary to analyze thousands of base pairs to calculate an adequately confident answer.


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Electrical transmission vs Chemical transmission
"The advantage of electrical transmission, apart from speed, is it can favour synchrony in firing. For example, in the brain stem a nucleus called the inferior olive can generate oscillations due to gap junctions."
Can somebody explain this idea? I do not understand the meaning of oscillations in this context. Do they mean that the neuron can send impulses and receive them at the same rate ? Is that what they're trying to put across ?
Source:Lecture Handouts

Please include a reference when you quote from a source; failing to do so is plagiarism.

Its from my lecture handouts


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Is there a mechanism of timing or delaying the expression of gap genes?
Summary

Gap genes are expressed in presence of the right combination and amount of
  transcription factors. But is there any additional mechanism of timing the expression of the gap genes to ensure that they are expressed at the right time?

Context and Detailed Question
Let's look at gap gene expression in Drosophila:

Firstly, bicoid and nanos are expressed and diffused from anterior and posterior ends respectively and form gradients;
Then, hunchback gets expressed, with bicoid acting as promoter and nanos acting as suppressor;
Then, Krüppel gets expressed, with
hunchback acting as both promoter and suppressor - meaning that there must be enough hunchback, but not too much.

(or a video: https://www.youtube.com/watch?v=uaedzlrnBGY)
Makes perfect sense, unless you look at it from dynamic, biochemical perspective:
Firstly, bicoid and nanos slowly build up in the embryo:

As soon as there's enough bicoid at the anterior region, hunchback immediately starts building up too: I mean, it can't just choose to wait for bicoid to establish its gradient or something - if there's a promoter for it, it should react accordingly.

And so it "chases" the bicoid gradient, in a manner of speaking, and will continue to chase it until it stumbles into nanos protein, which suppresses it.
All this makes sense so far.
The only problem is that at this point, there's just perfect amount of it for Krüppel at the anteriormost region, so Krüppel should start being expressed there:

Eventually, there'll  be too much hunchback at the anterior region, so Krüppel should cease to be produced - but some quantity of it should be expressed there nonetheless. The final gradient should look like this:

The only way to avoid it is if Krüppel kindly waited until the hunchback establishes its final gradient before even attempting to be expressed. But how is this possible? Is there some mechanism that prevents Krüppel from being expressed too early - and if so, then what releases it? Or maybe there's some mechanism of timing, that prevents genes from being expressed too early?
This Krüppel example is just one examples of several, when there must be some timing control in order for genes to be expressed properly.

I'm voting to close this question as off-topic because this is not the kind of precise answerable question that SE Biology is for. It is basically an argument against a model of gene expression followed by an “am I right?”.

@David 1. It's a precise answerable question (if there is a known mechanism that prevents kruppel from expressing too early, then a person who knows about it can answer).

Where did you see an argument against the existing model of gene expression?

Where did you see "am I right?" or even me proposing anything? I explained the thing about dev. biology that I don't understand and look for help. If you know the answer, you could just answer; or if you think that I misunderstood something, you could just explain where I am wrong.

OK, I'll withdraw my close vote and restrict myself to some constructive help and advice. 1. Your question is complex and very few people on this list are likely to be able to answer it. 2. They would have to read through text and 11 diagrams to get to the actual question to see if they could answer it. I think that few are likely to do so. The very least you should do is to start your question with a summary of what it is, before telling people what to consider. I have started this for you. You can delete it if you like, but I would advise you to improve on it instead. And your title.

I have absolutely now idea about drosophila embryo development, but you/your diagrams seem to assume that all these genes are - dynamically - expressed as along as their promotor is active (enough) at a given position in the embryo. I would suggest you to also look into the temporal dynamics of these genes as well - I wouldn't be surprised if these 'gap' genes only start expressing when the nanos/bicoid gradient is already fully established, maybe looking into that direction can help you find an answer.

@David, thanks. I've tried to make question and summary more clear. As you say yourself, the question is very specific and complex, and it took me two days just to formulate it properly - so I found no other way to make it clear but to include diagrams and stuff...

@Nicolai, thanks, I've found a few articles by googling temporal dynamics of gap genes, I'll see what they say. I also expect that they should wait for gradients to establish first, but I couldn't find what could be responsible for it so far. No articles that I've seen so far mention it and just say that it's all about gradients of transcription factors.

Not sure which papers you've found, but off the top of my head these address similar topics:
https://doi.org/10.1371/journal.pbio.2003174
https://doi.org/10.1371/journal.pcbi.1005285
There's also a video lecture by Johannes Jaeger in which I think he addresses similar questions/provides an overview of the above papers and previous work: https://www.youtube.com/watch?v=kVSf9Hjl9Jk
Too busy right now to read and watch these again in detail, so may not be helpful, but off the top of my head seem to address this kind of question.


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How is the Gibbs Free energy of Redox reaction during Electron transport of the Mitochondria utilized to pump protons across mitochondial membrane?
I understand basics of the electron transport chain..that electrons "donated"  from NADH and FADH2 moves through redox centers within respiratory complexes I,  III, and IV (II is not involved in proton pumping)..Each step releases some energy..How is this energy harnessed by the respiratory complexes to pump protons across the mitochondrial membrane (against the gradient) to build up the Proton Motive force (which is ulitmately used by ATP synthaze nanomotor)?*.
Does  the Free energy  cause  conformational changes in the Respiratory protein complexes*, and the conformational changes ultimately pumps protons against the gradient? Does the details of  how the    Free energy is utilized depend on the Specific respiratory complex?
I am looking for a mechanistic explanation how the energy of redox reaction  is harnessed to pump protons against the gradients.

There are a number of questions in your post, which would require a fairly long answer. Please use the [edit] function to concentrate on the most important question, as the policy in SE is one question per question (more within reason if strongly related, some of which aren't in yours.) Thanks.

For the mechanistic part of your question, a good place to start might be Paul D. Boyers' Nobel lecture Energy, Life, and ATP

I suggest you read a biochemistry text book. I would recommend Berg et al, and an old edition will suffice. You can pick up the 5e second-hand for about £5 on eBay (a search for Stryer Biochemistry gives more results).


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Through what mechanism does ingesting Saturated Fat (but not Mono unsaturated Fat/PUFA) increase Serum Cholesterol.?
I know that the saturated fats you ingest is broken down in the intestines by the bile acids from liver and then re synthesized as triglycerides after crossing the enterocytes. Then these triglycerides along with cholesterol (either from diet, or from the liver in form of Bile acid)  is packaged into lipoprotein particles called chylomicrons..and they leave the intestines through the lymphathic Systems.  These  chylomicrons deliver triglycerides (converted to FFA) to adipose, muscular and other peripheral tissues.The remnants of the Chylomicrons are taken up back by the liver at a LRP receptor?
Once these Chylomicrons remnants are taken up by the liver..it somehow triggers greater  synthesis of ApoB particles and VLDL, as well as down regulation of LDL receptors on liver. Then the VLDL particles (loaded with Triglycerides and endogenous cholesterol?) leave the Liver and deliver FFA to peripheral tissues (similar to Chylomicrons)...and progressively lose their Triglyceride content and become IDL (reptaked by the liver). and finally LDL..since LDL receptors are also downregulated and their is presumably no other equally effective mechanism for LDL reuptake this leads to a net increase in LDL particles in Serum and measured Serum cholesterol. My question is How does Chylomicron remnants returning to the liver trigger the synthesis/Genesis of greater amount of ApoB and VLDL production? Do these remnants act as a signal to the liver to produce more VLDL/ApoB, or are Components from Chylomicrons  used to produce the VLDL, and how about LDL reuptake downregulation.
I am an engineer with no background in physiology/biochemistry. Could you please provide a relatively layman's explanation of the mechanism. Thank you.


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What is the highest known trophic level for a consumer?
Or rather, what's the longest known food chain between a producer and an apex predator?
I've found a few similar questions and answers online, but none of the questions clarified some of the nuances of the question meaning all of the answers I've found are rather vague (e.g: 'about 10' or a more specific value without a specific chain, "we don't know", 'it depends', 'in the ocean' or 'infinitely long') or just random guesses (x2).
You might be able to consider the food chain of cannibalistic species or two species which consume each other to be infinitely long, so I'll assert that a food chain can not contain the same species twice. Also don't consider food chains that are only theoretically possible, I'm interested in what food chains actually exist and actively occur between widespread species. This also means not including species which eat just about everything, unless the species being eaten is one of their primary prey.
There probably isn't a definitive answer to this or a way to prove that one food chain is the longest, but I'm just interested in how long a food chain can get.

Hi and Welcome! You may not know that this site requires evidence of prior research (quote and link to source/s) in an attempt to answer your own question (this is a Q&A site, but one with slightly higher expectations.) For example, have you searched for the role of environment on food chains, etc.? If so, what have you found? Showing evidence or research greatly increases your chances of getting an answer.

you might have an easier time by making the trophic level version of the question the title, the food chain one all but unanswerable.

@anongoodnurse I wasn't sure how to site my sources properly, since StackExchange seems to just treat Markdown references as links but I used some sources multiple times or had multiple sources for one point, but I've done my best

That was an excellent edit to include sources. Since you did your part, I'll try to find out. I fully expect, though, not to find one definitive/reliable longest food chain length. The more complex the ecosystem, the more likely to be more "steps" in the food chain (E.g. a desert is less complex than a salt marsh.) I'll avoid the ridiculous or artificial. (E.g. coyotes > ospreys > ship rats)

OK, I did try. The common answer is "unknown", one reason being that food webs are seasonal, another is that the same species can be lower or higher in the food chain depending on size, population, etc., and oof!!! The most complex ecosystem on earth is the tropical rainforest, but I found more trophic levels in the ocean. But none were fixed; they change and are interconnected. Ugh. I'm sorry; I would have liked to have given a better answer.

@anongoodnurse Don't worry! I was fully anticipating there to not be a definitive answer thanks to the many variables involved. And you've clearly done far more research than me haha. Since it seems most of the variables relate in some way to time, maybe it be possible to identify a worst-case and best-case scenario?

I just decided I don't know enough to say much of anything. I read a number of papers, but I'm still kinda flummoxed. See here for an example of how complex oceanic food webs are. You should see the tables, some with hundreds of superimposed webs.


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Number of membrane proteins of a particular type per cell
Is it possible (or meaningful) to count how many proteins (protein copy number?) of a certain type a given cell has on its surface?
For instance, say there is some membrane integral protein X. Is it possible to take a population of cells, and arrive at a number (say 100) that reflects the average number of X per cell in the population?
I'm trying to look for publications that have done something along these lines, and I've had no luck so far. This made me wonder if this is even a meaningful idea at all, so I decided to see clarification here. (Apologies if this is a trivial question.)

The dimensions of every cell are different. So, The number will definitely be different for integral membrane proteins, and other cell constituents.  Mass-spectroscopy can be used to calculate cellular protein fractions. I'm not sure specifically for integral membrane proteins.

Nobody is going to publish a paper where the main result is the number of proteins of a particular type in a cell. It’s not what modern science is about. Any protein for which there is a quantitative assay would allow one to deduce this in the usual simple arithmetic manner. I used to drive my students mad making them do this sort of sanity check. Welcome to the club.

@David I think you're mistaken, unless I am misunderstanding your comment. In the time since I posted this question, I've managed to find a few papers that have addressed this topic (albeit, admittedly, not perfectly, and at a general level). See, for example, Ho et al. 2018 (https://www.cell.com/cell-systems/fulltext/S2405-4712(17)30546-X).

For the budding yeast pheromone receptor Ste2 this has been done long ago: https://pubmed.ncbi.nlm.nih.gov/3023832/
There is also later work that used fluorescently labeled ligands, allowing for these analyses on a single-cell basis to study cell-to-cell variability.

If you know the stoichiometry of a particular ion channel and do something like patch-clamp, where you know the surface area being clamped, then you can measure the ion-flux per unit time and from that infer number of the channels in that area. From this you can make some inference as to the number of ion channels on that particular surface of the cell.
However, this doesn't equate to the total number at all, as the different surfaces of cells have different numbers depending on their functions. For instance tight-junctions might have a different number from apical surfaces which will have a different number to basolateral surfaces.


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Butterfly Raises Abdomen Like A Scorpion
Since a few weeks I am observing a little butterfly in my living room and normally I put insects out but it's cold outdoors and I thought it's secure inside. It occassionally flies around, especially since last 2 days and now I saw it is behaving differently. It has raised it's abdomen rectangularly (90 degrees) and it looked greenish with white stripes. When I tried to make a picture with flash on, it lowered it's tail and the color has also changed to a brown. The picture shown is just a couple minutes later taken without flash. I'm worrying if it's afflicted by a worm and I am thinking about if it's better to put it to rest in that case!?
As I am writing this line, it has lowered its tail further.


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Emotions in Animals Based on Neuroscience
I know very little about the subject, so please forgive any misunderstandings in the question. First of all, by emotion, I mean feelings of pleasure and suffering and not merely just sensory recognition of damage to the body or things like that. If I understand correctly, the consensus among scientists is that all mammals can feel pleasure and pain based upon all of these animals having similar brain structures to humans that have been correlated with feelings like pleasure and suffering. https://www.emory.edu/LIVING_LINKS/publications/articles/deWaal_2011b.pdf.  The way I'm hoping to potentially find an answer is by asking if it's known that there are certain structures in the human brain that are necessary for feeling pleasure and suffering and if it's known that are any animals that do not have these structures or similar structures?

Hi and Welcome! You may not know that this site requires evidence of prior research (quote and link to source/s) in an attempt to answer your own question (this is a Q&A site, but one with slightly higher expectations.) For example, you can search using terms like "dog emotion and MRI", and quote from the article. Showing evidence or research greatly increases your chances of getting an answer.

look up the amygdala

What is it about the paper that doesn't answer your question? A link alone gives us no information.

It is so broad that I wrote my thesis on it! The evidence is also inconclusive and dividing. I think this is too broad for this site. Here is a fairly recent review on the subject https://www.sciencedirect.com/science/article/pii/S0149763419305391


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Sanger Method - DNA sequencing
I'm having a little bit of trouble understanding the Sanger method of DNA sequencing. How can you determine the order of the sequence just by the length of the fragment the ddNTP is attached to?
For example, say in our sequence the first base is A - so the ddNTP would be T, but what if randomly the first fragment is very long and the T is at a position that corresponds to the end of the sequence - would we say that A is at the end of the sequence?

Sanger sequencing doesn't use random fragments like many of the high-throughput sequencing techniques. Instead, it uses a series of progressively longer fragments, all of which originated at a dedicated primer site. Because they all have the same origin, the final nucleotide of a particular fragment will be a known distance from that priming site.
Today, PCR amplification is used to produce enough of the template DNA and to specify an arbitrary* location for the priming site. As bases are added to the elongating strand, a fraction will incorporate a fluorescent ddNTP, which terminates that particular fragment. All the other fragments are still elongating and so have the opportunity to incorporate a fluorophore as the next nucleotide.
Each fragment of a particular length should have incorporated the same fluorescent nucleotide. All of the fragments are then passed through a capillary which separates them by size (with enough precision to identify fragments differing in length by a single base pair), and the signal strength of each fluorophore color is recorded at then end of the capillary.
From this trace of fluorescence intensity the sequence of the original template can be reconstructed.

*Mostly, there are still considerations needed around selecting an optimal priming site.

What has PCR to do with Sanger sequencing? PCR hadn’t been invented when the method was introduced.

That's correct, the original Sanger protocol used bulk DNA from bacteriophage ΦX174, then used the fragments from restriction enzymes as primers. Following the advent of PCR the technique could be expanded to samples that otherwise wouldn't contain enough DNA, and allow for a much wider selection of priming site. Now, it's standard to use the products of a PCR reaction as the input for Sanger sequencing. I've edited the answer to clarify that it's the location of the priming site that creates a uniform starting point for elongation.


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Blooming at moonlight
At the moment a popular question in the physics SE community is about night-blooming cereus: this flower blooms at full moon, that is it is capable of making difference between the moonlight and sunlight.
The question has attracted a lot of guesswork, with some people even claiming that the cereus doesn't know about the moon, but simply blooms at night - the blooming at full moon however seems to find experimental confirmation. It is thus more plausible that the flower distingushes between the light intensities of the moonlight and the sunlight, as suggested here.
The closest question that I found in this forum is about flowers open during the daytime and closed at night (or vice versa). I suppose one could construct a more sophisticated model based on the mechanisms described here, but I would appreciate an expert answer.
To restate the question:
How does night-blooming cereus distinguish between moonlight and sunlight?

I'd really like to get an expert answer to this interesting question. Would you consider offering a bounty?


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Limma - Voom function for microarray data
I am wondering if anyone can have a look at the voom plot I got below and let me know if this is indicative of an issue with my design?
I understand that it should be more of a J-shape rather than a straight line.
Any help is appreciated.
I am not sure if this is because its microarray data instead of RNA-SEQ count data?

You might be better off requesting migration to our sister Bioinformatics site

Hi, yeah that's where I posted originally but was asked to post here lol


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What is the correct nomenclature for expressing a genotype where a recombination event may occur?
Given an example punnett square:
 -------------------------
 | x   | A-b     | Y     |
 -------------------------
 | a-B | A-b/a-B | a-B/Y |
 -------------------------
 | A-b | A-b/A-b | A-b/Y |
 -------------------------
 | a-b | A-b/a-b | a-b/Y |
 -------------------------

What is the correct nomenclature to express the genotype prior to putting it into a punnett square? The parent's genotype looks like a-B/A-b x A-b/Y except I want to show that a recombination event can occur, yielding the third row in the punnett square table.
This is relation to my previous question about how to calculate recombination frequencies.

I would suggest "genotype".
A Punnett square is a visualization technique to help us think, it doesn't change the terminology.
If what you mean is the 1N genotypes represented in the rows/columns that combine to make the 2N genotypes, you might consider "haplotype" (haploid genotype). The haploid cells with those genotypes might be called gametes, but that refers to the cell and not to the genotype.
If you are specifically interested in those genotypes/haplotypes in which a recombination event has occurred (or not), you could call them recombinants or non-recombinants. In some cases you can encounter specialized terminology, for example in yeast tetrad analysis you encounter terms such as "tetratype", "nonparental ditype", "parental ditype". But those are not generally used outside the yeast field, I believe.


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Drinking salt water
I have been told that one should never drink sea water no matter how much thirsty
It turns out that drinking saltwater adds lot of salts to the body that need much more water than the amount consumed to be removed leading to dehydration
A few questions arise in my mind

Why can't our kidneys excrete a little more concentrated urine than usual to remove excess salts (sea water is not saturated unless perhaps the Dead Sea water)
At maximum a more concentrated urine will damage the bladder or some portions of the kidney but that will not kill us as fast as dehydration.
Anyway the kidneys should know that the body is already having a shortage of water (that is why we are thirsty enough to drink salt).

Also should not absorption of salt stop in the intestine after enough has diffused passively
And if it is being(in case concentration is high but not than of blood) being actively absorbed it should stop after desired amount has been absorbed

If it too concentrated and threatens to cause plasmolysis the intestines should actively absorb water right?

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please take the [tour] and consult the [help] starting with [ask] for details.

"Why can't our kidneys excrete a little more concentrated urine than usual to remove excess salts" Things have limits and sea water is beyond that limit. Just because I can run a bit faster than usual doesn't mean I can continuously speed up forever. "Also should not absorption of salt stop in the intestine after enough has diffused passively" Think about what you're saying here. When does diffusion stop? When concentrations are equal. Is that too salty for the body? Most definitely. I'm pretty sure you already know both those things but you do not seem to be adding 1 and 1 together.

This has been asked and answered before. Search for "drinking sea water" in the search function at he upper left of the page; you will find some answers.

Please familiarize yourself with how this site works — your first two questions are already closed and now you are using the comments to try to start a discussion. A comment is ephemeral and intended for suggesting improvements to a post — do not use them to ask follow-up questions. ——— Note, from the [help/dont-ask], If your motivation for asking the question is “I would like to participate in a discussion about ______”, then you should not be asking here.


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How does comparing shuffled proteomes to the unshuffled ones help us understand independent protein adaptation?
From 'Protein and DNA Sequence Determinants of Thermophilic Adaptation', by Konstantin B Zeldovich, Igor N Berezovsky and Eugene I Shakhnovich (Published: January 12, 2007 | https://doi.org/10.1371/journal.pcbi.0030005):

Proteins are encoded in the nucleotide sequences of their genes, and
thermal adaptation presumably leads to increased stability of both
proteins and DNA. Therefore, signatures of thermal adaptation in
protein sequences can be due to the specific biases in nucleotide
sequences and vice versa. In other words, one has to explore whether a
specific composition of nucleotide (amino acid) sequences shapes the
content of amino acid (nucleotide) ones, or thermal adaptation of
proteins and DNA (at the level of sequence compositions) are
independent processes.
To resolve this crucial issue, we applied the following logic. If
amino acid biases are a consequence of just nucleotide biases and not
protein adaptation, then proteomes translated from randomly reshuffled
genomes will feature similar “thermal adaptation” trends in amino acid
composition as observed in real proteomes. In contrast, if amino acid
compositions are selected independently, then such control calculation
will result in apparently different amino acid “trends” in randomly
reshuffled genomes than observed in reality.

Can someone explain the logic of these authors in the second paragraph? Because I do not understand.
Firstly, I understand that DNA can adapt somewhat independently from proteins due to codon bias, and protein expression can adapt independently from DNA due to epigenetic factors (epigenetics is not mentioned in the article). However,
how does comparing the amino acid composition of a proteome translated from a randomly shuffled genome to the original, unshuffled proteome provide insights into independent protein adaptation?

I think they explain themselves pretty clearly; think about the two possible scenarios they identify, and how their shuffling experiment will give different results in the two scenarios.

@BryanKrause thanks Bryan I have several times, but I still do not understand how the second scenario in particular suggests what the authors are claiming it suggests. This is probably me at fault, but for some reason I can not understand.

Firstly, the researchers say: "proteomes translated from randomly reshuffled genomes will feature similar “thermal adaptation” trends in amino acid composition as observed in real proteomes", this is only a chance, there is a chance that the thermal adaptation trends will be entirely different. I suspect this is probable, because DNA only has four unique nucleotides, read in codons, if one nucleotide in a codon is changed then the entire amino acid could change. This is why I would actually expect "apparently different amino acid “trends”" in the first scenario.

Furthermore, if the genomes are randomly shuffled, how would this suggest: "In contrast, if amino acid compositions are selected independently, then such control calculation will result in apparently different amino acid “trends” in randomly reshuffled genomes than observed in reality."? I would expect the opposite, if the genome was reshuffled and we observed the same amino acid composition, then I could see how protein adaptation is somehow independent from DNA adaptation, as I would expect the amino acid composition to be different, due to new codons being created by the random DNA shuffle.


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Why is There a Necessity for Two Rounds of Cell Division and Four Daughter Cells in Meiosis
Why does meiosis involve two rounds of cell division instead of stopping after meiosis I, where each daughter cell would have one chromosome randomly selected from each pair of homologous chromosomes? Theoretically, this could be achieved without DNA replication prior to meiosis I? Why do we need four daughter cells rather than two? Where in meiosis, effectively, one chromosome from each homologous pair goes into two of the four gametes, due to the chromosomes in meiosis I being composed of two sister chromatids. I am clearly oversimplifying the process and overlooking some important components.

In an attempt to answer my own question, I asked myself: whether the two daughter cells from meiosis II (I am referring to one pair that is produced from each parent cell), were identical. I realised I had forgotten to consider recombination. While it may be true that sister chromatids are identical copies of a chromosome created during DNA replication, crossing over during meiosis I can create genetic diversity between sister chromatids. Crossing over occurs between non-sister chromatids of homologous chromosomes. As a result, even though sister chromatids are separated during meiosis II, the daughter cells produced may not be genetically identical due to crossing over that occurred during meiosis I. The result I assume would look something like this. However, I realised recombination would still be possible, albeit with two unique gametes, rather than four.
If at any point I say anything incorrect feel free to point that out.

I saw a potential answer here, however, the answer is arranged in a way that is unclear and difficult to read for me.

If I understand correctly, your idea is to say, it would also be possible to start with unduplicated chromosomes (no S-Phase), perform crossing over to increase the genetic variety and then to distribute the single chromosomes into different cells - and now you want to know what's the difference to regular Meiosis and "why" it happens that way?
As you hopefully know, "why" questions are not really scientific. We cannot really know why something happened. We can only speculate that this could be a reason or provide an advantage for evolution. One explanation why it would be advantageous to have S-Phase before and use Meiosis 2 to reduce the chromosome number is (as explained in the question you cited) the following:

Crossovers (CO) play a huge and important role for generating gametes and is the basis of genetic diversity.
COs are generated by double-strand breaks (DSBs).
Most DSBs are not converted into COs and need repair through different mechanisms.
The sister chromatid helps as a template for that.
My speculation is that without a second sister chromatid during crossovers, the cell would simply die due to DNA damage.


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Can nervous disorders be cured? Will enough research be the answer?
I have searched every nook of the internet and I couldn't find a clear and to-the-point answer. Well my story is that I am a young BSc student who wants to do research on neurological conditions because as far as my knowledge goes neurologists cannot do anything about ANYTHING, things like dementia and brain damage lead the person to become completely destroyed and then eventual death is what every doctor has to see. As of current.
So I am asking if we can develop eventually effective treatments for let's say OCD or Alzheimer's? Or that will never happen because of other factors in the ecosystem and it's the rule of the nature that some people are just unfit to survive? If that's possible, and about to happen in my life time -- i.e., I can contribute -- I am in. I am gonna get a doctorate in one of the life sciences and start doing something. Like discovering genes, or understanding the pathophysiology, or discovering drugs, whatever I am competent in and able to. I just cannot see people suffer like that.

Yes, levodopa type treatments for parkinsons.
epilepsy:
In 2017, 116 children were randomly assigned to undergo epilepsy surgery or receive medical treatment. After 12 months, 77% of the children who had undergone surgery were seizure free compared with 7% who received medical treatment.
Check news and histories of advances in neuroscience and neurology.
Every year drugs improve, it's best to stay objective in the face of mind dysfunction, meditate.

But will enough research lead to such advances that neurological conditions will be cured? If not, can the patients be significantly benefited in the near future? Thanks in advance.
Edit : I'll try to stay objective my best.


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When does DNA replicate actually?
I read on Wikipedia that when the cell enters prophase during mitosis , the DNA has already been duplicated , that is the DNA is replicated in the chromatin form , but here I see the picture which shows the already condensed DNA ( now chromosome ) divide into sister chromatids. When does DNA divide actually ?link to wikipedia -https://en.wikipedia.org/wiki/Prophase

Wikipedia is an iffy source to use. Points for adding illustrations though! Can you add link(s) so that anyone who wants to can go and read the articles themselves? If you have any questions or concerns about my thoughts on your answer, please visit the Help Center here https://biology.stackexchange.com/help

added the link.

Thank you! Are you able to reference something that isn't from Wikipedia. This article there looks pretty reputable and such; however, sometimes there is some "shady" stuff there, if you find something else, please feel free to link that here as well.

I can refer my textbook , but I would be thankful if my question is answered , I have stated my confusion quite clearly and I believe  I can get answers too.

My mistake... I thought you were answering a question not asking one. I totally misread, my apologies, your question is fine. I hope you have a great day! :)

According to This paper and most biology textbooks, S-phase or synthesis phase is literally defined by the beginning and ending of DNA replication.  The first picture does not accurately represent the nature of DNA replication and is instead a model to help people track DNA copies during stages of cell division.  DNA is replicated as chromatin and condenses to "double" chromosome form.  You can see some micrographs of DNA condensation in this paper.  You'll see that they don't condense as single chromatids, but they are already replicated.

That's exactly what should happen , It was constantly bugging me that how could the condensed DNA divide , it should be topologically difficult with all that packaging business , so they should divide in the loose form only , am I right in thinking like this ?

Yes, you're correct.  I'm not aware of any circumstances in which condensed DNA can replicate.  The first image from the textbook is meant to help student track copies of DNA through the cell cycle, but it does not represent the actual mechanics of chromosome formation.


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Can something cause both breaks and cross-links in DNA?
A double strand break in DNA is exactly that: the strands of DNA are severed. A cross-linkage occurs when something forms a covalent bond between two nucleotides in DNA. However, is it possible for something to form both a cross-linkage and a double-strand (or single-strand) break? For instance, could one part of a molecule cause a break while another reacts to form a cross-linkage?
For the purposes of this question, enzymes or proteins which do this (If there are any) also count.

Cisplatin forms DNA-protein crosslinks (so DNA-protein-DNA by extension) in vitro [1] and a review [2] says that cisplatin leads to DSBs (although I can't access the primary source at the moment). But you know, with the exception of ionizing radiation, mutagens usually don't directly cause DSBs. It's caused by repair processes or things like stalling at replication forks because of the mutagen.
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1874601/
[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047912/#!po=11.9919

Ultraviolet radiation can induce both DNA crosslinking and double strand breaks.
Here is a paper reporting sequnce determinants of UV-induced intra-strand crosslinks:
https://www.ncbi.nlm.nih.gov/pubmed/11342214
Here is a paper where the authors propose that UV-induced double-strand breaks are a consequence of repair of oxidative lesions, rather than a primary result of UV photochemistry.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488256/


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How do organophosphates actually work?
The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine at neuromuscular junctions, which ultimately results in respiratory failure. However, there is evidence that this may not be the case.
Firstly, a study reported that the nerve agent VX has been found to attack at least 132 different proteins, some of which were associated with metabolism.
Source: https://www.ncbi.nlm.nih.gov/pubmed/28267914
Also, another study showed that, even when the enzyme was protected against the action of organophosphates, nerve agents still exhibited toxicity.
Source: (http://www.rand.org/publications/MR/MR1018.5/MR1018.5.chap5.html) (Found in the Chapter 5 PDF, under "Non-AchE Effects")
Also also, another study was conducted on the matter. The test subjects were mice genetically engineered to lack acetylcholinesterase. The study found that the mice that totally lacked the enzyme not only lived (For over 34 days, no less), but were also twice as susceptible to OP poisoning as mice with the enzyme and exhibited the same symptoms.
Source:https://www.ncbi.nlm.nih.gov/pubmed/11602663
So, how do organophoshates actually act to cause the symptoms associated with OP poisoning? What proteins do they affect? There seems to be a great abundance of evidence that the effects of poisoning are not due to AchE inhibition.

Organophosphates (OPs) are cholinesterase inhibitors that lead to a characteristic toxidrome of hypersecretion, miosis, dyspnea, respiratory insufficiency, convulsions and, without proper and early antidotal treatment, death.
Most OP compounds are highly lipophilic. Sulfur mustard is a toxic lipophilic alkylating agent, exerting its damage through alkylation of cellular macromolecules (e.g., DNA, proteins) and intense activation of pro-inflammatory pathways

@com.prehensible If cholinesterase is a vital enzyme, then how come test mice that were engineered to lack it entirely could survive for over 34 days?

there are multiple genes for cholinesterase enzymes, for acétylcholine, butyrylcholine, This document states that they found that BchE was equally important as AchE. The knokout mice did die faster from VX. If you look on the reference it gives many, many different targets for OP's did you see it? it's very well written. http://www.scielo.br/img/revistas/jbchs/v27n5//0103-5053-jbchs-27-05-0809-gf04.jpg OP's are very volatile and they can put lots of chlorine and sulphur esthers inside the body, which react with 100ds of metabolites even DNA, the known list is given in the above pic

Hundreds of OP's have been made since the 1930's. Phosphoric acid is used in Coca-Cola and organophosphates are esters of H3PO4, you can study ester lipid/aqueous drug chemistry. They have many different targets: http://www.scielo.br/img/revistas/jbchs/v27n5//0103-5053-jbchs-27-05-0809-gf04.jpg
OP's are lipophilic. Lipophilic substances can dissolve into cell walls which are lipid bi-layers, straight into the DNA of cells and also into the nervous system.
They can travel through cellular membrane, alveolar and dermal membranes, through dermal glands, cell walls and from one organ to another. The degree of lipophilicity of drugs cause them to either stay inside the cell membrane or go through. Prozac also being lipophilic. The body is made of a mostly aqueous phase and also a lipid phase.
Many OP's contain Sulphur and they are bioactivated through desulfurative oxidation and turned into the corresponding oxon form by the liver so the organic chemistry inside the body is very complex: dealkylation, dearylation, phosphyrylation, carboxylation, hydrolysis and they are very reactive with metabolic compounds in different phases. They can be combined with absorption facilitators to pass the skin barrier and paired with radicals which are activated by the liver.
A recommended text on the toxicity: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-50532016000500809
OP and acetylcholine are both esters.
Here's a good chemistry animation of AChE enzyme inhibitor process: https://youtu.be/fIvF1rhp1nA
And this one, about non-competetive inhibition of AChE:
https://youtu.be/_jfGKbbZStw
general AChE info:
https://www.youtube.com/watch?v=-gIqZ8IxctE
AChE inhibitors that affect lots of organs such as peripheral and central nervous systems, muscles, liver, pancreas, and brain.
They lead to a characteristic toxidrome of hypersecretion, miosis, dyspnea, respiratory insufficiency, convulsions and without an antidote, death.
They can bind to fatty elements inside the body, like the central nervous system. They can exert damage through phosphorous-alkylation of cellular macromolecules (e.g., DNA, proteins) and intense activation of pro-inflammatory pathways.

Actions: (1) Phosphoryliodide can combine with phosphatidylcholinesterase to form a complex of phosphatidylcholinesterase and phosphatidylcholine iodide. The latter can be further cleaved into phosphatidylcholine iodide to free the cholinesterase and restore its activity.
2) Phosphodium iodide can also bind with free organic phosphate esters in vivo, and become a non-toxic phosphatidyl iodide phosphate, which is excreted from urine.
The mechanism of action is to inhibit cholinesterase and indirectly activate M-receptor, and the organic ester poisoning is also due to the inhibition of cholinesterase, which is equivalent to the original organic ester poisoning, atropine rescue overdose, and organic ester treatment.


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Do the antlers re-grow in the same pattern every year?
I am a software engineer and I am trying to develop a system to identify a deer by its photograph.
Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern next year and if yes, then what are the measurements that are of interest here?
Any pointers for me? Any software that can help me in recognizing a deer?

This has effectively been superseded by your subsequent question - in future you might want to consider using the [edit] function :)


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Is wiping with RNAse Zap enough to destroy RNAse activity?
From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH?
Some other links suggest there is some NaOH as well.
The Ambion site states that RNAseZap destroys RNAse activity on contact, but they also instruct to rinse with water twice after wiping RNAseZap on the surface being cleaned.
So, does RNAseZap actually destroy RNAse activity, or is it simply a "good detergent" to pick them up and rinse them away?
Thanks!
Carmen

It's hard to know what RNaseZap does since the ingredients list is a trade secret.  However, I expect it is a lot more than just detergent.  RNaseA is extremely hard to destroy; moreover it can easily renature once the denaturant is removed. Therefore, very minute quantities are sufficient to annihilate RNA experiments.  The historical method of purification was to boil solutions of it until all other proteins denatured and could be easily separated. I can personally attest that you can precipitate it in pure alcohols and it will spontaneously refold as soon as it is rehydrated.
I would not trust a simple detergent to get rid of it; you'll need something more volatile to be reliable.  A lot of "home made RNaseZap" recipes on the internet include hydrogen peroxide, which causes a variety of covalent modifications to the protein.  It also has the advantage of cleaning itself up (eventually turning into H2O).  The detergent is useful because you typically don't want any protein residue floating around your experiments, denatured or not.  If you have some dried RNaseA aggregates, it will also help break those up.
I work with RNaseA itself, so I can't personally vouch for the recipe below (since I'm not interested in destroying my sample), but it seems sound.  But if you have the cash to blow, just get the RNaseZap.  It's very widely used by RNA labs and you really don't want to chance a potentially expensive experiment on it.  Especially since you're constantly shedding tons of RNaseA from your skin, being sloppy will probably bite you eventually.

Mechanism of action for H2O2
plausible recipe

The Ambion's RNAseZAP is not a detergent but contains chemicals that denature RNAse, the step of rinsing with water is necessary in order to clean up the chemicals as well as the denatured proteins left.
It is highly recommended as it completely wipes out the RNAse and the experiment can be run safely. No need to risk time, money and samples.
So, to sum up, it is not a detergent, but a solution that denatures proteins.
Good luck!

Thanks! Is this denaturing irreversible?

The MSDS reports to contain only a 'trade secret' surfactant in the range 1-20%. Why you say it is not a detergent?

Which chemicals that denature RNAse could it contain?


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Why does rabies cause hydrophobia?
What feature of rabies pathophysiology causes hydrophobia? Why is hydrophobia unique to this one particular type of viral infection?

Related question

Rabies causes hydrophobia in the encephalitic stage which means when it affects the brain and causes swelling and inflammation of multiple areas of the brain. Hence, it affects the complex areas in the brain needed for swallowing. Initially into the course of the disease, the patient has involuntary contractions of neck muscles when he drinks water.  At later stages of disease, the patient starts contracting his muscles even at the thought of water. Rabies virus is a neurotropic virus which means that it travels through nerves because of its preference to attach to acetylcholine receptors in the neurons.  That is how the virus spreads from the bite site to the brain(via the nerves).

Why hydrophobia specifically and consistently? Most diseases causing encephalitis or other pathology to the brain has very varied clinical spectra.

Yes why specifically

This is a good answer above but would like to let this question sit a little longer. What are the swallowing areas of the brain etc...

The swallowing areas of the brain are located in temporal cortex, pons and medulla oblongata

Explains problem swallowing, but hydrophobia?

It starts off with difficulty swallowing water, progressing on to fear of water just on mentioning it.  I guess it affects the center of the brain subserving fear.  Why fear to water specifically, I do not know the answer.  As a clinician, it doesn't bother me much because it has no therapeutic implications. It only serves to me as a marker to suspect rabies.  There are many things in medicine which haven't or cannot be explained by reasoning but have shown to be significantly(statistically) associated. But I appreciate your inquisitiveness.

The evolutionary "why" is that the virus spreads through bites, and drinking water or swallowing would decrease transmission. As for "how" the virus affects the brain so specifically, I have no idea and would like to know also.

No doubt, the selected answer is sufficient for the question. But for the ones more interested in citations, here is a more credible answer.
When the rabies virus attacks someone, it begins with muscle cells, so that it is not detected by the host's immune system. There, it binds to neurons at neuromuscular junction1. Rabies virus, being neurotropic, binds preferentially to neurons, specifically the acetylcholine receptors on neurons. After binding to neuromuscular junction, it uses retrograde transport to travel to the axon, as its P protein interacts with dynein in neurons. As soon as it reaches in neuron cell body, it rapidly reaches the central nervous system, where it replicates in motor neurons and quickly reaches the brain2. From here, it travels to peripheral and autonomic nervous system and then reaches the salivary glands3.
Now, lets come from the how part to the why part. Rabies virus gets accumulated in salivary glands of the host so that it can get transmitted further on to the next host. And, as one might expect, drinking water or other fluids can decrease the virus's ability to get transmitted4. To prevent this, the virus causes painful spasms in throat and larynx so that not only saliva production in host is greatly increased, but also drinking, or even thinking about drinking, causes excruciatingly painful spasms in throat. Since the muscular movements during drinking (or eating) are involuntary, and the virus has already infected autonomic nervous system and motor neurons, it is thus able to control involuntary muscle movements of throat and larynx in the host5.
References:

Gluska, Shani & Zahavi, Eitan Erez & Chein, Michael & Gradus, Tal & Bauer, Anja & Finke, Stefan & Perlson, Eran (August 28, 2014). "Rabies Virus Hijacks and Accelerates the p75NTR Retrograde Axonal Transport Machinery". PLOS Pathogens. doi:10.1371/journal.ppat.1004348.
Cotran RS, Kumar V, Fausto N (2005). Robbins and Cotran Pathologic Basis of Disease (7th ed.). Elsevier/Saunders. p. 1375
Baer, George (1991). The Natural History of Rabies. CRC Press. ISBN 9780849367601. Retrieved 31 October 2011.
"Symptoms of rabies". NHS.uk. June 12, 2012. Retrieved 3 September 2014.
"Rabies". AnimalsWeCare.com.


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Looking for protocol to produce a drosophila primary cell line
I'm looking for a general (and easy, this is going to be for an undergrad class) protocol to isolate and culture primary cells from fruit flies.

Do you want primary cells or cell lines since they are different. My response should however aid with both.

We are time limited. We have about 3 weeks for this project im guessing stables takes up to months

This is the original 1972 paper describing the isolation of the S2 cells from Drosophila. However it would be best if you specify what application you are planning to pursue with the cells, which would make it easier to suggest which ones to isolate. I have personally isolated garland cells, which are visible with the naked eye and highly suitable for endocytic assays. It takes a few minutes to isolate them and all you need are two grade 5 or grade 4 sharp tweezers and 2nd or 3rd instar  Drosophila larvae and a dish and some PBS to submerge the larvae in. You don't even need to pin them! If you are interested I can edit this response and write their isolation technique as I can't find a good technique online.
EDIT:
I have not personally isolated S2 cells although I have extensively worked with S2 and S2R+ cell lines (which are embryonic). Garland cells are excellent to work with for endocytic assays using Dextran (fluorescent dye used for bulk endocytosis assays) and Dynasore [dynamin inhibitor] (and infact they were used to characterise Drosophila dynamin homologue, shibire, here and here and its temperature sensitive behaviour in Shi[ts] mutants and shi role in endocytosis) as an example shown here in fig 6 using S2 cells. I have never cultured the garland primary cells so I do not know their PD and how they behave in Schneider+FBS (since I only isolated them and performed andocytic assays with them while they were in schneiders) and I don't think anyone has (but have a look) so it would be a great protocol to stablish and publish in a methods paper. I'm more than happy to share the isolation technique with you, tried looking on jove or youtube for a video but failed to find one, and let you know what to look for if you wish. Just as a cautionary note, garland cells are multi-nucleated (i have seen up to 4) so it might not divide very well or at all so just bear that in mind.

So this is why I love stack e...thanks for this. So the end result is pretty open ended as of now. At that point in the course they will be learning about fluorescent microscopy. Last semester we had a lot of success using lysotracker in s2 cells and would like to expand the work they did with established cells, now in primary. I would love to have them make stables but I'm concerned about time (and serum). Im very interested in the method you used. Approx How many doublings a did u observe after isolation? We would acknowledge you if the manual goes in press. Thanks @bez I'm open to advice!

I have edited my reply. Please let me know if you require the isolation protocol for garland cells and I shall write it as an edit to my response.


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Can an axon recieve signal from other neuron or axon of other neuron?
As there is a very complex network of neurons in our brain so could it happen that an axon can recieves a signal from another parallel axon ?

There are indeed synapses called axo-axonic or axo-axonal that involve a synapse directly onto an axon from another axon.
There's quite a variety to these, so it's difficult to make any generalizable statements about them as a group besides the tautological fact that they involve a synapse from an axon onto an axon; like other types of synapse you'd want to first specify a brain region and source/target neuron type to start looking at their properties and likely network effects.


text:
Can someone explain this phenomena?
So many parakeets sitting on a tree with no leaves ?

What is your question? Can you please elaborate?

Why are so many parakeets sitting on a tree with no leaves. ?

Please [edit] your question to add all necessary details. Comments are only for requesting clarification. Anyway, can you add why you think this is unusual? Are all the parakeets in this area just sitting on this one tree?

Generally, birds reside on trees during evening and night but those trees do have leaves and hence birds build nests there. Are these parakeets sleeping, if yes then why on a tree with no leaves. And why is such big number ? Is this a specific kind of behaviour ?

Shubhanshu, as I said, please [edit] your question to address these points. Comments are not indexed and hence not searchable. They can also easily go unnoticed. Therefore comments are used only for temporary purposes. A post should be self-sufficient.

phenomenon —  singular. phenomena is the plural

Parakeets are social animals that live in large groups (flocks). Under ideal environmental conditions, they can form flocks composed of thousands of birds. http://www.softschools.com/facts/animals/parakeet_facts/1274/
The fact that this tree is without leaves is irrelevant to the Parakeets. They may or may not have caused it. They chose the tree as a place to relax. It could have been any other convenient place though. If you search google images for "parakeet flock" you will see them perching on various other surfaces in a similar manner


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What species of frog is this?
I was walking around outside my house when I found this little guy clinging to the outer wall of my house. The house in question is located in Indiana, United States. What is interesting to note is that the skin that is normally covered up by the frog's hind legs is yellow, but the rest of its belly is not, and this can only be seen when the frog is spreading its hind legs. You can see some of the yellow skin poking out from behind the left hind leg in the picture. This was at night, and the frog couldn't have been longer than an average person's index finger.


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What structural features make a molecule a potent opioid receptor agonist?
For instance, take morphine. It is used as a baseline for measuring the potency of opioid agonists. Its structure looks like this:

But then, take heroin, around three times as potent, its structure is this:

6-Monoacetylmorphine is around 30% more potent than heroin itself:

If, however, the acetyl group is bonded to the top instead of the bottom, the resulting substance is less active than heroin.
U-47700, a research chemical, has a totally different structure but has around 7.5 times the potency of morphine in animal models:

Desomorphine is 8-10 times more potent as morphine:

Oxymorphone is 10 times as potent as morphine:

The common explanation that I've heard for these substances being potent opioid agonists is that they mimic the endorphins produced in the human brain. However, Beta-Endorphin is 18-33 times more potent than morphine, and its structure is thus:

That looks absolutely nothing like any of the substances mentioned above. How can molecules with structures so radically different from those of endorphins mimic the action of endorphins? And how come U-47700 has a potency similar to the more powerful morphine analogues but looks nothing like them?
But then, there's Fentanyl:

100 times more potent than morphine, making it a more powerful Opioid receptor agonist than the body's own endorphins, and its structure looks nothing like them or any of the other ones so far. Other analogues are even more potent. So what is it about a molecule's structure that makes it a potent opioid? The only structural similarity that I can spot is the presence of a tertiary amine group in the structure. And how does U-47700 have a potency similar to the more powerful morphine analogues?

Are these comparative numbers you report receptor affinities? Or bioavailability?

I could only find receptor (relative) affinities reporte in much less concrete form: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555047/table/tbl2/

Specific parts — moieties — of an agonist molecule bind to the receptor protein, causing the receptor to change shape, which in turn initiates a signaling pathway inside the cell.
Some agonists are better at causing the receptor to change to its "optimal shape" for relaying signal. These are called "full agonists".
Other agonists cause a partial change in receptor shape and reduced signal. These are called "partial agonists". The strength of the resulting signal is called "efficacy".
In addition to differences in efficacy between agonists, the parts of the agonist that bind to receptors can have a different chemical makeup and so create a different environment of electrostatic attractions and van der Waals forces between atoms in the agonist and in the atoms in the binding site in the receptor. Agonists that bind more strongly will stay bound to the receptor longer. These are said to have higher "affinity". Agonists that bind more weakly have lower affinity.
It is affinity and efficacy together that determine potency, or how well an agonist works.
In a biological environment, as well, these agonists swim in a pool with other agonist and antagonist molecules. For example, your agonist of interest might do a good job of changing a receptor's shape, but if it binds weakly, it will "pop off" the receptor quickly — perhaps too quickly to trigger the necessary signal. Another, different agonist molecule comes in and binds more tightly, but it doesn't create as strong a signal. Or perhaps a passing antagonist molecule floats around and pops onto the receptor, stopping any signal from that receptor and also keeping any agonist molecules from binding again for a while.
The population of agonists, antagonists, and receptors all change the number and kinds of binding events that take place, which determines whether you get the signal you want, as strong as you want it.
While the opioid molecules you are looking at have different numbers and varieties of atoms, it is the molecule's shape and electrochemistry that matter. Most specifically, it will be the part of the agonist molecule that actually binds to the receptor that matters most: how well it causes a conformal change in the receptor, and how strongly it binds.
These molecules could look very different from one another, but ultimately it is the part of the molecule that binds to the receptor, and how well it binds, that matters.
I don't know about the receptor-ligand kinetics of how different opioids bind to pain receptors, specifically, but hopefully there is some terminology in this answer that helps with further research.

Another point that can be very important (not sure about this particular case) for the potency of drug/pharmacological molecules is its Pharmacokinetcis: drugs have to pass from their entry site through various organs until they reach the point where they are active and the efficiency of all these 'steps' is also determined by chemical properties & structure.

@Nicolai I believe I read a paper that attributed almost the entire difference for fentanyl to PK, so perhaps quite relevant indeed.

That's an excellent point and should make a great answer!

@BryanKrause: actually fentanyl has very low oral bioavailability, that's why it's injected/sprayed/patched. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555047/

@Fizz Is that bioavailability based on plasma? The thing about fentanyl that makes it potent from a PK standpoint is lipophilicity such that it partitions into tissue like brain. I could be wrong though.

Ah it's because of first pass liver metabolism. In any case, check out the table you linked in another comment. That shows the partition coefficient differences (which that paper says little about...) I was referring to, where fentanyl stands out a bit.

@BryanKrause: you're probably correct. The issue I'm seeing is that the OP didn't really say what his relative "potency" numbers were. (See my comments under this question.)

@BryanKrause: It thinks his potency number are based on DEA data. So maybe someone can answer: https://psychology.stackexchange.com/questions/23232/when-the-dea-says-a-drug-is-x-times-more-potent-than-another-what-do-they-mean

@Fizz Those potency numbers are commonly reported by clinical effect. They are referring to the (probably IV) dose required to get a similar pain relief effect to equivalent morphine. Partly why they are ranges and not more specific values. The remaining biology question is what actually causes the differences, and simple mu receptor affinity is not sufficient to explain it. So people argue about partitioning, effects on other opiod receptors, effects on non opiod receptors, etc.

I think you are confusing potency with receptor affinity.
The (unsourced) numbers you indicate appear to be DEA-style "potency", which probably refer to the effective dose (of some kind).
The fentanyl to morphine ratio on the κ-opioid receptor affinity, from human studies is only 1.35 to 1.14 (on average). In contrast the N-methyl fentanyl is estimated from animal studies to have a receptor affinity of around 18,000 (±3,000).
As pointed in the other answer, there numerous other issues besides receptor affinity that affect potency, like bioavailability by the various administration routes.
Receptor affinity alone is somewhat easier to deal with (e.g. in computational chemistry models), e.g. by "molecular docking":

Molecular docking, a type of virtual screening, places compounds or ligands into potential binding poses within the binding site of a biological target and assesses binding affinity with a scoring function. The scoring function evaluates the non-covalent interactions between the ligand and target to provide a binding energy (score) which can be used to rank compounds with increasing binding affinity

It's actually quite difficult to measure receptor affinity in practice; there's a large margin of error, better shown in this graph, from the source that that previous table is based on for human studies.

Also there are three opioid receptors to worry about. (The graph above is for μ.)
I think the reason why fentanyl (and its derivatives) is stronger than morphine in analgesic test is/are largely unknown. According to a 2014 paper

A large number of fentanyl analogs have been synthesized and structure activity relationships revealed, but the knowledge of their action is still incomplete and many questions remain unanswered. In general, the order of activity at receptor parallels that of binding affinity. However, the comparison of ED50 values, for μ- analgesics with their IC50 and Kd numbers at the corresponding binding site does not always correlate with experimental data. How to explain, why fentanyl (6), methylfentanyl (42), sufentanil (88), lofentanil (82) are more potent than it would be suggested from obtained binding values. Another example, the Kd of ohmefentanyl for the μ- site is approximately 5–10-times less than that of morphine, but it is nearly 7000-times more potent than morphine in analgesic tests. There is another contradiction, absence of correlation between lipid solubility and analgesic effect [195,196]. Another observation is that **in general fentanyls are compounds with the highest affinity for the μ-receptor and the most potency at that receptor. However not all fentanyl derivatives are highly μ- selective. They also produce actions through δ- and κ- receptors. Lofentanil (82) is the least and R30490 (90), are the most μ-selective compounds, among fentanyl series. Although their structures are very close, and affinities at the μ-receptor are similar, R30490 displays much lower δ- and κ-affinities than lofentanil.