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What is the average volume of the human Psychic tear? ("emotional tear")
My goal is to find out the volume of the average human "emotional tear" (Psychic tear - sadness, happiness), specifically when crying. I found a lot of information about Basal tears (constant lubrication), as well as Reflex tears (when slicing onions), but nothing about the volume of Psychic tears.
I should mention that in a 2016 study Is it possible to cry a river by the University of Leicester, the volume of one average tear that was used is the same as the volume of the average Basal tear - 6.2 micro liters. (Volume of Basal tears was also determined to be 6.2 micro liters in another study I found online)
I have a slight doubt that the average Psychic tear has the same volume as the average Basal tear, which is approximately 6.2  micro liters plus/minus 2 micro liters.
Could it be that both types of tears have the same average volume, and it is only the flow intensity that is different?
There seems to be nothing about this online after several hours of research. Any help would be greatly appreciated. Thank you.

Are you asking about the volume of a single tear drop or the total volume of the 'available' tear?

Yes, I'm interested in the volume of the average tear drop.


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GABA in plants (article about its mechanism)
I am studing to plant physiology exam and i cross over the statment about GABA in plants.
It said that level of GABA increasing my thermal shock. But mechanism of effect on plants is unknown.
Can anybody give me a tipe about proper article about it?

I am sorry for not doing my research part but i am quite busy.

Your comment perfectly nails down the main issue with your post. Respectfully, we are not here to do your work. Wether you are busy or not is irrelevant. We are all busy people and we would all be very pleased to have someone to work for us for free. I am VTC as homework question lacking effort. Good luck!

Unlike in Europe, in the US and Canada, there is actually loads of homework at the University. I dunno about other continents.

source: Stack Exchange

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

sort: votes


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Finding for evolution, comparing past flower numbers with present

In a hypothetical species of butterfly, wing spots are controlled by a single locus where BB individuals have blue spots, YY individuals have yellow spots, and BY individuals have green spots. Ten years ago, a previous collector randomly collected 1000 butterflies and reported finding 90 blues, 420 greens, and 490 yellows. You collect 40 blues, 320 greens, and 640 yellows. Has there been evolution in this population? If yes, is natural selection involved?

I have had many attempts at this question I calculated the p and q frequency for each using HW model.
For 10 years ago: 90+90+420/2000=0.3   BB
490+490+420/2000=0.7 YY
For now : 40+40+320/2000=0.2 BB
640+640+320/2000= 0.8YY
But I dont think I can know if evolution happened and natural selection from this (because Y allele in yellow for instance includes heterozygotes as well).
What do I do? Do I calculate the expected number of each and put it in Chi square test but how would I get natural selection from that? Please help

Has there been evolution in this population?
If $p$ differs in the population, then yes. If you $p_1$ and $p_{10}$ (the two different estimates at generation 1 and generation 10) are equal, then any deviation is caused by sampling error. Hence set $P_1 = P_{10}$ as the null hypothesis and performs a chi-square test.
Is natural selection involved?
For this we have to know the generation time and the population size. We can assume the generation to be of one year (10 generations). The population size $N$ could be estimated from genetic data of the sampled butterflies. The expected loss of genetic diversity per generation is $\frac{1}{2N}$ but you will need to consider any possible path by which one can go from $p_1$ to $P_{10}$ using a series of binomial distribution and sum up their probabilities. That being said, it is a little bit computationally expensive if $N$ is large but some Markov Model theory might give you some simplifications.

You see a question like this, you should just go ahead and calculate if the population is in Hardy-Weinberg Equilibrium, because that's almost certainly what's going to be asked.

For 10 years ago: 90+90+420/2000=0.3 BB 490+490+420/2000=0.7 YY

That notation is not helping.  B = 0.3, Y = 0.7
BB = 90/1000 = 0.09
BY = 420/1000 = 0.42
YY = 490/1000 = 0.49

For now : 40+40+320/2000=0.2 B 640+640+320/2000= 0.8 Y

BB=0.04
BY=0.32
YY=0.64
The allele frequencies are changed, which by definition is evolution.  But the populations were and remain in HWE, which suggests that all the requirements for that condition, which include there being no selection at present, are occurring.

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


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Wild bee hive indoors - can I move it?
Wild bees decided to build their hive in my shed, right above the table where I work on occasion.
The image is rotated 90 degrees left.
It started out as a single bee from what I could see two weeks ago. I thought fine, we won't bother each other and I like the company. But now two weeks later the bees are busily constructing and it is quickly growing larger. It started with a smallish dome, and new layers are being added from the outside. Every now and then a drop of some fluid falls out of the hive, and also small black grains, perhaps bee poop? Any ideas what these are?
Anyway, I have no idea how big this hive will become, so it is is probably a good idea to move it (it is around 15 inches from my head ;-)). Any suggestions?

I think there are professionals you can hire to do this. Are you sure those are bees? That looks like a hive made of paper.

Those aren't bees; looks like a paper wasp of some type. Though it varies by species they are sometimes more aggressive than honeybees. They can be beneficial as pollinators (though not as much as bees) and insect control, but many treat them as pests.

While honeybee relocation specialists exist, they won't do this job; this is an aboveground hornet or yellowjacket (Hymenoptera: Vespidae: Vespinae; the photo isn't clear enough to tell us which of three possible genera is involved) colony, which in this case will have to be (unfortunately, as these insects can be beneficial to a degree) exterminated; it's much too close for comfort.

Those aren't bees, they're a kind of paper wasp. As you observed, they start small and seem innocuous at first, but be warned, as the nests grow in size, the inhabitants become more protective of their nest and are more likely to see you as a threat to attack than as a peaceful cohabitant (at least this has been my experience.)

Nest construction starts in late spring and continues throughout the summer. The last brood raised includes males and next year’s queens. Due to the importance of these reproductives, the worker wasps become very protective and aggressive toward those who venture too close to the nest this time of year.

Somehow we seemed to have a number of attractive habitats for paper wasps (and mud wasps) and had to deal with them when too large or in a dangerous place (e.g. in a door frame.). A honeybee relocation service will do you no good in this situation.
You have a few options to consider, I recommend sooner than later. First, at night and while wearing protective clothing and gloves, you can simply whack the nest off at the base and run away as quickly as possible); Plan/clear your escape route in advance! Stay away for a couple of days as it often takes this long for them to completely abandon the young inside. If these are bald-faced hornets, their sting is quite painful, much more so than a bee or a yellow-jacket.
Or, if this doesn't bother you (it does bother me), you can light the nest with a burning roll of paper (it is, after all, paper, and will burn quite rapidly. The 'good' part of this is that the flame usually destroys the wasps' wings as well, and they're less likely to be able to attack you. This is best done on a cool night after all or most activity around the nest has ceased. The fire flares brightly and burns the nest very quickly without setting fire to adjacent structures, but a fire extinguisher should be kept nearby just in case.
Third, you can buy a spray, but I found them to be ineffective against the kind of paper nest shown in your picture, because the envelope protects the wasps inside. I used up two large cans of foaming spray (in spite of hating insecticides, as it wasn't a spot I could safely whack) without any obvious result. I ended up doing multiple whack-and-runs.
Finally, you can hire a professional, something I never did in my 28-odd years of dealing with them, but which is often recommended.
Yes, it's probably poop.


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Lizards Undergo Rapid Evolution: Please, tell me this is not a lie
This article states that transition from eating insect to eating plants is called and caused evolution.
The article neither provides images nor swears that they are telling the truth.
Has someone else tried the same method as the article's author? Those lezards were still eating insects in nineties in Algeria.
Can somebody living in Pod Mrcaru provide us with images of the same lizards?
Could this transition which is preceeded by human [... not nature] be compared to evolution?

Comments are not for extended discussion; this conversation has been moved to chat.

The article is referring to an actual series of studies, the divergent evolution is caused by the population being introduced to a small island free of predators. It is well known that small isolated populations can evolve quickly, change can spread much faster in small populations. Note the lizards still eat insects it is just the island population also eats some plants, they have other noticeable differences as well.
To answer your question Yes this is evolution, likely a combination of natural selection and genetic drift. Evolution is just a change in allele frequency (basically a heritable change) a group of organisms over time.
Like many news sites they do horrible job of sourcing their information, but is referring to actual science.

just to be clear, the comment in my answer does not refer to your answer but the one OP has marked.

[It is well known that small isolated ...] is this a law? I'm sorry it's not well known. [lizards still eat insects...] why wasn't this stated in the article? P.S answer me is this evolution?

Thank you John for your knowledge, time and energy. I'm accepting your reply as an alternative only because I trust you. I'll see and come back later. Thank you so much NatWH

@John In the well known link, (1) the author says "If you do it an infinite number of times, it will be 50%.". This is a fallacy, isn't it?

I can't find that anywhere in the paper, do you have a page number?

Since the existing answer barely even tried, I will give one. Rapid adaptive evolution on ecological time-scales is pretty much non-controversial, and has basically been understood since Haldane. The paper that this report is derived from is here (amongst others, see John's answer), and does appear to show morphological evolution over the course of some 37 years in response to different resource availability.

I really appreciate your answer and your time.

In Fig. 4. of the article, how can I convince myself that this is evolution rather than a normal morphological change (e.g. between two persons)?

Fig. 4 is a demonstrative example; I would look at the quantitative evidence in the earlier figures.

I swear of God, I could not be convinced. I'm sorry for your time. I'm going have a look at https://evolution.berkeley.edu/evolibrary/article/evo_01 and find some free glossaries

and please NatWH do not blame me. As you may admit, today's internet is full of lies. the Arabic article that targeted the object article was also full of (let say lies) falsification and information that neither exist in the object article nor in the official one you provided. I will study the article you provided. Here is the link http://www.ahewar.org/debat/show.art.asp?aid=346856


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How are the two mating types, a and α, for S. cerevisiae pronounced?
In reading about S. cerevisiae there are two mating types, one being the Latin letter a and the other being the Greek letter α.
How are these two types pronounced such that they can be differentiated?
In other words when I pronounce the text I don't want to say 'a' for both of them; there should be a different word or phrase for each one so that they are known to be different.
Is it simply that a is pronounced as a and α is pronounced as alpha?

Correct.
Haploid mating types in Saccharomyces cerevisiae are MATa (pronouce a as in day) and MATα (i.e. MAT-alpha).
For convenience you could also refer to the corresponding alleles as MATa or MATalpha (see also here)


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How does blood react to heat when inside the body
I was wondering:
What are the possible dangers of being burned on the surface of the skin.
Does it congeal (that's what my intuition tells me)? At which temperature would that happen? How heat-conductive is human flesh?
On the other hand, there's of course been many cases of severely burned people who did obviously not die afterwards.
This question comes from an argument i had the other day, when a friend burned himself by accident and we got into talking about what was actually happening with the affected blood (i.e. at the wrists, neck etc) and if it is dangerous (if you could actually die from an occasion where you burned yourself and then get a stroke or something)


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How to interpret the relationships of PTMs from BioGRID's data
On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file.
I have several issues with this file.

Foremost, I am not sure how to interpret the 'relationships'.

There are two columns 'Relationship' and 'Identity' that supposedly describe the relationships of PTMs.
    Relationship. A plain text descriptor of the type of relation represented. (Unique values: ['-', 'kinase', 'phosphatase'])
    Identity. A plain text descriptor of additional identity details if available. (Unique values: ['catalytic', 'regulatory', 'PTM'])

Lets say, a gene has a relationship (in in PTMTAB file, column 'Has relationship' is True) and in PTMREL file it is 'kinase' (in PTMREL file column 'Relationship'), does that mean that the gene is kinase or it is phoshorylated by a kinase?
Also what does it mean if the gene is additionally 'catalytic', 'regulatory' or a 'PTM' (in PTMREL file column 'Identity')?
Here's BioGRID's wiki page describing (but not detailing) the file format of PTMREL file.
https://wiki.thebiogrid.org/doku.php/biogrid_ptmtab_ptmrel.

If PTMREL contains data associated with PTMTAB file, why not simply combine it with PTMTAB file? Without knowing how to interpret the relationships of the PTMS, the users too, can not combine the two files.

Additionally, there are PTMs included in 'BioGRID TAB 2.0' too, and the number of PTMs (for a species) in that file are not the same as in PTMTAB file(!).

I understand that BioGRID provide this data 'WITHOUT ANY WARRANTY'. But still, since BioGRID is the most unified and constantly updated resource of gene interaction networks, users should know about basic usage of the data.
UPDATE:
After some data explorations, I could guess the meanings of the data.
If Relationship is '-' -> Identity is always 'PTM'. So, these are the PTMs that do not have known relationships.
If Relationship is 'kinase' or 'phosphatase' -> Identity is 'catalytic' or 'regulatory'. Now, here, I am not sure what do 'catalytic' or 'regulatory' mean.


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Evolution - The ability to control ear muscles
Among animals the ability to control ear muscles is pretty common, but only a few humans have the ability. Is it because we in general lost this ability ?

Yes, humans have lost the ability to move their ears toward sounds like many other animals such as cats and rabbits.
It is thought that our ancestors lost the ability to move their ears around 30 million years ago when

Ear size decreased and the associated musculature changed 1 (Steven Hackley).

A review from Steven Hackley outlines the evidence that the neural circuit remains in modern human brains. Apparently, the neural circuit still responds to directional sounds and may cause our ears to curl slightly (2 - 3 mm).

This adaptation would have very little pressure on gene pool selection, as it provides little to no advantage other than slight, likely negligible, hearing improvement.
As survival fitness in terms of hunter-gatherer qualities, such as those of keen hearing and sight, are today meaningless in terms of reproductive viability, this phenotype would not persist over time, in my opinion.

Welcome to SE Biology. I think you've only alluded to an answer for the question, which I read as Do we have an ancestral group that lost the ability to control their ear muscles? Your answer concerns why we could have lost the ability to control our ear muscles.

Hi, thanks for having me. He's asking 'is it because we in general lost this ability'. I'm saying 'yes, we as a species have lost this ability due to lack of genetic selection for the trait, although it still likely shows up in some gene pools sporadically'.  See definition of vestigial.

No worries. Editing to include what you have summarised in your comment would improve the answer.


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Is the ACh receptor more permeable to sodium ions?
The AChR is permeable to sodium and potassium ions only and has a reversal potential of 0mV.
However the Nernst potentials for sodium and potassium ions is ~ +60mV and -88mV respectively. Taking a simple average of these two potentials would give an expected AChR reversal potential of -14mV; but that is not what we see.
My question is whether the reversal potential is pulled up to zero because of a greater conductivity to sodium than potassium ions, and if so, how the AChR selectivity filter achieves this.
Thanks!

Short answer
No.
There are differences in Na+ versus K+ permeability, but you have it backward: potassium is actually slightly more permeable; however, these differences are not the only factors influencing the reversal potential, and also, the reversal potential for a nAChR need not be exactly 0 mV.
tl;dr to the long answer
You need to sum before taking ratios rather than take a difference of ratios when computing a reversal potential for multiple ions together.
Before we get into the weeds...
In most sources you will hear something like the reversal potential for a nonspecific ligand-gated channel like nAChR is "about 0 mV" - this is going to vary in different cell types, in different conditions, with different recent activity levels, with different versions of the receptor, etc.
What's important to remember in all this is that -14 mV is also about 0 mV... In the context of excitable cells, what is most important is the reversal potential relative to the threshold for firing a spike or activating other channels. That said, I'm not actually saying the reversal potential for nAChR is actually -14 mV, there are a couple other factors missing...
What you are missing
The big one you are missing is that the concentrations of the ions matter, not just their ratios. For the reversal potential of a single ion, all we really care about is the ratio inside and out, which is found in the Nernst equation.
Averaging the reversal potential for two major ion species, like you have done, gives you a pretty good ballpark estimate (afterall, -14 mV is also about 0 mV!).
To get the actual reversal, however, you'll need the Goldman Equation.
We can simplify the Goldman equation for just Na+ and K+ in fairly standard conditions to something like:
$61.5 \mathrm{mV} * log_{10}(\frac{P_{Na} [Na^+_{out}] + P_{K} [K^+_{out}]]}{P_{Na} [Na^+_{in}] + P_{K} [K^+_{in}]]}$)
If the permeabilities are both :=1, and the concentrations of Na and K are equal and opposite, then indeed you will get zero. However, if that was true, you would also have equal and opposite reversal potentials for Na and K alone in the cell: in the numbers you gave, that isn't the case.
I'm not sure what numbers you used exactly, but I'll use my own example. If potassium is 5mM out, 140 mM in, the reversal potential will be -85.6 mV for potassium. If sodium is 140 mM out, 12 mM in, the reversal potential will be 63.1 mV for sodium (you can check my math with the Nernst equation).
If you combine these numbers in the Goldman equation above, you will get -1.2 mV: closer to zero than your -14 mV estimate.
They are so close because the ratio (140+5)/(12+140) is a lot smaller than the difference of the ratios (5/140) and (140/12): order of operations matters.
This is assuming identical permeabilities

However, the permeabilities aren't actually identical
There are many papers measuring relative permeabilities in nAChRs, I just chose one randomly as an example (happened to be the first Google Scholar result).
Nutter and Adams 1995 found the relative permeability of several monovalent and divalent cations, with Na as a reference:

Therefore, potassium is actually slightly more permeable than sodium. However, there are also other important ions that could contribute, even if they are found at lower concentrations than either sodium or potassium, and the example ion concentrations you find in a textbook might not apply in the systems you are studying. A source that says nAChRs are only permeable to sodium and potassium really just means that they are not permeable to another other important high-concentration ion: chloride. They are also simplifying things a bit for you, which is okay.
If I use the Goldman equation quickly with these data, I get a reversal potential (with just Na and K, ignoring other ion species) of -5.9 mV: still "about 0 mV" and still closer than your original -14 mV estimate.
But how are different ions with the same charge showing different permeabilities?
This is better off as a separate question, and probably easier to address with a more extreme case, like in selective sodium or potassium channels. However, like in those channels, in channels that we call "non-specific", the particular arrangement of amino acid residues (especially charged ones) at the pore can favor particular ions because those ions differ slightly in size.

Nutter, T. J., & Adams, D. J. (1995). Monovalent and divalent cation permeability and block of neuronal nicotinic receptor channels in rat parasympathetic ganglia. The Journal of general physiology, 105(6), 701-723.

I'm really happy with this answer! I hadn't really appreciated the importance of the magnitude of ion concentration as opposed to just their ratios in setting membrane potential.  Thanks for taking the effort to correct my misconception:)

@ogu01 I really like the simplicity of the Goldman equation: sort of the "F=ma" of neuroscience and other disciplines where excitable membranes are important; I think it's really helpful as a student of these sorts of topics to just sort of "play" with it and make up your own scenarios and test them out. This will help the concepts make better sense. Best of luck to you!


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Resources for the study of the environment of Laramidia in the Late Cretaceous
I'm looking for resources (book, web, article, etc.) to learn in detail about the environment of Laramidia in the late Cretaceous, including flora, fauna, landscape, and climate. My goal is to get a picture of what it would be like to step out of a time machine into the North American West during the Maastrichian not long before the mass extinction event that ended the dinosaurs, and hopefully get an idea of how that environment varied by region. So far I've only been able to turn up a few brief articles, and some dense scientific reports (which I read the relevant parts of, but as a layman working without the benefit and context of professional knowledge have been of limited use).
I'm aware this question has some crossover with Earth sciences. But as it might fit pretty well on either site, and I've seen you folks answer more paleontology questions, I'd be grateful if you'd entertain it here.
How can I effectively research the environment of Late Cretaceous Laramidia? (Information directly about Laramidia is also very welcome, if secondary.)


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Do fruit juices have a diuretic effect & what governs this?
Was just contemplating this.
Juices tend to contain a lot of sugar.

Does the body absorb all the sugar in juices?
If the body does not, that sugar must be excreted by the kidneys alongside water thereby causing a diuresis, right?

NB I realise even if there is a diuretic effect that is outweighed by the large proportion of water in juices. But my question is whether there still is a small diuretic effect

In short: Drinking fruit juice by a healthy person with a normal kidney function do not likely have any significant diuretic effect.
Even if you drink, let's say, 2 liters of 10% fruit juice within 30 minutes, it would likely take about 2 hours for all the juice to be emptied from the stomach into the intestine and absorbed into the blood. Sugar delivered from the intestine will gradually increase blood glucose, but this will be balanced by the glucose taken from the blood by the cells, so, the blood glucose will not likely exceed 11 mmol/L, when glucose can start to move from the blood into the urine and cause diuresis.
I can back up this by the glucose tolerance test in which you drink 1 cup (237 mL) of a drink with ~35% glucose (>3 times as much as in a usual fruit juice). 2 hours after the test, the glucose levels in a healthy person (without diabetes mellitus) will be lower than 7.8 mmol/L, so below the diuretic level (11 mmol/L).


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difference between blastula and blastocyst
What is the difference between these 2 terms. I believe that blastocyst is for animals, but structurally is there any difference? And how would you be able to identify each?

A blastula is a hollow ball of cells, while the blastocyst occurs slightly later in mammalian development and has a defined inner mass and an outer layer of trophoblast.


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Expected bands in polyacrylamide gel
I have something in my notes that doesn't seem right.
If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two restriction enzymes I expect two cuts then then gel should show three bands. Then, if I use just one enzyme and I know the enzyme will cut just once, then should I expect two bands? According to my notes one band is expected.

If your restriction enzyme only targets a single site on the DNA sequence then it will split each DNA strand into two fragments. If the restriction enzyme cuts every strand then you will see those two fragments. Note that if the two fragments have the same length they could appear as a single band when separated using gel electrophoresis.
If the enzyme doesn't cut everything the uncut DNA will also be present. This is why you should always separate some uncut DNA in the gel electrophoresis.


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Does mushroom likes low air pressure room?
I know that mushroom likes high humidity and low temperature, but want to know that Does mushroom likes low air pressure room ? because of at low air pressure high humidity and low temperature can be achieved easily.


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Why is PCR possible to amplify DNA template before Sanger Sequencing for unknown DNA sequences?
Most of the informations show that both PCR and cloning can be used before Sanger Sequencing to amplify the DNA template. But how is it possible for us to design the primers if we don't know the DNA sequence yet? So, in my opinion, only cloning is possible to amplify the sequences. Can anyone tell me how PCR can work in this way? Thank you!

Can you link these informations?

Some comments in this question. There are different aspects which confuses me. https://biology.stackexchange.com/questions/40988/in-sanger-sequencing-why-do-we-resort-to-cloning-why-doesnt-pcr-suffice

PCR is used to amplify a sequence included inside two known regions. So, if you're able to clone (for example with recombination) two sequence forward and backward to your sequence, by using PCR you'll amplify also the sequence included.
This image in example will clarify my statement.

There are several tricks that can be used to PCR amplify an "unknown" sequence.
1) If the protein sequence is known, than it is possible to guess the entire range of DNA coding possibilities for a small region of that protein. Making the complementary primers for two regions is thus possible.
2) If you know several homologous of that gene several species, you can attempt to identify highly conserved regions within the gene. ie parts of that genes that does not change between species.
3) If the genome is small and your lab is well to do, you can just sequence the whole genome. Then you will have the DNA sequence and can thus design primers at your leisure.
4) If you have isolated the gene (via BAC cloning) but do not know the sequence, you may still PCR amplify it using primer that bind to the vector containing the gene of interest.
5) You may ligate dsDNA oligos to the unknown DNA sequence. Then use primers complementary to the oligos


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Growth mediums required for human cell cultures
So i would like to try a culture some of my keratinocytes just to see if i can do it. Ive read about a few different types of growth medium such as DMEM and RPMI but i am not sure about when to use which medium. So I am asking how do i detrimine which growth medium i need to use to culture human cells

So this paper probably has what you need.
Isolation and cultivation of human keratinocytes from skin or plucked hair for the generation of induced pluripotent stem cells
The first part of that paper covers just the cultivation of keratinocytes.
It's actually moderately difficult to culture keratinocytes, so if you just want to try out cell culture I wouldn't recommend this as your first step.
A good first step to learning the techniques of cell culture would either be bacterial, fungal, or yeast cultures because they are cheap, hardy, and don't require expensive equipment. Yeast culturing would be closest in technique to mammalian cell culture among the three  Yeast culture info here


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What species is the smallest bird?
What species is the smallest living bird in the world? What circumstances limit the bird size from the bottom?

There are definitely two questions here, and the question in the title and first part of the body should really be flagged for closure - it's easily googled - but the second is interesting and on-scope. Do you think you could edit it to the second part only?

this paper may interest you. minimum size may be related to maintaining their body temprature. https://www.journals.uchicago.edu/doi/abs/10.1086/282753

Related posts: https://biology.stackexchange.com/questions/21541, https://biology.stackexchange.com/a/66659

The smallest bird in the world is the bee hummingbird.
I think the minimum size is only limited by the size of organs. I mean that certain organs need to have a minimum size to maintain their function in the organism.

It is unclear to me how the "Wall effect" that you link under "organism" is relevant to your point. Is that an error?

The answered was probably thinking of something more like this, http://www.mrothery.co.uk/exchange/allkeynotesas.htm, but that is more of a limit on maximum size rather than minimum size.

@vkehayas yeah it is not much related to this topic. I quite misuse that it.

@L.Diago maybe update the link to reference Wikipedia instead, which not only gives the facts listed in your link, but also has pictures of them?

A better link: Bee Hummingbird.

I understand guys but that link was from guinessworldrecords you know. I  thought that it will fit better with the smallest bird in the world. :)

A complete answer should at least mention Kleiber's law.

I dont know but it doesnt fit to my answer.


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Harvest honey without damaging brood cells
I want to make a homemade beehive, I want to know how to differentiate honey cells and brood cells, therefore, I'd like to know how can I organize the beehive so bees will create honey and brood cells separately. By this way, I would be able to harvest the honey without killing the larvaes :)
Ancillary issues : Do bees need cells to sleep in ? Can I populate a homemade beehive with several bees caught from my garden ?
Thank you for your attention :)

Welcome to Biology.SE. I do not think this question is really about biology (but wait to get other users' opinion). You might want to consider pet.SE and sustainableLiving.SE (or even maybe greatOutdoor.SE).

You may have better luck on beekeeping speciality site like this https://beebuilt.com/pages/beekeeping-for-beginners

I think this question is about applied use of biological knowledge, more specifically bee behavior and entomology, and should be re-opened. Closing it is to me similar to closing general questions on medical treatments or medicine, since they are "just" applications of biology/biochemistry and not "really about biology" per se. Which we do not do at Bio-SE.

In domesticated bee hives, this is usually accomplished by excluding the queen from a section of hive frames (by the size of the entrance hole), so that these frames only contain honey and no eggs/larvae.
For instance, this can be achieved using a queen excluder.


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Can anyone identify this plant?
We found this seemingly ornamental plant somewhere in the midwestern United States; does anyone know what it is?
It's fairly low to the ground.  Thanks!

If you add some more information about this plant for example widness of leafs,  specify the somewhere part of your question and you might get your answer.

From the general appearance, and from the opposite leaves (seen if you look carefully in the enlarged photo) I think this is Euoynmous europaeus (Wikipedia entry).  Specimens I've seen can grow like a ground cover, similar to your picture, but they also get shrubby/woody.  It is not native to the US.  We'd need more details/pictures to be sure, but I'm guessing from how you worded the question these might not be available.

Euonymus europeus has green twigs that are square in cross-section. There are hardly any other species (in Europe) that have this, so it is a very distinctive feature.

It will also climb a vertical surface.

I think it is Vinca minor, or periwinkle. I'm from IL and it is a common landscaped ground cover around me. It is opposite, low growing, and woody. Check out https://www.illinoiswildflowers.info/weeds/plants/periwinkle.htm to confirm, I can't give any more of a detailed answer without a more detailed picture.


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Immediate cause of death due to dehydration
When we don't drink we get dehydrated and after some time we die. What is the cause of death on the lowest level?
I would assume the dielectric properties around/in the heart tissue get imbalanced and the heart stops beating.
Then lack of oxygen in the brain. Then...?

The simple answer is dehydration kills you by causing the blood flow to become completely ineffective.
Dehydration limits the amount of water in the bloodstream causing an increase in blood viscosity, and thereby an increase in blood pressure.  As this process gets more extreme the body has a difficult time getting the blood to the places it needs to be, and will limit blood flow to non-essential organs (kind of similar to what happens when it's cold outside and your fingers go numb).  At the same time waste is beginning to build up as the kidneys cannot filter the blood effectively, and the internal temperature rises because of the lack of sweating.  This process gets more extreme until one of your essential organs cannot take it anymore and shuts down, likely the liver first.
Most everything I got for this answer was from a PopSci Article. Although there is also a nice 1935 study with many measurements from real people.

Thank you for your answer. Could you please explain the reason one dies after the liver stops working? How long would one die after liver failure?

There are over 500 functions of the liver, many of them vital, including producing hormones, detoxifying blood and generating digestive fluids.  A failure of one function won't kill you, but an odd combination of several can combine to cause additional effects, such as electrolyte dis balance or blood clotting that in total overwhelm the body.


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Crispr/CAS9 genome editing is actually processed at which phase of Cell cycle?
all,
Is it only happens in certain phases, like S, G1,...or it can happen any time....or maybe, it has some perferences.
Put it in another word, does it going to processe edit if the cell is not growing ?
Thanks for any helps or comments.
Best
Bill Zhang


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Why don't cells double gene expression after S-Phase?
In the cell cycle (G1-S-G2-M), all of the DNA is replicated during the S or Synthesis stage. The cell may then spend some considerable time in the G2 phase before splitting in the M phase. Since there is double the amount of genetic material in the G2 phase, what mechanism if any, prevents the amount of gene expression from also doubling?

When the double strand is duplicated, the old strand (or, in other terms, the template) is methylated : this modification is enough to prevent the bind by the RNApol system and, by so, the transcription.
By methylation, DNA-repair systems are able to detect which is the newer strand, to discover and fix replication errors.
Here you can find additional infos


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How to estimate the amount of protein that are going to be synthesized?
I'm studying protein synthesis to understand how the body use the different amino acids to build proteins.
In particular I would like to learn how to (roughly) calculate the total amount of protein synthesized knowing the amount of amino acids eaten.
I think the easiest case is that of complete protein with PDCAAS value of 1. I guess that in this case the amount of proteins synthesized is equal to the amount of protein previously ingested, isn't it ?
So consider the more complex case of incomplete proteins, i.e. proteins with limiting amino acids.
For example consider raw lupins, 100g contain about 36g of proteins, with these essential amino acids:
  Amino acid   |   g in 100g of lupins
----------------------------------------
Tryptophan     |  0.29
Threonine      |  1.33
Isoleucine     |  1.62
Leucine        |  2.74
Lysine         |  1.93
Methionine     |  0.26
Phenylalanine  |  1.44
Valine         |  1.51
Histidine      |  1.03

source: https://ndb.nal.usda.gov

If I eat 100g of it, how to calculate the final amount of proteins that will be synthesized in my body ? (for simplicity don't consider the protein digestibility)
I guess the first step is to find the limiting amino acid(s) of the lupin, but how can I find it/them ?

Whatever makes you think the amount of protein synthesized is equal to (or even proportional to) the amount of protein ingested? Ever heard of urea?

I think it's impossible to estimate because of many reasons.
1) Amino acids are used not only to build new proteins in body. They can be used for other processes.
2) There are thousands of different proteins has been synthesized in cells for different purposes. These proteins differ both in number of amino acids and in what exact amino acids are included in exact protein. You have showed table for 100g lupins, for other proteins this table will be with different numbers.
3) It is impossible to estimate the needs of exact body in exact moment in exact components for exact processes. So it is difficult to evaluate the result of how what we eat will be used by body with good precision.

Thank you for pointing this out, didn't know about that. So how can all the sport dietitians give nutrition recommendations about protein intake if this cannot be estimated ?

I am not dietitian. So I express only my opinion. Recommendations is a result of simplification. General recommendations are not precise enough. They don't take into account individuality. Special recommendations are dictated by your purpose and body feedback. For such radical situation as disease, you have symptoms that give signals. For basically healthy state, you don't have good indicators. Some predictions can be made based on practical knowledge. Experienced dietitian can be more effective in predictions in specific situation. But on some level it's always trying and experimenting.

I understand, but in the case of a diet for increase muscle tissue, it is obvious that an increased protein intake is needed. As I wrote in the main question, i'm not interested in the precise quantity, but rather in an estimation. In this case (4-5 days a week of training) I guess the body needs everyday more protein than the average to build and maintain the increased muscle tissue. So, in this particular case, is not easier to estimate the protein synthesis? Should I ask in the fitness board?


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What determines which symptoms an allergen will cause?
Allergies result in many different symptoms such as sneezing, runny nose, itchy eyes, coughing, rashes, swelling of the face, stomach pain, vomiting, dry skin, anaphylaxis, etc.
An allergen can cause different symptoms for different people who are allergic to it... and different allergens can cause completely different symptoms for the same person. What characteristics of an allergen and/or the person determine what symptoms will arise?


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Control for Bisulfite sequencing
I am wondering how can I control my converted DNA!
I converted my DNA with bisulfite then I amplified the converted DNA with specific primers of BSP and purified my product and finally sequenced the product!
In which step should I control my DNA? And what is the protocol?
thanks for any advice.

Wait, so you're looking to retroactively add controls (not feasible) or add controls for future processing? If you already went through the entire process with no controls, I'd be uncertain as to how you're convinced the process went smoothly to begin with.

To initially optimize PCR conditions: Mix 50% methylated bisulphite-converted DNA (50 M)
and 50% bisulphite-converted unmethylated DNA (50 U) to test for proportional PCR amplification with bisulphite conversion specific
primers and PCR master mix.                                                                                This is from nature protocol,I dont know how should I control the PCR product because we just have one paired primers and there is no difference between methylated  and unmethylated product! should I design another primers that bind to CPG Island?


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At what rate does synaptogenesis occur in adults?
From many articles, I can find the rate of synaptogenesis at its highest: roughly 580,000/minute (weeks 6-23 after conception). However, I'm having trouble finding the rate with which it occurs in adults. I find articles stating that it is higher in areas like the hippocampus than other areas and depends on things like exercise and stimulation, but no numbers.
What is the rate of synaptogenesis in a adult brain?

I did not find the estimate in the cited document (perhaps you confused synaptogenesis with neurogenesis in p. 3?). Anyway, one would need to specify whether that refers to the whole brain or a brain region. I can only provide numbers for mice, if that's useful to you.

@vkehayas You are right, I did misread the neurogenesis reference on page 3.  The logic will still hold (we start with 0 synapses, and we have N after D days, so N/D synapses per day), but I'll have to adjust the numbers.  Mice numbers would be useful, especially hippocampus and whole brain numbers (from what I understand, the hippocampus  has very high rates of synapse creation compared to others, so that number and the whole brain number would provide useful bounds).


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How fast does activity affect synaptogenesis?
How long does it take for the increased activity due to a novel stimulus to cause an increase in synapse generation?
There are many studies which show that the number of synapses in the brain increases within 24 hours of doing a novel task, so I know the number is less than 24 hours. I'm interested in questions like "If I do yoga for an hour, will the later part of the hour benefit from synapse creation caused from earlier in the hour?" Obviously I don't know if yoga in particular would benefit from said synapses, but if synaptogenesis is not up-regulated in less than an hour, then I can certainly rule such an effect out.

Synaptogenesis at such a fine temporal resolution is currently still best studied in animal models and reduced preparations where the activity levels can be more precisely controlled and advanced imaging methods can be used to monitor morphological changes. A series of studies with relatively high temporal and spatial resolution have been carried out in vitro and in vivo with two-photon microscopy on dendritic spines, which are considered as a proxy for the existence of synapses, since ~98% of them contain one.
The fastest effect after stimulation is the enlargement of pre-existing  or newly-formed spines and their synapses, as fast as ~2 min (Matsuzaki et al. 2004, Harvey et al. 2007, Hill and Zito 2013). Next, immature structures (often called filopodia) are starting to form within the first ~15 min (Maletic-Savatic et al. 1999). It is not yet clear what percentage of those structures bear an actual synapse, however they certainly have the potential to obtain one. A more gradual increase in the number of spines that persist for several hours and are very likely to contain a synapse occurs in later stages, ~30 min after stimulation (Engert and Bonhoeffer, 1999; Nägerl et al., 2004, 2007). However, note that the overall spine density is almost never affected in vivo (Holtmaat and Svoboda 2009), which indicates that compensating mechanisms counter-balance any synaptogenesis, so you should not expect to see an overall increased number of synapses.

References
- Matsuzaki, M., Honkura, N., Ellis-Davies, G. C. R., & Kasai, H. (2004). Structural basis of long-term potentiation in single dendritic spines. Nature, 429(6993), 761–766. https://doi.org/10.1038/nature02617
- Harvey, C. D., & Svoboda, K. (2007). Locally dynamic synaptic learning rules in pyramidal neuron dendrites. Nature, 450(7173), 1195–1200. https://doi.org/10.1038/nature06416
- Hill, T. C., & Zito, K. (2013). LTP-Induced Long-Term Stabilization of Individual Nascent Dendritic Spines. Journal of Neuroscience, 33(2), 678–686. https://doi.org/10.1523/JNEUROSCI.1404-12.2013
- Maletic-Savatic, M., Malinow, R., & Svoboda, K. (1999). Rapid dendritic morphogenesis in CA1 hippocampal dendrites induced by synaptic activity. Science (New York, N.Y.), 283(5409), 1923–1927. https://doi.org/10.1126/science.283.5409.1923
- Engert, F., & Bonhoeffer, T. (1999). Dendritic spine changes associated with hippocampal long-term synaptic plasticity. Nature, 399(6731), 66–70. https://doi.org/10.1038/19978
- Nägerl, U. V., Eberhorn, N., Cambridge, S. B., & Bonhoeffer, T. (2004). Bidirectional Activity-Dependent Morphological Plasticity in Hippocampal Neurons. Neuron, 44(5), 759–767. https://doi.org/10.1016/j.neuron.2004.11.016
- Nagerl, U. V., Kostinger, G., Anderson, J. C., Martin, K. A. C., & Bonhoeffer, T. (2007). Protracted Synaptogenesis after Activity-Dependent Spinogenesis in Hippocampal Neurons. Journal of Neuroscience, 27(30), 8149–8156. https://doi.org/10.1523/JNEUROSCI.0511-07.2007
- Holtmaat, A., & Svoboda, K. (2009). Experience-dependent structural synaptic plasticity in the mammalian brain. Nature Reviews Neuroscience, 10(9), 647–658. https://doi.org/10.1038/nrn2699


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Why is Artemisinin Compound Therapy preferrable over Artemisinin therapy with regards to drug resistance?
How does adding other anti-malarial drugs to artemisinin, to obtain a "combined" therapy result in reducing the frequency of emergence of resistance?

And it is given in the form of artemisinin combination therapy,
  combined with another anti-malarial drug, with the goal of reducing
  the frequency of emergence of resistance. (Cf source).

The idea is rather simple. When an antibiotic is used, it becomes a driver to select for a mutant that has resistance towards the antibiotic. Let say the probability for that happening is P1 (Lets say 1 in 10, 0.1).
When you use two antibiotics with different modes of attack, the probability of acquiring resistance to both is P1 x P2. (Let say P1 =0.1 and P2 = 0.15). So P1 x P2 = 0.1 x 0.15 = 0.015
Hence the probability of becoming resistant to both antibiotics at the same time is very much lower. And as the antibiotics are always used together, the time a bug needs to develop resistance to the therapy becomes longer. The duration which you can use the drug is increased.

When was this discovered?

From Google, the concept has been around since the 1960s. I found an article in New England Journal of Medicine, 1960. However, it appears we only start to start considering antibiotic-antibiotic combination in the 1990s when MR started appearing at high frequency.


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Tools to find miRNA ID
How can I get accession numbers of bread wheat miRNAs by their sequences? What are the tools or website that can be used?

Somewhat out of character, I have given a (short) answer to your (even shorter) question, but you really should read the help on asking questions. You are expected to do some research before posting and show in your question what attempts you have made to help yourself. I do not work on wheat (or any plants, for that matter) but I know how to use the Google search engine. Did you search for "microRNAs and Triticum aestivum"? There are quite a few papers that come up that presumably could provide leads.

If you have a sequence, run a nucleotide BLAST search at NCBI, specifying Triticum aestivum (taxid:4565) as the organism.
The miRBase page for Triticum aestivum has details of wheat microRNAs, and a page where you can do a sequence search with either BLAST or SSEARCH (as @WYSIWYG kindly pointed out).
Perhaps the Triticum aestivum page at PlantGDB may help.

Reg. point#2: miRBase has BLAST and SSEARCH (Smith-Waterman) for searching by sequence.

Thanks @WYSIWYG. I had thought that there must be, but presumably I didn't scroll down far enough. Have modified my answer. miRBase seems to be the place the poster should go.


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Green insects on gooseberry plants
I have green insects that eat the leaves of my gooseberry plants:

Location: Toronto, Ontario.
The insects seem to only eat the leaves of the plants (not the fruit).
They have been present since mid-May, and I expect that they'll be present until mid-June, based on past experience.
They do not have spots.

What is the name of this insect?

The species name of this insect is the gooseberry saw fly. There are three related species, I think this is the pale spotted gooseberry sawfly because it has a pale green head. They usually have black dots as well, but this might develop when the larvae grow. At least, this is what I observed once in my garden.


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What can I see with a microscope at what magnifications?
I'm 26 and where I grew up the schools were complete crap so I've never really used a microscope much or learned much about them. And I want to learn some science and look at some microscopic things, like organisms in water, how tiny  bugs or dirt looks up close, blood cells, and whatever else there will be to discover.
So my questions are about magnification  and what I will be able to see at various magnifications. How much magnification would I need to get a detailed look at tiny insects like a gnat or tiny aphid? Or to see microscopic organisms in water, or our blood cells, or the fibres in my microfiber glasses cleaner. And If i was looking at stuff like blood cells, or food, would i be able to see anything like viruses or diseases? (And as an extra question, any good books for self learning about microscopic organisms like that?)  I was looking on amazon and found 500x max up to 2500x max, and would like to be able to see living microscopic organisms if possible.

Decide what you want to do; A  2X to 40X binocular is fine for insects and other stuff . But things like blood cells require serious microscopes. And magnification is a small part of defining the characteristics of a microscope .

You'll be able to see something that is 1 micrometer as a slightly formed (meaning you can decide whether it's more oblong ore more round) dot. So any structure that is bigger than that can be better observed. Unfortunately, viruses are far smaller, and many interesting cel organelles are too.

Also, many things (like parts of cells) are not visible until they are stained. There are many stains that are suitable for beginners (others are quite toxic or teratogenic). I'd recommend buying a book from 1970 or before (no re-issue), because many stains and chemicals are nowadays deemed too dangerous (although they are not that dangerous if used in amateur-microscopy volumes) and normal light microscopy technique has not changed since then.
With a used microscope from a reputable manufacturer (inquire beforehand whether the tubes are of a standard size so you can get replacement oculars etc.) you are on a good way. Schools and universities will sometimes purge their stock, which is where you can make incredible deals.
Get a microscope with mains-fed light, ideally LED. Some 'tricks' like Dunkelfeld are very interesting to use, but require a good light source and non-broken iris.
Also look at the table, it should have a smooth, no-hysteresis (meaning if you go left, and then right, there should be no 'slack' to take up before the picture moves the other way) x/y platform, ideally with a measure attached.
Total magnification is ocular*objective, and many microscopes offer the possibility to attach a camera, either additionally or as replacement ocular. that is a great thing, as you can take pictures and zoom in (real magnification will not change, but still, some things are easier to see that way) or later tweak the colors or contrast.
Depending on whether you mainly want to look at things that can be put between two glass slides (cells, bacteria, small parts of insects, ...) or at 3D things (insects, flowers, minerals) you can either buy a two-ocular microscope or binocular (3D) or a one-ocular microscope.
Objectives and oculars are small tubes with many lenses built into them - this means humidity and even rot can slip between those, so be sure to check used material (especially from learning institutions) for clear pictures.

My own experience, as a complete amateur who just bought one for curiousity's sake, is that anything over 400-500X is like doing your daily commute in a car with a 500 HP engine.  All that extra power is just going to waste.
20-40X is good for looking at insects (if you can get them to hold still :-)), feathers, and various materials.  200-400X gets you to microorganisms like protozoans in pond water, blood cells (which are pretty uninteresting, IMHO) or plant cells.  I have never tried to look for bacteria, and I don't think there's any hope of seeing viruses with a light microscope.
Another thing I've discovered is that if you wear contacts, or have floaters in your eyes, you're going to have a good bit of trouble distinguishing what's on the slide from what's inside your eyes.  I think one of the USB cameras might help: I haven't tried one yet, but it's on the wish list,

I recommend no more than 40 X in a macro binocular, zoom or turret . Nikon is a good name that makes some inexpensive lines. For about $ 500 you could get a good one with light source. I have used over a hundred optical devices ( not counting birding binoculars). From 2 X hand glass to mega X scanning electron microscopes. Over 3,000 hours looking through microscopes in my 40 yr career. What you may not have considered is that for every hour on a microscope , a technician spent about 4 hours cutting , mounting, polishing and etching a metallurgical sample. Prep is just as necessary for biological samples, cutting, slide prep, staining and stuff I don't know. This expensive preparation is required for about anything viewed at 50 X and more, and maybe for lower X. Light sources also become much more expensive as you get to 50 X. So stay below 50 X to start. Or get a job in some sort of lab .


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Secondary structure and function in mRNA and single-stranded virus RNA
Although some mRNAs and the RNA of single-stranded RNA viruses do have some secondary structure, this is much less than in rRNA, tRNA etc.
Why is this so? What prevents their folding to the extent of the RNAs mentioned?
And surely mRNA cannot have very much secondary structure. It enters the ribosome in a linear fashion, so if it bound to itself, wouldn’t that stop translation?

To the best of my knowledge all RNA has secondary structure. Some conformations are stablized by RNA binding proteins.

Welcome to SE Biology. As a new user we expect you to read the Tour and take a moment to find out how the site operates. An appropriate place to start is the Help on "How do I ask a good question?" where you will read "Have you thoroughly searched for an answer before asking your question? ...Tell us what you found and why it didn’t meet your needs." If you had researched you would have found that mRNA has secondary structure. What have you read about viral RNA?

I didn't assert anything, I am just clueless, because if it self bound, wouldn't it stop the translation if it entered the ribosome? As far as I know, there is no mechanism to unbind mRNA.

The details of how viruses function are not agreed on. If you ask any questions about HIV, such as basic things like what it looks like, what genes it has, or the mechanism of action, you will get dozens of conflicting answers even if you ask the most senior PhD biologists. So there is no scientific answer to your questions.

I have modified your question to remove the false premise I criticized. I think this rescues it to the extent I shall post a brief answer myself. I have withdrawn my close vote. You are free to roll back the edit if you really wish.

"As far as I know there is no mechanism to unbind mRNA". I am afraid your knowledge is deficient.  I assume that by "unbind" you mean break the hydrogen bonds that are responsible for base pairing in mRNA. Even the DNA double-helix with long stretches of perfect base pairing can be unwound by DNA polymerase, RNA ploymerase, restriction enzymes, transcription factors etc. The essence of life is that it is dynamic, and at the molecular level this is contributed to by the weak interactions responsible for the higher order structure of proteins and nucleic acids. These can be made, and broken.

Well, for me unbinding or breaking a hydrogen bomb means, for me, exciting the system such that there is no more binding. The strength, for me, should not matter for the naming of the reaction. But, if you say so I have to accept, as it might be a practice in the field. And the answer is exactly what I was looking for. Now, I can research things further.

Summary

Both mRNA and the RNA of ssRNA viruses can have secondary structure, which is often important in regulating translation
The extent of secondary structure of RNAs depends on the base composition and sequence, so that RNAs of various degrees of folding are possible.
Weak RNA–RNA hydrogen bonding can be competed for by weak RNA–protein interactions, so that a dynamic situation is possible — secondary structure in some circumstances which is unwound in others.

Evidence for Secondary Structure in mRNA and viral RNAs
Work in the late 1960s and early 1970s on the translation of the polycistronic single-stranded virus RNAs (MS2, R17,Qβ etc.) provided evidence for their secondary structure. The extent of masking of the ribosome binding sites (Shine and Dalgarno regions) of different cistrons affected their translation, and treatments and mutations that destroyed the secondary structure stimulated translation. This 1980 paper by Iserentant and Fiers and this 1982 paper by Hall et al. provide entries to that literature.
Eukaryotic mRNAs do not normally have ribosome binding sites, although those of certain RNA viruses like polio do, and these have distinctive secondary structure (ribosome landing pad) — see e.g. this paper from Sonenberg’s group. However the majority of eukaryotic mRNAs have extensive secondary structure at their 5'-ends, which requires a specific helicase — initiation factor eIF4A — in conjunction with eIF4B and eIF4H to unwind — see e.g. Svitkin et al., RNA (2001).
Secondary Structure varies with Sequence
A little reflection is enough to convince oneself that the extent of self-folding of a single-stranded RNA depends on its nucleotide sequence. The extent of hydrogen bonding of, for example, an (AG)n polymer (A does not base-pair with G in a Watson–Crick helix) would be expected to be much less than that of an (AU)n polymer where A–U base pairing can occur. Likewise, continuous stretches of complementary bases are likely to result in extra stabilization by base stacking, and hence in a more stable secondary structure than the same number of interspersed base pairs. The fact that the secondary structure of a mRNA can be altered by changing the nucleotide sequence without changing the amino acid sequence of the protein product is illustrated by the algorithm described in this paper by Gaspar et al., Nucleic Acids Research, (2013).
Competition by Proteins
It has already been mentioned that proteins (eIF4A and other initiation factors) are involved in unwinding eukaryotic mRNA, and there are numerous examples of the interaction of proteins with specific nucleic acid structures (including the ribosomal landing pad (aka internal ribosome entry site — IRES), previously mentioned above and shown below).

[IRES for Hepatitis C virus RNA, showing areas of interaction with various proteins. From Hellen and Sarnow, Genes and Development (2001)]
The general concern that mRNA secondary structure would impede secondary structure has some basis, but the movement of the ribosome can disrupt secondary structure, as the initial RNA phage experiments indicated. One should remember that after each peptide bond is formed, the ribosome causes the translocation of the mRNA by three nucleotides with respect to the A and P sites, so that it is continuously applying a motive force to the mRNA.
Turning to viruses, tobacco mosaic virus (TMV) — a positive single-stranded RNA virus — was the first virus the structure of which was determined by X-ray crystallography. There is, therefore, a wealth of detail as to the organization of RNA and protein in its virion — this PDB ‘Molecule of the Month’ article (illustrated below with the RNA in red) is quite accessible (in both senses). (A schematic of the virion of a different virus — vesicular stomatitis virus — VSV — is also shown.)

The assembly of the TMV virion involves initial protein self-assembly followed by the looped RNA (secondary structure) being fed in and winding round the inner core. The secondary structure origin of assembly of the TMV RNA is shown below.


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I am looking for examples of polyandrous insects?
This is for a homework assignment, and yet I am not able find any references that can help me find example of polyandrous insects.
Does anyone have any references or suggestions on where to look?

https://www.ncbi.nlm.nih.gov/pubmed/10973716 what about this one

The concept is sort of difficult to apply to insects, since they dont form pairs. However, females mating with multiple males is common (maybe the norm).


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Are the hyphae in mushrooms unicellular or multi-cellular?:
The mycelium is just a collection of hyphae.
Are these hyphae unicellular or multicellular?
If there's any problem in my question please inform me. Thanks!

Welcome to SE Biology. This seems like a homework question and these require that you show you have tried to find an answer yourself.

The haphae of mushroom are multicellular

@Michael_A I got the answer


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Immature lawn mushroom
These have been popping up all over our yard in South Western Australia. I have been digging them out before they mature as I have small children. But with 7 acres I can only check so much.
My question is: Is it possible to eliminate them as being harmful mushrooms from this picture before seeing them at maturity?
Some have been growing in isolation, others in clusters.
Note: a few weeks ago, from near this spot, I removed a white mushroom on a stem with its cap still closed and white gills when I opened it. I have also found a few different types of puffballs around

Are you able to obtain an additional photograph of the stipe (stem) of the fungus? If not, may you please describe the properties of its gills and hymenium - cells which eventually produce spores?

To get a good answer you will need to observe the growth of the mushrooms and post pictures at different stages. Puffball mushrooms will "pop" when poked releasing a cloud of spores. Some mushrooms look like a puffball when young but then open like an umbrella later.


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Why is GenBank growth slowing down?
https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are submitting their data unannotated (WGS submissions are allowed to be unannotated assemblies)?

It is not really slowing down. The graph that you see in that link is semi-log. So the exponentiality of the growth has reduced. It is not surprising because we have much more data than what we had 10 years back but the rate is not going to increase at the same rate (10 to 1000 is a great change but 1000 to 5000 is not despite the fact the the number of new sequences is greater in the latter). However, new data is being continuously added and the linear growth has not saturated yet.
See these graphs that I replotted from the data in your link.

Nonetheless, the number of new sequences will also slow down in future because we would be approaching the maximum.


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Fixing plant leaf tissue for tensile tests
I'm a new master's student in mechanical engineering, and I'm researching crop biomechanics. We need to do some tensile tests on samples of corn stalk sheath, which involves securely and evenly gripping a sample at two ends in a machine and pulling slowly until the sample experiences mechanical failure.
My advisor thought we might simply be able to use an adhesive such as super glue to fix the sheath samples to the tensile test machine, but he found that super glue doesn't adhere well to the sheath because of a waxy layer on the surface.
As someone who doesn't have a botany or biology background, I'm wondering if there are adhesives out there already that would serve such a purpose? Or perhaps another way of fixing the sheath to the machine? Normally tensile machines are used to grip metal or polymer samples, and have simple claw-like grips at either end.

Just as a thought: if it is epicuticular waxes that are causing the problem (or the cuticle itself), you might be able to get better traction by dipping the ends you want to grip in 70% ethanol or nail polish remover


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Why is pepsin able to operate at low pH?
Pepsin is a protease that operates in the acid pH of the stomach. Many proteins are denatured at low pH, and most enzymes — whether or not they denature — require a higher pH for activity.
Why is pepsin not denatured at low pH, and has catalytic activity at low pH, but not at higher pH?

Are you confusing inactivity with denaturation? Have you investigated how high and low pH can denature proteins (or inactivate enzymes without denaturing them)? Don't just say "if this happens to X why doesn't it happen to Y?", but show you understand why it happens to Y.

I think i may be referring to inactivity, why does pepsin become more inactive in more basic environments?

OK. I have edited your question so that it does not mix up activity and structural native state, and focussed particularly on pepsin so perhaps it is no longer a duplicate. You can revert if you wish.

The aspects of this question relating to the effect of pH on enzyme activity have been dealt with previously on SE Biology questions and answers:

Why does pH have an effect on enzymes?
How can ionized amino acid form be important for the catalytic activity?

Their relevance to the situatio of pepsin can be summarized:

The forces stabilizing the native three-dimensional (tertiary) structure of proteins include ionic and partial ionic (hydrogen-) bonds. It is thought that high concentrations of charged hydrogen ions or hydroxyl ions compete for the ionic or polar residues involved in these interactions disrupting the structure — denaturing it.
The effect of such ions will vary from protein to protein depending on the number and strength of these interactions. One presumes pepsin has evolved a structure with interactions that are less susceptible to a high concentration of hydrogen ions and therefore does not denature at low pH.
Catalysis often involves ionization of groups on the enzyme, not merely to bind substrates, but also to participate in the reaction. Typically the reaction mechanism involves flipping from ionized to deionized state or vice versa. Hence, the optimum pH for an enzymic reaction is often at the pKa of the ionizing group (in the environment of the protein), as this is the pH of half ionization.
The reaction mechanism of pepsin, an aspartic protease, involves two aspartate residues, each of which has a low pKa, explaining why pepsin works optimally at low pH.

The catalytic mechanisms of other proteases (serine proteases and cysteine proteases) do not involve ionization changes in aspartic acid, which is why they operate at higher pHs.

A good question. As you have accurately described, pepsin is indeed a protein, more specifically, a protease enzyme - a catalyst which assists the break-down of protein at certain amino-acid markers such as tryptophan and phenylalanine. As you are likely aware, proteins are composed from approximately 20 amino-acids, as shown below.

However, the chemical properties of a protein are constituted by its folding - its three-dimensional shape. This answer describes some superficial differences between protein families and the mechanism and function whereby pepsin is capable of functioning at a low pH.

Disregarding any post-translational modifications - the alterations made to a protein following translation from mRNA - proteins are made from a determined sequence of amino-acids, named its primary structure. Different classes of proteins shall have a different sequence and proportion of various amino-acids. For example, collagen fibrils are composed from a greater proportion of the amino-acids glycine-proline-hydroxyproline.
A sample of pepsin extracted from a pig (Porcine pepsin) demonstrated a higher yield of asparagine.
Secondary structure - the inter-molecular bonding between amino-acid side-chains including hydrogen-bonding and disulfide bridge. As you correctly described a protein denaturing, it is these bonds which are broken, thereby altering the protein's shape.
Although there be four principal protein structures - primary, secondary, tertiary and quaternary - the first two are most critical to understanding the ability for pepsin to withstand low pH. Pepsin is originally secreted into the stomach as a proenzyme - an inactive precursor to an enzyme - called pepsinogen. When food is ingested, both pepsinogen and hydrochloric acid are released into the stomach. Returning to our primary structure, pepsinogen possesses 44 additional amino-acids compared with the active enzyme. During acidic conditions, the pepsinogen auto-catalyses its own cleavage from the additional strand, folding into the correct form.
Therefore, other proteins in high acidic conditions lose their unique three-dimensional structure due to the breaking of these inter-molecular bonds. In a sense, denaturing only specifies a transformation into an inactive protein but could be stated for pepsinogen which is 'denatured' into pepsin which attains its activity in this 'denatured' form.
For more information regarding pepsin, I would advise the following Wikipedia page as an initial resource: https://en.wikipedia.org/wiki/Pepsin
For information regarding collagen and porcine-pepsin composition, the following sources respectively may help: https://www.ncbi.nlm.nih.gov/books/NBK21582/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC427253/?page=2
I wish you good digestion!

So after all that I have indigestion because I don't see any answer to the question in what you have written. Can you summarize in one or two sentences?

@David It appeared that the Original Poster needed to discriminate digested proteins from the enzyme pepsin itself. So, proteins have primary and secondary structure which provide the protein with its shape. Dietary proteins are denatured because of the breaking of secondary structure while pepsin (pepsinogen) is activated at low pH. Admittedly, because I did not explicitly refer to high pH, I will edit the post and insert this additional response. Thank you.


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human gene PCR primers database
I wonder if there is a place on the internet to get PCR primers for a specific gene.
For instance, exon 15 in CFTR gene. I don't want to design myself because I am sure sombody else already did it.

Answer is, obviously, yes.
Primerbank

Here. You can search primers using accession number or Gene-ID

Note that those are primers for real-time PCR, not regular PCR.

You need primers for one exon only?  Why can't you get the sequence and flanking sequence, and put that in to primer3?
http://bioinfo.ut.ee/primer3-0.4.0/


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Why can't we kill ourselves by holding our breath?

Is it possible to kill yourself by holding your breath?

This question is obviously copied from Quora, but I had heard it as a fact that we cannot kill ourselves by holding our breath and I'm looking for a referenced answer.

NAA, since it relies on something other than breath-holding.. but you could kill yourself if you do the over-pressure+hold breath trick to make yourself pass out and happen to hit your head badly when you land.

Or fall into water face-down, for a less gruesome death.

How do you know that we can't?

@SEwontLetMeDeleteProfile Because, even if we do it long enough to pass out (which is difficult except for under specific circumstances), we will immediately start breathing again.

The question "why" is ambiguous. Answer "because we evolved this way" is equally good but likely not what you're looking for.

Short answer
Healthy people cannot hold their breaths until unconsciousness sets in, let alone commit suicide.
Background
According to Parkes (2005), a normal person cannot even hold their breath to unconsciousness, let alone death. Parkes says:

Breath‐holding is a voluntary act, but normal subjects appear unable
  to breath‐hold to unconsciousness. A powerful involuntary mechanism
  normally overrides voluntary breath‐holding and causes the breath that
  defines the breakpoint.

Parkes explains that voluntary breath‐holding does not stop the central respiratory rhythm. Instead, breath holding merely suppresses its expression by voluntarily holding the chest at a certain volume. At the time of writing, no simple explanation for the break point existed. It is known to be caused by partial pressures of blood gases activating the carotid arterial chemoreceptors. They are peripheral sensory neurons that detect changes in chemical concentrations, including low oxygen (hypoxia) and high carbon dioxide (hypercapnia). Both hypoxia and hypercapnia are signs of breath holding and both are detected by the chemoreceptors. These receptors send nerve signals to the vasomotor center of the medulla which eventually overrides the conscious breath holding.
The breaking point can be postponed by large lung inflations, hyperoxia and hypocapnia, and it is shortened by increased metabolic rates.
Reference
- Parkes, Exp Physiol (2006); 91(1): 1-15

In addition: even IF you could hold your breath 'till unconsciousness, because it's a conscious act you'd start breathing again as soon as you're out.

My understanding (from dim-and-distant Chemistry O-Level days) was that it's primarily the build-up of carbon dioxide that prevents you holding your breath long-enough to pass-out/die... breathing into a bag containing a CO2 adsorber would/may allow this to happen.

@TripeHound Hyperventilating, to reduce CO2 build up, is one of the main causes of Shallow Drowning - it not only can, but does happen.

How universal is this?  I've heard various times that young children will use breath-holding as a coercive tactic against parents, and the best way to deal with it is to just let them keep at it until they pass out, at which point they involuntarily start breathing again, and they'll very quickly learn not to do it anymore.

@MasonWheeler I've heard similar stories, but couldn't find peer reviewed work on it; my answer is based on a sound paper in a credible journal, at least afaik

"Healthy people cannot hold their breaths until unconsciousness..." I've seen this done.

Which brings us to "Always listen to experts. They'll tell you what can't be done, and why. Then do it." --- Lazarus Long

Although - note that Parkes doesn't say this can't be done, but that it wasn't observed while attempting it, and that it appears it can't be done.

Does this mean that when people who are trapped underwater drown that they were conscious when they drowned. Even if they attempted to hold their breath that they had no choice but to breath in water. What a horrible thought as I knew a person who drowned after getting caught up in weeds.

@cgTag Yes, if they didn't hyperventilate or have some other health issue. Though note that you only really breathe in a small amount of water - the trachea gets sealed on contact with water - and this phase usually only lasts for a few seconds before unconsciousness sets in (the reflexive breath triggers only a short while before cerebral hypoxia in most people). There's still some time to save the victim afterwards - near drowning isn't rare. There's even some extreme cases in cold water where people survived the anoxia for minutes without any permanent damage (even 60 minutes!).

Counterexample: At least some people can train themselves to hold their breath until they pass out, and if this occurs underwater they will almost certainly die by drowning.
When I was in military service I became friends with some U.S. Navy SEALs.  They go through a notoriously difficult training and selection process (BUDS) that has been well documented.  Among the program's "evolutions" are tests in which candidates have to solve problems to access SCUBA units while submerged in pools or water tanks (and while being harassed by instructors).  It is common for candidates to pass out during these tests, because if they surface for air they fail the test.  (And these are people who self-select as very motivated to not fail at any cost.)  Apparently the tests weed out candidates who are prone to panic as they lose oxygen and can't override their physiological instinct to breath.
I spoke to one graduate who passed out during one such evolution (but succeeded on a second attempt).  He noted that after that incident he lost any fear of drowning, because he realized that if he ever found himself in a situation where he was running out of oxygen he would not feel panic and would just fall unconscious before drowning.

@Trilarion: Yep, just added link to news report on the subject.  Notable quote from that article: “What you’re seeing in the data is more rigorous documentation,” Davids said, suggesting that five students losing consciousness in four months wasn't unusual at BUD/S.

A similar effect (Wikipedia, check the references) is why swimming pools often ban distance swimming underwater: hyperventilation reduces CO2 in the body, even to the point where lack of oxygen causes blacking out first, but more often enough that the swimmer doesn't have time to surface after the urge for air becomes strong. If  the SEALs are hyperventilating first, and determined to stay under, no wonder they're passing out.

I'd expect that training could make this more achievable. Even so, when I witnessed this done it was a female classmate in 6th grade. It's at least possible for the untrained.

Hyperventilation is a special case: The urge to breathe is not triggered by lack of blood oxygen, but by excess of blood CO2. Hyperventilating substantially decreases your blood CO2, but only marginally increases your blood O2. In other words, it delays your urge to breathe without significantly delaying your need to breathe.

This counterexample does not support an ability kill yourself by holding your breath. You pass out, then something happens because you aren't conscious (you drown, under water). The same thing would happen if you held your breath until you passed out while driving, balancing on a tightrope without a net, sitting in a burning building, skydiving before pulling the ripcord, or running from a murderer. In all of these situations the official cause of death would not be holding your breath.


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What are the roundish objects in this sketch of a tracheid?
I got this picture from the Wikipedia entry for Tracheid. What are the roundish objects in the sketch?
Also are tracheids sclerenchyma cells?

It's a good idea to do some reading before posting. Your question whether tracheids are cells is answered in the very first sentence of the article that you took the diagram from: "Tracheids are elongated cells…"

The 'roundish stuffs' you are seeing are called 'pits'. The Dictionary of Botany defines a pit as '[a] cavity in the secondary cell wall, allowing exchange of substances between adjacent cells'. The pit itself is composed from a aperture, named the pit cavity and an environing membrane called the 'pit membrane'. The pit is comparatively analogous to the plasmodesmata connecting protoplasts by thin connecting vessels. The difference exists in the presence of pits within the xylem while plasmodesmata arise between other non-vascular cells additionally.
To respond to your second question, where sclerenchyma cells are strengthened, lignified cells, tracheid cells are indeed the 'tracheary' or vascular specialisation of sclerenchyma tissue.
For information regarding the Dictionary of Botany, the website is available from: http://botanydictionary.org/pit.html
Information concerning ground tissue is available from: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ground-tissue


text:
Understanding beat annotations of arrhythmia ECG dataset
I'm trying to understand the rhythm changes in the MIT BIH dataset.
In annotations, there are 2 main types. Beat annotations and rhythm annotations.
Rhythm annotations (aux_notes field) contains rhythm changes. After each rhythm change point, there are empty strings till the next rhythm change.
Does that means all beats after the rhythm change are in the same rhythm till the next rhythm change?
For an example, take a look at the below wave with annotations (202 record of MIT BIH dataset from 21:19 to 21:49).

In the above diagram does the beats between '(N' and '(AFIB' are all normal rhythm beats? and does the beats after '(AFIB' are atrial fibrillation rhythm beats?
Here,

'(N' means a Normal rhythm annotation
'(AFIB' means an atrial fibrillation rhythm annotation

Postscript
You can reproduce the above diagram via this online tool. Parameters are,
Choose input window

Database = MIT-BIH arrhythmia database (mitdb)
Record = 202

View/edit window

Go to = 00:21:19
Window duration = 30 seconds


text:
Where does the mass come from when you grow plants in water?
How do plants like green onions seem to grow forever when put in jar of water?  I understand that plants get a lot of their carbon from the air (as per this question) but surely they need more than just carbon to grow new leaves.
The answer in the linked question mentions that plants in general get their mass from sources like water and nutrients like nitrogen and phosphorous, and ions.
However, if a plant is growing directly in [distilled] water where will it get those nutrients (like phosphorous and the ions) from?
Where does that extra mass come from?

Right there in the first answer to the question you linked to is a statement that shows that over half the mass added by the plant comes from a particular source other than air.

The sources it mentions are water and then specific nutrients like nitrogen and phosphorous, and ions. However, other than the water where do those other items come from

If you put the onion in distilled water only, the plant will not get any more nitrogen, phosphorous, or ions. The onion has some stores of these atoms, though, and will continue growing a good while since the bulk of needed molecules (cellulose, sugars) are formed only from carbon dioxide and water.

Short answer
Plants with storage compartments can grow for extended periods on water alone.
Background
It indeed seems the question is indeed different from the suspected dupe after all.
According to Turesson (2014)

Seeds, tubers and roots are the most common sites for [...] energy storage and the forms in which energy is stored are predominantly oil, starch and sugars. Underground storage organs mainly store starch and sugars, while seeds from different plant varieties accumulate high levels of starch and also oils and proteins.

So storage compounds like "seeds, tubers and roots" can sustain prolonged growth in the absence of pretty much anything, except water; just consider the familiar seedlings of cress on cotton wool (Fig. 1). There's basically nothing there, just water.

Fig. 1. Cress grown on cotton wool and water. source:Dreamstime
Reference
- Turesson,  Carbon Allocation in Underground Storage Organs, Doctoral Doctoral Thesis (2014), Swedish University of Agricultural Sciences
Alnarp

The most common elements in organic chemistry are carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus.
Water provides hydrogen and oxygen; air (on Earth) provides oxygen, carbon (mostly CO2), and nitrogen. This leaves out only sulfur and phosphorus.
Therefore, any plant that needs only trace amounts of sulfur and phosphorus (or already comes with all that it needs) could grow reasonably on air, water, and light. Bear in mind that another limiting factor is trace amounts of magnesium in chlorophyll which can't be replenished on air and water.

I'm failing to see how this answers the question. Further, an answer needs to be backed up by sources.


text:
Immunofluoresence and vaccines
Can you use indirect immounofluoresence to verify if a vaccine will work against a virus?
Using the vaccine antibodies against the virus, plus a second antibody with fluorophore that will join the first.

I don't think that experiment would prove that the immune system will be sufficiently stimulated by your vaccine to elict the desired response.

A vaccine isn't antibodies.  It's bits of virus or microbe that elicits a response from the immune system, the most important component being the creation of specific memory cells which are ready to react if the real invader is introduced.

You can use an immunoassay like a homogeneous sandwich FRET assay: You can use donor-dye-labelled fluorophore antibodies that are able to recognise specific antigens on the virus to bind the virus antigen, then introduce a second set of antibodies labelled with acceptor-dye fluorophore. If the vaccine works and produces an immune response in the in-vivo model that destroys the virus, the antigen that joins the donor-labelled and acceptor-labelled antibodies is also destroyed and can no longer “sandwich” the two antibodies close together within the Förster distance to exhibit FRET.


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Having a lot of trouble identifying this insect

It was found in central Alabama

This is a true bug nymph; it may be an Assassin Bug (Reduviidae), but I'll admit to uncertainty there.

A friend of mine, ecologist, also suggested that it's a young Reduvid bug, and that it's supposed to suck blood.

Its legs are too thin, ain't Reduviidae supposed to be more robust? Maybe it's from an herbivore group.

I'm inclined to think it's not a Reduviid - those flared legs remind me more of something plant-eaterish; maybe something in the Coreoidea.  The problem is that Heteropterids are a bugger to know well, and that's just the adults.  The juveniles are a real pain.  Better to submit it to one of the ID sites like Bug Guide.

cool it looks like a cousin of the golden egg bug.

This is a true bug (Heteroptera) larvae as the dorsal scent glands and the wing pockets show (see image below).
I suspect it to be a member of the family Coreidae as it exhibits typical (larval) characteristics of this family: a rhomb shaped body and long legs and antenna.
A reduviid larvae, as some of the commentators suggest, would have a strong, often bow-shaped rostrum (proboscis) that I assume should be visible from the perspective of the photographer. Also, reduviid bugs usually have a relatively long head composed of a long neck and nose.

Compare more images of coreid (knowyourinsects.org) and reduviid bugs (knowyourinsects.org).

Image sources (in reading direction):  Mictis profana Graham Wise CC-BY-2.0 | Coreus marginatus AfroBrazilian CC-BY-SA-4.0 | Arilus cristatus Judy Gallagher CC-BY-2.0 | Rhynocoris annulatus Slimguy CC-BY-4.0


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What options exist to quantitatively detect enzyme activity in non-model insect tissue?
Evolution/genomics person here: what are the options to measure the activity or presence of broad categories of enzymes--like peroxidases or catalases--active in a specific tissue (in a non-model insect)?
I understand that antibodies, e.g. ELISA, may be one approach but am unsure if it's the best option or what the alternatives would be. Are any sequence based-approaches available, if I know the peptide sequence (or at least a specific function domain, ie Pfam ID)?

"I understand…". I don't think so. Antibodies are specific to one protein (you hope). They cannot be raised against a "broad category of enzymes". I think your question requires a little more thought.


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Lower affinity drugs longer time for pathways to rebound?
Do lower affinity drugs take a longer time for pathways to rebound?
Affinity has to with strength of activating a receptor others options.
Do those with stronger affinities result in more likelihood to rebound?

This article is a good starting point for this question.
It states:
"The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not."
The dissociation constant is explained fairly well by Wikipedia.
So, the higher the affinity of a drug with it's target, the stronger it binds.
I'm assuming that by "rebound" you mean that the pathway will regain its ability to function normally.
When someone takes a quantity of a drug, it disperses throughout the body. At any given time, at any given point in the body there is some concentration of the drug. If the affinity of the drug to it's target is very high, lots of molecules will bind to the target, whereas with a low affinity drug, fewer molecules will bind.
As time goes on, the body will filter out some of the molecules, and the remaining drug molecules will diffuse to fill the space where the filtered molecules were located. As this process continues, the concentration of the drug will decrease, lowering the dissociation constant of the drug-target equation, which means that fewer of the molecules will bind, and some of the bound molecules will be released to maintain equilibrium. The longer this process continues, the closer to "normal" the pathway will become, until the concentration of the drug is negligible.
Keep in mind that all of this is dependent on the rate at which the body eliminates the drug (and how quickly the drug degrades on it's own). See here for equations and such. While concentration of the drug is a large factor in it's effects, the half-life of the drug may be a better indicator of how long it takes for a pathway to rebound than affinity of the drug. For that matter, affinity is probably a factor in the length of a drug's half-life.

Another way of stating what my question is asking is withdrawal time for these drugs although I am more interested in simply the rebound of the pathways and not the actual withdrawal effects.  There is no doubt this occurs considering if you stop taking benzos you can experience insomnia on and off for weeks and months.  You answer didn't really answer this question.

In that case could you try to phrase your question differently; it doesn't seem to ask the question effectively. Go in to more detail about what you're looking for. Even your above comment isn't particularly helpful; are you asking if withdrawal time of a drug is dependent on affinity? Additionally, please define "rebound".

Another user gave me the rebound pathway term so it seems to me there is discrepancy on what people agree on.  Yes I am essentially trying to determine withdrawal time based on affinity although withdrawal effects can be caused from a host of issues and not simply how long for a brain receptors to start functioning how they were prior to taking the drug.

Ok, that clears up a lot. Now are you asking how to predict withdrawal time mathematically based on affinity, or if there is a relationship between the two at all?

yes.  I have read time taken might effect it also assuming there might be some universal formula or something.

I don't suppose you remember where you read that?

Robert Whitaker's book talks briefly about the dopamine receptors.  It suggests it takes 3 times longer for the receptors to rebound then actually taking the drug.  It isn't a very authoritative source.

"Over time, Chouinard and Jones noted, the dopaminergic pathways tended to become permanently dysfunctional. They became irreversibly stuck in a hyperactive state,  and soon the patient's tongue was slipping rhythmically in and out of his mouth (tardive dyskinesia) and psychotic symptoms were worsening (tardive psychosis). Doctors would then need to prescribe higher doses of antipsychotics to tamp down those tardive symptoms. The most efficacious treatment is the causative agent itself, the neuroleptic"

Considering the uncertainty involved in drug-brain interaction, and how little we know about the brain, I'm not sure that I can give a good answer. If the drug in question only effected one pathway it would be simpler, but there's 3 pathways involved here. I suspect it may be dependent on the individual drug and pathway being studied. I've been unable so far to find any solid conclusions.


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From where does the oxygen in glucose come in photosynthesis?
Is it carbon dioxide or water? I'm talking about the oxygen present in glucose and not the oxygen that is released after photolysis of water.

RuBisCO attaches one molecule of CO2 onto Ribulose-1,5-bisphosphate (RuBP). RuBP gets split to two molecules of 3-Phosphoglyceric acid (3-PGA). Via reduction to Glyceraldehyde-3-phosphate (GAP) the link to glycolysis is established. By doing the Glycolysis reactions backwards, you reach Glucose.
This is the reaction of RuBisCO (from humboldt.edu):

EDITED to correct: One molecule of RuBP, one molecule of CO2 and one molecule of water are converted to two molecules of 3-PGA. This compound then is either used to refill the Calvin cycle by production of new RuBP, or is inserted into glycolysis, where it can be converted to Glucose. So, as David correctly points out, the oxygen comes from water as well as from CO2.

Thank you @David, my bad, I missed that. I hope the edited answer is better.

Fine. I'll remove my original comment.