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Glycolytic non-oxidative pathway
I am currently digging in some books to understand the three major metabolic pathways involved in physical training. The most difficult one for me is the glycolytic non-oxidative pathway (also more commonly known as the anaerobic lactic pathway) and I would like some help from people versed in this field.
In this pathway, as far as I understand, glycolysis produces pyruvate. In this process, NADH and H+ ions are produced along the way.
Then, if there is still a high energy demand (i.e. glycolysis is still necessary); NADH binds with pyruvate to form lactate and free up NAD+ which is necessary to sustain the glycolysis (otherwhise, pyruvate would be consumed via an oxidative pathway i.e. oxidative glycosis or slow glycolysis). This can theoretically continue until glycogen is depleted or severely diminished as far as I understand.
The problem comes then from the H+ ions produced during the glycolysis. These ions cause acidosis of the muscles if not removed. However, they can be removed if sufficient oxygen is present to form water. And here is my main question :
Why, during high intensity exercise, would oxygen be insufficient to take care of the H+ ions produced by the glycolysis ? Is it because muscles used during high intensity are not the best ones for using/transporting oxygen? Is it also because these H+ ions cannot be transported towards neighbouring muscles able to oxidise H+ ions ?
I understand this is a difficult question and maybe there is no precise answer at the moment. If you could point me toward a good ressource that deals with this question, I would be glad. I currently base myself on McArdle book on exercise physiology.

This is a great question, but not really on topic for fitness. I am migrating it to biology, where it may get a higher level of attention.

I am going to try to walk through this problem, in a step-by-step manner in relation to exercise, starting from at rest, and ending at the point in which the body is no longer able to maintain its energy-charge.
At Rest
The body mainly utilises oxidative phosphorylation to maintain its energy-demands. In cells where great amounts of energy need to be produced very quickly, eg. cells that are actively replicating, glycolysis is the preferred mode of energy production because this pathway is able to very quickly produce large amounts of ATP, and lactate is able to quickly diffuse in to the bloodstream. Lactate will travel in the bloodstream, to the liver, to be recycled back to glucose through an anabolic process called gluconeogenesis. This recycling pathway is known as the Cori-cycle. Essentially, what is happening is, parts of the body that are in need of high amounts of energy, will "dump" their wastes to the bloodstream, to be dealt with by other organs.
Science and Skiing VI, 2015, pp 17-30. George Brooks of the University of California summarises lactate recycling quite nicely here.
Beginning Exercise
Muscle cells will begin to quickly utilise ATP-stores, and release glucose from the glycogen-stores, and release oxygen-stores from myoglobin.
As these stores begin to become depleted, the body will begin to go in to overdrive, in an attempt to restore itself to a resting-state. Thus, your heart-rate will increase, breathing will become faster, and glycolytic pathways will be activated through feed-forward mechanisms.
During Exercise
I have touched on this before, in another post that you may find interesting. I believe that if you read through this though, that you will understand why there is low levels of oxygen, and what the body does to attempt to circumvent this.
There will be very low levels of oxygen throughout the active tissues. The body will do everything it can to try to restore this, but it will ultimately fail to do so. Thus, the only real option it has is to rely on glycolysis in the tissues that are causing "problems". The rate of ATP-production is most dependent on the rate at which a cell can take glucose in to the cell.
The electron-transport-chain is only able to synthesise ATP at its maximum velocity - this maximum velocity is proportional to the concentration of oxygen. The rate of glycolysis is, however, essentially, only affected by the rate at which lactate can be removed from the cell and the rate at which glucose can be absorbed by the cell.
Of course, the muscles that are being used will only be concerned with producing energy. Therefore, all of the lactate that they produce will be dumped in to the bloodstream, where it will travel to the liver, in the previously mentioned cori cycle.

Overall, the issue is not in the muscle-cell's ability to regenerate NAD+. This is the easy part, seeing as there is no net-change in the concentration of NAD+ when glucose is converted to lactic acid. And also, things such as malate-aspartate shuttles, citrate-pyruvate shuttles, and glycerol 3-Phosphate shuttles can be used to maintain redox-balance. These are only but a few examples of how to maintain redox-balance.
You must also remember that carbohydrates are not the only class of molecules involved in these cycles; degraded proteins and fats can also be used to supply the TCA-cycle with alternative means of energy-production. Pyruvate probably would not even be able to be converted in to acetyl-CoA anyway, since pyruvate dehydrogenase requires the presence of oxygen to function.
Problems however do arise once the body is unable to deal with all of the waste that it is producing. There will reach a point, where the liver cells will be physically incapable of accepting any new lactate-molecules. And so, lactate will accumulate in the bloodstream. With an accumulation of lactate in the bloodstream, lactate will be unable to diffuse to the outside of the cell. Thus, cells will be unable to convert pyruvate in to lactate.
The reason why ATP-regeneration eventually fails to keep up with the rate of ATP-usage, is because the rate of conversion to lactate decreases. The rate of conversion to lactate decreases, because the concentration of lactate increases
I tried to make a little illustration of what I mean above, below. Hope this helps to conceptualize it.

In this second picture, there is too much lactate for diffusion to occur.

Supporting information
Taken from Quantifying intracellular rates of glycolytic and oxidative ATP production and consumption using extracellular flux measurements; Mookerjee et al. 2017
"These maximum values of JATPglyc and JATPox define the bioenergetic capacity of the cells. As shown in Fig. 5D, the maximum individual capacities of JATPglyc and JATPox in the bioenergetic space plot intersect at (62.5, 46.5) for a theoretical maximum bioenergetic capacity of 62.5 + 46.5 = 109.0 pmol of ATP/min/μg of protein. At this maximum point, the glycolytic index (GImax capacity) would be 62.5/109 = 57.3%, making C2C12 myoblasts primarily glycolytic when running at their maximum ATP production rate. Compared with the actual value of JATP production in the presence of glucose (55.2), the bioenergetic capacity was 109/55.2 = 197% of the rate with glucose (Fig. 5D). This bioenergetic capacity of 197% of the rate with glucose (alternatively, a reserve capacity of 109.0 − 55.2 = 53.8 pmol of ATP/min/μg of protein) reveals that the C2C12 cells under our experimental assay conditions with added glucose were operating comfortably within their capacity to generate ATP and were well set up to respond to any acute increases in ATP demand by increasing either glycolytic or oxidative ATP production, or both."
In these experiments, the researchers were trying to figure out what proportion of ATP would be created by glycolytic and oxidative pathways in muscle cells (and other cell-types). Their findings, were that, indeed, the majority of ATP production in muscle cells comes from glycolysis.
During exercise, this difference in amounts of ATP production between glycolysis and oxidative phosphorylation would probably be even greater.

I noticed that someone does not like this answer. If you could provide feedback on how to improve this or tell me why I am wrong, it would be greatly appreciated. Thanks.

Bob - I did not downvote you.  However this is incorrect (not completely so please don't take offense -- just missing some key factors). @xusr is on the right track. Will add on in a sec

True. However, it is not really about the amount of ATP that can be produced. It is about how quickly that ATP can be produced. By using glycolysis, the cell will be able to produce a greater amount of ATP than it would be able to if it were trying to cycle through the entire TCA-cycle & ETC. Also, the TCA/ETC does not shut down.. Not at all; it will however utilize alternative substrates, such as amino acids or fatty acids. The amino acids and fatty acids will be present in sufficient amounts to fuel the TCA relative to the amounts of oxygen that is present. And, as I said, when a cell is

using glycolysis to produce lactic acid. This lactic acid will be dumped in to the bloodstream to be processed by different organs - mainly the liver. Cancer cells use a similar mechanism - for those of you who have studied cancer, you know this.. Cancer cells do not use oxidative phosphorylation, because they can grow much more quickly by relying on glycolysis, and allowing the rest of the body to deal with the lactic acid.

@Mike-DHSc , Yes please do add on. I'm interested to see what you think.

@Bob Yes exactly where I was going -- I'm not a chemistry guy - I'm a PT so you'll run laps around me in that area.  You actually hit most areas (and some I didn't even pick up on the first time around) - was trying to find an excerpt from a book that explains it well but no luck.

I'm posting 2 images now -- maybe you can make better sense of them then me.

@Mike-DHSc Great! I'll take a look. But, which part was the part that you thought was incorrect? I'd like to look in to that a bit more also.

One sec I'll add them shortly

From What I understand (I am an engineer, not a chemist), I'll tag along with Bob. What I understand is, during intense exercise, your body is doing whatever it can to maintain its balance. So oxidative processes (using fat mainly I guess) are running at 100% (VO2max) but are not sufficient to produce ATP quickly enough (the ATP production rate is not enough to compensate ATP use rate). So non-oxidative processes such as ATP-PC (quickly depleted) and non-oxidative glycolysis enter the game. Oxidative glycolysis is not able to proceed because

non-oxidative is more efficient in terms of ATP production rate (not in terms of ATP yield per glucose molecule) and the body favours this one in view of the energy demand

@FenryrMKIII No, it would mainly use glucose, not as much fat. And, "efficiency" is relative to whichever state the body is currently in. While at rest, oxidative phosphorylation is more than enough to maintain appropriate ATP-levels, and you get ~36ATP per glucose molecule, so in resting cells this is much more efficient because it also allows preservation of resources. I don't really think you can say any one pathway is "more efficient".. Cells will always try to react in such a way that is optimal to a given situation - and if burning through the bodies glucose-stores to produce lactate

happens to be the optimal option during exercise, that is what the cell will do. To think of certain processes as being the "most efficient" leads people to believe things like "the paradox to anaerobic energy production during exercise". So yes, you are right on the money with: "your body doing whatever it can to maintain its balance".

Let's forget the word efficient. Rather, non-oxidative glycolysis is the pathway that is able to provide ATP at a sufficient rate so that ATP stores are replenished sufficiently fast compared to their use. Now one thing I don't understand from your answer is how can the body use glucose with oxidative processes while under intense activity ? Since in such situation, according to my understanding, glucose is needed for the non-oxidative glycolysis and oxidative glycolysis being the only other pathway to use glucose,

it is not possible for the body to perform oxidative glycolysis while non-oxidative is underway

@FenryrMKIII "Non-oxidative glycolysis ... provides ATP at a sufficient rate", correct! And, I do not think that the body would use very much glucose for oxidative phosphorylation - since the enzyme (PDH) that converts glucose in to AcCoa will not be active due to the low levels of oxygen. Instead, I think the TCA cycle would more so be powered by amino acids and fat (although minimal amounts of glucose might still get theough).

To my understanding, conversion of glucose to AcCoa is not active because the body knows (I don't know how exactly) that he needs to sustain non-oxidative glycolysis (not because oxygen levels are low, oxygen is in fact very present to my understanding given the intense activity). If he goes the AcCoa way, then pyruvate is used and no lactate is formed. Therefore, NAD+ is not replenished to fuel glycolysis and it stops and there is an ATP production hole. In the end I think we agree: during intense activity, non-oxidative glycolysis and oxidation of fat and amino acids provide the ATP.

Well, oxygen is "busy" being the terminal electron acceptor of the electron transport chain (ETC) - which is fueled by NADH/FADH2 produced by the TCA cycle.. But yeah, close enough!  As you can see, it's a very complicated question you have asked.

That is why I asked it :) Because in the books I have, the way they explain it is not clear enough and they contradict themselves sometimes.

No! The oxygen levels have decreased, IIRC the pO2 (in the blood tissue, at least) can drop down by something like 50torr - which is enough of a pressure drop to inactivate PDH - that's what causes the preference of glucose towards glycolysis. But, yeah, oxygen is definitely still there - just not as much of it, so the TCA/ETC will still work, just not as well as it was working prior to exercise.. Everything else that you said after "If he goes the AcCoa way, then pyruvate..." I agree with.

Can you please stop excessive commenting and discuss over in the chat?

pyruvate dehydrogenase requires oxygen as a cofactor to function No, it does not. In biochemistry a cofactor is a non-protein component of an enzyme's active site. The linked paper explores the way in which hypoxia influences the regulation of PDH through phosphorylation.

@AlanBoyd Good catch, thanks. Better?

Thanks @xusr, but I'm going to have to ask you to kindly start reading more carefully, ie. stop skimming through. Because, no where did I ever say that O2 is consumed/produced in the TCA. And also, you don't need to become Alan's echo - we already noted the whole phosphorylation thing at least three hours before your comment.

Fantastic question!  Hopefully this somewhat helps.  It's very difficult to simply this process as it's quite complex.
During high intensity exercise, energy demands exceed either:

The O2 supply
The rate of use exceeds the at which it becomes available.

So the respiratory chain cannot process all of the H+ joined to NADH.
Continued release of anaerobic energy during glycolysis depends on NAD+'s availability to oxidize 3-phosphoglyceraldehyde -- otherwise glycolysis grinds to a halt.

During anaerobic glycolysis -- NAD+ "frees up" when excess hydrogen's combine temporarily with pyruvate to form lactate.  Lactate formation requires one additional step catalyzed by lactate dehydrogenase.

The storage of H+ with pyruvate represents a temporary "collector" of the end product of anaerobic glycolysis.  Once lactate is formed it diffuses away into the interstitial space and blood for buffering and removal.
However, this avenue for energy is temporary.  Blood lactate and muscle lactate levels increase and ATP regeneration fails to keep pace with the rate of use.  Fatigue sets in and performance diminishes.

EDIT

H+ = a free electron
Increasing the concentration of free H+ ions = lowers the pH (so a pH
of 1 is very acidic and has a very high concentration of free H+
ions, a PH of say 9 has a lower concentration of H+ ions and is less
acidic).
Oxidation is losing electrons – reduction is gaining electrons.
During glycolysis NADH is oxidized.  The regeneration of NAD+ (this
is the reduced form of NADH)  during the reduction of pyruvate to
lactate is required for glycolysis to continue under anaerobic
conditions.
Several key steps in the oxidation of glucose to pyruvate involve the
reduction of the electron/energy shuttle NAD+ to NADH. It's required
to reoxidize the NADH to NAD+ in order to avoid consuming the
available pools of NAD+ and to thus avoid stopping glycolysis.
Put differently, during glycolysis, cells can generate large amounts
of NADH and slowly exhaust their supplies of NAD+. If glycolysis is
to continue, the cell must find a way to regenerate NAD+, either by
synthesis or by some form of recycling.
Let me know if that helps!

UPDATE
So these slides will have to do for now (best I have available to post).  Put very simply in anaerobic conditions - there comes a point where there is not enough NAD+ available to convert pyruvate to lactate.
Would H+ ions just accumulate and increase local acidosis?

Two errors in the edit: H+ is not an electron; NAD+ is the oxidised form; there is only one step in glycolysis where NADH is generated.

@Bob Well, obviously, but that isn't what the sentence Several key steps in the oxidation of glucose to pyruvate involve the reduction of the electron/energy shuttle NAD+ to NADH. conveys, at least to me.

Okay. So, have you heard of alternative splicing? Basically, different organs/tissues can have proteins that perform the same function, but the efficiency at which the proteins function will vary. So, in your first picture there, it is showing that the LDH-protein in the heart is less likely to use glycolysis to produce lactate - since, because the heart is quiet vital to life, damage to this organ needs to be minimised. In your second picture there, it is showing that pyruvate will not be converted to acetyl-coenzyme A in the absence of oxygen - which is required by pyruvate dehydrogenase.

I disagree though with: "there comes a point where there is not enough NAD+ available to convert pyruvate to lactate." this should not be a problem - because of the reasons I listed in my answer. The problem arises when there is a build up of lactate - because the equilibrium will not allow any further shift from pyruvate. So, basically, yeah - "H+ ions just accumulate and increase local acidosis", although it isn't actually the problem.. the problem is the presence of lactate. "H+" does not actually exist as a free ion.

"This avenue for energy is temporary because blood lactate and muscle lactate levels increase and ATP regeneration fails to keep pace with the rate of use. Fatigue sets in and performance diminishes.
Anaerobic Conditions mediate fatigue by inactivating various enzymes in energy transfer and impairing the muscles contractile properties."  I'm reading otherwise...

@Mike-DHSc Yes, but this has nothing to do with the concentration of NAD+. Remember, each time you convert glucose to lactic acid, there is no net-change in the concentration of NAD+. The reason why ATP-regeneration eventually fails to keep up with the rate of ATP-usage, is because the rate of conversion to lactate decreases. The rate of conversion to lactate decreases, because the concentration of lactate increases.

@Bob ah I see -- you seem to have a very strong understanding exactly what's going on.  What you've outlined matches what I'm reading.  I put too much stock in NAD+ Regeneration being some type of rate limiting step.  You're correct - thanks!

I am also looking for more references to add to my answer. I probably should have done this in the beginning, because I do realise that this particular topic seems to contradict a lot of the things that classic biologists take to be gospel. If you find anything interesting, I would like to read it also. One of the references that I am reading right now claims that glucose - uptake is one of the main limiting step in the initial stages of switching to mostly glycolysis. I'll post it once I think I've found a sufficient amount of supporting information.

A cited detailed explanation would definitely be helpful.  I primarily read rehab / health / fitness studies articles etc.-- for work and fun.  If something in that realm comes up I'll let you know.
Wish they had a member reviewed medical based forum on this site to answer questions and add that type of information.


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How much current is required to stimulate a neuron?
Extracellular stimulation of neural tissue is done using electrode. Amount of current determines neurons how far from the electrode will be excited. How much current is required to stimulate the neuron in immediate vicinity? Such information is not available on internet.

"Such information is not available on internet." - wrong, but okay, I understand it's hard to find. The problem with your question is it is ill-defined: what do you mean by immediate vicinity? That term is meaningless. It also doesn't say anything about the rest of the setup: how far apart are the electrodes, how big are they, what part of the neuron is nearby? If you really want to know the minimum current to make a neuron spike, all you need is the input resistance, resting potential, and threshold, but that's for current delivered directly across the membrane.

immediate vicinity means neurons in contact with the electrode. single electrode. how big? why? say 100 micron dia. axon is  in contact.

"If you really want to know the minimum current to make a neuron spike, all you need is the input resistance, resting potential, and threshold, but that's for current delivered directly across the membrane. " interesting.please tell me the calculation. rest potential -70mV, threshold -55mV and what is input resistance-  resistance of electrode wire? let us say it is 100 Ohms or R if you would like.

Because not all of the current will actually go through the membrane of the cell, especially if the ground is far away or not in the same direction. Input resistance is the input resistance of the cell. If you just want a ballpark estimate for some engineering project, typical extracellular stimulation intensities are in the microamp range, but the current you have to deliver across a membrane to make a cell spike is in the picoamp range, depending on cell type and other conditions.

To calculate for one cell, knowing the input resistance of the cell (not your wire), all you need is Ohm's law, knowing you want to change the voltage by, in your case, 15mV.

"the current you have to deliver across a membrane to make a cell spike is in the picoamp range" does this require electrode inside the neuron like the glass pipettte electrode.

"To calculate for one cell, knowing the input resistance of the cell (not your wire), all you need is Ohm's law, knowing you want to change the voltage by, in your case, 15mV. " For this, are two electrodes required,one inside cell and one outside? in that case why resistance  has to be known? just both electrodes should be at 15mV difference.

You always have two electrodes - in your case, your ground someplace is one of them. And yeah, I'm talking about inside the neuron with an electrode of some sort. For outside, you have to consider everything else, which is basically all the other places your current could flow. Imagine a massively parallel circuit where only one of the paths actually goes across the membrane you are interested in.

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How does Reissner's membrane rupture cause Ménière's disease symptoms?
In Ménière's disease, an ednolymphatic hydrops (EH) in scala media leads to a distention and, eventually, rupture of Reissner's membrane. This results in an influx of K+-rich endolymph into the Na+-rich perilymph of scala vestibuli.
Supposedly, this causes an "injury to the sensory and neural elements of the inner ear, which manifests clinically as sudden hearing loss, tinnitus, and vertigo."
What is the pathophysiological mechanism? Aren't these elements part of the Organ of Corti, not in the perilymphatic space?

It would be nice if you could cite your sources for most of your information. This appeals to the community that you have done your research.

source: my ENT textbook and BMJ

It would be better to mention it in your question itself with links that can guide the community to the sources so they can read more if needed. See Here on how to link your sources.

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Why did black swans to evolve black colouring?
What environmental factor caused black swans, which are native in Western Australia, to evolve black feathers ? Note swans are either black or white, there are no brown or grey colurings, which can be commonly found in various geese and duck spieces.

Because somewhere, sometime in the distant Australian past, either it helped them hide from, or deter, predators and/or helped them hide from prey increasing their chances of feeding and/or made them attractive to others and/or somehow a gene linked to color conferred some quality which increased their chance of survival. You missed the Black Necked Swan.

Also, is there any disadvantage in having black feather? Because characteristics like "the color of something" may just appear by simple point mutation and stay if not counterselected. Often they have a social effect, for example it's easier to recognize your pups if they have a different color.


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How to correctly preserve organic matter with ethylene and polyethylene glycol?
I am trying to preserve and dye flowers, especially roses. Let me walk you through the process I am trying to optimize:
1) Soaking flowers in 96%-ethanol for a day to dehydrate them. This step removes a lot of the color from the petals - red roses for example become faint pink. The flower itself becomes brittle to the touch, since almost all water is removed.
2) Putting the dehydrated flower into a mix of 96%-ethanol, polyethylene glycol 400 and reactive dye which is used in textile industry. I am still experimenting with the ration of ethanol:PEG. Soaking duration is a couple of days. In theory, the PEG gets into the cells of the petals - this preserves the petals and gives them most of their flexibility back.
3) Removing the flower from the mix and rinsing it for a minute in 96%-ethanol. This should remove the excessive PEG on the surface of the petals. Otherwise it looks glossy and stays sticky.
My problem begins at step 1): If I remove a flower from the dehydrating ethanol-bath, the petals turn opaque in a weird way. Some connected areas of a petal start to change their appearance abruptly (some sort of bursting, cracking, rupturing)! This starts some seconds after removing the petal from the ethanol and after a couple of minutes, almost all of the petal has turned opaque. Usually the outer edges of the petals don't turn opaque. I am not sure about this, but could it be, that the ethanol somehow destroys the cells of the petals? Is this a behaviour that is to be expected or am I doing something wrong? I think I would benefit a lot if I could understand where this abrupt change of quality comes from.
it doesn't matter, if I remove the flower after step 1, 2 or 3, the result is always this abruptly turning opaque behaviour.
Since my goal is to dye them to look nice and pretty, I need to find the mistake I am making. I was hoping you experts could help me.
You find two pics of already dyed petals attached.
(I wouldn't mind if they stay all transparent. In that case the petals should not turn opaque. But I also wouldn't mind if they become opaque - but on 100% of their surface. Also at the outer edges. This actually may be better - I think it looks nice this way.)

I find that using mixture of PEG 400 and Ethanol 2:1 reduce the transparency. You also need to bake the pental in microwave 360w for 15 seconds. Still some small transparency but acceptable.

Hello, nice answer! This question was deemed worth of an answer, so why not upvote it? Vote early, vote often to encourage new users and keep the community alive!

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Why can't primary RNA be used as a direct template for a protein?
Why can't primary RNA be used as a direct template for a protein

Please explain what you mean by primary RNA. This is not a standard term in molecular biology.  Preferably add a reference or quotation so it is quite clear. Also, what do you mean by "Why"? Mechanistically or philosophically/logically?

@GerardoFurtado then you might want to edit the question for the rest of us.

@GerardoFurtado I think half the problem with bad answers on this site is unclear questions. This is bad in many ways. Not only those I have indicated, but also that the poster has shown no evidence of having tried to solve this himself as described in the help. Furthermore, if he is asking about eukaryotes and his question is "why exons?" (philosophical) then he should have searched the site. The question would be a duplicate.

@a.baldwin Is this question about alternative splicing? Similar to the other commentators requests, please edit so no-one on SE has to guess what you are asking and you shall get answers :)


text:
AntiTrypsin Enzyme
In a smoking patient, is the lung over digested because of a combination of smoking and a defect in the antitrypsin gene (prevents digestion from protease)? Or does smoking act the same as a patient with a defect in the gene?

Do you have any proof for this claim? Usually proteases are not active in lung tissues.

Wikipedia has a fine article on the disease.
https://en.wikipedia.org/wiki/Alpha_1-antitrypsin_deficiency
from that article

Alpha-1 antitrypsin (A1AT) is produced in the liver, and one of its
  functions is to protect the lungs from neutrophil elastase, an enzyme
  that can disrupt connective tissue.

Neutrophil proteases are active anywhere neutrophils are.  People who don't smoke can get COPD just from having the double recessive form of this disease (no active alpha-1 antitrypsin).  But if that is the case with you and you also smoke you get accelerated COPD.  COPD is already an inflammatory disease associated with mucus and neutrophil action and the damage this causes is no doubt augmented with the lack of protective alpha-1 antitrypsin.
If you suffer this condition you can get infusions of alpha-1 antitrypsin  - sort of like type 1 diabetics get insulin.


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Function and Mechanism of Height Genes
I have an inquiry regarding the exact function of height genes.
To my knowledge, although they are heavily regulated by epigenetic factors, height genes can have either an "on" or an "off" allele, and the probability of the person being "tall" shows positive correlation with the number of "on" height genes alleles he has.
However, I could not find any resources showing the exact function or mechanism of these genes' function. Do these genes code for a specific protein when they are "on"? And if there are any, how do these proteins increase the probability of the person being "tall"?
Thank you.

Can you link to the sources that postulate "on/off" genes or to what some of those genes might be? That would help potential answerers follow the paper trail to the function of those genes.

There is no such thing as "height genes". There are, however, genes that have a quantitative effect on height, such as SHOX which interacts with bone development. Others have a dominant effect, like EGF3, which causes achondroplasia when it is mutated. However, the expression of genes that control growth is highly regulated by environment and epigenetic factors. It would really help if you linked some kind of source, or some group of genes.


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Artificial reduction of NADP into NADPH by means of an electrical current
I've recently been attempting to artificially drive the formation of NADPH via the NADP reduction mechanism utilized by Ferredoxin-NADP Reductase in the Light-Dependent Reactions of Photosynthesis in plants. My goal is to reproduce the synthesis reaction in vitro only by means of an electric current.
Is there any way to replace the electron pair supplied by PSI in vivo, with one from a current going through a wire? Would conducting electricity through a solution of Ferredoxin, FNR, NADP, and a weak acid yield any desirable results?

It SHOULD work, theoretically. If it doesn't, try using strong acid (not so strong that it'd degenerate other chemicals) ;)

@another'Homosapien' Thank you for your answer! So you are fairly certain that simply conducting electricity through a solution of the chemicals would lead to the spontaneous synthesis of NADPH by the FNR enzyme? I have to conduct this experiment for a research project, and I would like to have confidence that my ideas would "work". Also, what is the most efficient way of detecting NADPH in an aqueous solution?

@another'Homosapien' So I don't have to "bind" ferredoxin to the metal electrodes, right?

I said it SHOULD work, not it WILL work. There could be some problem at any step. I am not expert in using biochemicals in vitro, so I can just say that yes, theoretically it is possible. Ferredoxin carries electrons from PS-I to NADP, and since PS-I is the only source of electrons there, so ferredoxin is attached to the membrane. But as electrons would move from one place to another in solution, ferredoxin need not be attached at electrode.

@TomD Would a 100mM solution of acetate produce a pH below 5? Also, would serial dilution do for the experiment, since 100 micromoles for the NADP is a bit too sparse for our lab equipment? I don't know if your setup would yield a significant result, either. Finally, I would like to know how you came up with your numbers regarding the concentration of the chemicals. Could you clarify a bit more? Thank you!


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How does the human body power itself?
This query can be divided into sub-queries:

What form/s of energy does the human body "run" on?
Why/for what are these particular forms of energy required?
From what can these types of energy be derived?
How efficiently (less waste) does the body use energy?

Looking for a simple, effective answer with little to no jargon (distinction between pertinent use of terminology and showboating).

This question is very broad, and you can easily google part of it and show your research. If you narrow this down and add your research, I'd be happy to withdraw my close vote  and my downvote, and even to answer it.

If you had read the info about this site you would have seen that is for students of biology. Biology is a specialised subject with its own language. This is not jargon but a vocabulary to describe specific entities and concepts not encountered by the layman. To suggest its use is "showboating" is insulting to members of this list. If you have such a detailed list of informational requirements you need to learn some metabolism from a standard text, or find a website that provides a naive account of such processes, replete with half truths and false analogies.

The question is broad and can hardly be fully answered in a single post. I will be very brief hoping it will help you and push you to seek for more knowledge.
Humans, like all other animals (or almost all) are chemo-organotroph. This mean we get our energy from the food we eat and we release this energy through oxydation. It is therefore chemical energy that we're using. We are then storing this energy into another chemical called ATP. Note that not only humans use ATP but any living thing on earth uses ATP (or GTP I think). ATP is then used (ATP loses one phosphate group and becomes ADP) to perform specific action (such as the use of a trans-membrane pump or the contraction of a muscle fiber).
You should have a look at wikipedia > Primary nutritional groups as well as  wikipedia > chemotrophs and eventually this post.
For more information, please consider having a look at wikipedia and if you can't find feel free to ask your question in a new post. Always attempt to narrow your post down to a single, clearly defined question.


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What exactly causes SSRIs, SNRIs, and tricyclics to induce akathisia?
Such as too high neurotransmitter levels (serotonin/dopamine/other) or the method of drug delivery or some other reason?

Please keep in mind I know very little about this subject, I apologize for the vagueness


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Can gene-gene interactions result in gene expression?
I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge.
The format of the input data is shown in the image.
Now according to what I studied, a Gene Expression Matrix has its rows represent genes, columns represent samples such as tissues or experimental conditions and the numbers in each cell refer to the expression level of a particular gene in the particular sample.
And that Gene Expression is the process in which information from a gene is synthesized to obtain Gene Products. The process of Gene Expression is that it undergoes a transcription process where a transcription factor attaches itself to the gene and then results in the formation of gene product.
But the input data apparently shows gene-gene interactions.
As a result of this I am extremely confused.
Any kind of help would be greatly appreciated. Thanks.

Let us continue this discussion in chat.

I don't know anything about your algorithms. But i will try to explain your the format of data that was given to you. I don't know your background in Biology, so i will assume it is not your expertise field and will make some simplifications of the subject.
What is gene expression?
To understand what is a gene expression, you need to understand what is a gene:

A gene is a sequence in the DNA (composed of 4 bases A,T,C and G) that can be transcribed by a protein, in your context we will say it always start with a start codon (a codon is a triplet of DNA bases) and stop with a stop codon. It is usually around a thousand bases long. The transcription will give you a RNA, and that RNA can be translated (note the difference with transcribed) into a whole new protein.

Now the gene Expression is a measure of the amount of RNA from the gene you are looking for. In a cell you can have around 10000-100000 copies of that RNA; the raw count is not really stable as you can have extract two cells or three and it will change your "expression". Most of the time we normalize the count by the count of a bunch of known genes called housekeeping genes. The particularity of these genes is that their expression is quite stable.

The figures you have are a ratio between RNA copies of your gene of interest and RNA copies of a stable gene (in term of expression).

What does G1(-/-) and wt mean?
Usually when we (biologist) call a sample wt it means wild type, in other words, a normal individual. G1(-/-) means that this sample is from an individual with the G1 gene inactive (could be obtained by genetic modification).
What is a gene-gene interaction?
An example of interaction first: let's imagine a gene coding for an enhancer (booster) of transcription. the presence of this gene allow another gene to be expressed in the cell, if this gene isn't present or isn't transcribed, the other gene won't be expressed either.
How can we see interaction there?
Let's look at line one, the control (normal individual), We see that G4 (column) is almost unexpressed (0.07). In normal conditions, this gene is not expressed. Now let's look at mutant G1(-/-) and G6(-/-), we see the expression of G4 is rising (0.37;0.23) compared to the control (wt).
We can suppose than G1 and G6 are acting as inhibitors of the G4 gene.

The short answer is yes, of course there are gene-gene interactions.  I'm not sure what the point of the experiment would be if there were not.

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


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Understanding presynaptic and postsynaptic inhibition
One way to classify neural inhibition is based on the inhibition being "presynaptic" or "postsynaptic".
As far as I understand, the two different types of inhibition refer to the following:

Presynaptic inhibition: A neuron N1 is inhibited "indirectly" insofar as the presynaptic excitatory neuron's action on it are dampened. This is typically achieved by neurotransmitter's impact on the presynaptic excitatory neuron which inhibit Ca2+ channels, and consequently prohibit vesicle release of neurotransmitter's into the synaptic cleft - hence the excitatory impact on neuron N1 is reduced.
Postsynaptic inhibition: A neurotransmitter acts directly on  neuron N1's receptors, leading to hyperpolarization of the membrane potential and hence a reduced probability of firing.

My questions:
(1) When we speak of "inhibitory post-synaptic potentials" (IPSPs), is this hence
always in the context of post-synaptic inhibition?
(2) I often read of "interneurons" (and it seems that this concept is used typically to refer to inhibitory neurons). Is inhibition by interneurons also always post-synaptic?

Post-synaptic vs pre-synaptic inhibition
Yes, inhibitory post-synaptic potentials (IPSPs) are always in the context of post-synaptic inhibition, because they are post-synaptic potentials. They occur because of inhibitory neurotransmitters (for example, GABA) are released and bind to post-synaptic receptors, particularly ligand-gated chloride channels. We often just call this "synaptic inhibition."
Pre-synaptic inhibition, on the other hand, would reduce the frequency/amplitude of excitatory post-synaptic potentials, by reducing neurotransmitter release at excitatory synapses (for example, glutamatergic synapses). You can also have pre-synaptic inhibition at an inhibitory synapse, where the pre-synaptic inhibition is actually disinhibitory from the perspective of the post-synaptic cell (inhibiting inhibition).
In summary: post-synaptic inhibition is reducing the rate or probability of action potentials; pre-synaptic inhibition is affecting the quantity or probability of vesicle release.
Interneurons vs inhibitory cells
Inhibitory interneurons are a major class of interneuron in the neocortex, but not all interneurons are inhibitory (layer 4 spiny stellate cells, for example, are excitatory interneurons). In addition, not all inhibitory cells are interneurons; some brain regions have inhibitory projection neurons, for example the cerebellum (Purkinje cells) or striatum (medium spiny neurons).
Inhibitory cells are those that release inhibitory neurotransmitters, so they are best thought of as involving post-synaptic inhibition. Chandalier cells in cortex are a bit of a special case, because they synapse onto axons and interfere with action potentials that way, but I would not lump them in with presynaptic inhibitory mechanisms.
Sources of pre-synaptic inhibition
In general (because there may be exceptions, and almost certainly are in invertebrates who have very "weird" nervous systems from my mammal-biased worldview), presynaptic inhibition arises from three places: autoreceptors (self receptors), retrograde signalling from post-synaptic cells, and neuromodulation. One could fill textbooks with information on all the mechanisms, but I'll give one example of each of the three types:
Autoreceptors
Glutamatergic synapses, for example, can have pre-synaptic inhibitory metabotropic glutamate receptors. These are G-protein coupled receptors, not ion channels, and they typically respond when a synapse is very active. They are effectively a brake on over-activity: if a cell is firing too much, the effect of its firing will be decreased by pre-synaptic inhibition mediated by these self-receptors. This principle is common for other neurotransmitters, too. (Wu & Saggau, 1997)
Presynaptic inhibition by post-synaptic cells
Although we think of neuronal signalling as one way, that's not entirely true. Post-synaptic cells have mechanisms to communicate with the pre-synaptic cell, and this can include inhibiting that cell.
Endocannabinoids are one mechanism: they are released by the post-synaptic cell and can reduce pre-synaptic release probability (Maejima et al 2001; Melis et al 2004). At an excitatory synapse, that makes them inhibitory; at an inhibitory synapse, they would be disinhibitory.
Pre-synaptic inhibition by neuromodulators
Pre-synaptic cells can also be affected by local concentrations of neuromodulators, like dopamine (Bamford et al 2004). Dopamine isn't necessarily released directly onto a cell but more into the surrounding area. Dopamine D2A receptors, for example, are found presynaptically at cortico-striatal synapses. Release of dopamine in the striatum reduces glutamate release at those synapses coming from cortex.

Bamford, N. S., Robinson, S., Palmiter, R. D., Joyce, J. A., Moore, C., & Meshul, C. K. (2004). Dopamine modulates release from corticostriatal terminals. Journal of Neuroscience, 24(43), 9541-9552.
Maejima, T., Hashimoto, K., Yoshida, T., Aiba, A., & Kano, M. (2001). Presynaptic inhibition caused by retrograde signal from metabotropic glutamate to cannabinoid receptors. Neuron, 31(3), 463-475.
Melis, M., Pistis, M., Perra, S., Muntoni, A. L., Pillolla, G., & Gessa, G. L. (2004). Endocannabinoids mediate presynaptic inhibition of glutamatergic transmission in rat ventral tegmental area dopamine neurons through activation of CB1 receptors. Journal of Neuroscience, 24(1), 53-62.
Nadim, F., & Bucher, D. (2014). Neuromodulation of neurons and synapses. Current opinion in neurobiology, 29, 48-56.
Wu, L. G., & Saggau, P. (1997). Presynaptic inhibition of elicited neurotransmitter release. Trends in neurosciences, 20(5), 204-212.

That was such a great answer that I took my time to read through all references. Thanks! I have a last question: Isn't a simpler presynaptic inhibitory mechanism just having the following chain of neurons: (inh neuron) --> (excitatory presynaptic neuron) --> (postsynaptic neuron). In this manner, the postsynaptic neuron is stimulated less when its presynaptic excitatory neuron is inhibited, and the presynaptic inhibition is a network effect?

@Pugl That would just be post-synaptic inhibition of the cell in the middle. It's presynaptic to the final cell that you are calling "postsynaptic", but it's post-synaptic to your inhibitory neuron. Probably the best way to distinguish would be to say that post-synaptic inhibition is referring to cases where you reduce the firing rate/firing probability of a cell; pre-synaptic inhibition is when you influence synaptic release to change the effect of a cell firing, without changing the firing rate/firing probability of the (pre-synaptic) cell.

Stated another way, post-synaptic inhibition is affecting action potentials; pre-synaptic inhibition is affecting vesicle release.

Exactly, I meant presynaptic to the final cell, thx! And that's a great and very concise definition you gave.

@Pugl I'll add it to my answer.


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does Trichloroacetic acid remove fats from milk
I am trying to detect melamine in milk. As a part of preprocessing, I add 200 ul of TCA to 1 mL milk,and after filtration I get a clear solution. Does the filtrate contain fat. I feel I am having interference from fat even after extraction.

It is likely that the fats are present in both the filtrate and the ppt. because as far as I am aware this test does not distinguish fats/ lipids into micro or macromolecules...You find the macromolecules in the ppt. But the micro in the filtrate so yes, there is a chance of interference as you have concluded.


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Can changes of transposable elements in Drosophila be detected using RNA-Seq?
Not sure if this is the right forum for such a question, but please refer me to the correct one, if possible.
Does anyone has experience in working and detecting transposable elements using High-throughput techniques?
We would like to  identify the sequence of our TE and were wondering if this is possible via such methods (bulk- or scRNASeq)?
any ideas of others methods to run reach this goal would be appreciated.
thanks

With RNA-seq you will capture only retrotransposons. If that's your goal, then I would suggest enriching isolated RNA somehow,  (e.g. using microbeads that have a library of complementary sequences). Keep in mind: Some RNAseq workflows require polyadenylated RNA.
Why not use whole genome sequencing? Blumenstiel 2014
Or why not do something like this (it's just a quick idea, please back check with professionals):

Design multiple primers against Long Terminal Repeats or Terminal Inverted Repeats
Amplify transposons from Genomic DNA from drosophila
Excise Band from gel, extract transposon sequences of preferred size
Fragment DNA
Ligate sequencing adapters. Amplify. Your high throughput sequencing library is now done
Apply to sequencer

Please know that switching from bulk to single cell might increase your cost by a factor 50. (One cell costs very roughly 100 dollars, so sequencing 100 cells costs 10 000). So you need a good reason to switch to single cell.

thanks for the answer and also the link to the paper. It looks interesting.
I didn't plan on doing scRNA, it was just to know if this might be a better option than bulk.
Just to understand it better, you mention I can only identify retrotransposons with RNA-Seq. Is this because of the polyadenylation necessity?

RNAseq sequences RNA. It doesn‘t need polyA, necesserily. It only measures Retrotransposons since retrotransposons are the only transposons that are RNA at some point in their lifetime.

@AssaYeroslaviz  - note that the most differences between RNAseq and other NGS techniques lies in library-generation (includes e.g. reverse transcription). The sequencer itself always sequences a 'similar' DNA-library in the end that was ligated to adapters, no matter if the isolated source is mRNA, gDNA, miRNA, PCR-products, etc.


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Proteins in Milk, Oat , Eggs and Soy
I have read that there are proteins in oat which are similar to those in soy, milk and eggs. I know nothing about biochemistry, and I'm struggling to decipher the info i find..
the closest Ive got to an answer is albumin - which i believe to be a group of proteins, all present in the above?
Can you be intolerant to albumin? or a derivative of?
a simpilar version of the question - what is the name of the protein(s) found in milk/oat/eggs and soy, if any?
the reason for my question, my daughter has a milk/egg/oat (protein) intolerance and I'm just interested to find out if its a particular protein (or group of), or if its an intolerance to random things.
Many thanks!

Say, wouldn't this be better at chemistry.SE?

@MARamezani Cross posting is not frowned upon by the SE devs

Hmm, I've nothing but to say thanks @MarchHo! Still, this question asks about proteins that exist in milk, and egg, and oat, mainly. Let's leave it to see how it plays out. Unless an answerer directly points at intolerance issues that can rise, with referring to something other than what chemistry can answer, this question will be off-topic.

@MARamezani proteins are biomolecules, allergies are a biological mechanism, why would this be better on Chemistry than Biology?

Allergies are often caused by the immune system reacting to a part of a specific protein, therefore it is in fact a specific protein in the food that is causing the allergic reaction to occur.
Milk allergies are caused by casein and whey (Source: Mayo Clinic)
Oat allergies can be caused by avenin (Source: EJCI)
Soy and egg allergies are caused by their respective albumin proteins. Additionally, egg lysozyme can also cause allergy. (Source: Cleveland Clinic, Food Allergy)


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Why does agrose gel runs horizontally, and SDS-PAGE gel runs vertically?
It seems in electrophoresis, agrose gel always runs horizontally, and SDS-PAGE gel always runs vertically, why?

Be careful saying always, as in science you can rarely make an all-encompassing statement like that. Gels are traditionally run in those formats, but there are exceptions for a variety of reasons.

When you stand general agarose gel vertically, the gel is slippery coming out from the bottom; although, some run vertically.
To polymerize acrylamide, it is good idea to avoid air because oxygen inhibits polymerization of acrylamide. You would get an air tight condition, pouring acrylamide between glass plates, but how could you run gel made between glass plates. When you set such gel plates horizontally, how do you load samples? Then, it is easier to set gel plates vertically.

Yes, if you poured acrylamide into a horizontal slab mold it would take a very long time to polymerize, AND that top surface would dry out (unless you had a buffer layer on top of it, or plastic wrap, or similar).

Why does the agrose slippery out from the bottom if it runs vertically?

@sunboyharry Agarose does not adhere enough on glass plates to hold its position. I can not explain it via the physical and chemical properties, though.

Generally, one would want to run all the gels vertically to save the space. The gel slab has to either support itself or be enclosed in a supporting structure, like between glass plates. Simple agarose electrophoresis wouldn't benefit from enclosure into a precisely defined glass enclosure, and agarose is not strong enough to be run vertically - the slab will not support itself.
Thus PAGE gels are run vertically and agarose - horizontally.

To pour and run an agarose slab gel vertically the inner surface of the glass plates needs to be frosted (with microscopic imperfections).


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Would a stray ant re-home into a foreign colony (of the same kind) and will the colony accept an alien ant?
Let's say an ant got into my pocket as I was sitting in the park today. At home, I shook off my coat and the ant fell out and scurried out to my garden, which has ant colonies of the same kind.
Would the ant try to assimilate into that colony and would the colony accept it?
How would each know about the other's non-relation?
Thanks

Ant behavior is controlled by pheromones. They do not "know" things but an ant from a different would be recognized as a source of energy and probably killed and eaten.

With fairly high confidence, the ant would probaly be accepted. While normally ants live in colonies, you can move ants between colonies as long as they are part of the same supercolony. https://en.m.wikipedia.org/wiki/Ant_colony

If they are from a different species, they won't accept each other.
If they are from the same species, it depends of the species:

Some species won't accept any other ant born in a different colony, such as Lasius Niger
Some species form a supercolony which can gather ants from the same species over hundreds or thousands of kilometers, such as the Argentine ant on the coast from Spain to Italy.

To know more about ants, I advice this excellent book: Wilson et Hölldobler, The Ants, Belknap Press, 1990, (ISBN 9780674040755)


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Why are cells affected by time?
We as individuals die when we get old. But why are cells affected by time? We are constantly providing energy to the cells through food, but the cells die after a certain time. Why does this happen?

Anabolic processes vs Catabolic Processes. When you search on Google. what happens to cells overtime, there are many articles you can read through answering your question.

Sir if I do not get any vote stack exchange will ban me.

Individual cells don't live forever because they are damaged by their environment, for example by chemicals, radiation and mechanical wear and tear, or by other organisms (see this review). In multicellular organisms, such "worn out" cells are typically dismantled by programmed cell death and new cells are generated to take their place.
The life span of animal cells varies widely depending on their location and function. For example, epithelial cells lining the skin and intestines are exposed to a harsh environment, and consequently live only a couple of days. At the other extreme, neurons, which are safely lodged in the protected brain tissue, can live as long as the individual (or even longer).
Note that the life span of a given cell is very different from replicative age, which refers to the number of divisions a cell lineage has undergone, measured from some progenitor cell. Most animal cells are allowed only a limited number of cell divisions (known as the Hayflick limit) and thus their lineage is "mortal", while that of microorganisms are not.

Short answer: Not all cells do age and die, many symmetrically dividing unicellular cells are essentially immortal. In asymmetric species the occurs in many lines from the retention of old worn out cellular machinery. Triggered limited cell life only evolves later as organisms need to regulate multiple cells. It is likely a side effect of having cells specialize. However this origin is not conclusive, this is actually a vigorously debated subject in biology right now.

Can you cite some example of species where cells are considered immortal? I think life span is difficult to even define for unicellular organisms with symmetric cell division --- in one sense, such cells "die" in each cell division. For species with asymmetric division like budding yeast, cells generally age and die over time I think. See for example https://www.nature.com/nature/journal/v183/n4677/abs/1831751a0.html

"unicellular cells are essentially immortal" there's a search bar at top right corner (if you're on desktop version). Type "do bacteria die of old age?", hit enter and see what you get...

@another'Homosapien' Good catch I'll add a qualifier. symmetric dividing unicellular cells are essentially immortal. many asymmetric are not.

@Roland http://www.cell.com/current-biology/fulltext/S0960-9822(13)00973-1?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982213009731%3Fshowall%3Dtrue and https://www.ncbi.nlm.nih.gov/pubmed/20537537

@John, both of those studies actually claim that the cells studied have asymmetric cell division (defined by the old/new growth pole) and still do not age. That is very different from your statement "many symmetrically dividing unicellular cells are essentially immortal". My point was that the concept of cell age is meaningless if cell division is fully symmetric, as no cell is can be "older" than one division. (If symmetrically dividing cells would age and die, the species would die out ... )

@Roland I was just giving links for immortal lines, There is not a clear division between symmetric and asymmetric division it is a spectrum just like everything else in biology. Some cell lines are capable of both E coli is one of those. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010982/.

Regular cells are built to expire themselves when they detect too much damage (taking one for the team).
There are plenty of examples of cells that refuse to do so. Often, they're called cancer cells.

I love questions like this! my reasoning is that while cells certainly have processes and mechanisms that exploit entropy, the bitter reality is that eventually something like our own cells will be subjected to entropy and will ultimately die and be disassociated. Every second a cell produces ATP to survive it is put under more and more oxidative stress and this is why cells age and ultimately die. It is also why less metabolically taxing lifeforms like a plant, can live for hundreds of years, as opposed to a mouse, which lives for like 3 years (an animal with a high metabolism)
my english is terrible so in short: energy is oxidation, oxidation reactions are entropy favored, this causes things to age. higher metabolism = more oxidation = shorter lifespan. Plants dont get up and run so they can live longer than animals which do

Sorry, but it sounds like you don't understand entropy. All reactions are driven by increasing entropy (that's the second law of thermodynamics) and oxidation is not special in this regard. And this has nothing to do with (oxidative) damage to cells. Also, the life spans of animals and plants is irrelevant here --- the question concerns the cell level.

Think of it this way:  If you took the whole sum of reactions taking place in a cell over 24 hours would
That Total
Change in Gibbs free energy be positive or negative ? It is the natural progression for ordered systems to evolve to a disordered state. Perhaps I am wrong about the oxidative stress in a mouse vs that of a plant, but you are being pedantic and not looking at the bigger picture. Entropy is the sole reason why TIME MOVES IN ONE DIRECTION and it applies to everything cells, planets, laptops, etc.

No, I think your bigger picture is wrong. The entropy law does not explain why cells degrade and die, because cells are not closed systems. As long as a cell has an energy source, it can maintain its state forever as far as thermodynamics is concerned. Cells die for other reasons.

the question is why are cells effected by time? Don't reduce biology to "all or nothing" level of thought, oxidation is oxidation, regardless of its Intent (metabolic oxidation does release damaging radicals regardless of its intent ) it drives the dG to become even more negative as well as other external sources etc. you may bring in glucose for example but I am talking about the sum total dG. If not entropy to explain why time moves in one direction, then what do you think is the reason cells are effected by time?


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If a venomous snake somehow gets it's own venom in its body, will it be affected by it?
Here is a hypothetical situation I had been thinking about that sparked my curiosity:
Let's a snake is just slithering around, not being attentive for some odd reason. It happens to pass a mouse, in which it didn't see (this is all just hypothetical), and the mouse freaks out and starts to run. When it does, it trips over the snake's tail, and, not knowing what is happening, the snake snaps back bites the mouse and gives it a good dose of venom. (Now, to my question).If the snake ate the mouse, would it's own venom, now in the mouse, hurt the snake?
(Since they are native to where I live, let's say the snake is a Water Moccasin)

An excellent question.  This fun mental floss article addresses that question, but from the perspective of one snake biting another snake:
Snake on snake violence

“The conventional wisdom is that they have circulating antibodies in their blood,” says Stephen Mackessy, Ph.D., a Professor of Biological Sciences at the University of Northern Colorado and an expert in venomous snakes. “This would protect them from their own venom, as well of venom from another snake in their own species.”
Hypothetically, if a speckled rattlesnake bit another speckled rattlesnake, the immunity they’ve built from being exposed to low levels of their own venom—kept in glands behind their eyes and secreted when they bite—would protect them from a fatal wound. (Even though the glands are closed, they still contain blood vessels that allow the venom to circulate in their system, causing mild exposure, Mackessy says.) But a speckled rattlesnake that meets up with a cobra might have a different day entirely.

The same principle should apply to venom ingested in dead prey. Antibodies against the venom would protect the snake. For what it's worth, I think your way of phrasing the question is more interesting and relevant than the way it was phrased in the mental floss article.

Thanks! (If no one else answers, I will probably check mark this one)

@TheMattbat999 I think it's safe to say no one else is answering this one. If there is anything this doesn't address for you, let me know.

@DeNova I am so sorry. I totally forgot! I will accept it!


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Propagating errors for percentage reduction
Need a bit of help for this particular problem.
I have three averages collected from three genotypes (A, B, and C) and their associated SD (a, b, and c). A is my control.
I have been asked to represent the data as a percentage reduction as compared to A. How do I propagate my error?
Calculation:

% Reduction for A = (1-A/A)100%
% Reduction for B = (1-B/A)100%
% Reduction for C = (1-C/A)*100%

Thanks a ton!


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How to watch a Zebrafish embryo in detail?
How much microscope zoom would I need to watch the development of a Zebrafish embryo in certain detail? Thanks guys!

It might help if you clarify what you mean by "certain detail".

Observing the development of cord and eyes would be a good start.

From personal experience, it should be sufficient to observe zebrafish at 10-20x magnification for broad structural changes during development.  If your microscope has a 10x eyepiece, then that would be 1-2x zoom. If you are observing sub-cellular changes, you would benefit from higher magnification.


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What would happen to the body if it suffered no injuries?
In this (super cute) animation: 'Jinxy Jenkins & Lucky Lou' (youtube), the girl, Lucky Lou, is shown to be so lucky, she seems to have never suffered an injury. This is, atleast, what I get the indication of at 1:26 when she looks at her hand in a mixture of confusion and awe.
And this got me thinking, what kind of applications would it have for a human body, to live to about 20-25 without having ANY injuries happen to it? And I mean NONE, not even muscle aches, scraping of hands or knees, no nothing.
I may be wrong in this, but I have perhaps been led to believe that when an injury occours, whilst the body repairs itself, it also goes through some steps to toughen the injured area.
Would the body be noticably more fragile, or would it have virtually no effect?

It is a myth that injuries toughen your body. Broken bones and scars are not stronger than the original, and neither is any other injury beneficial. Have you heard the saying, "Whatever doesn't kill you makes you stronger"? That's optimistic nonsense. Sometimes what doesn't kill you leaves you paralyzed.


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properties of lamps for indoor plant growth
Ikea has a brand of hydrophonic start kits called vaxer. Part of their offering consists of lamps that aid in the cultivation of the plants (example1, example2 and example3). There are other companies offering lamps that should help plants grow. Here is an example on ali-express.
When I compare the lamps from ikea as well as others I find it hard to figure out what lamp may be preferable for my hobby projects at home. I recall seeing a documentary where it was suggested that plants prefer red and blue light because that is the colour they themselves do not emit back. This makes me wonder why the ikea lamps don't have these colors.
I'm new at this field but I may be interested in investing in some lights for some indoor hobbying. When considering this though, what are properties of these growth lights that are important as far as plant growth goes?
In my particular situation I am not concerned with heat but more the correct type of light and the costs of electricity.

You might find more people with expertise in this area at Gardening.SE

I am not a biologist, but I have read up on this a little bit. I recommend that you do a bit of research online at your library or online because it can get somewhat technical. There are several variables to consider. You are correct that the bulbs emit different colors of light. Plants species may have different needs for different colors during their growth stage & their flowering /fruiting stage. You should investigate what your plant needs. The amount of the light emitted by the bulb is measured in a unit called lumens- this is usually on the package. More lumens= brighter light. For indoor hydroponic, there are expensive lighting systems using a variety of bulbs & lamps, like fluorescent, halide & sodium, each with specific uses & (dis)advantages. One recent development are LED grow lamps. The LED's advantage is that instead of having 1 large heavy & hot light bulb like with a halide or sodium lamp, you have many little LED light that can come in different colors, allowing flexibility in different life stages. The LED lamps also consume much less electricity & don't create a lot of heat- but they are more expensive. OK, good luck with your project. Also, if you like hydroponics, learn about aquaponics, an offshoot of hydroponics that incorporates an aquarium into the system. The water flowing through the plant's roots circulates down into the aquarium and back up again, so that the fish poop helps to nourish the plants and the plants' roots act as a filter for the aquarium water, creating a type of symbiotic ecosystem between the plants & fish.

Vaxer is a total gimmick apparently. it's just cheap 1cents chinese LED's branded as IKEA grow lights at 15 euros... it's about 10w for 55w equivalent, 800 lumens,
Phillips currently sells 11w 100w equivalents for the same price. for 1520 lumens. Cree has a19 lamps which are less intense and which are 13w for 100w equivalent. in terms of money you can also buy red-blue 20w vac cob chips for 2.50USD and 50w vac cob chips for 3.00USD, to 50w dont last as long and are hotter.
Many home experiment comparisons have whites beating red/blue leds. There are no clear figures and research papers on the topic. it's all about efficiency for producing a PAR plant spectrum. Photosynthetically active radiation
You need penetrating LED's too, reflected PAR (Parabolic alu reflector) and unclouded diffuser to get best penetration into the plants.
Your best bet for efficiency is to get a white 120 lumens per watt light. Its a good way to achieve the PAR spectrum for plants. The plants may benefit from Green light for other pigments like Anthocyanin.


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What are the differences and similarities between fimbriae and adhesins in microbes adherence factor?
Adherence factors in microbes is to attach to a host cell or to an extracellular matrix.
So what is the difference and similarities between fimbriae and adhesins?

Fimbrae is a catch all term to denote the hairlike projections on many gram-negative and some gram-positive bacteria, but exludes flagella. Adhesins are a subtype of fimbrae that serve as organs of attachment to cells or mucosal surfaces. Another type of fimbrae are pili, functioning in conjugation, the transfer of DNA from one bacterial cell to another  (Koneman, I can't even find the year on this crazy book. Used to be the bible of determinitive bacteriology. So many hours.)


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Why does SDS-PAGE use for protein, and agarose use for nucleic acid?
My question maybe very primary, but after I learned this part, questions always follow me.
SDS-PAGE gel works for detect protein, agarose gel works for detect nucleic acid, so here is my question:
1. Why does SDS-PAGE works for protein, and agarose gel works for nucleic acid? Is it any possible to use SDS-PAGE to detect DNA? Or use agarose to detect protein?

Why does the SDS-PAGE gel always runs vertically, and agarose gel runs horizontally? Are they necessary?
Is any other material could be use in gel electrophoresis?

Mad Scientist explains why you would make different choices regarding size and desired resolution. Polyacrylamide gels can provide a higher degree of resolution for small molecules, you need to realize that proteins are small. A good-sized protein is around 400kDa., where as a 1000bp DNA molecule is 650kDa. Agarose pore structure is larger, so you use it for larger molecules like DNA. Another reason is toxicity. Polyacrylamide is a toxic substance, Agarose is a sugar, so if you can avoid using polyacrylamide, you do; sometimes you can't.

You can use polyacrylamide gels for RNA and DNA, and this is the common way to examine shorter nucleic acids. Agarose gels can be used for larger nucleic acids like plasmids that are a few thousand base pairs long, polyacrylamide gels work better for shorter nucleic acids around a hundred nucleotides long.
You don't need SDS for nucleic acids, they already have a negative charge at the phosphate backbone. Polyacrylamide gels for nucleic acids also don't use a separate stacking gel like in SDS-PAGE, it is just one single gel.

You just answered the first question, it makes sense to me, thank you. But could please answer the 2nd and 3rd questions?


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Why might food go bad in an oxygen-free environment?
I was recently watching a video from the International Space Station (Making a peanut butter sandwich in space), and I noticed he mentioned that a tortilla kept in an oxygen-free environment could last up to 18 months. Impressive, but it got me thinking: Why would some foods ever spoil if kept in a state where molds would not be able to grow? Would it be that other micro-organisms in things like the moisture present in the food eventually take their natural toll? Just a curious thought I had while watching through these awesome ISS videos.
Thanks for any answers!

First of all, you assumed that this tortilla went bad after 18 month, not that austranaughts just decided to eat it?
More importantly, there is thing called anaerobs. Just like your muscle don't use oxygen in times of acute stress (force requirement), so there are organisms that don't care much about oxygen. As it happens in muscle, it happens in yeast during fermentation when sugars are turned into alcohols and released energy is used to propel molecular machinery. So, if there are sugar molecules on tortilla, there are still microbes that willing to prosper on it.


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Where do all the NAD+s come from?
In the mitochondrial respiration (of plant cells) NADH is reduced from Nad+ as part of the TCA (converting malate to oxaleoacetate).
But where do the NAD+s come from?
The TCA cycle is working even in isolated mitochondrias by adding malate as a substrate, which indicates NAD+ must be present already.
I am also wondering if ADP and NAD+ can be transfered through the inner membranes of the mitochondrion without specific channels?

Reduce, reuse, recycle…

There is of course a pathway that synthesizes NAD+ de novo, usually from tryptophan, aspartic acid  or vitamin B3, or salvaged from compounds like nicotinic acid, nicotinamide. You can read more about it here: https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide#De_novo_production
The fact that TCA works in isolated mitochondria is not necessarily the effect of de novo synthesis. The reason for that is the cycle-like fashion of NADH production in the TCA and consumption of that NADH for electron-chain reactions (which recreate NAD+) or other reactions involving oxidoreductases. Redox reactions do not change the overall amount of the coenzyme. But in a living cell, some reactions will irreversibly consume NAD+, ADP-rybosylation may be an example. Still, the cell prefers the salvage pathway over amino acid pathway, because it consumes way less energy.
ADP and NAD+ cannot pass through the membranes without channels. Both are polar molecules and only non-polar molecules such as steroids can freely pass through the cellular membrane without any help from transport proteins.


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Can you do DNA seq with Microarray?
Is it possible to do the entire DNA sequencing with Microarray or would you have to use Sanger or NGS methods for that?

Microarrays generally capture gene products, such as mRNA (via cDNA), which have been extensively processed. Because of this, you lose genetic information such as introns or regulatory elements. In fact, what you'd end up with is the transcriptome of the organism, and it would be impossible to sequence the DNA from this. NGS methods are superior for this, still, and there is a good overview of the advantages of RNAseq over microarray here, for example. To sequence the DNA you will probably use NGS.

Source: JCI


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Can photorespiration do any good?
When CO2-levels are to low plants start to photorespirate instead of photosynthesise. This cost them losses in energy, and adds CO2 to the atmosphere instead of O2.
I wonder if the photorespiration is entirely "bad" for the plant or is there any beneficial outcome as well?

Honestly, I do believe that photorespiration has hidden advantages for plants. Yet, the answers to this question will most likely be primarily opinion-based.


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What is the difference between Regulatory Gene and Modifier Gene?
If both controls the expression of another gene by physically or genetically interacting with the target gene, which attributes make "Regulatory gene" different from "Modifier gene" or vice-versa?

Leaving a comment when down voting would help. I upvoted.

Different terms in different fields
I think that the two concepts are very similar but are used in different fields. The term "modifier genes" is often used in quantitative genetics and in evolutionary genetics while the term "regulatory gene" is often used in molecular genetics.
Example of a modifier gene that is not a regulatory gene
The concept of modifier gene can also be used in modelling when considering genes that "modify" the recombination rate (e.g. Otto and Barton, 2007; or other properties of the genome) in a quantitative manner. As such, a modifier gene is not really a regulatory gene (as it does not regulate the expression of another gene). As such I consider definitions like this one from ndsu as being too restrictive.
What I think about when I hear these terms
I would tend to think as a modifier as a more general concept than the concept of regulatory gene. Also, when I think of a regulatory gene, I think of this gene by the mechanism by which it affects other genes while when I think of a modifier gene, I think of the statistical effect of this gene on genetic properties of the organism.

Thnx for ur comment @Remi.b. Can it be that "regulatory gene" does not have any functional phenotype? It just can modify another gene? On the other hand "modifier gene" has its own functional phenotype and at the same time, it can have an epistatic relationship with another gene?

I am not sure I understood your comment but please see edit in my answer.


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Which spider species is this, and is it dangerous?
Sorry for a quite bad picture. I was afraid to get closer!
Seen in Croatia, inlands, not near sea. As he is on the picture there with the legs stretched out, I'd say he was about 8-10 cm in length.

It is a female, the males of this genus are quite distinct. The genus is Argiope, and the specific epithet most probable is bruennichi. It is not a clinically important spider.


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How can rapid growth cancer get nutrients in vivo?
When I was little, before I get into biological studying, I read a news talking about cancer would be totally cured after decades. I still remember that researchers had a theory to claim if they could limit the blood vessel generation near to tumor, then the rapidly growing cancer cell couldn't get enough nutrients and would kill them. However, this theory seems not to work well. Cancer cells or tumor still have another way to get enough nutrients to live, or at least, maintain themselves to survive and endanger the host. So, my question is how can rapid growth cancer get nutrients without blood vessels in vivo?

Long back in 1971 Falkman and others put forward new therapeutic implications of targeting blood vessels supplying nutrients to tumors.   Treatment you are mentioning is called 'Anti-angiogenic therapy '. However current challenges in this therapy are resistance to antiangiogenic agents and non specificity. Plus there was huge 'normalization effect' which was actually helping other blood vessels around tumor. To answer your question, Cancer cell makes their own blood vessels instead relying on host machinery. There are many other factors also why this kind of treatment is not successful yet.

Now, I do remember this saying... So there is impossible way to give "Anti-angiogenic therapy" to limit tumor growth? cuz it is so logical...

It is not impossible. This therapy needs more research :) Even in review which I cited in answer talks about how to tackle these problems.


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Measure of environmental impact on phenotype
Let me begin by disclaiming that I am nowhere near a biologist by competence or education and that I am simply interest in some of its fields of study as a matter of general curiosity. So excuse my ignorance.
I've been recently pondering the concepts of genotype and phenotype. This page succinctly summarizes the difference between the two.
I was curious if there are scientific measures, and how accurate they are, for the impact of environment on the phenotype of a specimen. Hypothetically, if the environment had no effect, the phenotype would be 100% determined by the genotype. But, in a simple approximation, phenotype = genotype + environment. Does modern biology have a measuring system for how much the environment affects the ultimate observable features of an organism, on top of what its genotype does?

In between a long comment and an answer...
For a review of the theory behind the causal variables of phenotype, one might want to have a look at Biology Why is a heritability coefficient not an index of how “genetic” something is?.
One can investigate the impact of a specific environmental variable onto the phenotypic variance but the environmental as a whole is typically computed as whatever is left when other sources of phenotypic variance have been explained. As such you might want to read about estimations methods for heritability and maybe esp. the post How do heredity and regression to the mean work with respect to intelligence?.

Phenotype is often discussed at a fairly coarse level. In biology classes we ponder simple genotypes from Mendelian genetics, and discern that the pea plant with the YY genotype bears yellow pea seeds.
Consider a suspension of tumor cells being grown in a petri dish, however. A fairly straightforward way to asses the phenotype of the cells is by confocal microscopy
Say you grow the same cells, but some at normal oxygen and some at lower oxygen. Refer to the following figure:

In B, the investigators are using fluorescent antibody label, as you'd use in flow cytometry, to perform confocal microscopy. At 1% oxygen for up to 21 days, the phenotype of the same cells profoundly differ (reference). Flow cytometry can also be used to identify difference in phenotype that arise from environmental factors.
Take for example T cells isolated from you blood. I can change the phenotype based on surface receptors detected from flow cytometry, by adding different cytokines to the culture medium. If I add interleukin-12, I'm most likely to differentiate my T cells to discernibly type-1 helper or cytotoxic cells. I can tell due to the presence or absence, or abundance of markers such as CCR5 or CXCR3.
And if you sequence these cells, you get the same material. Epigenetic changes are harder to wrap your head around. In the hypoxia example, the lack of oxygen is thought to change the phenotype by modifying the way the cell machinery can access and express key genes associated with the hypoxia phenotype.
The take home point here, is that in order to discern the techniques that are available to you, it's important to define the system you're researching. For example, I have no idea how they determine the environmental impact on animal species. But, I can sit here and rattle off techniques to analyze single cells or systems of cells.


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Has lamarckism been discredited?
Lamarckism is a pre-darwinian theory according to which an organism's traits acquired to adapt to the environment are passed onto its offspring. A couple of years ago, I attended an event with Richard Dawkins and Jerry Coyne, both preeminent evolutionary biologists, in which I remember them agreeing that it is basically B.S. and that acquired traits don't get passed but instead propagate themselves through natural selection. As a non expert in biology, it does not make sense to me that acquired traits would make their way into the genotype and then get passed on, which coincides with what Dawkins was saying. But I am a non expert.
I also have read a few things about epigenetics and it sounds strangely similar to lamarckism. Steven Pinker also discusses all these things in The Blank Slate and he gives a notion that thare is some idealistic ideology behind promoting ideas that we can radically change an organism by environmental conditioning and "save" those changes into the genotype. He says that ideology is to justify government programs aimed at rapidly enhancing mankind whereas natural selection, which proponents of such ideas may deem reactionary, simply is not so optimistic.
My questions are:

Is lamarckism, or inheritance of acquired traits, been conclusively discredited?
What does lamarckism relate to epigenetics

Can you provide any example suggesting that Larmackian inheritance is not discredited? Also perhaps search here at https://biology.stackexchange.com/search?q=lamarck and see if your question is answered by anything you find there?

I dunno if it has or not, that's why I'm asking

SE Biology is a question and answer site about biological problems that are capable of objective answers. A question on whether a theory has been discredited does not fit this bill. If I say "yes, all of my scientific colleagues agree", then I am only expressing an opinion. A better question is "is there any evidence for Lamark's claim that (e.g.) by stretching its neck a giraffe elongated its neck and this caused a change in the DNA of the gametes that was inherited by the next generation". It is up to the proponents of a theory to provide evidence. There is plenty for Mendelian genetics.

The question is interesting at many levels. Of course, in biology and in any other science there is no absolute or 'objective' truth about some given phenomenon if we really care to look at the nuances. Lamarck seems to be vindicated mainly by a wave of empirical work on patterns of transgenerational inheritance, particularly in the field that is known as epigenetics. You can read a good intro-level review here for some recent developments, some particular examples here, or a more conceptual reading here.
As an evolutionary biologist myself, I will say that most other biologists acknowledge that epigenetics and transgenerational inheritance are important and have solid empirical support, but (for various reasons) some of them are hesitant of calling that 'Lamarckian'.
By the way, Dawkins was a very effective science popularizer, but he does not practice science nowadays, and many of his ideas lie in what is known as 'scientism', which is a blind confidence in science as an absolute truth that is inflexible. The same applies to many positions of Steven Pinker, deGrasse Tyson, etc.

@baca the comment is relevant because the OP explicitly mentions them. And I'm discussing their ideas (i.e. scientism) because it is important in the context of the question (just as discussing Lamarck's ideas).

Dawkins is pretty straight forward about absolute truth not existing in science, his positions it is merely the best way of collecting and assessing knowledge we currently have, which most scientists would agree with.


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Do any animals prepare food?
I was just wondering if any animals (are smart enough to) enhance the flavor of their food by, for example, mixing ingredients or seasoning or letting it cure in some ways. In the first episode of Life (on Netflix), they show a monkey who dries some oily nuts for a week but that's just to make it easier to break the shell. But do any animals prepare their food in any way similar to human cooking?

You should accurately define what you mean by any way similar to human cooking. For the moment it is unclear whether you example from episode of Life would be a good answer or not. Maybe you are interested in the use of heat in order to pre-digesting food before consumption.

Any form of changing it from the raw state

Then, the answer is in the question! Yes, monkeys for example dry nuts until the shell is easier to break. I am voting to close as unclear.

Though I know how this sounds, it's true: my dog would steal duck eggs and bury them here and there (I sometimes came across them in my garden), and when, according to her own mysterious tastes, the buried duck eggs had reached their peak of "fermentation", she'd unearth them and eat them in the garage (thereby offending our olfactory sensibilities.) That was an animal capable of shopping (there were other kinds of eggs) and preparing food. Short of busting a fire, that's not so different from cooking. I'm sure other animals do similar things.

Your question consists numerous questions: 1. Are animals smart enough to prepare foods? 2. Do animals prepare food? And by prepare, I think you're asking about A. cooking, B. seasoning, and/or C. modifying (e.g., like the monkey you describe).

My horse will "prepare" hay by dunking a mouthfull in her water trough, swishing it around a bit, and then eating it.

Bees make honey and then eat it.

And she's now taught the other horse to do the same thing - or he's copied her.

Some animals do like;
Ants prepare their meat not by heating but by marinating it with digestive enzymes to create a glistening protein slurry. With their hourglass figures, adult ants have such tiny waists that solid food can't pass through to their abdomens. Biologists already knew that the blob-shaped larvae predigest meat. Some scientists had suggested that the adults feed meat to the larvae and return later for some regurgitated protein slurry.
some animal chew and regurgitate for their young, monkeys have been observed washing potatoes, and other animals bury and allow food to rot before consumption.
But cooking is certainly unique to humans. There’s no other species that does it. There’s obvious reasons for that because we’re the only ones that can make fire which is a pre-requisite. In a away fire comes first and cooking becomes a process after it. It’s becoming clear that really cooking provides quite a number of advantages. Richard Wrangham from Harvard has been doing a lot of experiments looking at how cooking can change the nutritional value of food. What it seems is that the process of warming food up: in a sense denaturing it has a number of effects. One is that food is much more tender. That we know. If you eat a cooked carrot instead of a raw carrot it’s much easier. We can spend less time chewing, we can swallow it faster and we can digest it faster. It seems that it’s an extension of things we see in other animals. Animals who use techniques often in their stomachs to tenderise food seem to try and make it more easily absorbable. If we turn to the other question of when all this happened the real question is when do we first find evidence of fire? That seems to be about half a million years ago or so. We don’t find direct evidence of cooking then but we do see over the next 100,000 years or so the beginnings of things like burnt stone which suggests that meat is cooked. It’s probably goes quite a long way back in our evolutionary history and some people would argue it’s really a very major change in the way we are able to live and survive.
The second possible advantage for cooking is that it improves digestion. We’ve done a model study here particularly with Zhongquan Sui when she was here – she’s now at the University of Perdue. She found that yes, cooking does to a certain extent improve digestion. You only need cook something for a fraction of the time that you actually do in order for it to be digested properly. The cooking times that people adopt when they normally say this is cooked seem to reflect strong mechanical changes in the food. In other words, these are things that affect you perception of food texture and allow you actually to eat it very much easier, very much shorter eating times than you would do if they’re raw. That I think I would give as the essential answer at the moment.

References:

http://www.sciencenews.org/view/generic/id/6910/title/Ant_Iron_Chefs_Larvae_fix_dinner_but_dont_sneak_snacks
http://www.thenakedscientists.com/

It would be good if you cite an article from a scientific journal rather than a popular science site. These sites would have cited to the original study, if not then the blog cannot be considered trustworthy.


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Why are viruses considered microbes?
My question is simple. Why is a virus considered a microbe? Considering a microbe is considered to be a "living" unit of life, which viruses are not.

"Life" is either a) arbitrarily defined or b) poorly defined.

Who considers a microbe to be "a living unit of life"? Do the people who use the word "microbe" use strict scientific definitions of life? In my experience, "microbe" is not a scientific term (although it may have been one once), it's a folklore word for "tiny bugs which make you sick". When a grandma tells her grandchild "cover your mouth when you sneeze, you're spreading microbes everywhere", she neither knows nor cares whether a biologist would classify the microbes as alive. Your question seems to need no biologic answer, but an epistemological one.

I think these sort of questions arise because we are generally too lazy to properly define terms. I've asked a similar question before: "Why isn't a virus alive"? We need to carefully define "life" every time it's brought up: Genetic code? Membranes? Ability to replicate? High cognitive power? Each has problems & caveats, but without a measurable feature, it's a moot discussion. I'd suggest reading The Seven Pillars of Life by Koshland, 2002.

Some recently identified viruses are considered alive due to their more complex organisation such as mimiviruses. Take a look at This it's pretty interesting.

What is a microbe?
A microbe (or microorganism) is a microscopic organism. Anything that is considered alive and that is small enough is called a microbe.
Note that this definition has two issues.

There is no universally accepted definition of life.
There is no universally accepted size threshold for being called a microbe (to my knowledge). I would go with a threshold of about $10^{-5}$ meters.

Is a virus a microbe?
A virus IS and IS NOT alive depending on the definition. Note btw, that the definition of what is alive is not a matter of Biology but a matter of Philosophy. Most of the time, viruses are considered as not being alive. It is important to understand that the definition of life has absolutely no impact on biology and is nothing but a question of nomenclature.
If you want to call a virus a living thing, then yes, viruses are microbes. As stated on the wiki article:

Some microbiologists also classify viruses (and viroids) as microorganisms, but others consider these as nonliving.

You can find a discussion of why viruses are generally considered as not being alive here.
Unit of life
The concept of "unit of life" has not much meaning in biology and, to my experience, is most often used as a nice image for teaching young students what a cell is. Most of the time that I heard of "unit of life" (mostly when I was in secondary school and eventually high school) was used to describe a single cell making up a multicellular individual such as a cell of your blood for example and not a unicellular individual.

Viruses are not alive until they are inside the body of the host organism (plant or animal). Viruses are active once they are inside the host and reproduce inside the host. They are a link between living and non-living.

Viruses are small bits of genetic code in a protective covering. Viruses are not "alive," that is, they cannot replicate, unless they are inside another organism. A virus is definitely too small to be seen without a microscope. Since viruses are so small (tinier than bacteria) they may be considered microbes. However, since they are not "alive" outside of a host organism, it is debatable whether they are really organisms at all. For convenience since they are neglected in other areas of biology, viruses are discussed in microbiology. Most viruses are known because they cause disease.

The claim [some organisms] are not "alive," that is, they cannot replicate, unless they are inside another organism is pretty bas IMO because following this logic, an endosymbiont cannot be a living thing. Plasmodium wouldn't be a living thing for example. Note also that stating Viruses are not alive reduces the discussion to a single definition while several exist (it has the advantage to highlight the result most common definition though)

@Remi.b: My personal definition, as a theoretical ecologist, is that if you can meaningfully study its ecology and evolution, then it's alive. :) That easily includes viruses. Of course, if you define "ecology" and "evolution" broadly enough, that definition can also cover a lot of things we would not usually consider alive, such as languages and ideas. I'm not really sure if that's an argument for or against it.

@IlmariKaronen As a theoretical evolutionary biologist, I like your definition! However, it is not the most common definition. In any case, I think pretty much everybody agrees that excluding from the realm of living things, everything which reproduction depend on other life forms is quite a bad idea!


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Affinity Column of membrane bound receptors
I understand affinity columns can be used to study the ligand/enzyme affinity. But is an affinity column able to be used for membrane bound receptors? I

This is a classic reference where Stanley Cohen and Graham Carpenter used an affinity column made out of the epidermal growth factor (EGF), and used it to purify the EGF receptor: JBC 1980

Purifying Challenging Proteins
So this is definitely something you can do, but first you need to express proteins that have a tag the affinity column is going to recognize. You can engineer a 6x his tag pretty standardly, but the procedure I'm looking at says a long 8-10 his tag might be better for insoluble proteins. You also want to be careful to place the tag at the C-terminus to avoid messing with the membrane anchoring signal at the N-terminus.
You can express these in bacteria, for example, and you'll disrupt the membrane and solubilize the proteins of interest using detergents. You have to be careful here because while some of the solubilized proteins can retain their native conformation in solution, harsh treatment with detergent can remove critical lipids affecting stability.
The purification step for his tags involves an affinity column of immobilized nickel, which binds to imidazole on histidine. After pushing the associated binding, wash and elution buffers through the column containing the sample, you should in theory have your purified protein product. You elute by washing imidazole through the column, which should competitively displace the his tag and wash the protein of interest out.
Should you lack tagged protein to begin with, you'll need to use a number of purification steps like gel filtration, ion-exchange, etc., and a little knowledge about your target protein to get a good purification though, like it's ligand for affinity binding. Give that presentation a read through!