text:
How do the brain and nerves create electrical pulses?
The information between the brain and peripheral nerves is sent via electrical pulses or signals, How then does a non-metallic human cell manage to conduct an electrical
signal?

This question has brought up a discussion on meta.

I would argue that if someone is so "expert" as to be driven away by a question like this, then good-riddance. Sure, you want to stay on topic, but come-on! This was a terrific question, and a REALLY informative and well thought out answer. A little less technical than the ideal? possibly, but closing it is an overreaction.

@Dr.Dredel please see the discussion on meta and comment there

This is quite a big question! I'll try to outline the basic view.
First, let's review how neurons signal between each other. The canonical way for a neuron to send a signal to a downstream neuron is by generating an action potential, the "electrical impulse" you have heard of. This action potential causes the release of neurotransmitter at a point where the two cells are very close to each other called a synapse. The downstream postsynaptic cell receives the neurotransmitter signal and converts it into a small electrical signal. If enough of these small electrical signals happen in a short time, they sum together and are likely to initiate an action potential in the second cell and the cycle repeats all along the circuit.
How is the electrical signal generated? The basics of how this works was worked out most famously by Hodgkin and Huxley in 1952. The short story is that the plasma membrane is selectively permeable to ions. Let's build the concept from the ground up.
The toolbox

Imagine a sphere of plasma membrane that represents a simple neuron. For starters, we assume that this membrane is bare lipid with no membrane-associated proteins. Because of the hydrophobicity of the bilayer, charged particles cannot diffuse through the membrane.
The cell is bathed, inside and outside, in a solution containing many ions (charged atoms), including sodium (Na+), potassium (K+), chloride (Cl-), and calcium (Ca2+). As we noted above, these ions cannot go through the membrane without "help".
Now we add an ion pump protein into the membrane which will pump sodium ions out and potassium ions in. This particular pump, the Na-K ATPase, creates an excess of sodium ions outside the cell and an excess of potassium ions inside.
Now we add a potassium ion channel to the membrane. This protein creates a pore in the membrane that only allows potassium ions through. This particular protein's pore is always open. Now things start getting exciting...
What do the potassium ions do now that they can go through the membrane? Ions will move based on the forces created by their electrochemical gradients. The pump created a chemical gradient by putting excess K+ inside, so the K+ ions start to flow out through the ion channels. But K+ ions are positively charged, so when they flow out, positive charge starts building up outside and negative charge builds up inside. This electrical gradient opposes the chemical gradient, tending to pull the K+ ions into the cell while the chemical gradients pulls K+ ions out. The influx and efflux reach an equilibrium at the Nernst potential, where the electrical and chemical forces equal out. For physiological concentrations of K+ ions, the K+ equilibrium potential is about -80mV or -90mV. This means that K+ ions will flow until the outside of the cell is 80-90mV more positive than the inside of the cell. We started at 0mV, so K+ ions mostly flow out.
We now have a membrane potential, a difference in electrical potential between the inside and the outside of the cell at about -80mV (usually closer to -70mV or -60mV in "real life"). In particular, this membrane potential is the resting potential that exists when the cell is not active. We can simplify for now and think of the resting potential as being set by a resting permeability of the membrane to potassium ions, but not to sodium ions. We call this membrane polarized, and thus depolarization is when the membrane potential becomes more positive, and hyperpolarization is when the membrane potential becomes more negative.
Now, we add to the membrane a voltage-gated sodium channel, an ion channel that passes only sodium ions but is usually closed. The voltage-gating means that this ion channel is sensitive to the membrane potential. At the resting potential, the pore is closed and the membrane is still impermeable to sodium ions. When the membrane potential becomes slightly more positive, the channels opens and sodium ions can flow. This channel is also inactivating, so that when it opens it only opens for a short period of time, letting in a limited amount of sodium.
What way will sodium flow when we open this channel? Because of the negative resting potential (-70mV) and the excess of sodium ions outside due to the pump, both the electrical and chemical gradient will drive sodium ions into the cell. The sodium equilibrium potential is usually around +60mV.
To complete the machinery for generating an action potential, we also add a voltage-gated potassium channel to the membrane. It works just like the voltage-gated sodium channel that is also closed at rest and opens when the membrane potential becomes more positive. This channel opens a bit more slowly than the sodium channel does, but it does not inactivate.

Generating an action potential
Ok, so how do these parts come together to create an electrical impulse?

The cell sits at its resting membrane potential, with all of its voltage-gated channels closed. It receives a signal from an upstream cell that causes a slight depolarization. The action potential will initiate when the membrane potential hits the threshold potential.
At the threshold potential, the voltage-gated sodium channels open letting sodium ions flow into the cell. The sodium flux pulls the membrane from the resting potential (-70mV) towards the sodium equilibrium potential (+60mV). These values are far apart, so the driving force is large and the membrane depolarizes rapidly. This is the action potential upstroke.
The depolarization also activates the (slightly slower) voltage-gated potassium channels. The potassium ions flow out and drive the depolarized membrane (about +20mV at the action potential peak) back towards the potassium equilibrium potential (-80mV). At the same time, the sodium channels are inactivating so that sodium is no longer depolarizing the membrane. The repolarization rate is usually slower than the depolarization rate. This is the action potential downstroke.
The whole process of the action potential depolarization/repolarization cycle takes about 2-3 milliseconds in an "average" neuron. Once the cell reaches resting potentials again, the membrane is basically reset. The voltage-gated channels are turned off. The ion pump moves the potassium ions that flowed out and the sodium ions that flowed in. That patch of membrane is ready to fire another action potential!

As a final note, I'll mention that the voltage-gated sodium channel provides a mechanism for the action potential to propagate down the axon. The action potential is initiated in one location of the cell, and creates a depolarization. This depolarization causes the voltage-gated sodium channels in neighbouring regions of the membrane to open and generate an action potential cycle of their own. This is how an action potential travel down axons (and sometimes dendrites too).

In the answer above, I simplify and say that the resting membrane potential is the potassium equilibrium potential. This is generally not the case, with most resting potentials sitting somewhat more positive indicating the involvement of more ions/channels than just potassium. Yes, resting potentials do vary between cells. I take -70mV or -60mV as my "rule of thumb" resting potential because it generally holds for many primary excitatory neurons such as hippocampal and cortical pyramidal neurons.

That's very interesting, but I'm really wondering when you write "we add" what does it mean? Is there some helping cells giving needed ions to the neurons? Is it somehow transmitted throw the way the neural signal goes (during the impulses)? Or are the nutritions just released into the cerebrospinal fluid like a hormones?

@Probably I'm building a simplified model of a neuron in the answer. When I say "we add" I mean "add this to your mental model of the parts of the system".

Yes, I understand, thanks, I was just asking more into depth. Luckily, I've asked this question already and got this good answer here: http://biology.stackexchange.com/questions/37317/how-do-neurons-receive-the-ions-needed-for-creating-electrical-pulses

So, let us introduce some keywords.
The "electrical pulse" that "is sent from between brain and nerves" is called an Action Potential (AP). This is then propagated along a nerve fiber until the target organ.
Basically, a neuronal cell has a body and several long extended structures that "sprout" from the cell body. Dendrites receive signals from other cells and they convey signals towards the cell body by creating small electrical currents. The axon is a single "sprout" that is usually much thinner and longer than the dendrites and it conveys action potentials from the near the cell body to target cells and organs. Some axons can be as long as 80-90 cm (imagine!)! At the place where axon leaves the nerve cell body there is a small protrusion called the axon hillock.
The AP originates at a special part of the axon called the axon initial segment (AIS). The initial segment is the first part of the axon as it leaves the cell body and sits immediately after the axon hillock.
The electrical pulse is the short electrical discharge, that can be seen as a sudden movement of many charged particles from one place to another. In our cells we have ions of Na+ (sodium), K+ (potassium) and Cl- (chloride) (and in some cases also Ca2+) that constitute these charged particles.
There are two types of driving forces for these particles: besides the potential gradient, e.g. the difference in the total charge in two different places there is also another force called concentration gradient, e.g. the difference in concentration at two different places. These force can point into opposite directions, and thus by exploiting one force (let's say concentration gradient) we can influence another one.
What we need here again is a so-called semi-permeable membrane, this is just a barrier for ions, but only for specific ones. We need this because our main ions -- Na+ and K+ -- are both positively charged. Therefore the cell membrane acts as a semi-permeable membrane, letting K+ into the cells and Ca2+ ions outwards but not the opposite. Therefore we have two concentration gradients: Na+ (outside is the peak) and K+ (inside is the peak).
In order to start the pulse we need to initiate a massive ionic drift from one place to another. This is done by the cell, and the first event here is the drastic change (increase) of the permeability for Na+ ions. Na+ ions massively enter the cell and their charges, moved into the cell, form the upstroke of the action potential.
The protective mechanism of the cell immediately start working against the Na+ invasion and open the reserve shunts -- the K+ channels. K+ leaves the cell, taking away some charge and this is revealed as the decay of the action potential. But potassium channels are generally slower, that is why the decay of the pulse is more steady, not as sharp as the upstroke.
You might be wondering now: what triggers the rapid change of membrane permeability then? There are several factors here that may contribute into this process.

Potential change of the membrane. Sodium and potassium channels are voltage-sensitive, meaning if you manage to change the resting potential of the membrane, formed due to concentration gradients and normally being about -90..-80 mV (millivolts) up to about -40 mV it will trigger the sodium channels. This is how the impulse propagates -- having originated at one place it just decreases the resting potential of the adjacent membrane area, sodium enters the cell there and the AP travels along the nerve. The AIS is the site of AP initiation because this part of the cell has a very high density of voltage-gated sodium channels.
Chemical agents, called neurotransmitters, can be detected by receptors on the cell membrane. Some of these receptors are ion channels themselves and open directly when neurotransmitter is bound. Other receptors act through intracellular signals to open ion channels. This is how the signal appears at the sites of nerve cell contacts -- neurotransmitters, like acetylcholine or adrenaline, just act here as triggers for membrane permeability.

Nice overview, but I wanted to mention a few clarifications. Do you mean axon hillock instead of axonic hill? Also, it is in the axon initial segment (slightly further along the axon than the hillock) that AP initiation actually takes place. Dendrites are shorter but usually larger in diameter than axons. I would use the word neurotransmitters instead of mediators.

@yamad: You are absolutely right! Just feel free to edit my post. I am not a native speaker and haven't written anything about biology for quite some time, so my vocabulary can be rusty and imprecise. Thank you for your corrections!

No problem! You speak/write English better than most native English speakers. Just made some substantial edits to try to make things clearer. Hope it helps.

Thank you for your warm words! I usually go over through my posts next day to polish them up, I will integrate your remarks soon.


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When does Coelom form exactly?
Related to my other question.
I know that the coelom is derived from mesoderm.
Coelom seems to form during organogenesis within 3rd and 8th week of embryogenesis.
However, that answer is not either enough exact or it is wrong.
I am reading the thing in Kimball 5e and Gilbert 9e, but cannot find an exact mention about the thing. I know for sure that the coelom develops within gastrulation and organogenesis, since it is forming from mesoderm.
When does coelom form exactly?

What species you have in mind?

@MartaCz-C It is not specified in the question given to me. Probably chick and human. I am not sure whether human's abdomic cavity can be classified as coelom so unsure about human

In humans, the coelom forms by the splitting of the lateral plate mesoderm, which occurs during weeks 4-5 (Sweeney, 1998).
Sweeney, LJ. 1998. Basic Concepts in Embryology. McGraw-Hill.

source: Stack Exchange

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

sort: votes


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What forms the human amniotic sac?
I am trying to understand the formation of embryonic disc for human and chick so the following question is related to here about formation of embryonic disc.
I had thought that the amniotic sac forms only from embryonic disc in humans, particularly of lateral mesoderm and ectoderm of embryonic disc. However, my thought seems to be wrong as my professor says that amnion form only for birds from embryonic disc, but from many different parts besides of embryonic disc for human.
What, besides the embryonic disc, forms the human amniotic sac?

In humans, the amnion (amniotic sac) persists from the primitive amniotic cavity1.  One side of this is formed from the cytoblast (a prismatic epithelium) and the plasmodioblast.  Together these two layers are the ectoplacenta or chorion.  They are also referred to as Rauber's layer.  These replace the lining epithelium of the uterus, whereupon internal cells undergo atrophy to create the amniotic sac.2
The other side of the amniotic sac is formed of the epiblast/ectoderm (internally) and the hypoblast (externally).  Within the epiblast the other layer is comprised of prismatic cells whereas the inner layer are flattened (the hypoblast/entoderm).  This double layer forms the bilaminar blastodermic membrane.2
I'd really reccomend that you borrow the referenced books from your university library as I found the diagrams much easier to understand than the text.

1 Gray, Henry. "Embryology: Formation of Membranes." Ed. Robert Howden. Anatomy Descriptive and Surgical. Ed. T. P. Pick. 15th ed. London: Chancellor, 1994. 90. Print. Colloquially Gray's Anatomy
2 Gray, Henry. "Embryology: The Ovum." Anatomy Descriptive and Surgical. Ed. T. P. Pick and Robert Howden. 15th ed. London: Chancellor, 1994. 82-83. Print. Colloquially Gray's Anatomy

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Are CN3, CN7, CN9 and CN10 the only Parasympathetic Cranial Nerves?
It has been my thought for a long time that this is the case, but I am unsure currently, since the parasympathetic tract of colon sigmoideum does not seem to have connection with CN 10. It connects with pelvic splanchnic nerves.
Discussion about it here.
If there is no connection from pelvic splanchnic nerves to CN 10, like CN 10 running within the nerves, then my though must be wrong.
Are CN3, CN7, CN9 and CN10 the only Parasympathetic Cranial Nerves?

Yes, only III, VII, IX, and X are cranial nerves that carry parasympathetic autonomic neurons. The key phrase is "cranial." Pelvic splanchnic nerves also carry parasympathetics, but they arise from the pelvis, not the brain.

Thank you! I was confused by the definition of the word itself "cranial". Parasympathetic Cranial Nerve only means parasympathetic neurons that arise from the brain. So the elements of brainstem like the lower parts of Medulla Oblongata still belongs to the brain.


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How Do Acid and Base Loving Plants Get Enough PO4?
Acidic and Basic soils experience phosphate sequestration through binding with either calcium, aluminum, or iron. How do plant that thrive in acidic and basic soils obtain the necessary phosphate? Blueberries are an example that I particularly enjoy.

Thanks to the University of Hawaii for posting this picture.

Phycology would seem to be an ideal place to study mechanisms of phosphate absorption at varying pH.

Why is pH6- pH7 the highest range for P availability ?It seems to me like the lowest.

@biogirl it would be because the phosphorous is more likely to dissolve in water at this pH than to react with iron, aluminum or calcium. This makes it available to the plant since it cannot absorb insoluble compounds.

Fixation of phosphorous occurs when the chemical equations tip in favour of less soluble compounds. Plants are able to absorb Orthophosphate ions, such as H2PO4- and HPO42-.

Orthophosphate is most available to plants at pH values near neutrality. It is believed that in relatively acidic soils, orthophosphate ions are precipitated or sorbed by species of Al(III) and Fe(III). In alkaline soils, orthophosphate may react with calcium carbonate to form relatively insoluble hydroxyapatite:

3HPO42- + 5CaCo3(s) + 2H2O -> Ca5(PO4)3(OH)(s) +5HCO3- + OH-

Environmental Chemistry, Seventh Edition -Stanley E. Manahan
This does tend to make it more difficult for plants to obtain their phosphorous when it is stuck to something that they cannot absorb, but it is not hopeless. These equations are equilibria, so they can be made to go both directions by adding or removing reagents from each side.

The plants will pull from the left side of the equations by removing the orthophosphate ions. More will be released to maintain the equilibrium.
In acidic or basic environments, rainwater will serve as a base or acid to push the equations from the right.
Decaying organic matter releases orthophosphates that the plant can absorb.

In this way, plants living in acidic or basic environments would still obtain enough phosphorous.


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Is it possible to make bacteria vulnerable to antibiotics it's resistant to?
Since bacteria becomes resistant to antibiotics after an unfinished course, is it possible to do anything to be able to get treatment with the same antibiotic again, and reverse the resistance in the bacteria?
Or, the bacteria with the resistance will stay resistant forever (until death)?
Edit:
There are some websites that are claiming that some natural remedies might be effective, like taking "Honey", which doesn't seem to be medical facts.

This question doesn't have any claim associated with it, but rather wants to know if a certain biological process is possible, I think that because of it this question should be on Biology.SE and not here..

Perhaps it is useful to first consider how resistance is gained:
If you treat a population of bacteria with an antibiotic, some may die and some may live.
If none die, they are obviously resistant.
If all of them die, then all of them were sensitive, meaning that the size of the population and the variation were not large enough in order for some of the bacteria to be resistant. One approach would be to try to get larger genetic variation by inducing mutations with some mutagen. In addition, you can take a larger population. This would in effect let you sample a larger part of the genetic space to see if you can find a resistant strain. Of course it is possible that this will not work.
If some die and some are resistant, the situation is slightly more complicated. One possibility is that those which lived are genetically resistant (their DNA is different). To see if this is the case, you take those which lived and treat them again with the antibiotic. If they all live, they are resistant. Another possibility is that they are scholastically resistant. This phenomenon is known as bacterial persistence. What happens is that there is a genetic switch that randomly bestows resistance in some fraction of the population, let's say 10 percent. If you now take this population and reapply the antibiotic, only 10% of the population will survive. This interesting mechanism allows the bacteria adapt more quickly, since they do not have to make modifications to their DNA.
I am guessing that if the bacteria are genetically resistant, they will stay resistant. If the bacteria are scholastically resistant, it might be possible to affect the genetic switch which causes the persistence. This, in addition to reducing the size of the population, might cause a situation where none of the bacteria in the population are resistant long enough to survive.

You've explained how bacterial resistance develops, but you haven't explained how it might go away (except an allusion in your description of bacterial persistence).

@dd3 Sorry about that, I misread the question. I will edit it slightly and will keep it just since it might be useful for someone.

Just an addition to the above answer........ In cases where resistance is because of overexpression of a certain gene such as an efflux pump, because of promoter mutations, the WT will outcompete the mutant because of the latter's additional cost of gene synthesis. In cases where a receptor mutation causes insensitivity to a drug then perhaps the mutant may underperform in processes where the receptor is vital. And WT can outcompete the mutant. If there is no trade-off for a mutation then it wont go away

Bitwise has explained how antibiotic resistance develops in bacteria.  To address how it might go away: as long as the antibiotic is around, there is selective pressure on the bacteria to preserve the parts of their genome that confer antibiotic resistance.  If, for example, some bacteria developed mutations that made them no longer antibiotic-resistant, these bacteria would die, and thus, only the antibiotic-resistant bacteria would reproduce.
For antibiotic-susceptible bacteria to develop and persist, you'd need to take away this selective pressure (no more of the antibiotic around to kill the antibiotic-susceptible bacteria) so that there would be no particular advantage to carrying non-mutated copies of the antibiotic-resistance gene(s). Of course, the natural rate of mutation is not that high, so I think it would take time for antibiotic-susceptible bacteria to reappear (unless there was a mutagen around).
EDIT: antibiotic-susceptible bacteria would become more prevalent if there was a way to select for them, over antibiotic-resistant bacteria. For example, if there were conditions under which maintaining antibiotic-resistance genes becomes unfavorable, antibiotic-susceptible bacteria would reproduce more often/faster (see the term fitness), and thus become more prevalent. However, this does not change the mutation rate - only selects for things that have already evolved.

The other answers describe the situation well for an individual, however there have been cases in the past where antibiotic resistance has emerged and been outgunned by medical advances to overcome this specific resistance.  A good example of this co-amoxyclav.
The original Amoxicillin, a  β-lactam antibiotic, was previously effective against a good range of bacteria.  However antibiotic resistance then developed when some bacteria began producing  β-lactamase, an enzyme which degraded the  β-lactam ring rendering the drug (and all within its class) useless against them.
This resistance was then countered when a way to inhibit the β-lactamase the bacteria were producing was discovered.  Clavulanic acid does this, leading to the mixture of its potassium salt with Amoxicillin.  The mixture (coamoxyclav) allows the amoxicillin to still be effective against the previously resistant bacteria, as the resistance they have been developed is being inhibited in parallel.
For this reason in a hospital setting it is more common to prescribe Co-amoxyclav rather than a beta-lactam antibiotic in isolation.


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Why do we have oncogenes?
Oncogene is a gene which in certain circumstances can transform a cell
into a tumour cell.
Everything we have has reason and meaning.
Or there was some use in past.
What's the reason for we have oncogenes?

"What's the reason for we have oncogenes?".... Because they are essential for cell division. Please do some research before posting a question.

@WYSIWYG Implemented on 1st comment. Why are they essential for cell division? I thought they cause cancer.

@WYSIWYG Found this on wiki " Most normal cells will undergo a
programmed form of rapid cell
death (apoptosis) when critical
functions are altered. Activated
oncogenes can cause those cells
designated for apoptosis to survive
and proliferate instead." Also, >An oncogene is a gene that has the potential to cause cancer. Nowhere written for normal body functions.

Found >An oncogene is a cancer-causing gene. We have about 20 thousand genes in each of our cells, some of which are involved in fostering or promoting cell proliferation. When one of the proliferation-promoting gene suffers damage, it begins to urge the cell to proliferate uncontrollably rather than to do so in carefully measured amounts. Such a damaged growth-promoting gene is an oncogene.> on another site.   http://www.talkabouthealth.com/what-is-an-oncogene-and-what-does-it-have-to-do-with-cancer

A hyperactive allelic variant of a proto-oncogene is an oncogene (except for the virally encoded ones. It is all a stupid nomenclature). Highly expressed proto-oncogenes can also cause cancer. Since it is a variant, it cannot be grouped separately. Basically a good gene gone rogue. You have these genes that help cell proliferate which can mutate to become hyperactive. I cannot blame you here. It is a bad definition.

Whatever be the definition (of either oncogene/proto-oncogene), please clarify your question. Perhaps something like "what functions do (proto-)oncogenes have in a normal cell?" But please include some research in the question. Do not use comments to provide that clarification.

From wikipedia

A proto -oncogene
   is a normal gene  that could become an oncogene due
   to mutations or
   increased expression. The
  resultant protein encoded by an
  oncogene is termed oncoprotein.
  Proto - oncogenes code for
  proteins that help to regulate cell
  growth and differentiation.

So, we actually do not have oncogenes. Instead we have proto-oncogenes.
Due to mutation or virus, these are converted into oncogenes.
Since, proto-oncogenes are required for normal cell division and differentiation, they are necessary. Also, these can change to oncogenes any time. So, we always have to live with probability of this conversion.

Given that you wrote and answered your own question so close in time I'm suspecting this is just a rep grab. This post should be a community wiki, and you should also credit material, rather than just stealing it.

Credit must be properly given where it is due, regardless of the source.


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Why do RNAi pathway proteins exist in the nematode when they can cause them harm?
When dsRNA is injected in plant, Dicer cuts it and prevents disease.
Why would the plant parasite, M. incognita - a nematode,  die when dsRNA was injected in it? It should have saved it.
Again, to be more clear M. incognita has Argonaute protein and other RISC components for eliciting RNAi. This causes its death.
Then, why does the worm have such factors which cause its death?

There are many studies that have used RNAi against the plant parasite M. incognita. The fundamental idea is that RNAi is directed against one of the vital genes of this nematode. Since, RNAi causes downregulation of the target gene, the nematode dies (or becomes ineffective in infecting) because of the loss of function of these important genes. As you might know about the process of RNAi, dsRNA (or hairpins) are cleaved by Dicer and the small single stranded RNA products, called siRNAs, associate with Argonaute proteins to form RISC (RNA induced silencing complex). The RISC will cleave RNAs complementary to the siRNA.
If you see any of these articles you will notice that the dsRNA is not injected into the nematode; it is expressed in the plant. Nematodes (such as this one and C.elegans in which it is quite well studied) can take up dsRNA from the environment via the RNA transporters present in their cell membranes (See this post).
Now, coming to your question on "Why do RNAi pathway proteins exist in the nematode when they can cause them harm?"
endo-siRNA and miRNA mediated silencing pathways have critical roles in the nematode development and other miscellaneous functions (See this review). As you already know, RNAi can also serve as a defence against dsRNA viruses.
It is us, humans, who have exploited this pathway to develop tools for molecular biology and for targeting parasitic organisms. There is certainly a likelihood that the host plant may express the dsRNA against the nematode during the course of the evolution of its anti-parasitic defence system (it is however not the case now). Not just RNAi, there are many other examples of endogenous pathways of a pathogen being exploited to kill the pathogen.

"See This review" actually solved my problem.  Thank you. You are really great.

@AnubhavGoel "How do you get such links? "..... because of some years of experience.

@AnubhavGoel perhaps we can talk about this over chat.


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Why is the internal capsule dark in this transverse section of the brain?

Why is the internal capsule dark in this transverse/horizontal section of the brain?
If it is white matter, then why isn't it white?
P. S. : Formalin was used for fixation.
Why the same color was not for remaining white matter.

Short answer
White matter is called white matter because it is relatively white compared to gray matter. However, in fixated specimens it is not as snowy white as in textbook pictures.
Background
The internal capsule is a paired V-shaped structure that is visible in horizontal brain slices (Fig. 1). It is a subcortical structure mainly consisting of fiber tracts connecting the cortex to the brainstem.

Fig. 1. Horizontal (transverse) brain slice showing internal capsule. source: Utah University
In Fig. 1 the structure is quite white'ish, but in the following two images you can see it is not always the case.

source: The Human Brain: Chapter 5: The Cerebral Hemispheres

Fig. 3. source: Medicos Notes
As you can see, the internal capsule is not always nice and white. Fig. 2 particularly shows a reddish taint of many white matter structures.
The internal capsule is well-vascularized (Schamann, 2003) and strokes in this region are associated with muscle weakness and loss in sensory sensitivity (source: Stanford Medicine). Hence, the red coloration may well be due to red blood cells that have not been completely washed out of the brain beore it was fixated. Also, non-specific coloring may happen over time in fixated specimens and many fixation artifacts can occur that lead to alterations in gross morphology (Chatterjee, 2014).
References
- Chatterjee, J Oral Maxillofac Pathol (2014); 18(S1): S111–6
- Schamann, Stroke (2003); 34: 2264-78

That is fine and something that is obvious.  Can you please be little more specific, why is it grayish (its not reddish)?  What was effect of formalin on internal capsule and tapetum only, and not on remaining white matter?

Hard to say,  really. Was it formalin treated? How old is the prep?  How often was it used?

In aged fixed tissues, red blood cells appear much more brown than red, though I am not sure if that's a likely explanation here, I am not familiar with @AliceD's suggestion that the internal capsule is particularly vascularized. In general, the specimen pictured does not look like it is in great shape. There is very little color distinction between white and gray matter, for example. It's possible some of the change in coloration is simply because of the orientation of different fiber tracts and the resulting susceptibility to drying/aging, really more of a texture difference than color.

It was fixated in Jan 2016 using formalin.

It was used last year for one month and again this year for one month.

@AnubhavGoel I'm surprised it looks so bad after that little time, but maybe it was not as fresh when initially fixed - just in general, it does not look good. Was it stored in formalin, too, or in ethanol?

@AnubhavGoel - I'm also surprised by the bad state it is in. I think this is part of the reason the coloring may be off

@BryanKrause It was Stored in formalin

@AnubhavGoel I think it is typically thought to be better to preserve tissues long-term, especially brain, in ethanol rather than formalin (after intial fixation in formalin/paraformaldehyde). Long-term formalin storage can essentially "overfix" the tissue. I'm not certain that is what happened here, but without seeing the tissue before and around the initial fixation that's my best guess.


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Which enzyme curdles milk in human infants?
Following, this question -
Do humans produce rennin?
Rennin does not exist.
And
What inactivates pepsin in infants?
Rennin exist.
What do I know is-
Rennin is found in calves and acts on milk to curdle it.
Pepsin acts as rennin at pH of 6-6.5 and curdles milk.
Humans have pepsin, in infants as well as adults. Pepsin can perform both functions in humans.
So, in infants, is curdling of milk done by rennin or the rennin like activity of pepsin?

@JM97 I read that answer before, but it says rennin exist in infants while in my question I am following a link which advocates, it does not. In, this post I wish to culminate both these, link together what really perform this function.

@David Please dont make this post duplicate to 2 posts that advocate 2 opposite things..

@Anubhav Please see the EDIT in another homo sapiens answer.

@AnubhavGoel — The two posts that between them certainly cover your question do not advocate anything. They ask questions. The answers may express different opinions or assumptions, but that is par for the course. It would perhaps be better if those two questions were merged to provide a more useful single resource, but that may be difficult to do now. You are asking for a clear cut answer when the answers to the other questions indicate there isn't one. I suggest you read them carefully and take from them what you can. Then it hardly matters which your post is classed as a duplicate of.


text:
Does sperm weight causes sex ratio?
Chromosome X in female sperm is heavier than male Y chromosome. Does it causes difference in fertility of sperm and heavier female sperm is unable to fertilize better than male sperm?
This is given in AK Jain of physiology, chapter on reproduction.
I doubt this explanation.

Probably not! There are certainly some physical reasons to doubt it. Looks like the mass difference between X and Y sperm is on the order of 0.1 picograms: X chromosome "weight"?
First, mass differences are not likely to affect swimming and motility of sperm, because sperm are at low Reynolds number -- the forces of fluid drag vastly overwhelm inertial forces. See, e.g. Purcell's lecture "Life at Low Reynolds Number" (http://aapt.scitation.org/doi/abs/10.1119/1.10903 but also available online). For this reason, even much larger differences in mass are not likely to matter to swimming.
If motility is not the issue, you could imagine that, during the fertilization or insemination process, sperm might be under the force of gravity, leading to different sedimentation rates. A sperm's sedimentation speed is equal to the force on it divided by its friction coefficient $\gamma$,
$$v_{sperm} = \frac{(m_{sperm}-m_{displaced}) g}{\gamma} $$
where $g$ is the gravitational acceleration and $m_{displaced}$ is the amount of mass displaced by the sperm. You can estimate $\gamma$ with Stokes' law (https://en.wikipedia.org/wiki/Stokes%27_law) as about $6\pi R \mu$ with $R$ being the sperm size and $\mu$ the fluid viscosity. We're interested in the maximum possible difference in speed, so we'll choose $R$ to be at the small scale of sperm size, $5$ microns and $\mu$ to be that of water $\mu \approx 0.01 \frac{g}{cm s}$. This gives us $\gamma \sim 10^{-4} g/s$. The difference between $v_X$ and $v_Y$ is then
$$v_X - v_Y = \frac{(m_X - m_Y) g}{\gamma} \approx 0.01 \,\textrm{micron}/s$$
This means, for there to be a significant difference between X and Y sperm you'd have to keep them sedimenting under force for quite a while. This can be used (especially in a centrifuge, where you can increase the gravitational force) to select between genders - but it seems unlikely to happen in vivo.
To see why this is a small speed in practice, you have to ask whether the sperm would also have diffused a larger distance or managed to swim while it was sedimenting. Sperm velocities are on the order of tens of microns per second, so anything that changes the sperm swimming speed by even 0.1% is more important than the mass difference in sedimentation.
Putting this together, it suggests that mass differences are not a likely origin for sex ratios slightly deviating from one - if they are tuned, it would make more sense to change sperm length or swimming stroke. In fact, I believe there are some small geometric changes between X and Y sperm - but could those geometric changes happen simply because there is less chromosomal material in the Y? That, I'm not sure.

It would be better to add this : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440662/

Thanks JM97 for link. I would have accepted that as answer.


text:
How many almonds a day can cause toxicity for vitE?
Vit E in high doses is dangerous for tissue. How many almonds a day taken regularly can cause this?
RDA
Males : 10mg/day
Females : 8mg/day
Pregnancy : 10mg/day
Lactation : 12mg/day
15 mg = 33IU for vit E
Requirement increase for higher intake of pufa
Pharmacological dose: 200-400 IU/day

Almonds contain  hydrocyanic acid, apparently as much as 25 mg/kg (8mg/kg standard deviation). However, it would take at least 2 kg of almonds (roughly 1650 kernels) to reach a lethal dose, which is highly unlikely to be digested unintentionally. You may die before vit e toxicity.


text:
Do Asian giant hornets (Vespa mandarinia) prey on other nests of Asian giant hornets?
Asian giant hornets are known to attack nests of other bees and wasps, but should they encounter another nest of their own, would they attack it?

Yes. According to this clip uploaded to YouTube on the Smithsonian channel, Asian giant hornets will attack and pillage other nests (of Asian Giant Hornets) if no other food source is readily available.


text:
How to find mutations related to disease for a protein?
I have done research on the protein (CYP3A4). I have its function, purpose and diseases (breast cancer, prostate cancer, testicular cancer, lung cancer). I am however having trouble finding the mutations of the protein and how it correlates with the diseases, specifically breast and prostate cancer.

What is your question? If you want to know more about the protein the way to go is to read papers about it.

Where do I find such papers

Does anyone know about my question and can help?

Pubmed, Google Scholar... As it is written, your question is just too broad (also unclear because there is no real "question"). Please clarify and narrow it down to focus on a specific issue.

I think I understand what you are asking so I will make a little guide to find what you need:
NOTE  the mutations you are searching for are probably on gene level so you can search your protein on Uniprot and then use the gene name to search on DisGeNET, you typ in the gene you are searching for:

Then you hit the search button and this will give you a result like this:

You can see that this site uses a sort of text-mining, in other words it is searching for the gene name associated with disease in articles. The score is an indication for how good the text-mining "worked". As mentioned in the manual:

We have developed a score to rank the gene-disease associations
  according to their level of evidence. DisGeNET gene-disease
  association score takes into account the number and type of sources
  (level of curation, model organisms), and the number of publications
  supporting the association. The score ranges from 0 to 1.

Then you have to click the browse details... in the down right corner. This will guide you to another summary page like this:

(NOTE I omitted a lot of rows to avoid huge images in the answer, so there will be more rows in your result). Because you were interested in prostate cancer I will click on Prostatic Neoplasms:

You can click on the 3 to obtain the 3 articles where the combination of the CYP3A4 and Prostatic Neoplasms was found. This will give you a list like:

As you mentioned in your question

"where do I find such papers"

You can easily click on the PMID this will guide you to the article, for example the first article:

CYP3A4 polymorphisms--potential risk factors for breast and prostate
  cancer: a HuGE review(link).

I think this will help you to find the papers related to the protein + disease, you can further read the papers to find mutations which cause these diseases.


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What is the evolutionary advantage of menstruation?
I was wondering why woman have fertile periods. Based on some simple reasoning I would expect that if woman were always fertile this would increase the chance of reproduction(one of the important things in life). But having menstrual periods would decrease this chance because only the period close to ovulation would result in fertilization.

So why did evolution result in woman having menstrual cycles?

Related http://biology.stackexchange.com/q/21715/3340

Human female ovaries only have a certain number of ova; none are manufactured in adulthood. Once they're gone (that's when menopause occurs), they're gone.
You can also ask, why did evolution result in a limited number of oocytes then? This kind of second guessing of physiology is endless.
In your scenario, an ovum would need to be released every few days in order to be fertile continuously. That alone would decrease the number of years that a woman could be fertile. Since a fetus needs about nine months to gestate, I think once a month fertility is more than adequate. The earth's population is already too large, which also translates as successful reproductively.
If a fetus could gestate in a month, I could see an advantage to constant fertility. But the disadvantages would also be great. How could a woman take care of so many babies? How could she possibly feed, say, six to nine babies a year with only two breasts? (Mammals that frequently have larger litters have more mammary glands.) How could her own body compensate nutritionally not only for the burden of feeding the fetuses but also of the babies?
Asking why didn't something evolve from a teleological standpoint rarely results in a satisfying answer. If constant fertility were advantageous, maybe it would be present.

But there are animals which don't have these cycles, so probably there should be another reason why we humans (and some other animals) got these cycles and others did not

@RickBeeloo - Are there mammals who don't have estrus cycles? Do these other animals physically care for their young through to near adolescence (age of "adolescence varies from species to species)?

Humans don't have estrous cycles, they have menstrual cycles (https://en.wikipedia.org/wiki/Estrous_cycle#Differences_from_the_menstrual_cycle ) so yes there are definitely mammals which don't have estrous cycles which is another good point in evolution (why menstrual cycles  and not estrous cycles or visa versa) @anongoodnurse

@RickBeeloo - Did I say humans had estrous cycles? I asked if you knew of any mammals that didn't have estrous cycles. You said, "But there are animals which don't have these cycles...". Since insects are actually animals, I know with great certainty that there are animals without estrous cycles. What you don't know doesn't make your argument more effective. There is no significant difference between menstrual and estrous cycles reproductively. One bleeds the excess endometrial tissue, the other reabsorbs it. Resorption may help avoid predation.

Yess I know there are animals which don't have estrous cycles and that's the whole point. Why are there mammals (like humans) which don't have an estrous cycle and mammals which do have estrous cycles, in other words what would be the advantage of having a menstrual cycle instead of a estrous cycle? I don't understand your confusion? @anongoodnurse

Reread my comment (which you did not answer); your question most certainly was not why do some mammals menstruate while others have estrus cycles (that's not "the whole point".)

@RickBeeloo you're talking in circles. Answer anongoodnurse's first comment.

Are there mammals who don't have estrus cycles? Yes humans. Do these other animals physically care for their young through to near adolescence (age of "adolescence varies from species to species)? Take snakes there is evidence that they take care of their offspring(https://www.reference.com/pets-animals/snakes-care-young-a731de15970742e4) And if I'm right snakes don't have cycles

The question asks about menstrual cycles. This answer going around the question because it conflates menstrual and estrous cycles.

@NickSandor - the original question did not mention menstrual cycles. It asked about periodic fertility. I answered the original question.


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Paired-end illumina sequencing
I'm tying to understand the mechanism of paired end illumina sequencing, however I dont't  understand why index primer 1 and index primer 2 are used.
paired end illumina sequencing (YouTube).

What do you mean with index primer 1 and index primer 2? Do you mean the barcodes? They are necessary to separate your samples after sequencing. Or do you mean the long adapters which are attached to your samples?

That's the problem hahaha, I saw on the video that they are only 3 basepairs long @TheGreenOne

Then you also did not recognize that it was not really scaled as the remaining part should be about 250 bp long for one direction.

Let me begin in the sample preparation to explain you the index primers.... and let me assume please that you want to sequence amplicons like 16S. Let me further assume that you have 96 samples, which means that you have one complete PCR plate full of samples. First you prepare your samples. You are doing a amplicon PCR, clean that PCR, attach the adapters which are necessary that the sequences can bind to the glas slide and at last you are attaching indexes.
You are attaching these barcodes individually for each sample.
Looks like that image:

source: https://www.neb.com/~/media/Catalog/All-Protocols/C411AB12AFB04000BED567FC17B2A4AA/Content/PCRPlate.jpg

Let's call such indices barcodes (index = barcode). As you can see, each sample gets its own combination of a indexing primer as you are using always to primers (i7+i5) for each sample. Whats important is, is that all these primers are individuals like:
Line:
1: AAAAAT
2: AAAATT
3: AAATTT

and:
A: TTTGGG
B: TTGGGG
C: TGGGGG

(In reality these primers are longer and more complex!)

After you have done such a indexing PCR and also cleaned your PCR (get rid of the polymerase, something like this) you have to pool your samples (put them all together) before you are sequencing. And thats the point why such indexes are important. Without indexing you would have no chance to get your samples separated (=demultiplexed) again after sequencing.
When you are sequencing paired-end then you are sequencing one time forward (barcode + adapter + the sequence you want to have) and one time reverse (barcode + adapter + the sequence you want to have). One big amplicon of e.g. 500 bps gives you two sequences: the forward sequence (also called forward read) and the reverse read.
Let's call the forward read: R1
And the reverse read: R2

After sequencing you have one big pool of sequences. What you are doing first is to demultiplex your samples. As you know now you have for each samples hundreds of thousands of sequences: each consists of two Parts: The R1 read and the R2 read. What you are doing now is to separate your sequences again: You know that you used for example the indexing primers AAAATTTT and CCCCGGGG (just examples!) for your first sample. So you know that AAAATTTT belongs to the forward (R1) read and CCCCGGGG belongs to the reverse (R2) read. This means, that, when you separate all sequences which contains at the "barcoding/indexing-position" these sequences, you know that these are sequences which belong to your sample 1. For sample two you used for example the barcodes AATTAATT and CCGGCCGG and then you know again: AATTAATT belongs to the R1 read and CCGGCCGG belongs to the R2 read. Filtering that sequences out and save them in an additional file you will get your sample 2 separated. And that's why such indexes are important and that's also the reason why you always have to indexes: one is used for the forward read, and one for the reverse read.
Additionally: Why basically we have to use primers is the following: If you want to sequence an amplicon you (or at least the machine) is only able to sequence about 250 bps in each direction. When you are attaching indexes (which are in each case needed) then you are able to sequence in both directions: forward and reverse. And afterwards, when you have demultiplexed your samples you can run an assembly to put the forward and reverse reads together again.

great explanation! Thank you so much @TheGreenOne


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Embryo development terms
I'm trying to couple the following terms:
cytoplasmic determinants, induction, positional information, hox genes, pattern information, morphogenisis, determination and differentiation.
I hope someone can explain me the connection between these terms,
thankyou,

When in doubt go back to definitions I say (as I am now).
cytoplasmic determinants: regulatory molecules located in specific distributions around egg cytoplasm
Induction: process by which the presence of one tissue influences the development of others
positional information, signals cells about its relative position to other cells.
hox genes
Differentiation: the process of a cell becoming a specialized type of cell through regulated gene expression
Determination: process by which portions of the genome are selected for expression in different embryonic cells
Pattern formation (aka morphogenesis) → events that determine the spatial organization of an embryo
Hox genes establish anterior posterior axis and regulate gene expression.
I would change,
cytoplasmic determinants → differentiation via determination → pattern formation (rather than information)
morphogen lead to pattern information (since these are the signals)
hox genes → morphogens → pattern information → pattern formation


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difference between motifs, domains, patterns, signatures and profiles
I can't get clear the difference between those terms, I see them a lot while browsing on Prosite, Pfam, Expasy e.t.c.
However, I can find documentation about them, but It still not clear what the difference is between those terms. I think it's something like:

motifs: Short residu stretch, not an indication of homology
domain: Could contain motifs, howevever most of the time is bigger, it can be used to identify homology if two proteins share a domain.

However I can't fit the patterns and profiles in this list.

Looking at the documentation you provide, I think that I can provide definitions for those terms as defined by EXPASY. Note that those definitions may just be an in-house system that EXPASY uses that you can't generalize to other databases for instance.
First, in section I.C of the documentation, they write "The use of protein sequence patterns (or motifs) to determine the function(s) of proteins is becoming very rapidly one of the essential tools of sequence analysis."
So it looks like for them patterns = motifs and motifs = patterns. Note again that "pattern" appears to be a somewhat informal term. I would certainly say that it is confusing that they use them as synonyms, but they do at least define them as such.
Second, I think that they are using the word "profile" in a very narrow technical sense, with regard to the way that they detect homology between proteins. The standard way to detect homology between proteins is using programs called Hidden Markov Models (HMMs). In section II.B, they write "A profile or weight matrix (the two terms are used synonymously here)...". So a profile is really just a weight matrix derived from a HMM that can be applied to any given alignment to figure out whether or not it matches homology. They go on to give an example of how this weight matrix is applied.
In simple terms, how the HMM works is that you give it a bunch of sequences that you know belong to the same family, and it will try to learn the frequencies of amino acids at each position and what order they come in. This model of the amino acid frequencies is the weight matrix they talk about. Then you make sure that the HMM works well (gives high scores for proteins in the same family, low scores for proteins in different families), and then you can apply the program to try to find new homologs.
Hope that answers the Q.

Thankyou, however It's not really clear what the difference is between patterns and domains? Because domains are also used to determine homology? @Maximilian Press

@Rick Beeloo, the scope of the question appeared to concern the definitions of profile and pattern. Nonetheless, the answer may be found again in the docs: "There are a number of protein families as well as functional or structural domains that cannot be detected using patterns due to their extreme sequence divergence; the use of techniques based on weight matrices (also known as profiles) allows the detection of such proteins or domains." So it seems that the domains are identified using the patterns/profiles.

I think it's like this:
signatures:

domains (which are detected using profiles)
motifs = fingerprint = pattern

Where motifs are short stretches of residu's which can be part of a domain, but don't have to be part of it.
Domains are functional unitits of a proteïn (which thus can contain motifs).

this is what you mean? @Maximilian Press , I couldn't wirte a structured summary of your answer so I wrote a new answer. However I will check yours as the problem solver don't worry

yes, I believe that is right- sorry, for whatever reason I was not alerted by this newer comment.


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Are there organisms which have compartments of different body temperature?
I was wondering if there are organisms which have compartments(inside the body) with different body temperatures. To clarify are there organisms which have tissue/organs which are surrounded by something (other cells, tissues) which have an other temperature.I'm not talking about fluctuation in body temperature, such as in ectotherm organisms. I have never heard about something like this and nor I could find information or articles about this (the reason why this question doesn't provide much background research). However I'm still wondering if there are organisms like this (or at least come close to this)?

Ps. please edit this question or comment if you can provide more background information regarding this topic

How broad is your definition of "compartment"? For example, in animals with external, scrotal testes, that compartment is a few degrees colder than core body temperature.

I was more looking for compartments inside the organism, I will clarify that in my question thankyou!! @kmm

I'm not specifically refering to something just in general so yes it could be a cavum/cavity for example @Hallur

A number of predatory fish - swordfish, for instance - keep their brains & eyes warmer than the rest of their body: https://www.newscientist.com/article/dn6861-swordfish-heat-their-eyes-for-the-hunt/

As @kmm suggested, the scrotum is a common "compartment" that is commonly a few degrees lower than the core temperature.
A key concept is the core temperature. That's only in the core.
I'm not sure if I understand your use of "compartments". Can an arm or a leg be a compartment? By definition, it is. A compartment is a section. A body part fits that definition.
Decades ago, I realized something fascinating about body parts and body temperature.
I had rescued a pregnant Siamese cat. In the litter she birthed, every kitten was a light ivory color everywhere. Over the next few weeks, the limbs, ears, tail, and face of each kitten darkened. At the time, my field was Molecular Biology, and my theory was simple: coloration in this breed was due to a temperature-sensitive enzyme. The kittens had come from an environment that had a constant (the core) temperature throughout: the uterus. Therefore a lower-temperature-sensitive enzyme would be inactive. After birth, their extremities were cooler, allowing the enzyme to produce melanin in the newly growing hair.
While I couldn't prove it in my cats, after some searching I found that someone else had already proven it in similarly colored rabbits.
So, yes, different sections (or compartments) of the body can have different temperatures.
 See Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus), Lyons LA, et al. Anim Genet. 2005.

I don't understand your kitten example because if all kittens were completely Ivory then this wouldn't suggest a different body temperature at different compartments (if only half of the kitten was black and the other half is Ivory I would understand this example)? The fading is more likely a transition from "cold" to "warmer" instead of compartilization

@RickBeeloo - I've added an explanation. Does it make more sense now?


text:
Why are not both alleles knocked out at the same time in knock out mouse?
I was reading this little 'article' about homologous recombination and knockout mouse. According to this article you first remove embryonic stem cells from a gray-fur blastocyst, then insert the construct and place them back into the blastocyst. Further the text states:

A knockout mouse has had both alleles of a particular gene replaced
  with an inactive allele. This is usually accomplished by using
  homologous recombination to replace one allele followed by two or more
  generations of selective breeding until an breeding pair are isolated
  that have both alleles of the targeted gene inactivated or knocked
  out.

However what I don't get here is that we have cells from an embryo, and thus have cells with both alleles. Hence, the regions surrounding these alleles will be homologous, so why would this step result in heterozygous (and thus require selective breeding afterwards) instead of homozygous mouse direcly?

It is a simple matter of probability. If the probability of replacing one allele is p then the probability of two alleles getting replaced would be p2 (note that the latter will be smaller because probabilities are less than one).
If you have a selectable marker such as GFP then you'll end up selecting both heterozygotes and homozygotes but the frequency of the former will be much higher especially when you consider the fact that the probability of homologous recombination mediated knock-out/in is very low in mammalian cells (10-7 – 10-5). Therefore, inbreeding is an easier way to obtain homozygotes than screening the ESCs. Moreover, selective breeding is inevitable because in the first round will just produce chimeras (not all ESCs are replaced with the modified ones).
Technologies like CRISPR are now being used to accelerate the rate of gene replacement.

Thankyou, I have one additional question. Why would you not just replace all ESCs? Or is this simply not technically possible?

@RickBeeloo It would be very challenging. Almost impossible.


text:
Infer distance since duplication from tree?
Question
I have a really simple question, but I'm not able to figure it out.
I made a tree (using BLOSUM62). Here is a part of the tree:

How can I calculate the distance till the duplication event occured between HBD en HBB?

just for HBB 36.21 and for HBD 38.79
or 38.79 + 36.21 = 75

More info
I determined if this set of sequences follows a molecular clock, and indeed this was the case. So I determined the rate at which these sequences envolve. If I can determine the distance between HBD and HBB I can devide this by the rate to obtain the time since the duplication event happened.

How could you calculate this one?

Assuming a molecular clock, the distance between the sequences and the duplication event is 75/2 = 37.5. Ideally, these sequences should have the same distance from the internal node (under a clock), and you could use a model that explicitly assumes a clock -- which will lead to ultrametric trees.  One example is the program promlk (or dnamlk) from the phylip package. A faster alternative would be the  UPGMA method, which also gives you an ultrametric tree.

How could you calculate the one from the image I added? Because this one is before another duplication event.

In this case, and in general, I strongly suggest you to use a method that forces an ultrametric tree -- that is, a (rooted) tree where the sum of branch lengths to the root node is the same for all leaves. In your newly added figure there's more than one way to weight the nodes (assuming, of course, a clock). You could or  find the avge distance of the first internal node (191+151/2) and then do the same again (result +38 is one and 182 is the other), or calculate avge between 182, 191+38, and 151+38. I do not recommend either averaging, preferring strongly a clock-aware estimation.

One last question. I estimated the rate based on a NJ tree using BLOSUM62. If I make a tree using UPGMA for example, it won't be valid to use the rate calculated using BLOSUM62 NJ rigth? Because this will other scores at the branches

If by that you mean that you used BLOSUM62 to calculate the pairwise distances and then used the resulting pairwise distances matrix as input to NJ, then you can just use UPGMA instead of NJ, and use the branch lengths from this tree. (Both NJ and UPGMA are using the same original info, i.e. the pairwise distances; only that UPGMA forces the tree to be rooted, ultrametric.) The branch lengths will be different, however, and in some cases even the topology. But you are assuming that the molecular clock is valid, and then UPGMA should work.

You may have done this already, but I would however use a maximum likelihood framework (e.g. protmlk). The branch lengths would, again, be different, but would be in general more reliable since ML takes into account reversals, site-wise convergence, etc.

First of all thankyou for you help! So what I can do is: MSA of these sequences, calucalting a distance matrix (using MEGA e.g.?), making an UPGMA tree, calculate the rate of change (plotting branch distance vs milion yeasrs since divergence and set up a linear regression) than using this rate (if it follows a molecular clock offcourse) to date the duplication events? Is the right way to go?

I guess so, yes!


text:
Topological property of DNA
I was reading a course about DNA Supercoiling, and I stopped at this definition :

[...] In the case of DNA, a topological property is one that is not affected by twisting and turning of the DNA axis and can only be changed by breakage and rejoining of the DNA backbone. (Source)

I didn't understand what they mean, can anyone clarify it please.

I think when you get to the later section entitled "DNA Underwinding Is Defined by Topological Linking Number", it will help explain what that means.

The classical explanation of topology is that donuts, coffee cups, and humans all have the same topology (this is a reference to the mammalian gastrointestinal system which is just a simple tube, the food goes in one end and out the other).  If you understand this analogy, then an intact circular rubber band (or elastic band) has the same topology as your covalently closed circular DNA plasmid.  You can twist and knot a rubber band all you want and you will never change its topology.

DNA supercoiling can be described numerically by changes in the linking number $L_k$, it's the most descriptive property of supercoiled DNA.
The linking number $L_k$ is equivalent to the sum of $Tw$, which is the number of twists or turns of the double helix, and $Wr$ which is the number of coils or writhes.
$$L_k = Tw + Wr$$

[...]  If there is a closed DNA molecule, the sum of $Tw$ and $Wr$, or the linking number, does not change. [...] Since the linking number L of supercoiled DNA is the number of times the two strands are intertwined (and both strands remain covalently intact), L cannot change.

I don't know how to explain it more but I think the main idea is represented in the image below.

Edit:
From DNA Topology: Fundamentals :
There are two important features of the $L_k$:

$L_k$ is always an integer.
$L_k$ cannot be changed by any deformation of the DNA strands, i.e. it is topologically invariant. The only way to change it is to introduce a break in one or both DNA strands, rotate the two DNA strands relative to each other and seal the break. This is precisely the role of DNA
topoisomerases.

Related question: Reason behind formation of positive supercoils during DNA replication/transcription.
Sources : DNA supercoil and DNA Topology.


text:
Are receptors integral membrane proteins or peripheral membrane proteins?
Integral membranes proteins serve as transporters. Peripheral proteins serve as cell adhesion molecules, antigens and enzymes. So what about receptors? Which proteins carry out the duty of receptors?

It may depend, but I know a detection system which has a receptor protein that is integral. Once it receives the signal it must somehow transmit that signal into the cell, which further suggests integral protein.

All the receptors I know about are integral, transmembrane proteins. It would certainly be possible for a receptor domain to exist on a peripheral protein that interacted with a transmembrane protein, but I don't know of any examples of this: an extracellular peripheral protein would tend to float away, which is a bit of a problem if they aren't intended for secretion.
There are certainly peripheral proteins that associate with the internal parts of transmembrane receptor proteins and may influence their function, but they are not themselves receptors.
I'm not sure about your question about "which proteins" - those proteins are most often named after their ligand followed by the word "receptor", or based on their function that is triggered by binding their ligand, or both (i.e., the AMPA receptor is a glutamate receptor that is also activated by AMPA; receptor tyrosine kinases are a family of receptors that are tyrosine kinases; the individual members of the family are typically known by their ligand).


text:
How to know what the expected value is?
I am confused as to how I was meant to know E for a X^2 test in the following question:

2.i and 2.ii give no more information.
Not knowing what to do I used E as 0 for the first row and 40 (3+37) for the second row, but that was just a guess. It was wrong and the correct answer for E is 20.
I suspect this has something to do with the 20 fields but I can't beleive that I'm just meant to know they expect one butterfly per field...
How was I meant to know E?

I'm voting to close this question as off-topic because it would be better suited for the statistics SE site, Cross Validated

The expected value is what the values would be if the tested conditions had no effect on the sample distribution. In your case, you are testing the effect of herbicides on butterfly populations. If the presence of herbicides wouldn't matter you would expect an equal number of butterflies on fields with herbicides as without.
So, the total number of butterflies being $37 + 3 = 40$, you would expect $\frac{40}{2} = 20$ butterflies on fields without and $\frac{40}{2} = 20$ on fields with herbicides.


text:
Is blood donation risky for patients with MGUS?
Monoclonal gammopathy of unknown significance (MGUS) is often considered a pre-cancerous condition.
Blood donors with MGUS are typically advised to discontinue blood donation as their blood may be risky for blood recipients.
This paradigm has been recently challenged (e.g. La Raia 2015), but also reinforced (e.g. Felldin 2016).
It is also possible that blood donation may be risky for donors with MGUS as well, as it leads to an overall boost and stimulation in hematopoiesis which may indirectly favor prograssion from MGUS to myeloma.
Is it true?

People in the UK are prohibited from donating with MGUS.

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text:
Which are the most important carcinogens in tobacco smoke?
I am researching the neoplastic effects of tobacco smoke and would like to measure a set of key molecules in the saliva of several study subjects after they have smoked.
Which are the most relevant carcinogens originating from tobacco smoke that are detectable in saliva? I don't think there will be time or room to measure metabolites, as the saliva samples will only reflect short-term (<60 minutes) exposure to tobacco smoking.

So you're after compounds present directly after smoking? Some metabolites may also be present (?) so I'm just trying to get this question clear. +1

#AliceD The saliva will reflect only short-term (<60 minutes) exposure, so I don't think there will be metabolites

This is not an easy question - as tobacco smoke contains something like 5000 different chemical components, from which 70-100 are carcinogen. The list includes: Oolycyclic aromatic hydrocarbons (PAHs), N-nitrosamines, aromatic amines, aldehydes, volatile organic hydrocarbons and metals. I haven't found articles which specifically concentrate on the carcinogens in saliva, but my guess would be that you find them all because of the "application route" of the cigarettes.
Most of these carcinogens first need to be processed from the livers cytochrome P450 system to reach their carcinogenic potential. The enzyme complex converts these substances into forms which can then covalently bind to DNA.
A list of several different of the carcinogens can also be found in the Wikipedia. For further information see the references.
References:

Hazardous Compounds in Tobacco Smoke
How Tobacco Smoke Causes Disease: The Biology and Behavioral Basis
for Smoking-Attributable Disease: A Report of the Surgeon General.
Tobacco Smoke Carcinogens and Lung Cancer


text:
Are Y spermatocytes faster but less resilient than X spermatocytes?
I have heard somewhere (but did not find any suitable reference) that spermatocytes carrying a Y chromosome are usually faster but less resistant than those carrying an X chromosome.
Is this true? If so, which are the actual reasons?
There is a remote but theoretically plausible explanation indeed for the difference in speed, as the Y chromosome is much smaller and lighter and thus would make the Y spermatocytes less heavy than the X spermatocytes. Possibly, the larger number of genes on the X chromosome (missing in Y spermatocytes) could imply that they can still have some incremental translational activity.

Spermatocytes only carry one sex chromosome - either $X$ or $Y$. They are haploid, not diploid. Are you asking why $Y$ spermatocytes "swim" faster than $X$ ones? Please add a citation to your claim that one is faster than the other.

@MattDMo Sorry for the typo, indeed I meant X vs Y spermatocytes. I have corrected the typo. I did not find any suitable reference for this, so it might just be and urban legend.

If you can show it is a suitable claim, then the question would be nicely suited for Skeptics.SE. (I am not saying it is off-topic here).

@Remi.b I am expanding it now. There is theoretical basis indeed (see edited entry).

@fileunderwater fantastic answer to  Why do we have more male infant born? addresses your question.

As a side note, the "lighter" argument is not particularly convincing for swimming, since sperm swimming isn't limited by mass, but by viscous resistance (see "Life at low Reynolds numbers").

I searched and found a letter which clearly mentions about misinformation that sperm with Y chromosome swims faster than X carrying sperms.I think this link may help https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440662/
The letter says "The widely held idea that spermatozoa bearing the Y chromosome (Y sperm) swim faster than those bearing the X chromosome (X sperm) seems to have originated from Shettles's work in 1960, using phase-contrast microscopy.He claimed to have observed, “two distinct populations” of spermatozoa. After attempting to count the chromosomes, he concluded that the smaller heads contain the Y and the larger the X chromosome. There were no intermediate types.
The following year he reiterated these findings, adding that smaller headed spermatozoa can migrate more rapidly and fertilize the egg more often in the distal part of the tube.
Reading Shettles's reports in Nature and other peer-reviewed journals, many researchers thereafter believed that Y sperm swims faster than X sperm. The finding particularly influenced research on sperm separation.
Although several attempts have been made to correct this impression, it was not until the development of computer-assisted sperm analysis (CASA) that reliable observations could be made. So far, researchers have found no morphological differences between human X sperm and Y sperm.4 Neither mature sperm nor their precursors possess significant morphological differences between X and Y genotypes, and Y bull sperm does not swim faster than X sperm."
You can see the reference and read more
1. Shettles LB. Nuclear morphology of human spermatozoa. Nature 1960;186: 648-9. [PubMed]
2. Shettles LB. After office hours: conception and birth sex ratios: a review. Obstet Gynec 1961;18: 122-30.
3. Moruzzi JF, Wyrobek AJ, Mayall BH, Gledhill BL. Quantification and classification of human sperm morphology by computer-assisted image analysis. Fertil Steril 1988; 50: 142-52. [PubMed]
4. Hossain AM, Barik S, Kulkarni PM. Lack of significant morphological differences between human X and Y spermatozoa and their precursor cells (spermatids) exposed to different prehybridization treatments. J Androl 2001; 22: 119-23. [PubMed]
5. Penfold LM, Holt C, Holt WV, Welch DG, Cran DG, Johnson LA. Comparative motility of X and Y chromosome-bearing bovine sperm separated on the basis of DNA content by flow sorting. Mol Reprod Dev 1998;50: 323-7. [PubMed]
Hope this help!


text:
What do you call members of a same species that show some morphological differences depending on their environment and/or diet?
What do you call members of a same species that exhibit a number of morphological differences depending on their environment and/or diet?
I was thinking of the term "different phenotypes," but I am not sure whether this applies.
I would like to apply it in the field of entomology.
EDIT
The ensuing discussion has funnelled the question down to:
When to use the term "phenotype" vs. "morph"?
I am also attempting to synthesise the different viewpoints in a tentative answer below. Comments and some amount of leniency are welcomed.

we would call that normal, the exception are rare and noticeable.

I think that "morph" is a substantially generic term that it would cover environmental as well as genetic variation. A cursory google search suggests that this is common practice in zoology:

a paper on lizards,
one on ants,
another on ants.

This paper discusses the phenomenon in general using the term "polyphenism", in the context of the phenotypic plasticity literature. That last link is to a review paper titled "Polyphenism in insects" (Simpson et al. 2011), which uses the term "morph" extensively.
This suggests to me that this is a well-known concept in entomology and no one will be angry/surprised when you use this term.

The ensuing discussion and additional reading shows that the delineation in usage between the terms "phenotype" and "morph" is not always clear cut.

An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, and the influence of environmental factors. Both factors may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. [Source]

According to the above, morphs would be clearly different phenotypes.
However, the difference in fur colouring in dog morphs is solely the result of the genotype and not at all the environment.
Polyphenism → Phenotypes, Morphs

Biston betularia caterpillar phenotypes on, respectively, birch (left) and willow (right), demonstrating a colour polyphenism as a result of its environment and diet.
Polymorphism → Morphs
Whereas the dark-morph or melanistic jaguar does not result from an adaptation to its environment or diet.

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text:
Relation between biomass and radius of roots system
Is there a known relation between the mass of a plant to the size of its roots?
For example, can I take the root size to be proportional to the biomass of the plant like in this relation: $$R = R_0 (1+EB) $$, where $R_0$ is the minimal size of the root (i.e. the diameter of the seedling), $B$ is the biomass of the plant, $E$ is some parameter, and $R$ is the length of a typical root?

Your question specifically asks for an equation which gives root radius and your sample equation is for typical root length, neither of which I'm aware of. However, there is a known relation between the above-ground biomass and the below-ground biomass of a plant, which varies with species and environmental factors. This is the root:shoot ratio.

This is a linear model where the constants represent differences in starting conditions (the intercept) and biomass partitioning (slope).

Roots and shoots are functionally interdependent and these two systems
  maintain a dynamic balance in biomass which reflects relative
  abundance of above-ground resources (light and CO2) compared with
  root-zone resources (water and nutrients). Whole-plant growth rate and
  root : shoot ratio are thus an outcome of genotype × environment
  interaction, but source of control is ambiguous.

The actual size of the roots - as in their extent - will depend on the soil characteristics, water table, the plant species, etc.
Source: http://plantsinaction.science.uq.edu.au/edition1/?q=content/6-3-1-biomass-distribution


text:
What are some characteristics of venules and arterioles?
I know that the vascular system of the human body is organized in the
two, "ever branching", structures of the veins and the arteries. These two
structures stem from their connections to the heart and stretch and
branch throughout the body.
The two structures are interconnected through capillary beds,
responsible for the interactions between the blood and the
extracellular liquid, surrounding the tissue cells of the body.
The capillary beds are connected to the arteries and the veins through
small vessels, venules, branching out from veins and arterioles,
branching out from the arteries.
The capillary beds consist of a web of capillaries, vessels small and
thin enough to allow exchange of nutrients and waste between the blood
in the vessels and the extracellular liquid surrounding the vessels as
well as the cells of the body.
Now, I realize that the capillary beds must be ubiquitous throughout
the body, sustaining every part of the body but the circulatory system
itself.
I am eager to find out more about the venules and arterioles. Looking
at the structure of veins and arteries, how prevalent are the smaller
blood vessels? Are the arteries and veins "fuzzy" with arteriole and venules or are the small vessels more sparse? Do they emanate from large vessels as well as smaller ones? How do their presence interfere with vascular interventions or
even drawing blood for blood tests?
I'd be happy for information in these matters.
Cheers
Mats

I think this question is a bit too broad to write a comprehensive answer to, and there will certainly be some variation between tissues.
However, here is one reference that might give you what you are looking for.
I used to make acrylic arterial casts, mostly of coronary arteries but also some dabbling in the pulmonary, renal, and hepatic systems. My experience with the coronary system is that most of the arterioles come off in a tree-like branching pattern from quite small arteries, but there are always exceptions. I think the "fuzziness" you refer to definitely depends on the scale of observation: the further away you are, the more "fuzzy" arterioles look: of course they will never be as "fuzzy" as capillaries, but certainly once you enter the muscles themselves there is a lot of branching, but that branching isn't necessarily uniform. That is, there may be larger branches running in one dimension, and smaller branches in another dimension.
In larger vessels you also have the vasa vasorum: arteries that feed the large arteries and veins themselves. Some of those vessels are certainly the same size as arterioles, and some branch directly off the main vessel, but I am not sure whether anatomists always consider those to be arterioles or if they are considered separate.
From the perspective of interventions such as surgery, etc, smaller arterioles aren't really any different from capillaries, and larger arterioles might need to be clamped off or cauterized, but there isn't really any way to avoid them if you are cutting into a vascularized tissue. One wouldn't avoid these vessels they way they might avoid larger vessels.

I would appreciate an explanation for the downvote, I am happy to make edits if suggested!

Thanks Bryan. Yes, I apologize for a poorly stated question. In spite of this, you helped me shed a little more light on the subject. I hope I am not responsible for any down vote. If I am please explain and I will rectify. I will accept this answer. It helped me. I will restate and ask a new, clearer question later on. Thanks again for your answer.


text:
How to calculate grams of fat used during hibernation?
In Humphries et al. 2002. Nature, the authors report number of grams of fat bats use during hibernation. However, their equations results in values in mlO2/g.
How can one convert the energy requirements to amount of burnt fat resources?
I found an equation $f = \frac{20.1 \times E}{3930}$, whre $f$ is fat in grams and $E$ is energy in mlO2/g (Hayman et al. 2016. Sci. Adv.). But the paper is without any explanation as to what the numbers mean, and why they are used. Does anyone know, how to convert oxygen consumption to volume of burnt fat?


text:
To understand why satellite cells are genetically inactive in Barr body
DAPI is used as a stain for DNA heterochromatic and euchromatic regions. The Barr body is heterochromatic.
In the slide of a normal human female cheek's somatic cells, there is apparently no other clear dark spot inside the nucleus than the Barr body against the nuclear inner membrane. - - I used an old microscope so my observation may be wrong as pointed in the comment.

How can you deduce from the given slide that the spot really contains inactive satellite cells that are not used genetically?
Why is the active X chromosome not visible by the same staining method? (It probably can be made visible by some other staining method.)

Just to clarify, do you mean "there is no other dark spot inside the nucleus?"  The Barr Body is not inside the nucleolus, and the nucleolus appears as a DAPI-dim (unstained) spot in interphase nuclei.

@KAM Yes, I mean that I did not see any other clear dark spot inside the nucleus than the Barr body. Other thing was blurr and not that clear. Thank you for pointing out the mistake: the Barr body is inside the nucleus next to nucleolus or more exactly against the nuclear inner membrane in interphase nucleus.

DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase.  In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus.  When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.
A great picture is here (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.

Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes.  The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.
I do not understand the first part of your question, though.  You cannot tell from a still image that the Barr Body is relatively inactive.  If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes.  If you clarify your question, I can answer better.

Do you mean that you can see Barr body and the active X chromosome as dark spots to the eye in the given slide? - Assume yes. Then my classmate was wrong in claiming that she can differentiate between the two X-chromosomes from the slide. Like you said you need to measure RNA production to verify the thing.


text:
How do you see the stage of the second meiotic arrest in oogenesis in the given video?
My old question raised this new question. After reading this page I can say now that metaphase is the stage in which the second meiotic arrest occurs within oogenesis:

The oocyte is arrested again in the metaphase of the second meiotic
  division.

It is difficult to visualize the thing in my head. I could not find a video of specifically for oogenesis but probably the general model for meiosis holds true. The problem I am having is that I cannot see the arresting steps in this general meiosis video.
How do you see the second meiotic arrest of oogenesis in the above video?
I cannot even see clearly the first meiotic arrest. I only know that it is in prophase for the first and metaphase for the second.

I seem to understand the thing now.
The video is utterly simplified for animal cell meiosis I and II.
In oogenesis, you get after every anaphase one cell with very little cytoplasm, polar body, and another cell with much cytoplasm. In the video, the amount of cytoplasm is equal so the thing is idealized.
The video is better to explain male gametogenesis: spermatogenesis, since the amount of cytoplasm does not differ after each anaphase.
The video is too going too fast to teach you oogenesis, since in reality the things are arrested rather long time. The second meiotic arrest in oogenesis can lasts 12 - 50 years starting after puberty. The rupturing secondary oocytes lasts then again less in the second meiotic arrest of oogenesis, since they start to develop into ovum after the monthly release.


text:
How do pineapples and lemongrass grow?
You can't plant the leaves, you can't plant the fruit, but, if you plant the part where leaves and fruit meet you will grow a whole pineapple plant.
The part of the pineapple where the leaves meet the stem is the point from which the whole plant seems to form. Cells below seem to become fruit and fruit skin, cells above seem to become leaves. If you look at a cross-section of this part of the plant you can see the way that the cells seem to move outward from this point.

(1)But is that really how it grows? Are the new cells added from the center or do new cells get added to the leaves at the tips and in the middle of the leaves?
(2)I know some orchid roots grow from the tip... but is this the case for all roots?
(3)I noticed that some lemongrass in my worm compost bin has grown roots! So, I transplanted it outside. Maybe I can grow lemongrass. Again, it was the part of the plant where the roots met the leaves that still had life in it.  This seems like a very powerful part of the plant. Is there a name for the part of a plant from which everything else grows?
UPDATE: http://en.wikipedia.org/wiki/Meristem
This is what the regions is called! But I still want to know if the plant "pushes" out the leaves from this central point or not... and are all root like orchid roots that grow from the tips?

First, allow me to provide the link to an old paper that deals with development in Ananas comosus, it should be freely available and answer this question in more detail: http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1936.tb06884.x/pdf
Now, to briefly explain the observation that a mature plant will grow from the region where the leaves of the pineapple attach to the fruit, it should be noted that the pineapple fruit develops at the top of the central stem of the plant in a developmental process known as influorescence (please see a picture of a pineapple plant). Since the top portion of the fruit is in fact the end of the primary stem, this region contains the apical meristem, a collection of stem cells that are apparently is sufficient to give rise to a mature organism. Pineapple development has apparently been a topic of constant research for nearly a century (due to its economic importance), so there are quite a number of papers that can provide much more detail, but many of these are not freely available.
In nature the primary means of pineapple propagation is the formations of lateral shoots, the growth of which consequently are accelerated by influoresence of the main shoot.
Now the actual way the plant grows is not quite as simple to answer, as plant development is often as complicated as animal development, but in general it is a function of cell division and elongation. In the root apical meristem, there is a region known as the quiescent centre which contains the actual root stem cells. Directly behind the quiescent centre is a region known as the merismatic zone, which features extensive cell division, and directly behind that is the elongation region where the cells grow, effectively pushing the root tip through the soil. In the region behind the elongation region, the maturation zone where the cells have reached full length, cells begin to form more rigid cell walls and differentiate into the different tissues of the root.
The shoot apical meristem is dome-shaped, the top of the dome is known as the central zone and is analogous to the quiescent centre of the root apical meristem, the sides of the dome are the peripheral zone, a region of rapidly dividing cells that give rise to the leaves, and the central region of the dome is the rib zone that gives rise to the stem structures. Elongation, differentiation, and maturation also occur below the meristem region, but involve the additional complexities of leaf organogenesis.
There should be considerable additional information on plant development online.


text:
How is a T lymphocyte specific to an antigen but not specific to an epitope?
In my immunology notes, it states that B lymphocytes (and other APCs) capture and present antigens to T lymphocytes that is specific for an antigen, but that the T cells do not necessarily recognise the same epitope. How can a cell be specific to an antigen but not to the epitope presenting on the surface of the antigen?
I've been in the process of discussing this with a friend and trying to make sense of Janeway's immunobiology and we've come to the theory that the APC recognises the antigen and takes it up, breaks it down and presents the epitope via the MHC where it is then recognised by the T cell. Am I right in saying that the antigen is broken down into many fragments that act as epitopes but each clonal expansion of T cells can only recognise the various epitopes of one antigen?

It's mainly because antigens have multiple epitopes, and so the T/B cells will recognize one epitope, but you'll get multiple cells recognizing multiple epitopes. The polyclonal expansion of these cells allow the attack to come at multiple angles of the same antigen at once.

Okay, I think I understand why T/B cells can bind multiple epitopes but I'm still confused about how this leads to them being specific to one antigen, as surely, different antigens could have the same epitopes on them? Or is each type of epitope only found on one antigen? Thanks for your help! @CMosychuk

Take a look at the following image. The shapes on the bacteriums surface are the antigenic determinants, aka the epitopes. Notice how they can differ: each antigen has many epitopes at once.

Thanks for the image, it really helps me to visualise it. I think my confusion is coming from the fact that on my midterm (will edit the post and tag homework, I read the rules after posting) it says that "Concerning T lymphocyte/B lymphocyte co-operation in humoral immune responses to T dependent antigens:
The epitope recognised by the T cells and B cells must be identical (FALSE)
The antigen recognised by the T cells and B cells must be identical.  (TRUE)"
And it's the second statement that's confusing me. I don't understand that bit, does that make sense? @CMosychuk

"...it states that B lymphocytes (and other APCs) capture and present antigens to T lymphocytes that is specific for an antigen" - Shouldn't it read"...present epitopes to T lymphocytes..." or "...present peptides" (that's what they are? Which leads to: Do presented peptides have/include epitopes, or: embed one and only one epitope). -  Ref. @CMosychuk – Elizabeth May 30 '16: Do you mean:  if B-Cells "edit" one and the same antibody they are specific for, they are being "activated" from different sides (even different strains of virus causing that activation)?

Perhaps it would simplify for you to think of a model system? Let's take HIV because it's simple. The antigen in this case is a protein called ENV and it looks like this.

All of those arrows are pointing "regions" of the antigen that an antibody will bind to. Since the B cell makes the antibody you can think of these regions as where the B cell will bind to. They call these regions epitopes.
Do you see how there are many different sites on one antigen? Well one of those epitopes can be for a B cell and one of those epitopes, which can even be on the other side of the antigen, can be an eptiope for a T cell. So while T and B cells recognize the same antigen, in this case HIV Env, they needn't bind the same epitopes.

I think where you may be getting confused is  when B cells chew up an antigen, the epitope they display on MHCII and display to T cells is not necessarily the same epitope it used to recognize the antigen. The B cell chews up the entire antigen, including T cell epitopes, and displays them on MHCII.

I think it's worth mentioning in that context that B cells only produce antibodies that refer to the epitope they recognize, not the ones they present to T helper cells (as I feel rather insecure about that...).

For this answer lets restrict ourselves to T dependent MHC II mediated responses.
So, an APC like a macrophage or a dendritic cell, takes in a pathogen by phagocytosis and degrades it inside the cell. Some of its broken proteins, which are antigens are presented on the MHC II of this particular APC.
The B cells also do something similar but they identify either free floating antigens or the ones that are expressed by phagocytic APCs. These antigens are broken down in the lysosome. These fragments now are expressed on the surface along with MHC II. This fragment may or may not contain the epitope that the B cell receptor (surface antibody) originally recognised the antigen with. Also, it is not that just one of the fragment is taken to the surface, most of them make it, each with a separate MHC.
The T cell that is going to now interact with this B cell may have a TCR (T cell Receptor) against the epitope in any one of those fragmented antigens on the MHC.
This T-cell is specific to that particular epitope of the antigen it bound to, similarly there could be another T-cell that could recognise some other fragment of the same antigen brought to the membrane by a different MHC II.
So, the epitope that the B-cell and the T-cell recognised the antigen with, needn't be the same. But logically, there's a possibility that they may be.

Note that:

The processing of antigen in the phagocytic APC is not shown in the picture.
B cell recognises antigens not that are displayed on the MHC II (this the T cell does) but those that are tethered on the APC membrane.

Image: Nature Reviews Immunology.

"The B cells (...) identify either free floating antigens or the ones that are expressed by phagocytic APCs." - 1. True that B cells do not take up whole viruses? 2. Any basic textbook reference for APC presenting, then B taking up? 3. Still true that cytotoxic T cells do not uptake, in contrast to B cells(!)?