text:
Can mexican salamander regenerate any organ?
Mexican salamander or few other species of salamander can regenerate limbs, tail etc. Do they have HOX genes for vital organs like liver, heart, brain, kidney?
If brain is damaged, can salamander grow it's brain to normal functioning again ?

I'm going to assume you meant Ambystoma mexicanum also known as the axolotl. There are other kinds of salamanders that live in Mexico, but the axolotl is widely-studied and sometimes called the 'mexican salamander'.
The axolotl has exceptional regenerative powers, and although I suspect this ability is shared among salamander larvae(even if not the adults) there's not much research into phylogenetic distribution of regenerative capability. So in the absence of a more refined answer I'm going to hope axolotl results generalize to other salamanders.
Axolotls, as long as they don't die, can regenerate nearly any part of their brain. As a rule, as long as they don't die they can regenerate from any injury. There are a couple exceptions(it's very hard to keep an axolotl alive without a heart, so that hasn't been tested) like the eye but in general they can grow back nearly anything.
The Hox gene research I've found was done explicitly on worms and frogs, but I would feel safe concluding that axolotl regeneration relied on a similar mechanism, and that therefore they have Hox genes for internal organs. I mean, they had to grow them the first time, right?

So until he not get  killed he is immortal ?

They still die of old age, unfortunately.

They have regeneration power so they can replace old tissues ? Its stranger they become old :|

They're still subject to cellular aging as far as I know. As they age their regenerative abilities fade, until eventually they die. Similar to humans, really, but our regenerative abilities are much reduced.


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Do mammals and birds have a common warm-blooded ancestor?
Is it homogeneous or did they converge?  Did we both evolve from warm-blooded reptiles that are extinct maybe?

I think the OP meant "homologous" rather than "homogeneous" ...

Welcome to Biology.SE.
Did you say warm-blooded?
The term warm-blood is very unclear. The correct terms are endo-, exo-, poikilo- and homeo- therm. In short…
Source of heat

endo = inside
exo = outside

Variation in inside temperature

Poikilo = varies
homeo = does not vary

Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. A fun example also are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur homeo-endo-therm individuals. Hope that makes sense to you.
By warm-blooded I will assume you meant endotherm.
MRCA of mammals and birds (and other things)
The Most Recent Common Ancestor (MRCA) lived 301.7 millions years ago (see on tolweb and on OneZoom). This MRCA was exotherm. In consequence, birds and mammals endothermy are an example of convergent evolution (even if they are not using exactly the same mechanisms).
References to go further into the evolution of endothermy in birds and mammals

Grigg et al. 2004
Hillenius and Ruben 2004
Ruben 1995

According to this, mammals and birds share common cold blooded ancestor. And also comment that reptiles are "Imperfectly warm blooded"

I added some info for the large dinosaurs. I wouldn't trust too much a paper that uses the terms "cold-blood" and "warm-blood". But anyway, we agree that the MRCA was exotherm I guess.

It does not appear borken to me. But I might have modified it right at the moment of yuor comment 2 days ago!

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Woodland outdoor microscopy advice
Let me start by saying I have never used a microscope outdoors, and in general I have never owned a microscope nor used one regularly.
However, I am currently developing and organising some activities for children, to be carried out in a woodland. I thought it would be really interesting to use a microscope to analyse and compare different samples: leaves, insects, etc. In a word, to do some "field microscopy" (I googled that, but doesn't seem to be a popular expression).

Is it possible?
Is it easy?
What type of microscope should I look for? We have quite a bit of funding, so feel free to suggest anything.

Thank you very much.

Worth considering DSLR and Macro lens. Take a look at macro photography samples. Advantage over microscope is that it is way easy to handle outdoors.

1: Yes it is possible
2: It's not as easy as lab conditions because of variable conditions, chances of equipment breaking, especially when small children are involved.
3: You can also look at a Foldscope. Its a small, but powerful microscope made with paper. It was developed by a scientist called Manu Prakash, and although it is still in its beta testing stage, I'm sure you would be able to obtain a few for your students. It is incredibly cheap, very customizable and really user friendly.
P.S.: With the amount I endorse the Foldscope, you would have thought they could have shipped one of the damn things to India for me.

There are a range of "nature microscopes" you can buy that will do this.
One cool new portable microscope with video storage is the Mustcam.

My suggestion would be to (have the children) construct some pooters (with a clear vessel to allow viewing) to catch small insects with and use magnifying glasses or hand lenses like this one which gives a range of magnifications.
For most of the things you would want to look at you would not need massive magnification (i.e. you wouldn't need a scope). Microscopes also give the issue of how to fix the object (if it's a living mobile thing) to immobilise it, and a magnifying lens is generally more portable and affordable.
A good tip for looking at very small things up close in the field is to look at them the with binoculars but using the binoculars backwards - it allows you to get a good close view.

You could go wild in a forest with a microscope if you had batteries.

Yes
Yes
200X

IMO you don't need more than 20-40x for bugs and leaves. Beyond that it gets hard to find and focus on the sample, and the optics have more obvious aberrations.
"Field microscope" is a good category to look for. You need a light source in the scope -- most have a small LED. I got a couple of these for my 6- and 8-year-old kids and they have surprisingly good optical quality and durability. I linked to Amazon because there is a sample photo in the reviews.  I'm a professional microscopist, so I'm picky about these things, but I was impressed.
With the field scope I mentioned you can pull off the stage (part that holds a slide) and just hold the scope up to the side of a tree or a rock. Super cool.
Also, look for some rotten wood, or an acorn with a hole in it, and break it up to find the insect larvae inside.

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Difference between vacuolar and symplast pathway
what is the difference between Vacuolar  Pathway and Symplast Pathway ? Is the symplast pathway does not take into account the vacuole to vacuole movement?

The vacuolar pathway involves the movement of water between vacuoles of neighbouring plant cells. The symplast pathway, on the other hand, involves the movement of water from the cytoplasm of one cell to the cytoplasm of a neighbouring plant cell without it entering a vacuole inbetween, so the symplast pathway has no vacuole to vacuole movement.

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Confusion about result of monohybrid cross in Mendelian genetics
I was studying monohybrid crosses in genetics where the character considered is stem height. Whenever I came across punnett squares, I used to calculate the probability of the genotype of the offsprings which can be formed as a result of a cross between 2 heterozygous plants. In the F1 generation, these are obtained by crossing homozygous dominant(Tall) and homozygous recessive plant(Short). Now when these plants of the F1 generation are crossed, each plant produces 2 types of gametes where each gamete is having only 1 allele of the gene.
Now my question is that when we cross these plants, is it necessary to get 'one- fourth' dwarf plants and 'three-fourth' tall plants? Doesn't the punnett square only gives the probability of the possible genotypes of the offsprings formed, while the real cross could result in say 50-50 percent tall or dwarf plants? Is it necessary that the actual cross follows the probability of predicted by the punnett square ?
If no then why is this statement given in my book that 'One fourth of the plants obtained in the cross were dwarf while the rest were dwarf'? Couldn't this proportion be anything  other than this proportion ? If so then how could this proportion be obtained isn't that a chance factor?

while the real cross could result in say 50-50 percent tall or dwarf
  plants?

Sure it's possible, but if you have dozens of offspring, the odds of you being very far away from the 1:3 ratio are very small.   If you look hard enough, you can find Mendel's actual results, and a chi-square test is the usual way to show that his results do not deviate significantly from the expected ratios.

That is these results( punnett square) are the most probable results

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Restriction Mapping of Plasmid Assignment

pUWL22 is a circular, double stranded, 10.5 kb plasmid. It contains a
  gene encoding an enzyme that confers ampicillin resistance in the host
  bacterium. Cloning into the kpn I and Sst I sites abolishes ampicillin
  resistance, whereas cloning into other sites on the plasmid does not.
  Digestion with the following restriction enzymes singly and
  combination results in the following data:

Enzyme Digest     ()()()()()()   Fragments Produced (kb)

Hind III  ___________________________10.5

Kpn I  _______________________________10.5

Not I  _______________________________10.5

Pvu II  ______________________________10.5

Sst I  _______________________________10.5

Stu I  _______________________________10.5

Hind III + Kpn II  ___________________8.5  _______________2.0

Hind III + Not I _________________8.0  __________________2.5

Hind III + Pvu II ________________6.0  __________________4.5

Hind III + Sst I _________________7.5  __________________3.0

Hind III + Stu I _________________7.5  __________________3.0

Stu I + Not I  ____________________10.0  __________________0.5

Stu I + Pvu II  ____________________7.5  __________________3.0

Now the actual questions:

A) Create a circular map of pUWL22, designating the Hind III site as
  the position 0 on the map. Once you have completed the map, indicate
  the relative position of the ampicillin gene.

My plasmid mapping:
What I need help with in indicating the relative position of the ampicillin gene. In the statement above it said "Cloning into the Kpn I and Sst I sites abolishes ampicillin resistance." Does that mean its inbetween Sst 7.5 and Kpn 8.5? Please tell me where it is and why its there.
P.S. I made a mistake on the on the Sst I enzyme, it's suppose to be @ 7.5 not 7.8.
The question after that is:

B) Propose 2 other double digests that could be done to confirm your
  analysis. Predict the sizes of the fragments that would be generated
  from these digests.

Please answer this and explain why.

Please note that you will get much better responses to your question if you explain what you have tried far or give your solution and ask if it is correct.  Also, it never hurts to include at least some formatting in your question rather than just a block of text.  Welcome to the site regardless xD

i drew out the diagram, that wasnt a given, im stuck on the part indicating the relative position of the ampicillin gene and question B.

I tried laying it out the best i could, thanks for making it nicer btw

A) Here is the correct map:

You made a mistake on your map at the PvuII site (it is not on 6.5kB from the start of the plasmid, but on 6kB).

Can the Kpn I not go on the 8.5 site, it still creates the 2 and 8.5, so isn't there more than 1 correct option for plasmid map?

Yes. What you need to do in order to make the correct map is try all possible positions of the restriction sites:

You start with HindIII and place it at position 0 of your vector.
The KpnII site can be either at 2kb (left of HindIII) or at 8.5kb (right of HindIII). Draw both versions of the plasmid.
You place the NotI site that can either be at 2.5kb or at 8kb. Now you have four different possibilities for the plasmid:

HindIII[0], KpnII2, NotI[2.5]
HindIII[0], KpnII[8.5], NotI[2.5]
HindIII[0], KpnII2, NotI[8]
HindII[0], KpnII[8.5], NotI[8]

Then you do the same for the rest of the restriction sites. When you get to the last two digests, there is only one option for the correct plasmid left in the following order, depicted on the plasmid map below.

I have to point out though that StuI and SstI can both be at 3kb (they can be next to each other). Then the 2 fragments from the digest will be ~3kB and ~7.5kB. So technically, there are two possible versions:
correct
a) HindIII[0], KpnII2, NotI[2.5], StuI[3], PvuII[6], SstI[7.5]
b) HindIII[0], KpnII2, NotI[2.5], StuI[3], SstI[3] PvuII[6]

If u can, can u please elaborate on question b as to why there is one correct option for the plasmid map? Also, what do they mean by double digest to confirm ur analysis?

A double digest means that you cut your plasmid with two different restriction enzymes at the same time. As you already have a putative map of the plasmid, you can predict which would be the expected bands. If you observe the expected sizes, then your design is correct and your analysis are confirmed.
To check which one is correct I would do a double digest with:
1) SstI and PvuII, generating a 1.5kb and a 9kb bands if design a) is correct or                              3kb and a 7.5kb bands if design b) is correct
2) StuI and SstI, generating a 4.5kb and a 6kb bands if design a) is correct or                             a 10.5kB band if design b) is correct

To confirm the "ampicillin gene" starts at kpn I 2.0 and end at the 3.0 stu I site right?? So the amp gene is 1 kB long?? So the relative position of the amp gene starts at 2.0 and ends at 3.0.
  Why is it that in the question it says cloning into the kpn I and sst I sites abolishes ampicillin resistance whereas cloning on other sites does not?
  What do they mean by this? Is the ampicillin resistance gene diff from the ampicillin gene??

The ampicillin resistance gene and the ampicillin gene are the same. It refers to an enzyme (beta lactamase) which degrades ampicillin, and thus the cells that harbour the ampicillin-containing plasmid can survive when plated on ampicillin.
Are you sure that the resistance is disrupted if cloning into SstI site and not StuI? If this is really the case, then the StuI site and SstI sites are next to each other, as first you have the SstI site, followed by StuI. The amp gene
The gene is a little above 1kb, so it starts upstream of KpnII and ends right after SstI, but it doesn't disrupt StuI. If something is cloned into KpnII or SstI sites, then the open reading frame of amp is disrupted, and the protein cannot be functional.

Heres the solution

i got 1 mark off for the position of Not I


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Why is wound contraction very slow?
I am working on mathematical model for healing of dermal wounds. For anyone who's a bit familiar with Physics and Math, for the model I use the Cauchy Momentum Equation as a basis, and from there I use already established literature to expand to a so-called morphoelastic model.
From a physical perspective, if a force is exerted, you would expect a material to start moving, upon which stresses arise, until a new balance is found. This all usually happens on a timescale of second. Now when wound healing is regarded, the contraction force is exerted by fibroblasts. I have read that wound contraction happens at a speed of up to 0.75/mm per day. On the one hand this is impressive, yet on the other hand it is very slow when viewed from the mechanical perspective.
So my question is: Is there a biological effect or phenomenon that slows down? Could it be that the migration speed of fibroblasts is the bottle neck? Or maybe skin is in some way tethered to underlying tissue? I know very little about biology, so any help would be appreciated!
Thanks in advance

Is it really that slow? What are you comparing it to? If you're comparing it to simple muscle contraction, you should note that muscle movement is transient and returns to its original shape when the stimulus/energy input ceases. When a wound is healing, it wants to change its shape permanently so it's more like tissue growth. (1/2)

If you compare it with growth of maize root tips, which grow at only 2.4 mm/day or dendritic spine growth, which is only 0.13-0.17 mm/day it doesn't seem that bad. (2/2)

As far as my biological knowledge goes (which is not very far), wound contraction happens due to stresses induced by ((proto-)myo-)fibroblasts. Before, during, and after wound contraction, collagen fibres are secreted in order to replace the injured skin. The new arrangement of the collagen is reflected by the mechanical properties of the tissue.
If wound contraction was to be attributed to a tissue growth-like process, the rate at which it happened would completely make sense to me. But from what I have understood, wound contraction is a mechanical process.

Your comment actually cuts right into the heart of morphoelasticity theory, where deformations are decomposed into an elastic (transient) and a plastic (growth) component

Short Answer : You can not pinpoint any single step for this delay. It is a combination of multiple processes.
Long Answer : I think there are multiple factors that can contribute to this. Dermal Wound healing is a multi-step and complex process typically includes inflammation, new tissue formation and remodeling (Gurtner et al 2008). Each of these stages involved very complex signaling pathways of various components. In addition, there are multiple types of fibroblast cells involved in this process. You are most likely talking about Myofibroblasts who bring the edges of a wound together. However, this itself is a very complex process involving interaction with the proliferation and migration of both mesenchymal and epithelial cells. This is further tightly controlled by Keratinocyte-fibroblast interactions (Werner et al 2007).
So what can you do? : The the physical analogy, which you are trying to implement here, has to apply within some assumptions. You can declare some fitting parameter(s) which can contribute to all the process and validate it according to good experimental data, probably with some kind of mutant data where the wound healing process is slowed down or accelerated. While deciding your assumptions, use as fewer assumptions as possible else you will end up creating Spherical Cow.


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What would happen if we had a device that produced oxygen inside of our lungs?
Hypothetically speaking, suppose there is a device that produces a limitless supply of oxygen. The device is inhaled by a human and is resting inside the (a) lung.
What would hypothetically happen if this were possible?

Welcome to Biology S.E.! If you need additional assistance on how/what to ask please visit The Help Center.

What is your question?

We'd probably choke…

Depending on the efficiency/production of the hypothetical device, it might be toxic

Could you elaborate on the situation in which you want information about the device? i.e. in an oxygen-deprived person/athlete/underwater/etc. Also, a little more information about the hypothetical device would be useful (does it maintain normal atmospheric oxygen conc., or produce excess?)

You might need to narrow your parameters a bit.
Just things to consider:

Our lungs are not hollow organs that can accommodate an oxygen producing machine. They are basically narrow tubes that get smaller and smaller until they end in a tiny balloon-like structure - about 700 million of them. Where would the machine go?
100% oxygen is toxic to the lungs, as it is to many other things as well.
How would the oxygen diffuse to all the other areas of the lung that need oxygen? Diffusion is a complicated process in a structure like the lungs.
from what would it produce oxygen? For example, would it extract it from water? How would the body deal with the loss of moisture from the air in out lungs? Where would the excess hydrogen go?
Hydrogen is highly flammable around 29%. Would we become fire-breathing?
How would the machine not hyperinflate and thus injure the lung?
How would we get rid of CO2? We would still have to breathe in and out.
Etc.


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Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?
When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are known. When there is a mixture of multiple ligands and receptors where each ligand and each receptor can interact with eachother, this is not so simple. For example, lets say you have the following set of information:
$$K_{11} = \frac{[R_1][L_1]}{[R_1L_1]}$$
$$K_{12} = \frac{[R_1][L_2]}{[R_1L_2]}$$
$$K_{21} = \frac{[R_2][L_1]}{[R_2L_1]}$$
$$K_{22} = \frac{[R_2][L_2]}{[R_2L_2]}$$
along with the $K_d$'s ($K_{ij}$) and the total concentrations of $R_1$, $R_2$, $L_1$, and $L_2$. I have not managed to find any publications where this has been demonstrated but I would be surprised if it hasn't been figured out by someone.

Are you familiar with differential equations?

The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is that they capture all the intuition without the tedious algebra.
It's interesting that you are asking for the fraction of ligand bound to receptors ($[RL]/[L]_{tot}$). Typically one is interested in the fraction of receptors that have ligand bound ($[RL]/[R]_{tot}$). This is for two reasons:

Typically the fraction of bound receptor is the physiologically relevant variable for a cell, determining the response of the cells to the ligand stimulus. Since the cell can only sense the concentration of ligand when it binds to the receptor, the fraction of bound receptor is the natural variable to study.
In most contexts, the number of receptors is much smaller than the number of ligands. This motivates the approximation found in pretty much all treatments of receptor-ligand equilibrium that the concentration of receptor-ligand complex is negligible compared to the total concentration of ligand. For cells, this is a fairly reasonable assumption. In this limit, the fraction of ligands bound to receptors ($[RL]/[L]_{tot}$) is always negligible. It's the fraction $[RL]/[R]_{tot}$ that is  interesting. Another reason this assumption might be adopted is that in practice, ligands tend to be soluble while receptors are insoluble. In this case, it is easier to control the concentration of ligand, adding it in excess to a pellet of receptors, and then measure the amount of bound receptors (maybe by radioactivity): in this experiment the total concentration of receptors is measured, not controlled, so you want your equation to be a function of your controlled variable, the concentration of ligand. This requires adopting the approximation above.

The situation in which there are two ligands binding to one receptor has been solved (in the limit that $[RL]\ll[L]_{tot}$): this case is known as competitive inhibition. In your notation, the fraction of receptor 1 bound to ligand 1 (ligand 2 is the "competitive inhibitor," i.e. rival ligand):
$$\frac{[RL]}{[R]_{tot}} = \frac{[L_1]}{[L_1]+K_{11}(1+\frac{[L_2]}{K_{12}})}$$
So I'm going to generalize to the case that there are $N$ ligands and I am interested in the fraction of a given receptor $R_i$ bound to ligand $L_j$. The equilibrium constant for this reaction is $K_{ij}\equiv [R_i][L_j]/[R_iL_j]$.
The receptor is also binding to all the other ligands, so that the free concentration of receptor $[R_i]$ is equal to the difference between the total receptor concentration $[R_i]_{tot}$ and the concentration of each bound complex $[R_iL_k]$ for $k$ from 1 to $N$. And the ligand is also binding to all the other receptors. In order to get a reasonable equation, we have to invoke an approximation very similar in spirit to the one mentioned above, namely, that the concentration of all ligand-receptor complexes is small compared to the total concentration of each ligand individually. Thus I can ignore the difference between $[L_j]_{free}$ and $[L_j]_{tot}$.
In this approximation, I expand out the expression for the equilibrium constant (using $[L_j]$ as shorthand to stand for $[L_j]_{tot}$).
$$K_{ij} = \frac{([R_i]_{tot}-[R_iL_j]-\sum_{k\neq j}^{N}[R_iL_k])[L_j]}{[R_iL_j]}=\frac{[R_i]_{tot}[L_j]}{[R_iL_j]}-[L_j]-\sum_{k\neq j}^N\frac{L_kK_{ij}}{K_{ik}}$$
Note that the sum is over $k$ from 1 to $N$ except $k=j$, which I pulled out of the sum early. I also used the definition of each dissociation constant to write the sum in terms of dissociation constants instead of $[R_iL_k]$, which makes the algebra a lot simpler.
This can then be simplified to solve for the fraction of bound receptors:
$$\frac{[R_iL_j]}{[R_i]_{tot}} = \frac{[L_j]}{[L_j]+K_{ij}(1+\sum_{k\neq j}^N\frac{[L_k]}{K_{ik}})}$$
Suppose instead of being interested in the fraction of receptor $i$ bound to a particular ligand $j$, one is interested in the fraction of receptor $i$ bound to any ligand. I'll call this quantity $[R_i\mathbf{L}]/[R_i]_{tot}$. We can figure this out by noting that
$$[R_i\mathbf{L}]\equiv \sum_{k=1}^N[R_iL_k] = [R_i]_{tot} - [R_i]_{free}$$
We obtain $[R_i]_{free}$ from the formula for each $K_d$:
$$[R_i]_{free}\equiv[R_i] = \frac{K_{ij}[R_iL_j]}{[L]_j}$$
And so using our equation for $[R_iL_j]$, we obtain (I'll spare you some of the gory algebra details)
$$\frac{[R_i\mathbf{L}]}{[R_i]_{tot}} = \frac{\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}{1+\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}$$
(these sums are again unrestricted, from $k=1$ to $N$ including $k=j$).
Happily, if there is only one ligand, these formula reduce to the regular result, namely $[L_1]/([L_1]+K_{i1})$. As another check, if all the $K_d$s are equal, then the fraction of receptors bound to any type of ligand is the same as the bound fraction for the same amount of a single type of ligand with the same concentration as the whole pool of different ligands ($\sum_{k=1}^N[L_k]$), and the fraction of receptor bound to a particular ligand $L_j$ is smaller by the fraction of the total ligand pool that is species $j$, $[L_j]/\sum_{k=1}^N[L_k]$.
If you are really interested in the fraction of ligands bound to receptors---that is, you are working in the limit in which there are tons of receptors compared to ligands, so that the number of receptor-ligand complexes is tiny compared to the number of receptors---then you can use the above equations just by switching $L$'s and $R$'s. In this case you would obtain
$$\frac{[R_iL_j]}{[L_j]_{tot}} = \frac{[R_i]}{[R_i]+K_{ij}(1+\sum_{k\neq i}^{N}\frac{[R_k]}{K_{kj}})}\qquad [R_i]\equiv[R_i]_{free}\approx[R_i]_{tot}$$
A caveat
To derive these equations, I made a pretty strong assumption that the total concentration of all receptor-ligand complexes (for different receptors as well as different ligands) is small compared to the total concentration of each ligand individually. In this limit, we can assume that the pools of free ligands of each species are so large that each receptor equilibrates with this pool independently of each other receptor (there's plenty of ligands to go around). You might be interested in the limit in which ligand binding and unbinding to one receptor affects the binding and unbinding to another receptors, so that receptors are not independent. I am not sure how to approach this problem. I'm skeptical that there will be any sort of closed form solution; in my preliminary thinking about this limit, I think I can imagine situations in which stationary equilibria are not possible: depending on rates, receptor A might partially equilibrate, depleting the pool of ligands, affecting the equilibration of receptor B, which would cause receptor B to "pull" more ligands away from A, in some sort of oscillation. However, that is just speculation, and I'd be very curious if someone could provide more insight to this case, in which receptors are able to "interact" through the pool of free ligand.
One of the take-aways of this whole analysis is that it is very helpful to be aware of the assumptions made in standard derivations that lead to the nice results we learn in biochemistry class, and how those assumptions might have to change if we generalize the system somewhat.

dzjeezz, my math is shaky, and I'm not really capable of upvoting your answer in terms of its content, but heck +1. Nice. Very nice. I really hadn't expected this one to be dealt with any time soon. kudos.


text:
question about directional selection
Cattle breeders have improved the quality of meat over the years by which process?
A) artificial selection
B) directional selection
C) stabilizing selection
D) A and B
E) A and C
I know the answer is D. It is obvious that is artificial selection but WHY is it also directional selection? how do we know? I know the differences between directional, stabilizing and disruptive selection but there is nothing in the question that explains the quality of meat in relation to directional selection. so HELP!

To help understand the problem, it might be good to restate the definition of directional selection that you know. What is directional selection?

There is a small issue in this question that is: everybody does not always use the exact same definition of stabilizing selection and disruptive selection. These two concepts are sometimes used to refer to phenotypic traits or to genes. For example stabilizing selection might either mean,

selection for the mean phenotypic trait of the population
or
selection for the wildtype allele, getting rid of all newcoming mutations.

Under simple genetic architecture the two concepts are equal.
Although for this question I don't think we even need to give a clear definitions between these two words, we'll use the phenotypic based definition (the first one above) in order to ease the intuitive understanding of the answer.
Let's say the trait breeders select for is mean quality and for ease again, we'll imagine this trait as being one unique trait that we can map on one axis from low quality to high quality. Here is a representation of that where the x-axis represent meat quality (left = low quality) and the y-axis represents the density of cows in the population which has the associated meat quality.

If breeders performed a stabilizing selection, it means that they would not improve the meat but only prevent the meat to change quality. In order to shift the quality of the meat to the right (to better quality), breeders need to perform directional selection.
I think the only problem that you had for solving this problem was the conceptual issue of considering meat quality just like any phenotypic trait. And if you want to shift a phenotypic trait on one side or another, you have to apply directive selection.

THIS WAS SO CLEAR :) I GET IT NOW!!
You are awsome and amazing.
Thank you very much.
Have a nice day, and thanks again for your time and efforts to construct this solid explanation :)


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Are there other mechanisms for mutation besides imperfect DNA replication?
I was reading http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/ and saw:

[...] the evolution of entire species can be changed by a single
  mistake in the replication of a strand of DNA (this is one mechanism
  for mutation).

... implying other mechanisms for mutation exist. Do they?

Absolutely. Ionizing (X-rays, neutrons, electrons, heavy ions) and non-ionizing radiation (UV), chemicals, etc. are able to induce DNA Damage, which is then imperfectly repaired. So it's not an issue of imperfect replication, but also of imperfect damage repair.

DNA methylation over CpG doublets can cause mutation since 5mC can undergo spontaneous deamination and covert to a thymine.


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Why are we using upper teeth and lower lip on labiodental sounds?
I came to wonder this when studying language (as well as other same theme question posted just few ago). For example the word "fantastic" we use upper teeth and lower lip to produce F sound, instead of using lower teeth and upper lip, which would work as well with a small practice.

I'd imagine I'm not the only one who just said their saying it to see if you're right.  It could be something to do with the bottom teeth being set behind the top ones I suppose, you have to use energy to pull your bottom jaw forward if you're doing it the other way.  Really interesting though xD

It definitely feels like an unusual jaw movement to do it with your lower teeth. The jaw is required to laterally move forward rather than longitudinally move, which is a more common movement in terms of other vocalisations and eating.

@RoryM Yeah, I hope nobody was looking a second ago when I was biting my lip and blowing! :)

lol, yes I found that funny experiment. But again more you do it, more natural it comes plus you may become economical with jaw movement. What is the variation of jaw placement on human skulls? Some have a different shape jaw and more in front than others.

This article might help, and is at least related. http://www.psych.mcgill.ca/labs/mcl/1528.pdf

@LanceLafontaine: Broken link (403).

@Mechanicalsnail, works for me.

@LanceLafontaine: By any chance are you accessing the site from within that university?

Nope. Anyhow, here's a PubMed link which should work.
http://www.ncbi.nlm.nih.gov/pubmed/8035233

The alternative articulation, called dentolabial, is more difficult to articulate, so it is very rarely used in human language. However, it apparently is common enough in disordered speech to be allocated an ExtIPA diacritic.
The reason labiodentals are easier: Humans normally have a slight overbite.

When the jaw and lips are in a "neutral" position, the lower lip is close to or touching the upper teeth, so with a small vertical movement of the jaw (together with tensing the lip) one can articulate a labiodental. Articulating a dentolabial requires moving the jaw a fair distance forward, to go around the upper teeth before reaching the upper lip. As Ben pointed out in the comments, front-back jaw movement is unusual, a less "common movement in terms of other vocalisations and eating".
Furthermore, since labial articulations are directly visible to observers, learners are especially likely to imitate others' exact articulation. Thus even though labiodentals and dentolabials sound similar, everyone in the population of speakers uses the same articulation (rather than having both articulations in free variation).
Perhaps dentolabials would instead be more common if most people were like this:

I wanted to suggest the slight overbite, but had no supporting information. Great answer!


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Why apes started to contemplate and become altruistic?
I was asking this first on philosophy forums, but it is suggested, that answer could be found from evolutionary view of point, so here we go:
Again my question raised when thinking of myths, their origins, mysticism and religious institutions. It is said that prieshood came to existence, when ape first landed from trees to earth collecting and gathering fruits, hunting and then started to plant and farm. Whole agriculture was build organizating leadership of the society among whom were the priests and shamans who tried to understand natural forces with limited knowledge and superstition. Accelerating need for planning future, not only own family's, but whole society's future forced thinking process of humanized apes to become more involved with contemplating. Did some of the deep thinkers find that there was a dimension on meditation which is next to impression of using herbs and drugs to bring mental experiences, were they hallucinations, visions, calmness or anything similar alive? Thus they became ascetics and adept on focusing mind toward itself while other part of high class of the society became adept on aiming mental activity outward, improving skills to master matter and physical nature. On ancient times both still shared same concept of need of supernatural forces to be placated or otherwise controlled to get or avoid certain every day results.
This also brings up a huge evolutionary problem so to say. While apes, if they were just lead by rather unconscious instincts, they would have reproduced and build on the principle of the strongest is the leader. But when reasoning, ability to think "cunning plans" as stated by Baldric on Blackadder came to existence, then the most clever often won the game. But what is clever on the other extreme of the religious practice, self sacrificing and altruistic ethics? It feels almost unnatural, that religions evolved to direction, where ethic and moral rules fights against physical existence or surveillance of the individual. There is a strong hope of afterlife compensation, which explains some of it, but I'm still a bit struggled, why (and when) apes started to retire to the forests to meditate and rather practice altruistic ethics, loving enemies for example instead of getting justice and their own benefit fulfilled in first hand, instead of reproducing and fighting for their lives and space?
To bring whole question to modern life, I think zen buddhism is a good example of such practices brought to other level. While on the most plain form they don't expect belief on the existence of the self nor karmic relations of the acts, they still rather follow high ethics of the teachings of Buddha and live simple middle way life just being aware and mindfull of the things happening at the moment, which is the ultimate goal of the practice and life.

We're not entirely convinced that there's enough biology in that question to make it a fit for this site, and even if there was it's very broad :)

No philosophy, biology, religion and antropology forums accept my question. One I haven't tried yet are pseudo sciences, gotta try ;)

You should consider cogsci.SE which already has some questions in related topics of game-theory and evolution. The site has provided answers to similar questions (the particular Q was badly framed) both an evolutionary and psychology perspectives. If you do decide to ask on CogSci, take time to focus and scientifically frame your question. You can edit and flag for migration.

I think this is a difficult question all around, which is why its a little uncomfortable for some to be entertaining questions which are often seemingly metaphysical in nature.
I think also that it is true that biology and neuroscience will have a big impact on the question, its also fair to say that the jury is still out on this question.
The genetic anthropologist Svante Paabo is one of the most engaging researchers in this question.  He started out studying the difference between the human gene sequences and the chimpanzee to try to suss out the specific genes which might be be responsible for out social selves.  So from this point of view, it might be that intelligence started at most about the time of human chimp divergence, 8-25 million years ago.
Finding the specific genetic structures that convey our unique cognitive or social abilities would certainly pinpoint that time much more accurately.  There is just 1-4% difference between the chimp and human genome sequences (depending on how you calculate it), but even 1% of a 5 Gb genome is a lot of differences and no intelligent mutant chimp has been found (that they've told us about!) .
Since then, a lot of interest has focused on assembling a complete Neanderthal genome sequence.  Since Neanderthals diverged from humans about 500k years ago, and there's plenty of evidence that they were intelligent, comparing the three genomes (human chimp and neanderthal) would help pinpoint the specific genetic elements which are distinctly human.
If it is a mutation or set of mutations as the current thinking implies, there is a good chance that it is a combination of strong selection and accident.  Its true that cooperation is often enjoys a strong selective advantage, but it doesn't make you smart or hospitable.  When we talk in biology we don't say altruism, we say cooperation.  If such cooperation happened only because of selection, we would see such behavior in other primates.  So if we see this, I would lay odds to look for a rather complicated story...
Another interesting person to read is anthropologist Terrence Deacon, who is trying to understanding the terms with which we define intelligence.  About ten years ago there were actually experiments that showed that chimpanzee some strong candidate intelligence genes related to cognition could be put into people (who needed gene therapy because they had lost cognitive function) and restore that function.  Apologies, this is anecdotal - i saw him give a great talk, but he's moved on a bit and can't find the references.
This is important I think because the fundamental definitions of human intelligence have failed over the years, from the old chestnut of using tools, to a recognition of mortality, to awareness, animals have surprised us, particularly primates.   I wonder whether we will be able to confirm these vital factors until we get a monkey asking for the keys to the car so that they can go get some pizza.

Thanks for suggest. I need to browse thru links and see, if there are any clues :)

I found this site which deals with the same question: http://www.fitnesshealth101.com/fitness/meditation/origin

The human genome is closer to 3.2 Gb rather than 5 Gb. I'm not sure about chimps, but I expect it's similar.


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Incremental denaturation of protein mixtures
When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time.
I assumed that Brownian motion degrades the protein structure more and more. But I noticed that, in practice, one has a mixture of proteins, and I wonder whether they may behave differently, causing some macroscopic effect?
As an example, taking the clear part of a chicken egg:
No doubt it contains multiple proteins. When heating it slightly above the denaturation point, it coagulates slowly.
I would like to understand in which way that is caused:

by proteins that denature at some temperature dependent rate - where all proteins behave very similar
by different proteins denaturing at different temperatures at a much higher rate than others, so that partial coagulation means some proteins are coagulated, and some are not
of course, it could be both combined, or a completely different way.

Related: How does protein denaturation work?


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Storing Taqman plates with polymerase in fridge before running
I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, including controls etc.). Since our thermocycler can only handle one 96-well plate at a time, it has been suggested that I make up the mixes all together, aliquot them into the plates, then store the plates at 4°C (well wrapped in plastic or Parafilm) until ready to run. I would imagine that the plates would be in the fridge for just one day, at max overnight.
My question is about the polymerase - can I add it ahead of time, and just take the plate out of the fridge and pop it in the thermocycler, or should I add it just before use? I've been kind of out of the DNA/RNA field for over 10 years, and I seem to remember from before that polymerases could have residual activity even at 4°C. Is this still the case, or have they improved to only be active at 60+°C or whatever your temperature is?
Alternatively, is there another ingredient I should leave out until just before amplification? cDNA? Probes? Something else? Also, does the storage time make sense? Is overnight okay, or should I run them all the same day? Is over the weekend okay? I don't want this question to extend into a too-broad "How do I do qPCR?" question, but any tips you have would be very helpful. As far as I'm aware, all the reagents are from Life Technologies/Applied Biosystems.
The reason I ask is because it seems to me that it would be much more accurate and reproducible to prepare the master mix with polymerase already included, instead of adding 1 μL of polymerase to each well just before running the assay.

I don't see why you can't just freeze all the samples, and then prepare the master mix and run the PCR in one single go. Purified cDNA is far more stable than PCR mixes.

I stored several pre-mixed (with all the components, the polymerase included) plates in a -20˚C freezer for up to 1 month and still worked beautifully. Was using Taqman reagents. Would opt for the freezer rather than the fridge. Just take out your ready-to-amplify plates a bit ahead of time to allow them thawing.

@MarchHo the cDNA has been prepared ahead of time and frozen. On the day of the qPCR, I prepare the reaction using 2 dye-labeled probes (gene of interest and internal standard), PCR master mix, template, and H2O. All this is aliquoted into 96-well PCR plates and stored at 4C. When it's time to run the next plate, it's taken out of the fridge, polymerase is added, the plate is put in the thermocycler, and run. What I'm wondering is whether I can add the polymerase when I'm setting up the plates, then just take the next plate out of the fridge, put it in the thermocycler, and run.

I would suggest freezing it at -20 rather than at 4. You will still have some activity at 4, and its best to avoid that.

It is much easier and better to set up the reaction again. After a run, the thermocycler (for Real-Time such as light-cycler) should generally be allowed some rest (1h). In this duration you can prepare your second plate. You can aliquot cDNAs in PCR tubes (or strip tubes) with your probes and keep them at -20. You can add taqman master mix with appropriate volume of water before the reaction and load the PCR plate just before running the PCR.

Not sure if this question is still valid, but it was marked as unanswered and frequently viewed, so here's a go :)
These days most polymerases (certainly for Real Time PCR) are so-called Hot Start enzymes (ask your manufacturer, because they save you a whole lot of trouble!). They are modified with a protein that prevents them from working until activated at 95 deg. Celsius. Be aware though that not all hot start enzymes require the same activation time at 95 deg. Celsius, and some enzymes lose activity when activated for 15 min. at 95*C instead of 2 min.
In my experience storing plates at 4 degrees (or room temperature) is not a problem at all, and most manufacturers advertise that the PCR mixes (including primers, probes and DNA) are stable at room temperature for 24 hours. You do however need to protect the mixtures from (sun)light because the probe might be damaged when exposed for longer times.
Personally, I would not recommend storing real-time PCR plates in the freezer, because condensate will most-likely form when you thaw your plates. This can influence the PCR, as real-time PCR uses light for the analysis of your samples.
If you want to save yourself some pipetting, but can't prepare plates in advance, you can prepare a primer-and-probe mix, which you can freeze in batches. In our lab, we keep a stock of primer-and-probe mix for every assay. Maybe this also works when you already add water and PCR mastermix, but I have never tried. I wonder how other people do this, so please leave a reply.
Hope this might help some people.


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What is the advantage of the way eukaryotes initiate translation?
The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ?
Edit : I specifically want to know why eukaryotic ribosome first attaches to tRNA and then to mRNA but prokaryotic ribosome can do this in either order. Is there any advantage of the former ?

Is there any aspect in particular you are interested in?  Such as Shine-Dalgarno versus Kozak, or what?

@Amory Edited the question !

As far as I understand it (and I'll preface this by saying that initiation is not my strongest point), but prokaryotes utilize the beautiful AGGAGG Shine-Dalgarno sequence.  Usually around 8bp upstream of the start codon, it is this sequence that the prokaryotic ribosome seeks out to initiate translation.  It does this through a complementary region in the 3' sequence of the ribosomal RNA.  Upon complementary binding, the ribosome and mRNA are correctly bound.  Convenient!
In eukaryotes, however, there is no consensus SD sequence, so a different mechanism must be used; the complex of 40S and Methionine tRNA serves this purpose.  The two together scan the mRNA, looking for an AUG start codon which the tRNA is complementary to.  This eventually brings the full ribosome (40S + 60S) together to start translation.


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I found these skulls in a old bottle in the woods. Can you tell me what they are?

Can you help me identify these skulls I found in an old bottle in the woods?

That top photo looks like a shrew skull.

Where and in what type of environment did you find them?

I found them in a bottle that I picked up in the woods in Illinois.

Its a Shrew skull.

Hainault Forest Website
Photographs by © Brian Ecott


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How to avoid air bubbles while pipetting?
I get air bubbles while pipetting small volumes. How can I avoid them ?

You can try to be slow?

You have to pipet up slow and make sure your tip is (and stays) completely submerged in the solution. On the other hand it shouldn't be put in too far.

You're still pipetting too fast, you should move the piston slowly and evenly to avoid air bubbles. Also make sure that you wait a second or two for the liquid to rise before moving the tip out of the liquid reservoir.
Pipettes can also behave rather weird with any liquid that differs significantly in any physical property from water, e.g. very viscous solutions.
You can find a few more tips in this document from Eppendorf or this one from Thermo Scientific.


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What is difference between several mRNA RefSeq for one gene?
I'm looking for mRNA RefSeq sequences for a given gene in the UCSC genome browser by searching gene name "HLA-F" in human (scroll to Refseq genes section). There are several RefSeq mRNA for the gene, what is difference between these RefSeq sequences and which one of them is what I want?

I'll walk you through the process of determining this:

Note that there are two gene names presented: HLA-F and HLA-F-AS1. The "AS" part means, "anti-sense", so it's on the opposite strand...so ignore all of the HLA-F-AS1s.
Note the associated chromosomes. chr6 is a normal chromosome, but things like chr6_cox_hap2 aren't. Instead, these are haplotype patches/chromosomes. The HLA regions are highly variable, so having only a single reference sequence ends up being problematic in many analyses, such as finding sequence variants. For your purposes you may or may not want to ignore these, it depends on what your goal is.
If you ignore the haplotype patches then you're left with 3 listings on chr6. These are the 3 isoforms of HLA-F. You end up needing to use the refseq IDs for each of these.

BTW, Gencode/Ensembl list 4 isoforms for HLA-F, rather than 3. Whenever UCSC disagrees with Gencode or Ensembl, go with Gencode or Ensembl.

Many thanks for your nice reply. Just one thing, would you please help me out how to get Refseq sequences of interest from Ensemble in a way that the CDS is recognizable from UTRs in the sequences?

Google "Biomart".

Would you mind justifying your last statement? >Whenever UCSC disagrees with Gencode or Ensembl, go with Gencode or Ensembl. Not that I disagree, but it would be better to give a reason for suggesting some source is better than another.

UCSC's annotations have historically been a bit of a mess. For example, they have genes with the same ID on multiple chromosomes and strands, which will break a number of tools. refSeq in particular tends to be overly conservative in what it includes, so typically using it results in missing a number of likely correct isoforms. For what it's worth, UCSC now defaults to Gencode for human (and Gencode is essentially the same as Ensemble)

@DevonRyan Thanks. Maybe this paper is also relevant.


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Hypothalamic breakdown and effect of temperature on membrane lipids
I'm in my last year of high school and doing a research assignment on thermoregulation. In the excellence level exemplar for the standard, a student made the statement:

Once the body's internal temperature is well above the optimum range, important enzymes start to denature, phospholipids start to destabilise, and cell membrane lipids begin to dissolve. As a result of this, important organs in the trunk of the body are unable to carry out important metabolic processes. If the temperature continues to rise it causes tissue damage which could cause disability depending on its severity. It also causes the hypothalamic thermostat to break down, meaning the body can no longer have control of the core temperature.

However, I have been unable to find any sources which mention destabilisation of phospholipids or the dissolving of membrane lipids. I have also not found anything on tissue damage or the cessation of the hypothalamic thermostat.
Are these things true? And if so, could someone please direct me to a reliable source which states this?

If you supply heat to a system, the entropy increases which results in destabilization of order. This is a general thermodynamic principle and you can refer any basic book on that topic. However, it is not essential that all molecules would be affected equally. There are heat-stable enzymes in thermophiles such as Thermus aquaticus which are resistant to heat. Also the membranes in these organisms are made up of stronger and more rigid isoprenoid lipids.
Even in mesophiles, lipid membranes with higher content of cholesterol are rigid and more resistant to thermal movements.
On Breakdown of thermostat:
The body can regulate the temperature only in a certain range; at higher temperatures these mechanisms will fail as well.


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Are spiders part of the study of entomology?
The definition of entomology says it is the science of studying insects.
I know spiders are not insects but does entomology include studying spiders as well?
Otherwise is there any name to the science of studying spiders (class Arachnida)?

Spiders are part of a taxon called Arachnida. Arachnida also contain scorpions, Oppiliones, acari, … The science of arachnids is logically called Arachnology
However, (wikipedia):

Entomology (from Greek ἔντομος, entomos, "that which is cut in pieces or engraved/segmented", hence "insect"; and -λογία, -logia) is the scientific study of insects, a branch of arthropodology. In the past the term "insect" was more vague, and historically the definition of entomology included the study of terrestrial animals in other arthropod groups or other phyla, such as arachnids, myriapods, earthworms, land snails, and slugs. This wider meaning may still be encountered in informal use.

In other words, in the informal sense entomology include arachnology but the strict definition entomology does not encompass arachnology.
You will find here on tolweb.org more information about the systematics of Arthropoda

I understand this. But generally the term Arachnology seems not very used; even the wikipedia's article seems incomplete or needs more "inline citations". In the other side, it was looking entomology includes spiders and some other non-insect animals in the past but it is not clear if it is still accepted or if any other animals should go in thier specific terms.

@ruffp I am not sure I understand your comment.. You know, all this is just a matter of definitions. And the definition of entomology has not real importance to science, just like the definition of biology itself is not of real important to biologists. So, what has to be known is that some people use "entomology" this way and some people use "entomology" that way. And yes, of course this kind of definitions are changing over time. It is indeed likely that entomology has evolved to be used in a more and more restrictive way as everybody accepted that spiders are not insects for quite a while.

I had this question when I start to use this site to ask questions about spiders and I did not know if I can tag them with Entomology because there is no Arachnology tag. I did not know as well if this question can be in the meta site or here, but because I wanted a general answer not specifically related with tagging on this site, I post it here.

As a general rule no. Spiders and other arachnids generally tend to have their own field of study called arachnology.

The term entomology is derived from the Greek words Entomo ("Insect") and Logia(word) . Considering that Entomo generally refers to insect(s) the question is whether Arachnids could be considered entoma in Greek as there is no other used term that refers to arachnids.

Although this answer gets at the etymology of entomology, it doesn't quite consider the usage which seems to be more important here, and doesn't have any citation for that usage. There are lots of words for which the etymology is not particularly instructive for the usage since usages change.


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Prokaryotic Ribosomes
During bacterial protein synthesis, when ribosomes attach to the cytoplasmic membrane and form a polysome, to what molecule are the ribosomes attaching? Is the polysome held to the cytoplasmic membrane by just a single connection between one ribosome and the particular attachment molecule?

Do "ribosomes attach to the cytoplasmic membrane"? Membrane-bound Ribosomes Define the Rough ER. Ribosomes are not membrane bound. A polysome represents a cluster of ribosomes, bound to a mRNA molecule.

Here is a good article on bacterial protein synthesis: http://mmbr.asm.org/content/69/1/101.full

According to "Microbiology: An Introduction" by Batzing, Ch. 2 p. 24, "During protein synthesis, bacterial ribosomes attach to the cytoplasmic membrane.."

According to Smith et al., 1978, bacterial ribosomes don't necessarily bind directly to the membrane, but through the nascent chain, in which case nothing is truly attaching to anything..


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H3K36me3 role in RNA polymerase II elongation
I found a paper describing the association of RNA polymerase II with the histone methyltransferase Set2 that methylates H3K36.
At the end they say:

While our results strongly implicate K36 methylation as having a direct role in RNAPII elongation, the precise role is currently unclear. We propose three possibilities: (i) K36 methylation generates a chromatin structure that is more permissive for RNAPII passage. In this scenario, the loss of Set2/K36 methylation would result in a chromatin structure that is more difficult for RNAPII to pass, which might appear as an increase in RNAPII occupancy along the gene through increased pausing. (ii) K36 methylation generates chromatin structure that is less permissive for RNAPII passage. In this case, K36 methylation acts as a negative regulator of RNAPII elongation, and the loss of this “mark” permits increased RNAPII passage.

I am a bit confused about the (ii) point. If the loss of this mark permits increased RNAPII passage we would not see the H3K36me3 pattern in the active genes. Why is then H3K36me3 said to mark active genes?

We have a more recent study, Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin and they seem to suggest that in accordance with your '05 paper, H3K36me3 in part contributes to the formation of tightly packed, inaccessible chromatin. You'll see there's a lot of crosstalk, but you would also think that transcription in heterochromatin might be poor.
Looking at yeast studies, though, it would seem that RNA Pol II is capable of transcribing through heterochromatin anyways so long as specific cofactors are present (Acetylation of H3 K56 Is Required for RNA Polymerase II Transcript Elongation through Heterochromatin in Yeast)


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Can animals make their own unsaturated fatty acids?
I know that animals can't make poly-unsaturated fatty acids (PUFA) and so require them from dietary sources. For eg.Omega -3 and Omega 6 fatty acids.
My questions : Can animals synthesize other unsaturated fatty acids from scratch? If not, does the unsaturated fatty acids in the phospholipids of plasma membrane of animals come only from dietary sources?

At least fish should be able to do this - most Omega-3 and Omega-6 fatty acids used for food supplementation are extracted from fish, namely salmon or cod.

Fish don't make it themselves either, they get it from algae through the food chain.

However, it is very energy-intensive and not at all efficient for heterotrophs to desaturate and elongate LA & ALA to EPA & DHA, so it is better for them to obtain these long-chained fatty acids from their diets. This is true from zooplankton to crustaceans to insects to fish, birds, and mammals (lots of refs for this).

Yes, animals can make their own unsaturated fatty acids.
Mammalian fatty acyl desaturases can introduce double bonds at the Δ5, Δ6 and Δ9 positions (i.e. numbering from the functional group). As shown in the diagram below, this means that we cannot introduce double bonds at the ω3 or ω6 positions (i.e. numbering from the methyl end of the molecule) in fatty acids of a reasonable length (see any Biochemistry textbook for confirmation).
I've illustrated the impossibility of us making α-linolenic acid as an example.

So can the plasma membrane unsaturated phospholipids be made from scratch ?

@biogirl Yes, the unsaturated fatty acids will be incorporated into new phospholipids at the endoplasmic reticulum then transported in vesicles to the plasma membrane.

Only linoleic acid ($\omega 6$) and $\alpha$-linolenic acid ($\omega 3$) are essential. Other PUFAs are synthesized from these by desaturases (as Alan Boyd pointed out).
I haven't come across any study that reports de-novo synthesis of $\alpha$-linolenic acid in animals. However, this study reports that mites can synthesize linoleic acid.


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Number of introns in a genome
Humans have approximately 21000 genes but they probably make more proteins than that. This has been explained by many mechanisms like alternative RNA splicing.
My question is - If what we call as "introns" and "exons" vary so much, then how is the  number of introns present in a genome determined ?

What do you mean? What we call "introns" and "exons" is actually quite well defined. It is the concept of "genes" that causes problems. Counting introns is relatively straightforward (as long as you have an accurate count of genes). It is not a very useful exercise but it is not hard.

@terdon I didn't mean to say that our concept of what we say as intron and exon vary. I meant that for each different protein from the same pre m-RNA , what sequences we call as introns and exons would vary.

Ah I see, well anything that can make it into a mature mRNA is an exon by definition. Anything that does not is an intron. So yes, the same stretch of genomic nucleotides can actually be both in different mRNAs.

Yes, the individual number of exons/introns will vary in a transcript, but what you can do is just count all possible exons of a gene
For example, lets say you have an alternative exon in these two isoforms. The XX's are exons
XX---XX---XX---XX
XX--------XX---XX
We would say this gene has 4 exons and 3 introns, even though one isoform only has 3 exons. Its the transcript that varies in number of exons, the gene remains constant.
Heres a slightly more complex example. Mutually exclusive exons
XX---XX--------XX
XX--------XX---XX
We would still say it has four exons. Pretend that every exon of every isoform is included and thats how you get the number of exons in gene. So for the above example, just pretend both mutually exclusive exons are included
XX---XX---XX---XX
According to this old paper there are 8.8 exons per gene (7.8 introns). Their gene number count is high because its older, but they estimate that there are 207,344 introns in the human genome.

Introns is not always "exons - 1", you can have spliced UTRs with a leading intron for example, or a trailing one in the 3' UTR.


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Risks in bacterial phage therapy
I just finished reading J. Craig Venter's book Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. The book is a little over a year old now, and Venter has an optimistic outlook that bacteriophage therapy will become an effective alternative to gene therapy and viral immunotherapy. He mentioned that the JCVI (J. Craig Venter Institute) is working on such projects. Are other companies also researching, and has progress been made? What are the expected risks? How can rogue, harmful phage mutations be controlled? Can this type of therapy be applied to cancers?

Check out oncolytic viruses

Have you read the wiki page on phage therapy? This technology is only used for treating pathogenic bacterial infections, particularly those that do not respond well (or at all) to conventional antibiotics. It is not related to gene therapy or viral immunotherapy, aside from the fact that phages are viruses, so I'm not sure what "effective alternative" means, as the three are used for entirely different things. Google "gene therapy" and "viral immunotherapy" to learn more.

The Eliava Institute in Tiflis (Georgia (a country)) has been at it since the 1930`s. A US company sells a phageproduct for desinfection of meat.
The risk of Phagetherapy is there, if the phage is ill choosen or contaminated with other phage it could introduce pathogenic genes to the target or other bacteria.
If those risks are eliminated there is very little risk in phage therapy aside from the fact that it may not work at all. Phagetherapy is most useful in regions where bacteria are normally found, in other places the immunesystem will make short work of it.
The faster and cheaper sequencing gets the more effective phagetherapy will become. Since a "bad" bacteria can quickly be isolated and a proper "phage cocktail" can be prepared. If we get to the point that we can sequence the whole microbiom of a person then i bet that Phagetherapy will be a very normal thing.
To your cancer question, i think its rather hard to apply it to cancer therapy except if u are looking to combat the cancer with a Intracellular bacteria...but then again. How u get the phage to it.
A excellent read on this topic is the Book "the bacteriophages".

In Venter's book he does mention that Russia has been the most active in phage work. With oncocytes if we become skillful enough to genetically engineer phages to their most minor details, can't we just bypass any involvement of a bacterium and just have the phage directly target the cancer cell? Create an oncophage?

I would think that the best way to archive that is to use oncolytic (or a virus that marks the tumor cell for the immunesystem) viruses (mammalian). Phages no matter how cool they are, are specialised towards bacteria. First the phage must get into the human cell. Then it must replicate or inject genome. Then replicate in a orderly fashion and at last get out of the cell. The structure of bacteria and eukaryotic cells is way too different. But oncolytic viruses are a VERY hot topic currently and im sure they will lead the way. Since a designed virus is easy to patent. Even big companies Win:)

Can anyone provide citations or further reading for this?

You run the risk of the killed cells suddenly releasing huge quantities of cytokines. If this occurs you may cause spike in capillary permeability and basically create massive sepsis. The bacteria will have to be killed SLOWLY to prevent them spilling their contents into the circulatory system. But, I have always believed phages could be engineered to control certain infections like urosepsis. But, any phage therapy may be single use only. I used to inject them into rabbits to prepare antisera used in phage growth experiments, I guess that is one of the reasons phage therapy is out of the mainstream. http://www.nature.com/news/phage-therapy-gets-revitalized-1.15348


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Does every human eye see the same visible spectrum?
It is said that human eye can see light with wavelength approximately between 400nm and 700nm.
Are these upper and lower bounds same for every human? If not, what are the means and standard deviations of these upper and lower wavelength values for human eyes?

Basically every human sees the same spectrum as we all have the same four types of photoreceptors: rods and a cone for green, red, and one for blue light.
In very rare cases there are women who have a duplication of one of their cone genes (usually the red one). If one of those duplicates mutates slightly, this results in a kind of fourth type of cone (see it mentioned here at Wikipedia), so they see a different spectrum.

This is not entirely correct, there are multiple variants of each of the three colour photoreceptors that have slightly different response curves. I do not know whether these variants result in different minimum and maximum sensitivities.

Also, you've somewhat confused the women having a fourth type of cone too. What happens in some women is that they have two variants of the same colour photoreceptor (red, almost aways).

I've also read studies on intraocular lenses that suggested that the humans eye sensitivity to light changes with age.

The variants would produce different maximum and minimum sensitivities. The bounds aren't sharp, they are soft. As light moves out of the visible spectrum the response gets weaker and weaker, but it's not just a sharp drop. So different variants of photoopsins would change those "boundaries".

Human eyes all use the same optical pigment photopsin, so they all have the same basic frequency response.
There are differences. For example cataracts will change the sensitivity of the eye to colour, and people with colour blindness have various defect to cone cells that affect colour response. However these are secondary effects.


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If the body continuously produces new sperm, how is there room for it?
If you never ejaculated, how is there room for the constantly generated new sperm? I mean, is there always room for more?

Your testes are a sort of waiting room where sperm hang out, and if ejaculation does not occur, they eventually die, just like red blood cells (or any of your body's cells). Once cells in your body die, they are broken down, and your body uses the components and nutrients to create new cells.
So it's a continual cycle of replacement and death.
Read more here

Hi @J.W., Welcome to Bio.SE, and thanks for the post! You would receive much better response (i.e., more upvotes) if you wrote a more substantial answer. It's great to link to a resource, but providing a bit more info here would make this a stronger answer. It's also great to use very accessible language in your answer (e.g., "waiting room" and "hang out"), but following this language up with more biologically appropriate terminology helps provide a greater sense of credibility to your answer. Please consider revising and adding more detail to your answer. Thanks!


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Why people like to see pornographic scenes, but do not feel the same about eating scenes?
This question may seem funny, but I think biology must have good answers.
I think no more explanation is needed.
I really thought about this and searched for an answer, but there is nothing yet.
If you know some thing about or have some thing which may lead to good answer(s) please express.
Also, do animals portray the same behavior in such situations?

:( Please don't be wrong with my question. I really think there most be a good answer to this in biology. thank you

Why do you say they don't feel the same way? Most people enjoy seeing sexual images of attractive people, and seeing these pictures makes them want to have sex. Most people also enjoy seeing pictures of particularly delicious food, and seeing these pictures makes them hungry. Seems pretty similar to me.

Look Octern, There is no eating movies to be like porno movies.

http://www.foodnetwork.com/

I think this could be off topic here unless you want some in-depth details into the biological side rather than psychological.

@MySky: there are plenty of TV shows about cooking, not to mention that there are thousands of food-bloggers.

This would probably be better in http://cogsci.stackexchange.com

@octern And yet I don’t see a multi-billion dollar industry around food videos. Sure there are cooking shows but their economic relevance compared to pornography … is … to say the least … you see?

Sexual arousal, in and of itself, is pleasurable in a way that hunger is not.
As to why this is, perhaps visual stimulation and anticipation improves the sexual function of animals more than it improves eating.  One possible explanation is sperm competition.
Either arousal state can be induced by visual stimuli.  However, the respective hormones work differently.  Ghrelin doesn't affect hunger and feeding(1) the way that dopamine affects arousal and mating(2).  Also, starvation has been found to decrease dopamine concentration(3) in those same areas that sexual stimulation increases it(4).

For these two phenomena to create the same feelings all of the time, the physiology that engenders these feelings would have to be the same.  All I can do is point out that these have been separate and distinct even in yeast and bacteria and invoke a likelihood argument.
The impulse for hunger is almost as old as living things.  In bacteria, cyclic Adenosine mono phosphate (cAMP) mediates hunger, though this does not appear to be universal.
Sexual reproduction appeared much later - in the single celled eukaryotes mating factors for instance are mediated by the MATa/alpha receptors.
In animals like C elegans the differences persist (hunger, mating).  This is not a precise argument, but there is the entropy argument - the odds of these 2 signals evolving together biochemically or genetically is quite unlikely given how separate they have always been.
That's not to say that eating food can't create a sexual arousal, but it does not do so all the time.  The sexual response appears to be plastic and adaptable to nearly any sort of stimulus.  The fact that in primates and many other animals, the pleasure stimulus is related to both mating and eating might make them seem like similar impulses, but when you go deeper it doesn't seem plausible.  So the two could hypothetically create the same feeling, but if you are asking why doesn't it usually... then there are lots of reasons why.
I find it helpful to reverse the question and ask - what would happen to a species where you could suppress the mating impulse by eating?  Probably not an adaptation that would survive long.

Why people like to see pornographic scenes, but do not feel the same about eating scenes?

Well, the whole point of watching porn is sexual arousal. (Or research for the curious, but that's another thing)
Watching someone eat delicious-looking food CAN make people feel hungry. I admit, I have a bad tendency of feeling hungry if I see good food, or if I see someone eating good food.
But I don't get the point of the question. Are you wondering if most people feel this way about watching someone eat, or are you wondering if people are AROUSED by watching someone eat? Lol. Some clarification would be useful.
EDIT: Ok, I think I get it now. You're wondering why aren't there any "food scenes" for food-loving people? Well, it's not as widely prevalent as porn, but it IS there for those who are into it.
Example: http://foodporndaily.com/explore/food/
^ One of my favourite sites, actually.

People can satisfy their sexual urges on their own (that is, without a sexual partner) through masturbating. They cannot satisfy their hunger on their own (that, without food).
I suppose people could eat one food while looking at another kind of food pretending that the food they are eating is the one that they are watching, but where's the fun in that?
Having sex with an attractive person is an indicator of biological desirability ----- namely that another human being wants you in the way you want to be wanted due to your accomplishments or social status. Thus, people watch or read porn to satisfy their need to be accepted or to make them feel as if they are such a person with accomplishments or social status or to compensate for things not going their way in life and subsequently masturbate to such porn.
As for hunger, a better analogy for porn would be taking those kind of drugs that make you feel less hungry.
So yeah, for sex, people watch porn. For hunger, people do not compensate for their inability to eat by looking at food that they cannot have. They would probably take drugs or something. I'm not quite sure if such a thing exists, but I swear one of my grade school teachers said that there was some kind of drug that makes people stop feeling hungry.
I think a better analogy for looking at food they cannot have is looking through pictures of a lustful or romantic interest with his/her romantic partner.
This may sound like a stupid answer that is more philosophical than biological from some loser with 1 reputation. I request commentary along with any downvotes.

Can you please make this a real answer with references?

@Chris This may sound naive, but who needs references to logic? If I prove to you 1+1=2, do you need a reference?

@Chris If I could, I would comment that the question is wrong. OP's analogy is wrong. The analogue of watching porn, falsely satisfying one's sexual desires without a sexual partner, for food is not looking at food but rather falsely satisfying one's hunger without food namely taking drugs.


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naturally occuring fatty acids
The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance of cis double bond in naturally occurring fatty acids? Why the naturally occurring fatty acids don't have double bond in trans configuration?

Trans double bonds in fatty acids may disrupt cellular membranes because of their shape. Normally the fatty acid tails on phospholipids are kind of lined up, allowing them to form a double layer. You can imagine them being more or less rectanglular, and 2 layers of these rectangles form the membrane, with fatty acid tails pointing in. Since cis double bonds don't disrupt the shape, they fit in ok. Trans double bonds kink the tail, and make the membrane less ordered. This is pure speculation, so I'm leaving it as comment.

@user137.. you are correct.. But it is not about kinking.. trans-fatty acids make the membrane rigid because they pack closely.

The diversity of fatty acids produced by an organism is limited by the diversity of enzymes which synthesize them. Unsaturated fatty acids contain carbon-carbon double bonds which do not isomerize. The capacity for humans to produce cis fatty acids is probably selected for because of their lower melting point which prevents arterial clogging. Cold blooded animals utilize cholesterol to increase membrane fluidity when their body temperature is low.


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How does a cell create/gain its initial ribosomes for protein synthesis?
I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes to pass on to the created organism?

@caligari2005 Uhm...why don't you make that an answer and I'll give you the credit for it? :P

From the comment section:
Cells divide and when they do the two daughter cells will not only have copies of the DNA but also of the organelles, the cellular machineries and the cell membrane which implies that yes the daughter cells receive also ribosomes. The replication happens during the interphase.

I transferred the answer from the comments only 2 days ago so that was actually quite fast :D

Nevermind then. ;p

Each daughter cell, following mitosis, will contain some ribosomes and DNA transcription machinery already, so it can already synthesise more ribosomes.
In the case of the fertilised ovum, when the organism is only a single cell, the first ribosomes will be those already present in the unfertilised ovum.
So cells never have to start from scratch with no ribosomes.


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Cell nanoparticle dynamics within blood
I am trying to mathematically model the dynamics of a particular cell in circulation and its binding to another nanoparticle that is intravenously injected. The concentration of this cell is very low (about 5 cells per mL of blood). I want to see how many nanoparticles are needed to bind to as many of these rare cells as possible.
So first, I am trying to model the cell dynamics in the blood flow. I am not sure how to start. I wanted to model the cell movement through the entire cardiovascular system, but I would have to simplify it. I am thinking of modeling the blood flow through some of the major organ systems, and estimating the absorption through the capillaries. I am thinking something like the physiologically-based pharmacokinetic model (PBPK). However, there would be some parameters that I wouldn't know about that I would need for the model (at least that is what I think, I am new to pharmacokinetics) Also for the actual fluid dynamics, I'm not sure how to model this, because the blood isn't just a fluid, and has many other cells, so I don't know if there are some other effects.
So, my question is, in what direction should I go to model the dynamics of this cell in circulation? I want to model the circulation in the entire cardiovascular system, because I need to also model the other nanoparticle dynamics, and how likely it is to find and bind to some of the receptors on the cell. Is there an example of a similar model that has been done?

I'm not terribly knowledgeable in this field, but I've come across it once or twice in my work doing pharmacokinetics/pharmacodynamics (PK/PD) studies on both large and small molecules. To my knowledge, there should be existing published studies on modeling the circulation of cells in blood. While you are correct that blood itself is a complex non-Newtonian fluid, its physics are pretty well established by now. Nanoparticles are also becoming more and more common, so hopefully you should be able to find multiple published reports on modeling them as well, then put the two together.

So, you should be fairly accurately able to determine the dispersion of your cell type of interest as well as the nanoparticles, then it's just a matter of calculating the probability of their meeting and the avidity needed for them to bind - say, for example, that the nanoparticle has a receptor-specific scFv coated on its surface, and the correlating receptor density on your target cell is such-and-such, and the Pk of binding is so many nM or pM or whatever. Good luck, I'm not a math guy (I just take care of the biology)!

This question is a bit opinion-based and would most likely be put on hold for that. However, this is my suggestion. Start with the simplest model and add complexities if the model is insufficient. Don't start with modelling the blood flow: you'll get into PDEs which are more complicated than ODEs. Start with an assumption that the blood stream is a well mixed vessel. You can consider different organs as compartments with different volumes (based on how much vascularised they are).

@WYSIWYG in what sense is it opinion-based? There are only 2-3 possible models that have been previously done. So, it might be a little opinion-based, but is it really bad that it would be put on hold?

I am not saying that it will definitely be put on hold. But different people would have different suggestions on how to model a certain system. Technically, there are infinite ways to model something. If your question is explicitly about reference request (previous models etc) then it is fine; you can add the relevant tag and clearly mention that you are looking for references.

To go the PBPK route:
I would recommend using the organism parameters and structure from the whole body platform model by Shah and Betts.

Shah, D.K. & Betts, A.M. J Pharmacokinet Pharmacodyn (2012) 39: 67. doi:10.1007/s10928-011-9232-2

They have assigned a plasma space volume, plasma flow, blood cell space volume and blood cell flow for each organ and the total body.  The base model structure for circulation is complete if you use the equations for the blood cell space in this paper as the foundation (Eq 2 and Eq 5).
Once the model structure is complete, step 2 is to model all processes that can affect the cell in each compartment.  If the cell is adhering to a nanoparticle, a compartment equation could then be:
d[cell]/dt = (flow in - flow out)/volume + Kon x [nano] x [cell] - Koff x [cell-nano complex]
To model the interaction of the cell with the nanoparticle you will need to model both within the same structure.  A review of PBPK modelling for nanoparticles can be found here:

Physiologically Based Pharmacokinetic Modeling of Nanoparticles
Mingguang Li, Khuloud T. Al-Jamal, Kostas Kostarelos, and Joshua Reineke
ACS Nano 2010 4 (11), 6303-6317 doi: 10.1021/nn1018818

A pharmacokinetic (top-down, classical) model for nanoparticles in the circulatory system may also give insight to how to model the processes that affect nanoparticles in vivo.  This model accounts for fluid dynamics, pore size and specific nanoparticle properties.

Kirtane, A. R., Siegel, R. A. and Panyam, J. (2015), A Pharmacokinetic Model for Quantifying the Effect of Vascular Permeability on the Choice of Drug Carrier: A Framework for Personalized Nanomedicine. J. Pharm. Sci., 104: 1174–1186. doi:10.1002/jps.24302

I am not understanding the compartment equation. Wouldn't it be one for each organ, modeling the concentration and flux of the cell into and out of the organ? I plan to keep the model simple and assume there are no major effects on the cell, in terms of growth, and elimination. However, maybe the elimination of the nanoparticle by immune response might be important.

You're right.  The words "compartment" and "organ" are interchangeable.  Every organ is modeled as a compartment.

Can you fully explain the differential equation you wrote down? Also what parameters do I need to know about the nanoparticle and the cell? Where can I find a good introduction to PBPK modelling?

What does the Kon and Koff model?

Kon is the rate constant used for calculating the rate that the nanoparticle and the cell adhere together, proportional to the concentration of each.  The term [Kon x nano x cell] gives you a rate in mol/time of nano-cell complexes that are formed.   Koff is the reverse rate constant.  https://en.wikipedia.org/wiki/Binding_constant


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Regarding tumors and their developement
If certain cells or tissue in a specific part of the body are for some reason overworked; like the cases of severe acid reflux damaging the throat repeatedly and the cells in the throat having to do growth and repair a lot more than they would with a healthy person -- or problems in the stomach attacking the stomach lining a lot, causing 'extra' growth and repair; could these situations of 'extra' growth and repair cause various cells used in these processes to mutate with all the cellular division and replication required? And maybe some of these extra-growth-and-repair induced mutations might cause the apoptosis mechanisms to malfunction?

If a cancerous cell has a horrendous amount of mutations and yet it still functions ( if abnormally) it must be able to keep existing without 'alerting' the immune system or interfering 'too much' with other subsystems. How is this possible? Wouldn't all the mutations if 'expressed' cause all sorts of 'activity' the cell or other neighboring systems might not be able to cope with?

There is indeed a positive correlation between gastric reflux disease and esophageal cancer, and also between stomach ulcerations and stomach cancer. There are more than one possible mechanisms for these correlations to arise, but what you are proposing is definitely a prime suspect.
http://www.webmd.com/heartburn-gerd/news/20130523/chronic-heartburn-may-raise-odds-for-throat-cancer-study
http://www.ncbi.nlm.nih.gov/pubmed/10658066


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What kind of microscope should be used to view biological structures (such as spores) roughly 5 µm in length?
I would like to be able to identify genera of fungi based on the shape, size, and colour of spores. So the requirements are:

Must be able to view a 5 micrometre object clearly with reasonable resolution
Must be true colour
Must facilitate the measurement of an object within reasonable accuracy (500 nanometres would be nice)
Should be inexpensive (\$100-\$400) fingers crossed
Bonus: Be able to take photos

What type of microscope do I need? What magnification/resolution? Is there a good rule of thumb relating size of object with magnification?
How do I find and purchase a decent microscope after defining my requirements? Any tips?
Blue light is ~450 nm, so does that mean I will not get very good resolution?
(For the sake of context: I have absolutely no formal experience in biology, but I have recently taken an amateur interest in mycology and might enrol in an undergraduate course as part of my degree at some point.)

From Wikipedia:
"With an optical microscope having a high numerical aperture and using oil immersion, the best possible resolution is 200 nm corresponding to a magnification of around 1200×."
So, I searched for 1000x optical microscopes and  found a AmScope 40x-1000x on Amazon. Has anybody used this brand? Will this be sufficient?

Ooh, this one takes photos: OMAX 40X-2000X Digital Binocular Biological Compound Microscope with Built-in 3.0MP USB Camera and Double Layer Mechanical Stage Is OMAX any good?

In this price range, I would avoid anything with very high magnifications > 600x or so. You'll find it very difficult to get enough contrast to see any details.

I think you have a good question, but if you want to get a good understanding of the issues you raise with it, then you really ought to consider spending some time reading this optical microscope primer. In my opinion, you need not bother with taking an undergraduate course at a physical university. As an intro to biology (which is not really necessary if all you want to do is look at small things in a microscope and understand what you're seeing), you might want to consider enrolling in this free class, but if all you want to do is look at small things and have a basic understanding of what you're seeing, I think all you need to do is read the primer.
If it was me, I'd read at least some of the primer before investing the money in a microscope. Otherwise you're just taking a blind leap of faith from someone's (perhaps biased) suggestion.

I agree with Kevin F, if I was you, I'd take a bit of training before buying something or even trying. Biology teachers or staff from the university are usually happy to provide you with a microscope to test something, so just ask. If you want a resolution that high, there are a lot of adjustments to do, commonly referred to as "Köhler illumination", because otherwise you won't get a nice picture.
To answer your question, you can basically forget microscopes at that price range for this resolution, let alone the ability to take photos. You would have to spend >$1000 to get something good enough. As in photography, this is largely due to the lenses. I don't have much experience with fungi, but you might want to have a phase contrast microscope to be able to see the specimens properly. You can buy microscopes with have a port for a DSLR camera, with which I've made good experiences.
For a 5 µm object, you could use a $60 \times$ lens (which, together with a $10 \times$ ocular makes a magnification of $600\times$), or even a $100 \times$ lens, when you want to resolve surface structures, but no idea, if the latter really works with your specimens, so you'd have to test that before buying.
So: First, get a bit of formal training, as suggested by Kevin F. Then, try it yourself without buying, and try it with your own specimens! Then, save money and buy. :-)

Agree 100%. Cheap lenses will just give blurry and distorted images. Beware of promises of 1000x, and color camera for $200... you will just be disappointed. The ideal would be going for something like the Zeiss Primo Star which goes for around 1500-2000€.

I know this thread is old, but I just wanted to say that before reading your suggestion of taking a look at my university's microscopes before buying one I had thought about the same thing and have been just told today by a lady at the university that I would need consent for research from a professor for that.