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Why do we absorb vitamins better from whole foods than from pills?
We can't rely on pills to provide us our nutrients because we don't absorb the nutrients from the pills as effectively. Presumably this is because pills are lacking components that are required for certain reactions to take place.
Why can't we just create a pill that does have all the necessary components?

I think your premises are wrong. I don't know of any food that is recommended in place of a pill, because it is supposedly better.

Why can't we just create a pill that does have all the necessary components?

I'm assuming you mean micronutrients (vitamins & minerals). A day's worth of macronutrients (energy and building-block providing chemicals - proteins, fats, sugars) are already very abundant and dense - a pill containing a day's worth would be the size of an egg.
Otherwise, we do. There are vitamin/mineral pills which have a very high absorbancy rate (usually those chelated or chemically bonded to various amino acids [words ending in -nate on the label]).
The big problem is that while the vitamins and minerals may satisfy your bare biochemical needs, that is all they do. They will not satisfy a hunger instinct (proteins and fats do that), and there are untold millions of compounds in the untold thousands of plants and products humans can pick up from the market. These compounds usually do not do much, but some are beneficial to our health.
So while multivitamins exist which provide you with a very efficient method of absorbing most of your vitamins and minerals, it's always recommended to get them directly from food since food will provide macronutrients (thus satisfying your hunger), the micronutrients you're curious about, and many potential beneficial compounds which are not necessary.
If you are still interested, Soylent Shakes are an attempt to provide all the micro- and macronutrients the body needs in an easier-to-consume form without all the messy cooking or multivitamin pills. Keep in mind the long-term effects of sticking to such a diet are more or less unknown, but it's as close as we can likely get to an "all-in-one" meal.

I'm assuming you mean micronutrients - Yes, I do.

So does that mean you could eat an diet that isn't nutritious but that fulfills your macronutrient demands, take a multivitamin (satisfying the micronutrient demand), and that would be perfectly healthy? (you said the micronutrients that aren't in vitamins but are in food aren't necessary. could you expand a bit on this?)

Ps: thanks for introducing my to Soylent. VERY interesting. I definitely have to research it some more, but I had no clue this existed and it seems to be a huge step forward for humanity if is indeed healthy.

@user6035 - Yes, you could eat an artificial diet of macronutrients and micronutrients that would satisfy your biochemical needs. It would probably be "healthy" in that you would probably continue to live without issues you weren't already predisposed to. How other chemicals and compounds contribute to our health are unknown (think antioxidants), but have the potential to contribute significantly. However, please consult medical professionals for further info if you intend to pursue this. Due to genetic variation your body might have greater or lesser needs than the recommendations.

Ah ok. Great point about antioxidants. That example cleared up for me what you mean about other chemicals and compounds. I'll continue to investigate before moving forward!


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Balanced vs Maximized Codon Optimization
I have worked with the optimization of several viral proteins, from different viruses/families, with different results.
When Menzella, 2011 was published I tried that method.  I found quite the contrary result, in that randomization did far poorer than straight maximization of codon usage.  I chucked this up to working within the context of viral infection (though it was also true in transient expression from plasmid transfection under CMV promotion).
I was quite excited by Pechmann and Frydman's Nature article which highlighted the importance of the location of the codon within the protein when regarding optimal vs suboptimal codon selection. Oddly enough we were able to deploy this information most successfully with the purposeful deoptimization of a protein.
Pairing a locational awareness, screening for secondary structure, and then maximizing codon optimization has had the best results for more than a year.  By maximization, I mean choosing the most optimal codon in every instance that doesn't violate:

Needed restriction sites
Predicated Secondary Structure
Location gradient to a lesser extent (ibid.)

This is all well and good, but we've been having problems with my institutions preferred vendor for gene synthesis.  A post-doc that just joined my lab recommended a company I had never heard of before, and they posed an optimization strategy I had never considered before.  Instead of maximizing codon optimization, they propose a "balanced" codon optimization that matches the normal distribution of codons in the target organism.
For example, the codon bias for alanine in humans breaks down (roughly) as follows:

GCC 65%
GCT 20%
GCA 11%
GCG 4%

As opposed to a maximization strategy which would seek to use "GCC" when ever possible and only when there was an issue switch to "GCT," the balanced stratgy would seek to replicate the above distribution as closely as possible.
Has anyone tried a balanced codon approach, especially when compared to a maximization technique?  My overall goal is to maximize expression of naturally poorly expressing protein.  I know that straight maximization can occasionally lead to poor expression for a variety of reasons (often fatal secondary structure), but this seems like it would hardly increase expression at all.
I would be further interested if anyone else had experience within a viral context.
I know that there have been a few related questions, mostly in the context of E. Coli.  I don't think this is a duplicate, but would be willing to remove if it is seen as such.  If I run into some extra funds I may test this empirically, but often when I'm trying such a test it's only in relation to 2-3 proteins, which might not be representative.

Do you want to control the protein synthesis rate? Something like you do not want it to be produced too fast because of folding issues? This article summarizes different mathematical models for translation. You can obtain optimal codon usage by fixing the synthesis rate.

This paper talks about codon usage and virus-host interactions. Is it what you are interested in ?

@WYSIWYG I want to maximize protein expression in a human cell line.  While I appreciate David's work, that's not what really is at play here. The empirical observation from the theories leaves more complex modeling to be done. I am mostly interested in the bold question, perhaps I included too much background.

I suppose I mention Menzella solely as an example of what makes me weary to try something different.  If I can reasonable suspect that it will end in failure, I'd just as soon not waste time or funds on it.

I suspect that this maximization and balanced codon usage will depend on your protein; there would be some optimal rate of synthesis at which it will fold properly. IMHO there cannot be a generalized model unless folding dynamics can be predicted solely based on sequence (which is very difficult).

@WYSIWYG I remain unconvinced that the rate limiting factor in many cases is the protein folding, but rather tRNA availability plays a much bigger role in production. Particularly considering time scales involved in active infection (let's say less than 48h as a high limit).

Well. You would want to use sub-optimal codon usage only if you would have folding issues. Correct me here if I am wrong. Else you should go for the maxima of codon usage (which is basically obtained from tRNA availability).

Codon usage optimization is still pretty much heurestic. The most common factor we think are important in E. Coli are:

optimization to highly expressed genes, i.e. maximization of codon adaptation index http://www.ncbi.nlm.nih.gov/pubmed/19359587/
keeping the optimal GC content http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107319
not introducing motifs that are somehow detrimental, e.g. restriction enzymes, or some dinucleotides http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642
adapting to available tRNA http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002
minimizing folding energy (in the first ca. 30 codons) and minimizing the amount of hairpins at the 5' end http://www.sciencedirect.com/science/article/pii/S0014579305010719
optimization of 'codon context' e.g. dicodons but also using nonoptimal codons between secondary structure for more accurate folding http://www.ncbi.nlm.nih.gov/pubmed/15772378
optimization of codon balance and also maybe the introduction of a 'ramp of slow codons' in the beginning of a gene to avoid 'traffic jams' of ribosomes later on. http://www.ncbi.nlm.nih.gov/pubmed/20403329

Most probably it's a mixture of all of those.
Disclaimer: We are working on a codon optimization strategy for e.coli/yeast/hela and it works in e. coli but is yet untested in human cells. If you want to take a long shot just shoot me a message and we could try it. Apart from this, I would also offer you to have a look at your sequence and see if there is anything 'strange' from the codon usage point of view and what I think what be the best optimization strategy.

It would be great if you provided some references to support your response!

Thanks for the answer. Small editing note, you included the "]" in several of the links (I could change it for you, but as new user you might want the practice).  Looking at references, none seem to be advocating matching the levels found in the host (even if it's E. Coli).  As far as the sequences, we're making about 14 or so different strains of a poly-protein, so that's probably not practical.

@Atl LED, thanks! Just wanted to get the answers out before christmas since I thought it might be time critical for you. I will change the formatting and will look for the mentioned reference as soon as possbile.

In a side-by-side comparison of 3 viral proteins (2 from paramyxoviridae, 1 from caliciviridae) each with both a "maximizing" and "matched" codon bias, we found the "maximized" version produced more protein the "matched" version in each instance.  Protein levels were quantified via Western and flow, cell lines tested were 293T, HEp2 (HeLa contaminate), and Vero.
This is certainly not wide enough testing for any kind of general statement, it's just what we found.  I think this will take a cell bio or pure micro-bio lab to fully study.  We're in infectious diseases, and this question would be off grant and off topic for the paper.  If we can find a way to squeeze it into a publication we will.
I'm going to accept Jan's answer because it contains more information on optimization, but with this answer in place to:

Address what we observed.
Note that Jan's doesn't offer any information on "matching" the codon bias of the target host (other than perhaps noting optimization is heuristic).

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Removal of the Initial Methionine in Venus for FRET
I'm working on building some FRET reporters.  In addition to a cleavage site (of varying composition from 15-18AA), a 1 AA linker, I'm using Venus and Cerulean.
Initially I was worried that 18AA would be too long, but it does in fact give a fair signal.  For reference, I believe the Förster radius (Ro) is 54Å.
I am now working on further optimization.  Does the removal of the intial methionine cause any problems for Venus if it is the second protein in the FRET pair?  The basic layout is:
Cerulean - Link - Cleavage - Link - Venus
And I'm wondering if cutting the Met from Venus might bring me 1 AA closer and therefore a slightly better signal.  I have seen it published both ways, and I was wondering if anyone had tried both or just knew theoretically that it wouldn't matter.

why do you want to remove the Met-1. Removal of 1 amino acid may only reduce the length by ~3Å (twice the peptide bond) and if i am not wrong Forster's radius is ~60Å and therefore the distance of interaction = 2x60Å. A 3Å reduction may not be very significant

@WYSIWYG I didn't mean to imply that the reduction of the radius was the only advantage.  It also gives me a better restriction site in the DNA, and is possibly more flexible in the AA sequence.

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What is the name of this plant?
This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?

Thanks, looks like it is something like this:
http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034
Related question:
https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610

Nice pictures! Thanks also for getting pictures of different plant parts.

Also see similar question on GL. (Highest voted three-word answer on the whole site.)

Shouldn't this question be moved to GL. As per this discussion on meta http://meta.biology.stackexchange.com/questions/151/plant-identification-questions

@PatrickB see this question: Is it a good idea to have an identical topic (plant identification) on both GL and Biology? I'm coming to the conclusion that plant identification questions can be asked on either site, but for different reasons.

This looks like some species of Phytolacca to me.
It's possibly Phytolacca americana, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but naturalized in Europe.
If you still have any in the ground, once they ripen, the berries are intensely purple and can be used as dye (or even eaten?)

Mark A. Nienaber & John W. Thieret. Phytolaccaceae.  In: Flora of North America Editorial Committee, eds.  1993+.  Flora of North America North of Mexico. New York and Oxford. (link goes to entry of P. americana)

Seems like it is an invasive species that can prevent others from growing.

It certainly grows very weedily here!

Oreotrephes You have a garden, therefore you should get over to GL now and then. =)

It is a Phytolacca, but not americana, because the flowers stand upright. P. americana has hanging flowers.

It is Phytolacca acinosa because the flowers grow upwards and the fruits are ribbed. Phytolacca americana has downward pointing flowers and smooth fruits.


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Why do crabs spit?
Last year I photographed this juvenile Sally Lightfoot Crab (Grapsus grapsus) 'spitting' (click for larger view):

I thought I'd look up more information on this behavior, but couldn't find any explanation regarding its actual function. I can imagine a few potential functions this could serve:

Secreting excess salt—just as Marine Iguanas sneeze.
A means of evaporative cooling—like the mosquito's behavior described here.
An attempt to eject irritants from the crab's mouthparts.
Possibly a means of self-defense.
Any combination of the above or something I hadn't even considered.

Has there been any research regarding the biological function of this behavior? On a side note, I'm curious about how widespread this behavior is—is it only this species or is it nearly all land crabs?

No idea but excellent photograph.

Watching some videos of them it seems like it could have a number of uses, possibly even as a fitness indicator to mates. Smelling your partner's sneeze - so romantic.

Breathing during digging

And if all that wasn’t enough responsibility for these claws, they also are used for digging. While most digging crabs use their back legs to burrow backwards into the sand, the shame-faced crab uses the claws like little bulldozers, excavating the sand forward so the crab sinks downward until it is completely covered by the sediment.
Burrowing underground is fine and all, but how does it then breathe? Again, it’s the claws that solve this problem as well. When beneath the sand, the crab regularly shoots a stream of water from its mouth (when you remove one from the water it spits for a few seconds, creating a little fountain that can be up to half a foot long. The crabs themselves are only about two inches thick.) The stream of water ricocheted off the inside of the claws, shooting upward and moving the overlaying sand grains, briefly allowing the crab to take a breath.

Expelling salt water

SALLY LIGHTFOOT CRAB
Born much darker (almost black) in color as to avoid predation,
Sally Lightfoot crab grows gains more vermillion, as it grows
larger. Nimble-footed and photogenic,these crabs make for
excellent models --though they may be a bit shy for close-ups,
scurrying away sideways, up slopes and even upside down.
Occasionally you may see a crab “spitting” from near its eye.
Actually,the stream of liquid you notice is the Sally Lightfoot
crabs way of expelling salt water that seeps into its exoskeleton.

Although neither source sites a reference, they support the hypotheses of secreting excess salt and ejecting irritants (sort of). Thanks for the response.

@p.s.w.g I know, I'll try to also find a reference later. And you are welcome :)


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Single long axon vs serial neurons
Based on the comments in this post and also this chat. For discussions and speculations please comment in the chat.
The basic question is what is the advantage of having a single long axon such as that of sciatic nerve (~1m) compared to a series of neurons?
The primary advantage is surely the conduction speed which will get affected because of chemical synapses. However, gap junction synapses can reduce that delay. The larger volume of the soma of the post synaptic neuron may also reduce the conduction speed, but signal strengthening can also happen. Cell architecture can be adjusted to minimize the loss of speed.
The obvious disadvantage of having a single large cell is that there would be tremendous burden on the nucleus for the cellular maintenance. There would be delays in transfer of non-electrical signals such as biomolecules from axon termini to soma and vice versa. Long axons also means continuous transport along them which in turn demands large number of molecular motors and therefore ATP. Moreover, a small injury can disable the entire conduction channel. It can be imagined that this trait (long axons) can also be selected against; injury leading to inability to move and thereby causing perishment.
EDIT (Based on comments to Anne's answer)
Time is of course a valid advantage for having a single axon as an information conduction channel. However, the energy or the maintenance cost is the factor that I am actually interested in. Maintenance cost would increase with cell volume (in fact surface area) and having serial neurons would demand more energy (cumulative) than a single axon (including costs of maintaining a nucleus). However a long cell would need much higher number of molecular motors to maintain the traffic flow rate. All responses that require transcriptional control would be slow (such as response to injury). Moreover a single soma also imposes a limit on the number of mitochondria. There should be a limit on how long an axon can be. I am especially interested in case of big animals (with long hindlimbs) that also have a good reflex (perhaps camels, even horses).
Has someone tried to analyse the tradeoffs of having a long axon vs series of neurons connected by gap junctions? If not is this problem worth modeling or quite trivial?

Saw this in Quora:

My first thought mostly agreed with the question details, except I'm
  pretty sure that the dorsal root ganglion (DRG) has a longer axon than
  the motor information carried in the sciatic nerve (which is the
  longest nerve in the body, but not axon).

Does this mean that sciatic nerve has serial neurons?

Forget conduction speed. What about signal fidelity? How much noise does each extra gap junction add to a signal?

@tel I am not sure about the noise at the gap junction (GJ). Can you tell me how is noise generated at the GJ?

I'm not a neruo guy, so I can't give you any specifics, but in terms of general information theory/2nd law considerations, every time you convert a signal from one form to another (axonal current to neurotransmitter gradient, say) your signal/noise ratio gets a little worse. You can recover the original signal somewhat, but it always involves an expense of free energy.

@tel Oh well.. but in the gap junctions the wave can move to another cell. There are no neurotransmitters involved.

If you want to reduce the variance in signal transmission with n serial steps, then you need to add more steps. Therefore to achieve signal transmission with really low variance, you either want a single axon (case A) or really lot of them connected in series (case B). May be overall, case A is not so bad compared to case B not to be selected for.

First, I must clarify that a nerve is not the same as a neuron. A nerve is a collection of axons (with each axon a part of an individual neuron) in the peripheral nervous system. Thus, when you mention “single long axon such as the sciatic nerve”, this is technically an incorrect phrase as the sciatic nerve is a collection of many long axons. If one of these axons is nonfunctional, this would not severely affect the function of the entire sciatic nerve. However, you are right that if the entire sciatic nerve is severed, then there would be serious consequences downstream.
Second, the primary advantage of conduction velocity is less dependent on length and more dependent on presence and degree of myelination (directly proportional to fiber diameter) and presence of nodes of Ranvier.
With regards to the content of your question, the advantage of length is exactly what one might think--- greater distance. The sciatic nerve is the longest nerve in the body in order for our nervous system to innervate as far as the tip of our toes. Having hundreds of side-by-side series of neurons compared to hundreds of side-by-side axons seems like a far less efficient system in a couple of ways in exactly the two ways you mention: energy and time.
Energy: Having serial neurons would require an increase the number of neurons needed to transmit a message. Having more neurons requires more Na+, K+ and Na/K pumps and individual channels, requiring more energy.
Time: Having serial neurons would also require an increase in the number of synapses between neurons— either electrical or chemical. If the synapses are chemical, then time is increased many-many fold. If the synapses are electrical, then time is slightly increased by 10-fold per synapse compared to chemical synapses, but this would still take more time compared to having a single axon with myelination and nodes of Ranvier which by about 100-fold faster than a single electrical synapse.
In summary, having longer nerves made up of axons rather than serial neurons is beneficial by improving energy and time efficiency, which allows our bodies to effectively innervate structures farther away.
Ref:

Regarding delay of conduction: Chemical v. Electrical/Gap  Ch 10 of Principles of Neuroscience- "Synaptic Integration in the Central Nervous System" (Siegelbaum,
Kandel, Yuste) 5th ed. McGraw-Hill Medical, c2013.
Regarding conduction velocity of myelinated versus nonmyelinated
cells

Regarding the ATPase absolute number increase in serial vs one long axon, I assume this will depend on the number of neurons in series. However, I read this paper, which says that increased length between each node of Ranvier has been physiologically associated with increased conduction velocity. This suggests fewer needed nodes, despite concentrated ATPases at these locations, and thus fewer ATPases. I haven't been able to find studies which compare ATPase concentration in the soma compared to nodes of Ranvier within axons.
Regarding energy use in soma vs axon, mitochondria are not only made in the soma but are concentrated in pre- and post-synaptic membranes (and growth cones). The more of these structures there are (as in serial neurons), the more presumed mitochondria. See mitochondria and neuronal activity.
Finally, my literature search could not find studies which showed longest possible energetically feasible length for myelinated or unmyelinated neurons.

Why would multiple neurons need more ATPases? The only difference is more cell bodies? Could you provide a citation for the gap junction transduction velocity? I would think it would be about as fast as myelinated conduction. If I am wrong than this is a likely answer!

@ChrisStronks I will add references tomorrow, I used quite a few so it will take time.

@ChrisStronks Multiple neruons need more ATPs as they will have other soma related function to which they have to cater to. More soma=more protoplasm=More volume of space where electrolyte balance need to be maintained=More channels active=More ATP

@Anne "primary advantage of conduction velocity is not dependent on length".. yes I meant in the context of uninterrupted myelinated axon. And length does have a role in velocity (see cable equation). Your point on time is correct but I am slightly skeptical about the energy part. What about larger animals; would there be an optimal length of a single axon?

@ChrisStronks Besides, energy is expended for other cell functions - facultative and constitutive cell functions which would not be expended otherwise

@CRags Requirement of ATP is more or less related to total volume of the cell which would be slightly more in case of serial neurons but not overwhelmingly high. Also a long cell would need much higher number of molecular motors to maintain the traffic flow rate. All responses that require transcriptional control would be slow (such as response to injury).

We are not talking about responses though. Purely from a energy point of view, more cells=more energy expenditure. The longer length of the axon does not mean more molecular motor. As the organ/part which is ennervated is at a fixed distance, one neuron or multiple neuron would have the same number of molecular motors. Infact in this scenario, multiple neurons would require more energy than a single neuron due to the above mentioned reasons.

What I would grant you is the time taken to resolve any disruptions. This would be undisputably longer for longer neurons

@WYSIWYG With neurons, diameter plays a much larger role than length. Nernst Potential and Nerve Conduction Speed

@Anne Did not discredit that. Was just saying that length does have a role :) And yes with the introduction of another soma the diameter will change; however increase in diameter is favorable for longitudinal current (as resistivity is constant; conductance ∝ Area); the problem is the case of less insulation i.e low transverse resistance leading to leaks. In any case I accept that time is an obvious advantage. My question is would energy be a tradeoff at some point: single soma also imposes a limit on number of mitochondria.

@Anne I am also confused here: myelination directly proportional to diameter. Can you provide a link for this; Do schwann cells have a limit on how much can they extend (the coiling during myelination). Of course they cannot myelinate the soma but this is still an interesting point. However I guess there can be ways to reduce membrane resistance without myelination- perhaps by having anchored cytoplasmic domains to confine the leak channels (this can be regulated at the soma). This is just my guess. I think I am raising too many arguments; forgive me I don't have much knowledge of this area.

@WYSIWYG Myelination + axon cross section = fiber diameter.  This applies only of course if we are talking about myelinated neurons. If you have a non-myelinated neuron, axon = fiber diameter. See yellow and green picture on the bottom the page.

@WYSIWYG Mitochondria and neuronal activity. You make a good point about limitation of mitochondria based on capacity of a neuron, and it is unknown whether more neurons in series would require overall less mitochondria than a long axon of a single neuron. However, the references states that mitochondria are not only made in the soma but are concentrated in pre- and post-synaptic membranes (and growth cones). The more of these structures there are (as in serial neurons), the more presumed mitochondria.

@Anne I understand the point about the fiber diameter and myelination. I thought you meant (in the answer) that extent of myelination is dependent on diameter of the axon. Yes mitochondria are localized in axon termini and are transported there via axons. I meant that neuron in series can accommodate more mitochondria to cope up with energy demands. Single soma would be overburdened. Sorry for asking another question: what is the longest axon known. I want to know till point having a single axon would be be an optimal solution (beyond which it is infeasible).

@WYSIWYG Longest axon in humans belongs to the neurons of the sciatic nerve, though some debate it's the DRG. In the world, probably the same structures in a blue whale or other creature we may not have discovered. How long can it get before it is not energetically feasible? That's an experiment yet to be done. Diameter was meant in context of fiber, not axon.

@Anne Can you add these points in the answer. I can accept it then. So I guess the question "How long can it get before it is not energetically feasible" is worth pursuing, at least theoretically. You sure there are no theoretical studies on this?

@WYSIWYG I edited my answer, hopefully that helps. As far as I have searched in pubmed, google scholar, etc haven't been able to find studies regarding energetic feasibility, unfortunately. Please let me know if you have any other questions.


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Can you change your gut microbiota by changing your diet? Would that affect calorie uptake?
I have seen peer-reviewed papers mentioning the daily changes in gut microbiota composition according to dietary changes. See for example this paper:
http://genomebiology.com/2014/15/7/R89
My question is related to this one:
Relationship between our microbiome and personalized nutrition
If, according to these recently published scientific results, it takes a day to change the gut microbiota to adjust to the dietary change, and the presence of certain microbes makes food assimilation more effective,
Does this mean that alternating a protein-rich meat and dairy diet with a carbs-rich diet every day would make our microbiota switch daily and not have time to increase calorie uptake?

Firstly, it should be noted that a stable, healthy microbiome is generally thought to be a marker of health; actively disrupting it through diet in an attempt to fight with it over nutrients is therefore not necessarily a good idea, as it can affect the health of not only your gut but also your immune system, etc.
Dysfunctional microbiomes are for example associated with behavioral problems in eating disorders.
Nonetheless, diet shifts have been used as a tool to attempt to control the microbiome and put it in a "healthy state". You can indeed use consumption of some foods to shift microbiome composition. Presumably if you did this in a sufficiently disjointed way, you could throw your microbiome into a sort of ecological chaos.
However, it would be much simpler to just constantly take antibiotics to ensure that your gut load of microbes was generally low. This still isn't a good idea, as it can lead to Clostridium difficile or E. coli infections or other bad things, but it would be a much more straightforward way of getting to the desired end state.

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enzymes that stabilize DNA loops
As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.
I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs.

My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.
This is a follow-up question to this one, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.
Any ideas?

I have read that cohesin is one of such enzymes, but works as a
  transcription factor by binding specific DNA motifs.

Cohesin binding is not motif dependent (like transcription factors) and is also dynamic. Though sequence may have a role it is, just as in the case of nucleosomes,  mostly the overall composition rather than a sequence based motif:
From this article:

Cohesin binding peaks correspond closely to peaks of high local AT
  composition, a base composition periodicity of ∼15 kb that is distinct
  from the ∼50 kb periodicity of base composition isochores, consistent
  with axis association of cohesins.

DNA-protein complexes can be crosslinked and subsequently the loops can be pulled down. However, this is tricky. You would need to cut the DNA at the loop ends in order to ligate them together. I don't know how to do that (Perhaps by using an antibody linked to an endonuclease).


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List of the biggest companies that work in selective breeding
Looking at this question, I've been wondering, What are the biggest private companies which work in both animal and non-animal selective breeding?
Let me know if Biology.SE is not appropriate for this kind of question.
Thank you

Seeking on the internet I found these two companies Hendrix Genetics and PoultryHub

This varies by the kind of animal or plant. I think one company would rarely do both.
For plants Monsanto comes to mind.  And Syngenta.
I'm not sure for animals.  For beef cattle in the US, this is done by individual ranchers (who may be corporations) that collectively share their genetic data creating a market which can predict the value of a bull.  The market for bull semen can be worth hundreds of dollars per impregnation.
Why are bulls valued at such a greater rate than cows?  Because semen can be preserved, transported and used thousands of times while a cow can only calf one at a time.

Thanks for this answer. I found two companies on the internet (see comment under my question). I'll wait to see if others can bring some other company names. I am surprised that individual ranchers make their own selection without any breeding plan decided at a national level.

in the US that would not quite work.  but the history is that cattle ranchers have been doing this for centuries and a company hasn't quite been capable of taking the business from them.  seed farmers have been okay with buying seeds from central sources for some reason.

you can add perdue chicken to the list too though.  they do breed a specific line of chickens for meat.  they don't let their farmers even hatch eggs.


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Why do we have two brain hemispheres?
Is there any explanation why we have two brain hemispheres? Is there any advantage of having two in contrast to having one (or three / four)?
From what I've read so far (not too much; I'm not a biologist) each half can take the job of the other half when it comes to injuries. Is that correct?
Are there animals which have more than two hemispheres?
edit: I have seen What was the evolutionary reason for cross lateralization of the brain?, but that question seems to be about the question why the left hemisphere controls right body parts and the right hemisphere controls left body parts. My question is why there are two hemispheres at all.

Possible duplicate of What was the evolutionary reason for cross lateralization of the brain?

You will probably want to read Do the Left Brain and Right Brain have different functions? too.

Bilateral symmetry evolved to be the predominant body plan. According to Wikipedia it accounts for about 99% of all animals. And while this is pure opinion, it kind of makes sense when you consider that almost everything starts from a single cell and we divide in two. And as the genes that control body plan are highly conserved in most organisms, then the simplest way to form a multicellular body that starts from a single cell and grows by dividing in half many times is to have two sides.

"From what I've read so far (not too much; I'm not a biologist) each half can take the job of the other half when it comes to injuries. Is that correct?" The brain does have plasticity, but there are limits, and if you have passed certain developmental targets, then it becomes very difficult to compensate. Over long periods of time and a lot of occupational therapy, some people have recovered some of the functionality, but it depends a great deal on where in the brain the damage was done.


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Organisms using thermal energy as their sole energy source
After seeing this question I remembered that in secondary school we watched a documentary stating something along the lines of "all organisms derive their energy directly or indirectly from the sun. *pause* Well, except a couple of organisms in the deep sea cultures that get their energy from small undersea volcanoes" . Now, after doing a lot of searching I was able to find the 'giant tube worm', however that still indirectly relies on energy from the sun as well as it relies on free Oxygen being available that in the end comes from photosynthesis (if my understanding is correct). So my question is two fold, am I correct in my understanding of the giant tube worm and if so, are there any organisms that function in a way that does not require any energy source beyond geothermal energy?

(PS. I don't have the reputation to tag this chemosynthesis yet, but do think that adding that tag would be useful)

I had to re-read your last sentence a few times to make sure I understood it correctly, but I think that now I do, and I can answer your question.
What you're talking about are thermophiles. They're small organisms that love hot conditions - up to nearly 250 degrees Fahrenheit. They can be found places with a lot of hot water, such as hot springs - and, yes, ocean vents. Many use sulfur as a fuel during chemosynthesis, oxidizing it to make sulfuric acid. They take the energy from the heat source to do this.
Not all thermophiles use chemosynthesis. Those in hot springs may get a lot of sunlight, and they can use photosynthesis. However, those in the deep sea cannot undergo photosynthesis, and are forced to use the energy from the vents to undergo chemosynthesis. In fact, entire ecosystems can be built off them!
Thermophiles may even have been some of the first organisms on Earth. Around the time that life is thought to have first formed, Earth wasn't a very hospitable place. As Ashwini Kumar Lal writes of the first forms of life,

Many of them are evolutionary relics called “archaea”, believed to be among the first homesteaders on the Earth 3.8 billion years ago. They are presumably
  the first version of life on our planet when its atmosphere was devoid of oxygen, and comprised largely of ammonia, methane, water vapour and carbon dioxide. They are microorganisms similar to bacteria in size and simplicity of structure, but continue as an ancient group intermediate between bacteria and eukaryotes. Heat – loving microbes, or “thermophiles”, are among the best studied of the extremophiles that can reproduce or grow readily in temperatures exceeding 45º C, and some of them, referred to as “hyperthermophiles”, are capable of thriving even thrive in temperatures as high as 110º C – more than boiling water temperature.

While we do not know (and may never know) the truth of this hypothesis, it is certainly plausible, given the locations where some extremophiles have been found.

References:
1: Microbial Life in Extremely Hot Environments
2: http://en.academic.ru/dic.nsf/enwiki/18641 (link no longer works, for some reason)
3: Origin of Life
Note: While I list several Wikipedia articles throughout the answer, I did not use them for the information in this answer. I think they're a good starting point to lead you to other sources, though.

It's 1:39AM here, so I will take a look at it tomorrow when my brain is up and running again, but just a very very quick question I can already pose now. So these bacteria do not require any products from photosynthesis? The reason I am asking is that I came across Chemosynthesis as well, but the example chemical process there is "12H2S + 6CO2 → [...]" which requires the oxygen I mentioned in the question. Or is that simply how it works in giant tube worms, but is the process different in some thermophiles? And if so, which (even a single example would be great)? I will be looking through

those references tomorrow, so I might discover more then myself. Just those are the question that came up in me when I read your answer. And PS. I confess, I did do most of my research on wikipedia... as it still is the best encyclopedia that's around.

@DavidMulder I figured; your info on the tube worms was similar to what it said. I, too, love Wikipedia, and sometimes use it for references on Astronomy, but I know Biology is a bit stricter about this sort of thing.

This seems to indicate that some material can come from other organisms - i.e. organic matter.

You may be confusing elemental oxygen (oxygen the element, made in exploding and late-stage stars, comprises almost 50% of the earth's crust by weight) with O2, the reactive oxygen gas. Carbon dioxide contains oxygen, but isn't necessarily produced by photosynthesis. Ditto water, etc etc

This makes no sense. No organism, or any other device, can use thermal energy as an energy source. It is thermodynamically impossible to convert heat to other forms of energy, because it would reduce total entropy.

@Roland The second law is valid only for a closed system. If heat is introduced into a system, work can indeed be done. For example, if you heat water, it can turn into steam, which can then be used to generate electricity. See also thermal energy.

@Roland The second law does not prohibit heat engines from existing; it simply limits their efficiency.

@HDE226868 Okay, that is true; my statement was too general. But heat engines rely on a temperature difference; here we're talking about microscopic processes, and the heat gradient across a bacterium must be minimal.  What would be the mechanism for an enzyme exploiting this? Can you cite any example?

Organisms do not survive solely on heat. The organisms you mention that are (more or less) independent of the sun obtain their energy by oxidizing inorganic compounds, like iron or sulfur. For example, some bacteria oxidize ferrous iron (Fe$^{+2}$) to ferric iron (Fe$^{+3}$), which releases some energy that can be used to "power" the cell. A list of various reactions used by these bacteria is found in this Wikipedia article.
The reason these species exist at hot thermal vents is not because the heat is helpful as such, but because iron, sulfur and other energy-rich inorganic materials are released into the ocean at these sites. The bacteria have adapted to tolerate the heat so that they can harvest the inorganic materials; but they don't benefit from the heat in itself.

The bottom part of your answer is correct but the top part is simply wrong. Heat CAN be converted to other forms of energy and this does not violate the second law but you do need a temperature gradient (https://en.wikipedia.org/wiki/Heat_engine). Every conventional powerplant operates on this priniciple.

See comments above. I don't think there are any examples of microorganisms extracting energy from heat gradients. But I realize you're correct in principle, I have edited the answer.


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Will a 0.2g/mL sugar concentration cause vomiting in humans?
This infographic claims that the sugar content in a can of Coca Cola would cause vomiting if not for the phosphoric acid.

In The First 10 minutes: 10 teaspoons of sugar hit your system. (100% of your recommended daily intake.) You don’t immediately vomit from the overwhelming sweetness because phosphoric acid cuts the flavor allowing you to keep it down.

Now this question came up on skeptics.SE and the remaining question is whether (flavourless) water with sugar would cause vomiting. Very specifically we're talking about 200ml of final concentration and 39 grams of sugar. I would try it out myself, but per the rules of skeptics.SE I am not allowed to do this so I am posting it as a question here.

No, we've had a 2M (360 g/ 1000 ml = .36 g/mL) glucose in water solution for a lab in Molecular Genetics and nobody threw up, even if it was unpleasant to drink. In 200 mL of water my solution would contain 72 g of sugar. I'd put his in an answer but I have no other evidence but personal experience and we only had a mouthwash cup full but it was of multiple different concentrations of the sugar water.

By sugar, you mean sucrose, right?

@WYSIWYG Well, very technically speaking you will find 'high fructose corn syrup' in traditional Coca Cola apparently.

Why in heaven's name would phosphoric acid prevent vomiting if this claim were true? Infographics are about as accurate an memes.

Sugar (be it sucrose, glucose, fructose or honey) does not have emetic properties in any concentration, unless there is a personal (and highly individual) psychological adverse reaction to sweet substances.

Sugar is not a local gastric irritant (like dishwashing detergent, or syrup of ipecac, copper sulphate, zinc sulphate; yellow mercuric sulphate, ammonium carbonate, powdered mustard and other local gastric irritants.) Some non-irritating substances (e.g. cod liver oil) may induce emesis because of a repugnant smell, taste, or texture. Few people find the taste of sugar repugnant. Gastric distension to the point of emesis does not occur with 12 or 16 oz. of fluid.
Psychological causes of vomiting include aversions (e.g. some people vomit when they see someone else vomit.) That would involve a cerebral cortex mechanism.
No sugar of any concentration is listed here as an emetic. If it were true, we would have a much less significant incidence of obesity.


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Are there genes in sex chromosomes that determine facial features?
My friends and I were bored enough to try out this activity.

Picture a teenage boy in your mind.
From this picture, remove any accessories (glasses, piercings, etc.), moustache or beard, then replace the hairstyle with that of a stereotypical teenage girl.
Are you possibly convinced if someone tells you that, this picture was originally of a teenage girl?

I tried it by picturing a few boys who are my friends, but still, I was never convinced because I feel that there's something inherent about the facial features of these boys that made them appear boyish rather than girlish.
If this is not some psychological effect caused by my acquaintance with the boys I pictured (as I know them well so I cannot accept the mapping of their faces to the opposite gender), then are there really biological factors, genes in sex chromosomes in particular, that result in differences in the development of facial features between males and females?
Apparently, "facial hair" isn't an acceptable answer...

Yes, having a Y chromosome does cause specific alterations to facial structure.
The Y chromosome doesn't contain much actual genetic information. Most of the information needed to activate the male developmental program (the female one is the default) is in just one gene 'SRT', the other genes on the Y chromosome aren't super important, such that you can get a normal looking (but infertile) man if this gene is transferred onto an X chromosome.
This SRT acts as a switch causing various changes, but one of the most important ones is the higher production of testosterone. Testosterone (and some other hormones called  'androgens' cause changes to a lot of things, and one of them is facial morphology. In fact weirdly, the bones in the face retain the capacity to grow in adults, so you can give someone hormone treatment and their facial structure will change (google this and you'll clearly see the difference in people's facial shape after hormone therapy for sex change procedures - especially around the jaw). There is also some correlation, in both sexes, between the amount of testosterone in someones blood and the 'manliness' of their face.
Your teenage friends are currently undergoing a natural process similar to artificial hormone treatment, and their faces will get more and more male looking as puberty goes on.

Any reference ?

For which claim? Most of that is pretty basic. For the association with T and male facial characteristics see e.g. this

@DermotHarnett - +1 for this answer. Usually when someone requests a source, it's good to edit it into your answer (per site guidelines). There are lots of papers to support this answer even more strongly, and even starting with testosterone exposure in utero (e.g. Whitehouse et al, Prenatal testosterone exposure is related to sexually dimorphic facial morphology in adulthood).

@DermotHarnett I'd be wary of claiming the "default" is female, considering (among other things) a single X chromosome will result in Turner's syndrome, not a characteristically distinct female or male.

The answer is a bit of a 'yes and no', though mostly 'no.
The Y chromosome has very few genes, but arguably the most pivotal is the sex-determining region Y or SRY gene, also known as TDF or testis determining factor.  The protein this gene codes for acts essentially as a master switch for male phenotypes by triggering the development of testes in the developing fetus.
One of the primary function of the testes themselves (aside from sperm production), is the production and release of testosterone.  It is the testosterone itself that causes masculinization/male phenotypes. Among these masculine phenotypic changes are a modified subcutaneous fat distribution and a thickening and widening of the jaw bone.
So in this respect, yes, the Y chromosome contains genes that influence facial structure.  However, the influence really occurs at a regulatory level, and there are no 'facial structure genes' per sé on that chromosome. In fact, having a deleted on nonfunctional SRY gene, among other potential causes), leads to a person having an XY karyotype, but often being phenotypically female (a lack of a second X chromosome in this case, however, usually leads to other functional problems including infertility).
Further, there is also a condition known as Androgen Insensitivity Syndrome, wherein a person's cells lack functional receptors for testosterone.  It is possible in this case, for a person to have an otherwise fully functional Y chromosome (including a working SRY gene), but be otherwise biologically female, as it is only the androgen hormones, to which the person's body does not react, that lead to any masculinization in the first place.


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The Origin of Mitochondria
For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were "engulfed" by another cell which acted like it's host. This is the endosymbiotic hypothesis.

"The endosymbiotic hypothesis suggests mitochondria were originally
  prokaryotic cells, capable of implementing oxidative mechanisms that
  were not possible to eukaryotic cells; they became endosymbionts
  living inside the eukaryote."

However, recently I looked at the wiki entry on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous.

"In the autogenous hypothesis, mitochondria were born by splitting off
  a portion of DNA from the nucleus of the eukaryotic cell at the time
  of divergence with the prokaryotes; this DNA portion would have been
  enclosed by membranes, which could not be crossed by proteins."

It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (This question here deals with some aspects of multiple-occurence/convergent endosymbiosis).
My questions are;

How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis?
Further, are there any other (plausible) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?

This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called Power Sex and Suicide. You would be interested to read it.
There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example:

There are no microfossil records for the evolutionary intermediates
Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously

So to answer how it exactly happened is quite difficult.
As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check this post.
There are eukaryotic cells that lack mitochondria (eg. Entamoeba histolytica ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner.
There is one more evidence to support the endosymbiosis theory:
There is this observation that organelles that are less numerous in a cell have retained more of their genome compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the Limited Transfer Window Hypothesis which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles.
This article suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (I need some time to mine up the reference. Read it a while back) but these are not the the ancestors of eukaryotes.

Just to follow up: "it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without ... mitochondria" -  how do we know that an early form of mitochondria didn't evolve which allowed the cell to become the larger eukaryotic cell we see today? (It is a bit of a chicken or the egg argument from me there [prokaryote-> prokaryote with mitochondria-> eukaryote, versus, prokaryote-> eukaryote-> eukaryote with mitochondria], and I don't necessarily believe that the early mitochondria came first, just playing devils advocate).

@GriffinEvo: yes definitely.. I didn't say that prokaryote with mitochondria is the precursor of eukaryote. The available information suggests that the eukaryotic ancestor got all its eukaryotedness in a relatively short span of time. It suggests that perhaps there was some non-ubiquitous microenvironment which promoted it.
The argument is that a large eukaryotic cell carrying out the mitochondrial function without having a dedicated organelle cannot thrive because of high energy expenditure.

@WYSIWYG I think you are talking about secondary endosymbiosis, but maybe I'm wrong.

@AtlLED.. I am aware of secondary endosymbiosis but I am not talking about it here.

authors: عبدالرحمن المغربي


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Are there functional examples of parallel DNA double helices?
The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this paper, for example. However, my question is: are there functional examples of parallel DNA double helices? Here are some implicit/additional/guiding criteria:

It should be double stranded. This excludes structures such as G-quadraplexes, which do have some parallel strands.
It does not have to be an extended helix. I don't have any specific length restrictions, but don't assume it needs to be hundreds or even tens of base pairs long.
The structure need not be solely composed of DNA. If a parallel helix is induced by, say, protein or small molecule binding, so be it.
By "functional examples", I mean that the parallel structure should have some effect on cellular processes. The structure can be studied in vitro, even using synthetic constructs, but it should have some functional significance in vivo (or, at least a proposed significance).

Note that although I only mention DNA above, papers discussing parallel RNA double helices in the same spirit would also be welcome.
Related question: why is DNA antiparallel? Can it be parallel?

I hope this question is interesting to others. Please let me know (or edit) if it can be improved.

At first sight I thought the question was crazy, but having checked the NAR paper in the answer you quote (it might be worth providing a direct link) I changed my mind. I suspect you may have to end up answering your own question though. Have you checked for more recent papers that cite the NAR paper? That might be fruitful.

@David Ha! I made the suggested edit. I only skimmed through the NAR paper. I also came across another which showed an intercalating drug promoting a parallel helix. I will post an answer when I have some time to read through the literature.

Surprisingly, a parallel DNA duplex has been reported! In a paper, Tchurikov et al have reported the presence of parallel complementary DNA in the non-coding region of alcohol dehydrogenase gene as well as between two Drosophila DNA sequences. The region, which is ~40 bp long, has 76% bases in same polarity along with complementarity. However, its presence in vivo and its significance are not known (they observed its existwnce in vitro).
Tchurikov et al, in another paper, have reported that parallel complementary RNA in E. coli plays some role in RNA interference and is indeed more effective than antisense RNA in silencing mRNA for gene expression regulation. They also propose the presence of such a system in vivo in E. coli cells. (Seemingly, this paper alone is enough to answer your question since it fulfills all your criteria).
In another paper, Szabat et al have shown that DNA, 2'-O-MeRNA and RNA oligonucleotides can adopt parallel duplex configuration at pH 5 and lower. Also, presence of LNA stabilizes parallel duplex configuration. This might seem helpful in processes such as RNA interference, though this study too was in vitro (obviously, in vivo LNA is not known).
Many such papers, like Westhof et al, Mohammadi et al, etc. have reported the presence of parallel duplex DNA.
References:
 1. Tchurikov NA, Chernov BK, Golova YB, Nechipurenko YD. Parallel DNA: generation of a duplex between two Drosophila sequences in vitro. FEBS letters. 1989;257(2):415–8. pmid:2479581
 2. Tchurikov, N. A., L. G. Chistyakova, G. B. Zavilgelsky, I. V. Manukhov, B. K. Chernov, and Y. B. Golova. 2000. Gene-specific silencing by expression of parallel complementary RNA in Escherichia coli. J. Biol. Chem. 275:26523–26529
 3. Szabat M, Pedzinski T, Czapik T, Kierzek E, Kierzek R (2015) Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2’-O-Methyl RNA and RNA Oligonucleotides. PLoS ONE 10(11): e0143354. doi:10.1371/journal.pone.0143354
 4. Westhof, E., and M. Sundaralingam. 1980. X-ray structure of a cytidylyl-3′,5′-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye. Proc. Natl. Acad. Sci. USA. 77:1852–1856.
 5. Mohammadi, S., R. Klement, A. K. Shchyolkina, J. Liquier, T. M. Jovin, and E. Taillandier. 1998. FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A-T/G-C sequences and their A-T/I-C analogues. Biochemistry. 37:16529–16537.

Nice finds! I look forward to reading the papers.

All articles I found discussing parallel helices are purely speculative with regards to biological significance; but, they are still interesting. Here are some that I found, in addition to the other answer.

Safaee N, Noronha AM, Rodionov D, Kozlov G, Wilds CJ, Sheldrick GM, Gehring K. 2013. Structure of the Parallel Duplex of Poly(A) RNA: Evaluation of a 50 Year-Old Prediction. Angew Chem Into Ed 52:10370-10373.
This paper presents the solved crystal structure of parallel poly(A) RNA and shows that Poly(A) Binding Protein (PABP) promotes parallel duplex formation. A biological role is hypothesized:

As the great majority of eukaryotic messenger RNAs (mRNA) are tagged with 100 to 250 adenines at their 3′ end, the polymorphism of poly(rA) is also relevant for present day cellular processes involving mRNA translation, storage, and decay. Under conditions of cell stress, cellular mRNAs are transported into RNA granules, increasing the local concentration of poly(rA). It is possible that nature evolved proteins such as PABP in part to regulate the occurrence of poly(rA) duplexes in cells.

There are several reviews that discuss the possible role of parallel RNA in the RNA world which revolve around the problem of replication using complementary, anti-parallel strands:
Taylor WR. 2005. Stirring the primordial soup. Nature 434:705.

Some mechanisms for replication in the RNA world have been put forward, and following the current systems of protein polynucleotide synthesis, all involve the creation of a complementary daughter strand using Watson–Crick base-pairing. But from a mechanistic viewpoint, such a model contains a fundamental problem: if a ribopolymerase were to make a complementary copy of itself, it would need to recopy this to obtain a new functional ribopolymerase. This implies that both the ribopolymerase sequence and its complement would have to coexist. But if these two copies came together, the result would be a double stranded Watson–Crick helix (as found in some RNA viruses) — not a new ribopolymerase. Even if both sequences had well determined secondary structures, the perfect complementarity of the Watson–Crick pairing would act as a sink, leading to a sterile population of double-stranded molecules.

The proposed solution is that early RNA polymerases may have created parallel complements to prevent such inhibition:
Taylor WR. 2006. Transcription and translation in an RNA world. Phil Trans R Soc B 361:1751-1760.

Replication strategies. (a) Replication via a reverse complementary strand leads to (b) a stable double-stranded duplex if the two copies meet. (c) Replication via a parallel complementary strand leads to (d) a relatively unstable double-stranded duplex if the two copies meet.

The propagation of information in a nucleic acid strand from one ‘generation’ to the next using Watson–Crick base pairing logically does not have to involve a reverse complementary strand. Providing that there is complementary base pairing, a parallel complement would also propagate the same information...
...all that need change from the viewpoint of replicase is the direction of its progression along the template. The resulting transcript could only be expected to base pair with the template over a short region before parting, but, faced with the problem of irreversible hybridization, this would be a desirable feature of the model.

This paper mentions some proposed functions of parallel stranded (ps) DNA, with accompanying references, but I can only access one of them:

Other functions have been proposed for ps-DNA in gene expression, recombination, RNA processing (14,18,20), the packing of single-stranded and dimeric viral genomes and the function of reverse gyrase (12).

This is the one reference that I could find from the above paper:
Ramsing NB, Jovin TM. Parallel stranded duplex DNA. Nucleic Acids Res 16:6659-6676.

The possibility that ps-RNA might exist is intriguing in view of the rich
  structural and functional repertoire of RNA species in general. Three canonical situations in which ps helices could arise by interactions of wholly or partially homologous strands or looping of single stranded nucleic acid of appropriate sequence are shown in Fig. 12. The topological implications of such structures are of great interest, particularly in relation to the potential roles of ps-DNA and ps-RNA in (nonhomologous) recombination, RNA splicing, stabilization of ribosomal RNA, and other cellular processes. In addition, it can be anticipated that specific ligands, particularly proteins, could intervene in order to stabilize and exploit the parallel stranded conformation.


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Basic step by step methods for PCR & Gel electrophoresis class
I'm teaching a class how to do PCR & gel electrophoresis soon and would like it if you could check through my basic step by step instructions - it's a while since I've done one. Is there anything there that is wrong, missing, or should be excluded in the following?

A)    Collect all ingredients from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.
B)    Make master mix by adding all ingredients (ddH20, MgCl2, PCR Buffer, F Primer, R Primer, dNTP) (excl. TAQ)
.......
W)    Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the wells.

(The students will use primers they designed to sex 6 DNA samples from 3 species of birds, males should produce 1 band & females 2 bands in the gel)

for the full version see the answer below

for one thing you have to add a stain to the gel to see it on the UV. ethidium bromide requires gloves and is toxic.  GelGreen/GelRed is expensive, but is a lot safer.  also remember to keep the mastermix frozen at -20C until use - aliquot it because you can't refreeze it more than ~6 times or so - it degrades.

Thanks @shigeta useful tip of freezing and aliquot in the mm. I forgot the loading dye is a prepared mix of loading dye and gelred

Might not be necessary for a teaching lab, but a better control might be to have one extra PCR tube without any template (No Template Control) to assess if there are primer-dimers or any other contaminations. If reagent cost/availability is a problem a control run by one student would probably provide enough liquid to run on 2+ gels (since I assume many of these reactions will go in the same thermocycler it's still a reasonable control)

So use the defined amount of Master mix and then add millipore water in the same quantity as the DNA in the samples? @A.Kennard

@GriffinEvo Exactly, and then do PCR on that sample alongside all the others and run it on the gel.

here's a good PCR troubleshooting guide.. https://www.neb.com/tools-and-resources/troubleshooting-guides/pcr-troubleshooting-guide

Looks good to me, with the comments others have shared. I think the most important part of preparing a lab like this is not only make sure you get decent results (although with master mixes and the like these days that's usually pretty straightforward), but to know exactly WHY you're doing each step, and to be able to explain that clearly to the students so they understand. Anybody can follow a protocol, but it takes a special person to connect the "how" with the "why" and explain it all in a unified story. Good luck with your lab!

Thanks @MattDMo I'll keep that in mind, perhaps I could set them up in groups, get them to follow the standard protocol to start with, then have them tweak the PCR reaction mix and thermocycler set up to see what that does, then have them write up the results describing the effect of and explaining why, for example, changing Mg++ concentration affected the end product.

@GriffinEvo I read the article u wrote on wordpress about this and I absolutely loved it ! Learning by teaching. Way to go...

I've run a test following this protocol to the letter...

PCR step by step:

Collect all ingredients (excluding TAQ) from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.
Make master mix by adding all ingredients (excluding TAQ) using fresh pipette tips for each ingredient and using the volume specified
in the PCR reaction mix recipe.
Vortex & lightly spin down on a centrifuge.
Add the required amount of TAQ to master mix (insert in to the liquid) and mix using the pipette to draw some liquid up and down.
Add master mixes to labeled PCR tubes in the required volumes as specified by the protocol.
Add DNA to PCR tubes (using fresh pipette tips for each DNA sample) again using the volume specified in the protocol. Label your tubes
carefully (and on both the lid and tube).
Lightly spin down the PCR tubes on a centrifuge.
Run PCR in the thermocycler according to your protocol.
Collect samples from thermocycler and place in fridge until needed.

Gel Electrophoresis step by step:

Make 1xTAE (enough to make the agarose gel and to place in the electrophoresis apparatus).
Make an agarose gel (about 5 mm thick) by melting agarose and 1xTAE in the microwave; allow the liquid to cool a little before adding it
to the mold.
Once the gel is cool, place it in the electrophoresis apparatus, cover it with 1xTAE (just covering the gel) and then remove the comb.
Collect the PCR products from the fridge/thermocycler.
Make spots of loading dye on parafilm. The loading dye is premixed with GelRed so your samples show under UV light.
Add one sample to a spot, mix it by drawing the liquid in and out of the pipette tip, and then carefully add to a well in the agarose
gel. Take care not to puncture the gel or spill any of the liquid out
of its well. Discard the pipette tip.
Repeat the previous step for each sample and for a negative control (master mix and milli-q water instead of DNA). Use a fresh tip for
every sample.
Load PCR Ladder, also mixed with loading dye, in to a well.
Connect the electrophoresis apparatus to a power supply, with negative electrode (black) nearest to the wells containing the
samples.
Set the power to run 80-120 volts.
Wait until about a finger-width gap appears between the blue and purple bands (approximately 20-30 minutes).
Disconnect the power and collect the gel carefully from the liquid.
Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the
wells.

And got a perfect result...

The order is Control, female, male, female, male, female, male, ladder. Males have one band, females have two. The final pair didn't show too well on the picture but were clear enough on the screen in the camera room. Thanks for the tips everyone! Sorry the picture is low quality.
Feel free to recreate these guidelines but remember to credit the Biology Stackexchange Community!

now that's dedication! Thanks for sharing this!


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Different level of toxicity between smoke
Has there been studies on the difference between the smoke generated from:

cigarette or cigar manufactured by brands which are proven to contain more than a hundred of dangerous additional components
tobacco/marijuana (more or less pure?)/any-plant-dried-leaves made cigarettes.

Apart from the nicotine both contain naturally, are the latter safer to inhale? in which scale?
The other question Effects of smoking tobacco compared to inhaling other smoke, reminds the danger of all source of intoxication, wall paints are also to consider.. and outdoors gas pipes, etc... But I'm doing a fixation on smoked drugs. I've been living in residences, sharing corridors with flats with more or less important smoke concentration, and had developped fumiphobia (but this is out of topic).
This is probably psychological but I'd never stay in the same room than someone smoking, but if someone take some dried leaves out of a plant,.. roll them in paper, fire it and inspire it. It never happened but I wouldn't be as much scared by the generated smoke. But if a study would show that manufactured cigarettes are between 1.5 and 3 times more 'toxic' then I would consider both cases dangerous.

I am not sure, if any comparisions have been made with other plant leaves, but unless these contain some pharmacologic active substances, I doubt that they are smoked widely.
There are comparisions between normal smoking and the smoking of marijuana and the short version is: Both are harmful. It depends on the temperature at which they are burned, how they where grown and so on. For smoking marijuana it also depends if you mix it with tobacco...
This fact sheet from the University of Washington lists a number of points on marijuana together with proper references.
Then there are some articles about smoking and marijuana in comparision:

A Comparison of Mainstream and Sidestream Marijuana and Tobacco
Cigarette Smoke Produced under Two Machine Smoking Conditions
On the Carcinogenicity of Marijuana Smoke
A possible chemical basis for the higher mutagenicity of marijuana
smoke as compared to tobacco smoke
Is frequent marijuana smoking harmful to health?

Thanks a lot for those data, indeed I heard the temperature is what is most harmful to smokers (not passive smokers though) but both share second-hand smokes


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Is dried grain dead or dormant?
Is dried grain considered dead or dormant botanically?
Related to a BH-SE question.

Relevant to the BH-SE quote, a seed considered biologically dead (cooked, too old, etc.) will not then produce a crop.

I would imagine this might vary by species, where the seeds of different plants could survive different degrees or duration of dryness.

Dried grains are very mostly viable means they are in a dormant state until and unless suitable condition are provided. More dried it will be viable for longer.
In fact there are seeds found in Siberia which are ~32,000 years and still viable.

Courtesy: National Geographic
Source:
US Emergency Supply: Introduction to Seed Viability

I got to thinking that there must be a distinction between grain and the germ. The grain must die in order for the germ to come alive. I am confident that the germ will not grow so long as the grain is alive. It is through the process of its dying and acquiring moisture from the earth, that the grain converts to sugar which supports the germ and enables it to sprout. The germ is in the grain, but separate & distinct from the grain, like a baby in the womb is in the mother, but separate and distinct from her. With grain, the mother must die for the germination to occur. With humans not so.

This response can be moved to BH-SE if it is more appropriate there.


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If oxygen deficiency is bad even for a short while, why do people swim?
This may be trivia to many of you.
Textbook says the oxygen deficiency, even for a short while can injure our cells. Then why do people go for sports like swimming? (where rhythmic breathing is required yet, there's a practical possibility of holding the breath longer than usual inhale exhale process) I am looking for a reasoning from cellular biology/patho-physiology/respiration aspect. And not because swimming or any other such exercise is anyone's choice/preference.
So my question is: during sport like swimming, does the oxygen level in our blood drop below a critical level, that cells might suffer from lack of oxygen?
Also found some relevant information here.
Currently referring to this online text : Swimming Fastest: Physiological Responses to Exercise.

My best guess is simply that holding your breath for short periods does not lower your blood oxygen to levels were cells die of asphyxia. It will take some time for your blood to reach critical levels of oxygen, i.e. acting as some sort of buffering.

I've edited your question to avoid closure. Please feel free to revert my edit at any time.

In this paper the authors measured decrease of arterial blood oxygen saturation in healthy and patients with sleep apnae (this latter part is not really relevant only the measurements in healthy individuals).

They found that fall of oxygen saturation depends on the initial saturation rate, but is not affected by the breath-holding time. As you can see on the graph at high initial saturation the fall rate per second is quite low. Here is the info in a table format:

At high initial saturation only mean 0.16% saturation drop occurs per second, thus in average a healthy individual looses 1% oxygen saturation approx every 5 seconds (I'd also like to note that the urge to breathe does not come from the lack of oxygen when holding breath, but from the accumulation of CO2). According to wikipedia normal oxygen saturation is between 100-95%, and only below 90% is considered hypoxemia /hypoxia (a medical condition where blood oxygen level is low). So if we look at the data in the table, it is safe to say that it takes approx 20s until the blood saturation level drops from 97% to 93% and another 5-6 seconds until it drops to 90% (with approx 0.5% saturation loss per sec at 93% initial saturation).
People who are conditioned by exercise have larger vital-capacity (they can breathe more air in for a single breath), thus have means to acquire more oxygen can compensate for the excess use of oxygen. During heavy sport activity like swimming it is unlikely that anybody will hold his/her breath for several tens of seconds.

I am going through your post and will revert once I have understand it enough to ask few side questions.

I don't mind reverting my edit, but be cautious not ask too many sub questions as it may make your question too broad or unclear. If your have side question that are not tightly related to the main question of your post I'd advise putting them into separate post. But encourage you to edit your post to fit your curiosity, and if needed I'll edit my answer to fit the edited question.


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Why there aren't any pandemic diseases by prions?
Learning biology in school, I became interested in the fact that there aren't any diseases by prions which are globally infectious (as far as I know), unlike diseases by viruses (ex. COVID-19, SARS etc.) or by bacteria (ex. plague, ...). Why is it?
cf. Here are some my hypothesis

Prions are not efficient pathogens because they don't have DNAs.
Such prions are not yet discovered or does not exist.
There exists lots of people who are immune to such diseases.

Are there any answers to the questions? Or is there any answers?

Add #4: Prions are bound up in cells, and not readily transmitted through the environments.  You might contrast respiratory viral diseases like COVID or influenza, that are transmitted through the air, with ones like AIDS that require exchange of body fluids.

Kuru, a neurodegenerative spongiform encephalopathy, is considered by many to have reached epidemic proportions in Papua New Guinea in the 1950s, caused by cannibalism of dead relatives, mainly by women & children. Carleton Gajdusek received a Nobel prize for his work on Kuru. (For a disturbing BBC documentary on Carleton Gajdusek, see Storyville The Genius And The Boys)

I think it requires cannibalism.

I thought CJD could be spread by surgical instruments (and that 'conventional' sterilization methods is not enough to 'kill' the prion)? (See Iatrogenic Creutzfeldt-Jakob disease via surgical instruments, for example)

@Jamesqf hepatitis and AIDS are pandemics affecting millions of people, so why would that vector not a threat? quote: Worldwide, 500 million people are estimated to be infected with hepatitis B or C. ... isn't that a pandemic, because it's not transmitted readily through the environment?

@aliential: The difference is in rate of spread, and limits on who it can spread to.  E.g. AIDS took ~25 years from the first known case (1959) until it was recognized as a virus, COVID took a few months from the first case to worldwide pandemic.

I think that you could argue that some prion diseases do form epidemics or outbreaks. In some cases it does appear that people have referred to BSE/vCJD as pandemics. There is even some journalism on the topic, and see also here.
Infection by prion from the environment does occur at some rate, and it is true that it is these prions are the more transmissible. See Table 1 in that linked paper for more information; it appears that the discovery of prion excretion through e.g. feces is relatively recent.
For less transmissible variants it is true that you usually have to directly ingest a fair amount of prion from (i.e. eat) an infected individual to be affected, which is a harder means of transmission because it implies cannibalism (which is not that uncommon biologically, but still).

Might be noted that the pandemic-like outbreak of BSE supposedly was the result of (unintentional) cannibalism, as cow feed producers included waste from meat processing in their products.

@jamesqf a good point. So which transmission mechanism is most efficient can be expected to vary a lot across environments; obviously a feedlot / meatpacking supply chain has a significantly different ecology from a "natural" population.

In order to get large outbreaks via cannibalism/consumption one typically needs not just cannibalism but group cannibalism, i.e. one individual gets eaten by several others https://royalsocietypublishing.org/doi/full/10.1098/rspb.2006.0449?casa_token=geTGhZcyauUAAAAA%3AHpSSymG2SBv6cfyuFXu5fztS6XifIweORmi36i7YA-LfXdyP72bO3kM6FBbNisnRmTXJhccS-7WR

Viruses mutate relatively fast, i.e. Aids mutates 100,000 times faster than Eurkariotic DNA. Actually, viruses mutate on average once every time they reproduce into a new copy / per genome replication.
The DNA segment that encodes healthy PRPC protein which can be hyjacked and converted by a prion has 3kb base pairs, and there are only 30 mutant version of PRPC known as prions detailed since 1970, compared to thousands of different versions of Covid-19 since 2019. The mutant prions dont use RNA, they actually latch on to the healthy versions inside the human body and changes them to mutants.
We can say that prions evolve 10,000 to 100,000 times slower than other bodily fluid viruses like hepatitis and AIDS. Those mutations serve to keep the viruses fit, resistant to new environments, new species, new biochemistries.

Prions don't have a nucleotide component, it is entirely protein, so prions and viruses (or any nucleotide containing organisms) aren't comparable directly in terms of evolution.  It's also that they are incredibly slow - takes years (decades?) to see the effects in any individual.

Precisely, the question was comparing prions to quote: like diseases by viruses (ex. COVID-19, SARS etc.) or by bacteria (ex. plague, ...). So I detailed the difference in replication process and mutation rate...

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


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Thermodynamics of Forming Peptide Bonds

Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein?
A) +ΔH, +ΔS, +ΔG
B) +ΔH, -ΔS, -ΔG
C) +ΔH, -ΔS, +ΔG
D) -ΔH, -ΔS, +ΔG
E) -ΔH, +ΔS, +ΔG
Answer:  C

I know that dehydration is endergonic (+ΔG).
I have two questions:

Why is entropy decreasing? In the beginning of the reaction, we have two amino acids. By dehydration, we have at the end two molecules: the two amino acids together and the H2O molecule. The same number of particles before and after.

Why is enthalpy change positive? You made a bond between the two amino acids. That is exothermic.

I don't think C is the answer. Answer should be D. There is a net lowering of enthalpy because it takes energy to break a peptide bond.

The energy used to catalyze the peptidyl transferase reaction is from the breakage of the bond between the amino acid in question, and the aminoacyl-tRNA it's attached to. The two reactions are coupled by the ribosome. The ribosome can then lower the entropy by positioning of the molecules (including water) in the active site as described here.
So we have our reaction ΔG = ΔH - TΔS
Your ΔG is positive because your reaction is endergonic, and the ΔH is positive because the peptide bond is the system, and you're absorbing energy to form it. The entropy is decreasing as such (removing enerygy = removing heat from outside the system), and the actual reaction for the formation of a peptide bond is unfavorable. As I mention above, this unfavorable reaction is coupled to a favorable reaction in the hydrolysis of an aminoacyl-tRNA to make it possible. What I forgot to mention above is that the ribosome is making this more favorable as well by decreasing the activation entropy for the reaction, and that's what they describe in the linked journal.

Please answer both questions to make the answer complete.

@yolo made what i thought were sensible edits.

authors: Екатерина Кирзова


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Effect of recombination on the rate of loss of genetic variation
Following up from this question: Does recombination increase the additive genetic variance for fitness?
(I'm thinking about the evolution of additive genetic variance and differences between the sex chromosomes and autosomes. Assume males are heterogametic (XY) and females XX, recombination occurs on the X in females, but not between X and Y in males. This means X chromosomes recombine at 2/3rds the rate of autosomes. Answers need not necessarily relate to sex chromosomes as many other factors should be affecting their evolution and additive genetic variance)
As far as I can tell, recombination should improve the efficiency of selection as variance in fitness of the population of chromosomes increases (because favourable mutations can combine more easily and deleterious ones do too) which should in turn reduce additive genetic variance (right?). But then recombination means many more combinations occurs which means additive genetic variance might be higher.
So, if I sample the additive genetic variance in a trait in a population where chromosomes that do recombine and a population where chromosomes do not recombine, where should we see the most variance (the recombiners or non-recombiners)?

(answers should point to theoretical papers please)

I found a key paper for myself from an issue of Nature Reviews Genetics last year. It discusses and reviews how recombination affects the rate of genetic variation at the sequence level.
A key concept is that of selective interference, which is what I had stumbled across in the question, this is when the efficacy of selection is reduced because "recombination fails to break down linkage disequilibrium at selected loci." Simply, a beneficial mutation in a system of no recombination is only as fit as the background it is in, if recombination is extremely high (no LD whatsover) then the fitness is defined only by it's own effects. This means that recombination can reduce polymorphism because selective interference will reduce the speed at which non-neutral alleles are fixed or lost.
However, recombination maintains polymorphism, because without it there is a greater potential for hard sweeps, soft sweeps, partial sweeps, and background selection to all remove genetic variance. For sweeps a beneficial mutation will drag any mutations it is linked with to fixation, the further from the allele the weaker that effect is.
It seems that over riding effect of recombination is to maintain genetic variance despite the increased rate at which an mutation can fix when there is no selective interference because it reduces the polymorphism reducing effects of sweeps and background selection.

"It is expected that neutral genetic variation will be systematically
  depleted in genomic regions with little recombination."


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What is the oligomeric state of Leptospira LipL32 protein?
Does anyone know the oligomeric state of the mature and functional lipoprotein lipL32 in Leptospira?
It's an outer membrane-bound protein. In its mature state, the signal peptide (residues 1-20) is removed, and the cysteine (resid 21) reacts and binds with the head group of a lipid. I've looked through many articles, from x-ray to western blots, and although I understand its structure in terms of the single protein, the results from the x-ray crystal data (as per the protein data bank) are my cause for confusion.
These are the results from LipL32 in the PDB. Three different structures, a multi-mer, and two different dimers.
Are these different geometries the result of the experiment, or is the protein's quaternary structure as one would expect in the organism?

If you are going to reference an outside resource, please provide the actual URL so people can see exactly where it goes. Do not use URL shorteners.

@MattDMo done - enjoy.

@AnthonyNash what MattDMo was referring to was to not use 3rd party shorteners. You can still shorten the link using standard formatting: your text (or using the "add link" button in the formatting panel, that way the mouse over works and you can see the link is actually heading to RCSB, and not some dodgy website, which is obscured when you use the 3rd party sites.


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Performing Flux Balance Analysis (FBA) or Metabolic Flux Analysis (MFA) on tracer metabolomic data
I have targeted tracer metabolomic data of a mammalian cell culture in 3 biological replicates, and 3 time-points (0, 10 and 60 minutes). Cultures were fed with 13C6-glucose. After manual curation I have reliable isotopologue measures for 7 metabolites in glycolysis, 5 metabolites in the tricarboxylic acid cycle and 7 aminoacids. Is my dataset suitable for performing 13C-MFA or FBA?
The metabolites in question:

Hexose
Hexose-P
Hexose-BP
3PG
DHAP
PEP
Pyruvate
Citrate
cis-Aconitate
Oxoglutarate
Malate
Fumarate
Glutamate
Glutamine
Aspartate
Asparagine
Arginine
Serine
Glycine

It would help to include which metabolites you have.

Thank you @David and Michael_A for your remarks and corrections. Here the metabolites I have : Hexose, Hexose-P, Hexose-BP,  3PG, DHAP, PEP,  Pyruvate;  Citrate, cis-Aconitate,   Oxoglutarate, Malate, Fumarate;  Glutamate, Glutamine, Aspartate, Asparagine, Arginine, Serine, Glycine.

The data are probably sufficient for something, but it's hard to evaluate without more details. What exactly are you trying to learn from this experiment?

thank you @MaximilianPress, indeed we would like to estimate metabolic fluxes in a similar manner as these researchers : https://www.researchgate.net/publication/332843369_Core_Metabolism_Shifts_during_Growth_on_Methanol_versus_Methane_in_the_Methanotroph_Methylomicrobium_buryatense_5GB1  . But we have mammalian tissue instead.  I have some knowledge of python, but I have never used cobrapy

I believe no one can answer your question entirely, except you set up a model in question. You need some metabolic network based on which you would formulate, for further computations, your balance equations (flux equations). If those equations with their boundary selected well, you may have a network where you could compute then with your observations (known fluxes) the unknown fluxes.

Thank you very much, I have found this library https://masspy.readthedocs.io/en/latest/education/sb2/chapters/sb2_chapter10.html which hopefully will help me to build the model as you suggested me. However, I guess I have to create myself a new stoichiometric matrix with my few metabolites, and therefore model the glycolisys+tca cicle with some "spureous" reactions that will be short-cuts when necessary (for example, oxoglutarate --> Fumarate)


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Need help with ImageJ thresholding
I'm trying to measure the colocalization of two proteins in a .tiff image taken with a wide-field fluorescence microscope. In ImageJ I have split the image into the two channels (red and green), and now I have to apply a threshold, however when I threshold both channels the bright areas corresponding to the cells are located in the darkest part of the histogram instead of the brightest part, as you can see in this image for the red channel:
https://www.screencast.com/t/QO2iVt0JM
Why ImageJ is assigning darker values to the cells rather than to the background? I'm having problems with this as I cannot properly select these cells for the colocalization analysis.
Anyone does have any clue? Any help would be greatly appreciated.

Check the "dark background" checkbox that is unchecked if the background is dark and you want to select the bright cells. Right now it is assuming the background is bright.

I was thinking about that too but it just inverts the colors, simply assigning white to the cells while they are still considered the darkest objects in the spectrum:
https://www.screencast.com/t/INdZ5pFLHgIn
Here instead how cells (or metal particles like in this case) should appear on an histogram:
https://www.screencast.com/t/TlFxRwsXubr

On the last picture, the particles are bright so they appear as a peak on the far right of the histogram, while the other peak on the left represents other objects in the background that have been excluded by thresholding them out. You may notice on the histogram that this left peak is inside a rectangular black frame representing the background. And as you can see the “Dark background” box is not checked.
With my image I get exactly the opposite, which is weird… and I don’t know what am I doing wrong.

@betelgeuse That's from your actual data then and can't be fixed with imageJ. Look at your histogram vs that one: it's doing the best it can do with what you gave it.


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The probability of indirect human fertilization (follow-up)
This question is a follow-up to
this one.
I've been wondering how small that probability is. As we all know, "safe" sex, that is (correctly) using a condom and all that, isn't perfectly safe. So, in order to put this question into perspective, I'd like to know which one (safe sex or indirect insemination) has the greater chance to lead to impregnation. In other words, can you explain the probability of this scenario in terms a layman like me can understand?
Thanks in advance!

This question appears to be off-topic because it is about sexual products and not biology.

I'm sorry if it comes off that way but the comparison to condom use is used as an attempt to put the other question into perspective, as I already mentioned.

Safer sex techniques are more risky.  Perfect condom use is associated with around a 2% pregnancy rate within a year.  According to that, even sterilization has a 0.1% (male) or 0.5% (female) rate.  Combining techniques is, of course, safer.  "Indirect," as you proposed in the other question, will border on an infinitesimally small chance, as answered there.

Not impossible though, see my answer here :).

@terdon Still the best news story ever.  I remember everyone freaking out when they read that.


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Is recombination suppressed in the males of all Drosophila species? Any other species?
Following up from this question, I am wondering if the phenomenon of genome-wide suppressed male recombination is limited to Drosophila melanogaster or is common to all Drosophila? The answer to the aforementioned question hints that this may be the case but has no reference on that, and doesn't directly state it.
For an added bonus, is this recorded in any other species?


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Degree of dosage compensation in Drosophila melanogaster
In this paper the authors state that the dosage compensation seen in Drosophila is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean degree of dosage compensation in Drosophila (melanogaster)? For example, if X linked genes are, on average, perfectly upregulated the X:AA ratio in males would be 1, while if they are nearly perfectly (but slightly under) upregulated it will be ~0.9.
Here is a similar (but different) question RE perfection in DC in general (here I am specific to Drosophila melanogaster).

please explain downvote

I checked for RNAseq experiments in male and female drosophila but couldn't find any. If you can find one study then I can tell what is the mean degree of DC.

There are studies here and here which explore compensation via the MSL complex (I think Straub et al. has the correct info but they reference the Hamada paper as well). I apologize, I haven't time to read them thoroughly myself, if anyone could give them a look over.