Is glyphosate carcinogenic? I'm trying to understand if glyphosate is carcinogenic. The information in internet is very confusing. There are many ecological oriented websites which claim it's carcinogenic which I suppose they could be biased, but also news websites stating that World Health Organization says "it's probably carcinogenic". In the other hand the European Union seems to sustain it's not, and it extended its license of use in a "heated debate". is it known if glyphosate is carcinogenic or not, or just there isn't enough evidence to sustain one thing or the other?

There is a difference between potential and risk. That's why different agencies came to different conclusions.

The IARC (International Agency for Research on Cancer, a body of the WHO) assesses the potential of a compound to cause cancer. They go through the research that point into this direction and if there is any hint that any dose of the compound might cause cancer they have to rate it accordingly. If you go through the IARC report on glyphosate, you find that a lot of the studies they looked into did not actually find a link between glyphosate and cancer in humans. Nevertheless, there are some studies that show that high doses of glyphosate can result in cancer in animals. So, the IARC had to conclude that glyphosate has the potential to cause cancer. They put it into the category 2A (probable carcinogens). In the same category you find red meat, hot beverages and being a hairdresser, because these things have the potential of causing cancer.

Agencies like the FDA, EFSA etc. are assessing the risk of cancer from "normal" glyphosate exposure. While it seems to be possible to get cancer from "too much" glyphosate, we are only exposed to a tiny fraction of that dose. While it's unavoidable that small amounts of glyphosate residues are found in our food, these amounts are most probably not harmful. At least, that's what most research concludes. The dose makes the poison. While eating fresh organic berries does not pose any risk to harm you, they naturally contain small quantities of chemicals that have the potential to harm you at high concentrations. Your body itself makes small amounts of compounds that have the potential to harm you (e.g. Formaldehyde).

That's why the debate is so heated. Environmental activists are taking the cancer potential assessment of the IARC and turn it into a risk for the consumer, which is untrue. If they would work with the same energy against other group 2A carcinogens, we would have to close down barber shops...

So, does glyphosate has the potential to cause cancer? Probably yes.
Does this provide a risk for the consumer/farmer? Probably no.


How much energy does human body fat contain? I have been reading the Wikipedia article about food energy, but as I'm not a biologist, I don't really understand it properly, so I came here to ask you guys.

My question is: If a human body needs X kcal of energy and it's taking it from the stored fat, how much fat (weight/kg) does it need to burn?

I know that 1 gram of fat represents 9 kcal of energy, but according to the food energy article, the efficiency of getting that energy isn't 100%, so the formula might be a lot more difficult.

I'm not sure what is the real efficiency value here. The article mentions more values, ranging from 18% to 40%.

P.S.: If this belongs to Chemistry.stack, please, tell me or move it there.

I am not sure if I am able to answer your question, but I will give it a try and hope that someone tells us if I'm wrong.

Biologists talk about different kinds of energy depending on where you measure it. The first measurement is the gross energy (GE) which is measured through bomb calorimetry and is basically how much heat a substance gives off when completely burnt. I have recently read in a compendium that the GE value of fat is ~9,4 kcal/g.

The next stage is digestible energy (DE), which is how much of the forage you actually can digest, which would exclude for example fibres.

Next stage is the metabolizable energy (ME), the energy which can be used in actual metabolism (DE - energy losses from transporting nutrients etc). This are the value you reported. (I don't have a source, but I've heard the same values from multiple recognized sources.)

Now is the part where it gets a bit trickier, as the final measurement of energy is the net energy (NE). This is defined as the metabolic energy minus the heat increment, which could be simplified as the energy losses through the conversion between different types of energy (ie. from long carbohydrates into glucose etc.) within the body. Even more simplified it can be said to be the difference between the heat production in a fastened person and the heat production in a fed person, thus being the heat produced by eating, digesting, absorbing and transporting food.

I argue that because the fat already is incorporated in the body it has a very efficient value, and very little transportation within the body is needed. And because the energy (ie, the fat) is internal, it is not accounted for in the heat increment and therefore the NE of internal fat is the same as ME.

And according to the wikipedia-article you linked to United Nations recommendation of the average minimum energy consumption per person is 1800 kcal/day. Thus the amount of fat required to meet the minimum energy requirements of a person would be 1800/9=200g of fat per day.

If you want to read more about the different energy-measurements and the heat increment here is a good link. And don't forget that energy alone is not sufficient for a person as we need protein, vitamins, minerals etc...


The Assumption of Weak Selection? I was reading this question and I failed to fully understand the introductory part of it.

The OP (@Artem Kaznatcheev) says:

  Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection.

I don't fully understand it. Can you help me making sense of why assuming weak selection allows one to Taylor expand the selection function. I am hoping someone would answer by presenting a mathematical model that at first does not assume weak selection and show why assuming weak selection allows the use of a Taylor series to linearize the function. I'd like to understand which terms fall down and which terms left with this assumption.

This is my take in this, without experience of using the Taylor series to analyse evolutionary game theory problems.

As you know the Taylor series expansion of $f(x)$ at point $a$ can be written as:

$f(x)= f'(a)(x-a) + \frac{f''(a)}{2!}(x-a)^2 + \frac{f^{(3)}(a)}{3!}(x-a)^3 + ... + \frac{f^{(n)}(a)}{n!}(x-a)^n + ...$

Often factors above second order are dropped as a simplification. However, to use the Taylor expansion, the function must be differentiable at point $a$, and to be differentiable it must be continuous.

As @Artem Kaznatcheev writes in his question, "...with weak selection meaning the game modifies overall fitness only slightly..." and "... it is typical to model organisms as having a base fitness that is modified slightly by the game interaction...". These statements imply that the overall fitness function/surface can be assumed to be relatively smooth and continuous (i.e. the payoff is negligible), which means that the Taylor series expansion can be used. If the game payoffs for a single game would determine a large proportion of the overall fitness, the fitness surface would be discontinuous.

An example where a Taylor series expansion is used to simplify the fitness function under weak selection is given in Andre & Godelle (2006) (see equation 20 ff).

You might also find this supplement to Nowak et al (2010) interesting (a rather controversial paper), especially page 8.


Were dinosaurs 'hot-blooded' or 'cold-blooded'? Were dinosaurs hot-blooded or cold-blooded? NOTE: The popular term 'hot-blooded' means having an internally maintained average body temperature, which is generally more than that of the surroundings, despite the variation of the temperature outside.  And obviously 'cold-blooded' is the opposite of 'hot-blooded'.

This is a question I have often heard and there is no one certain answer to it. There are several scientific hypothesis about the methabolism of dinosaurs, but none of them has been ever proved or completely disproved.

Arts of methabolism

First of all, the term "cold-blooded" and "hot-blooded" are not scientific. In biology the organisms are classified according to how constant their body temperature is:

homeothermic (from greek "hom(e)o" = equal, same) -- organisms, who manage to maintain constant body temperature.
poikilothermic (from greek "poikilos" = changing, changeable) - ogranisms, whose body temperature fluctuates over time. It is implied here, that  the body temperature follows the fluctuation of the environment temperature, even though this is strictly not correct (see below)

There is another orthogonal classification, which takes into account the metabolic properties of the organisms:

endothermic organisms actively produce heat in their bodies, whereas
exotermic organisms mostly rely upon external heat sources.

What do we know about dinosaurs' methabolism?

Unfortunately there is no one living dinosaur, so we can only reason about their methabolism basing upon the fossils (and possible DNA from moskitos trapped into ambers).

One of the most cited works here is the "Dinosaur Fossils Predict Body Temperatures" (link to the free full text), where the authors write:

  Perhaps the greatest mystery surrounding dinosaurs concerns whether
  they were endotherms, ectotherms, or some unique intermediate form.
  Here we present a model that yields estimates of dinosaur body
  temperature based on ontogenetic growth trajectories obtained from
  fossil bones. The model predicts that dinosaur body temperatures
  increased with body mass from approximately 25 °C at 12 kg to
  approximately 41 °C at 13,000 kg. The model also successfully predicts
  observed increases in body temperature with body mass for extant
  crocodiles. These results provide direct evidence that dinosaurs were
  reptiles that exhibited inertial homeothermy.

And exactly here we need the terminology I presented above to understand the findings:

Dinosarier were endothermic -- they were able to actively produce heat in their bodies.
The produced heat can only be taken away through their body surface. Due to the fact that the body surface increases quadratically (n2) with the size, whereas the weight grows cubically (n3), the bigger dinosaurs were the higher temperature their bodies reached. That could be one of the growth limiting factors and explains why especially big species preferred to live in water.
Even though the dinosaries were homeothermic, we don't know anything about their thermoregulation. Modern reptilia do not have the thermoregulation mechanisms that would keep the body temperature constant. Dinosariers, however, due to increased heat production might have less fluctuations in their body temperature, than smaller reptilia. This is termed as "inertial homeothermy" here.


What is the difference between cytosol and cytoplasm? I've generally seen cytosol defined as the solution inside cells minus  the organelles, cytoskeleton, etc and cytoplasm as the cytosol plus the organelles, cytoskeleton, etc. This naturally leads to the impression that cytosol is the cytoplasm minus all the solids. The problem here is that there are all sorts of other large molecules in the cells which could be thought of as solid. Are they also part of the cytosol or are they suspended in it? (I.e. are they part of the cytosol or are they non-cytosol components of the cytoplasm?)

Basically, I'm asking if the precise definition of cytosol is just anything in the cell that's not behind an endomembrane (save the exoskeleton) or if the dividing line is something else.

Subquestion: things can get even more terminologically confused because the cytosol is sometimes called the matrix. What the heck is the preferred terminology with this stuff?

IMO, the definitive answer to this question is given in a paper by J. S Clegg.  He traced the origin of the term cytosol to a book chapter by H. A. Lardy, and confirmed by email that Lardy had indeed coined the term. Their definition of cytosol is as follows:

  ... that portion of the cell which is found in the supernatant fraction after centrifuging the homogenate at 105 000 x g for 1 hour.

Thus cytosol is a centrifugation term, (ie a fraction obtained by centrifugation)  and  ' should not be applied, in any context, to the intact cell' (Clegg, 1983).

The cytosol  may roughly be though of as the 'soluble' portion of the cellular extract obtained after everything else, including the microsomes, have been sedimented. (For those not familiar with subcellular frationation, centrifugation at 100 000 g for 1 hr is the 'standard' method of sedimenting microsomes. If your enzyme is found in the 100 000 g supernatant fraction, you can be  pretty sure it is soluble).

When we are referring to the cellular aqueous fluid  that 'holds'   the organelles and other  components we should use the term cytoplasm.

At the bottom of Clegg's article, the editors of TIBS have supplied the following quote, attributed to F.H.C Crick & A. F. W Hughes (1950):

  If we were compelled to suggest a model for the structure of cytoplasm we would propose Mother's Work Basket -a jumble of threads, beads and buttons of all shapes and sizes, with pins and threads for good measure, all jostling about and held together by "colloidal forces".'

In being a  centrifugation fraction,  the term  'cytosol' is very like  microsome: the intact cell contains neither cytosol or microsome.

Ref

Clegg, J. S. (1983) What is the cytosol? Trends in Biochemical Sciences 8, (Dec, issue 12), pp 436-437


During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment? I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. I understand that it is labeled so in order to locate the fragment on a gel, but I don't understand why it is only labeled on one end? If the DNase cleaves it in two, wouldn't the other end be un-labeled and untraceable? Therefore kind of defeating the purpose of labeling it at all?

Preamble

Although there is a Wikipedia page with a general account of DNA footprinting, this perhaps does not put sufficient emphasis on the general strategy, making reference to the Maxam & Gilbert DNA sequencing method, with which contemporary students are not likely to be familiar. Elsewhere on SE Biology I have summarized the strategy of different DNA sequencing methods, so I shall use that as a starting point for this answer.

The Strategy of DNA Footprinting

In DNA sequencing there are two conceptual pieces of information one is trying to discover: the identity of a base, and the position at which it lies. A third point of importance is the practical technique one uses to realize a strategy. The method of DNA sequencing developed by Maxam & Gilbert used specific chemicals to fragment pieces of DNA:

The particular chemical used identified the base as the last one on one of the fragments produced.
The length of the fragment indicated the position with respect to one of the ends, which was used as a reference point.
End-labelling of one end of the original DNA allowed fragments containing the reference point to be visualized, distinguishing them from others that were unlabelled and hence generated elsewhere.

In DNA-footprinting we are not concerned with identifying the bases: the DNA has probably already been sequenced or we can do that separately. We are in interested in positional information, and we shall see that this also involves fragments — generated by the non-specific DNase — and their visualization, as in the method of Maxam & Gilbert.

This is explained in the figure below, my own modification of Coutney2008.jpg, in the Wikipedia article mentioned.

The frame on the extreme left addresses the question of labelling and visualization by showing the fragmentation of uniformed-labelled DNA by DNase. In this example the DNase cleaves at three points (arrows), generating four fragments of different sizes, A, B, C and D. If these fragments are separated and visualized by their radioactivity (by autoradiography) there is no way of knowing their position in relation to the reference point. So whatever our strategy is in relation to protein-binding (explained below) the positional information is not revealed. We cannot tell that fragment A contains the reference point.

Now let us turn to Frame 1, which is in effect the Maxam & Gilbert strategy without the base-identification. The DNA is labelled at one end and treated with DNase at a concentration that will generate a range of fragment sizes. The ones we are interested in are those that include the reference point, which is the end we have labelled. These fragments have been coloured pink. Other fragments (light blue) that do not include the reference point will be generated — including some of the same size as those of interest — but these will not interfere with our analysis as they are not labelled and will not be visualized after the fragments have been separated according to size on denaturing gels and subjected to autoradiography (see gel lane 1). (The unlabelled ‘light blue’ portions may have been fragmented further, but this has not been shown for clarity.)

The footprinting strategy is shown in Frame 2. The experiment of Frame 1 is repeated with the DNA-binding protein (bright blue oval) added. Now the region of DNA to which the protein binds will be protected from DNase. Thus, fragments terminating within this region will be missing and be absent from lane 2 of the gel. Hence the position at which the protein binds is specified as the distance of the missing fragments from the labelled reference point. (There are likely to be fragments of the same size as the missing ones in the mixture, but, to repeat, because of the end-labelling they will not be visualized.)


vestigial structure question If a species has a vestigial anatomical
structure that it no longer uses, would
you expect this structure to disappear
over many generations through the action
of natural selection? Always, sometimes,
or never? Explain your answer.

I'm having a hard time with this question. I don't know what should I do

If a species has a vestigial anatomical structure that it no longer uses, it may or may not disapear through natural selection.

Evolution is based on four mechanisms :
- mutation
- natural selection
- sexual selection
- genetic drift

A no longer used structure can disapear if a mutation makes it to. Then, if it confers a selection advantage (natural or sexual), then individuals without that structure will survive and / or reproduce better than the other. The mutation will spread among the population and structure may finally disapear.

If it does not confer benefit the individual nor decrease it's chances of survival or reproduce compare to others, mutation may or may not be conserved and so for the structure.

Genetic drift can accelerate disapearance of a structure, especially if the population is really small, even if it does not confer any advantages to the individuals. The mutation can rapidly spread through the population just by chance.

For example, in human body, the appendix is no longer used but still remains. It's absence does increase chance of survivol nor is attractive to sexual partners, so it doesn't imply natural or sexual selection structure. Genetic drift may or may not randomly make it disapear one day, no one knows.


Territorial behavior in humans? Do humans exhibit territorial behavior like other primates? I have seen people sometimes stare at others -- notably males -- and then physical fights spontaneously turn up. Is this territorial? It seems it either goes two ways: One person looks at another; the other looks back and either looks away or both look away; or they both hold a stare until one or both erupt in to physical blows and try to dominate the other or fight/assault them. Is this a display of human territorial behavior? I know some chicks do it too.

I've also read that in males more so that staring can be an "alpha" or "dominating" gesture to others -- especially if a stare is held at one in response to them either turning away or provoking a fight.

This can be seen in every area, but possibly more so in clubs, bars, or certain social settings.

From encyclopedia britannica

  Territorial behaviour, in zoology, the methods by which an animal, or group of animals, protects its territory from incursions by others of its species.

Following, this definition, yes territorial behaviour exists in humans. Here are three simple examples drawn from different (western) cultures

You seem to be confusing territorial behaviour with general, aggressive behaviour. Whether or not the behaviours you describe qualify as territorial behaviour requires one to make a psychological study to determine whether the individuals had a notion of territory that they wish to defend.


Can sugar be absorbed orally within seconds? Whenever I feel a little light headed or tired, it helps to eat something sweet.
Specifically, simply chewing or sucking on a sweet seems to aleviate the symptoms within a matter of seconds and then the sugar seems to kick in. So I was wondering whether it is just a psychological effect, or whether sugars are absorbed in our mouth and reach the brain (or wherever the sugars exert their effects?) within seconds. Or is perhaps the taste of sugar sufficient to signal the body that it can safely release some extra energy as resupply is imminent?

Yes we do. The first part of digestion starts in mouth. Digestion begins in the mouth, where chemical and mechanical digestion occurs. Saliva  produced by the salivary glands (located under the tongue and near the lower jaw), is released into the mouth. Saliva begins to break down the food, moistening it and making it easier to swallow. A digestive enzyme (amylase) in the saliva begins to break down the carbohydrates (starches and sugars).


Why do humans seem to be the only mammals that like spicy food? Peppers evolved chemicals like capsaicin to discourage animals from eating them, and that chemical itself can cause internal damage if consumed in large quantities, though this is usually only a concern for the hottest of peppers (which people do eat).

Still, why is it that humans seem to be the only animal that often "like" spicy food?

I think like many things spicy food became something that we used as a tool. Used mostly for preserving food, those countries where it gets very hot due to a tropical climate you'll find the food tends to be much spicer in areas where parasitic flies and other pathogens would contaminate the food faster. The spicier it is, the longer your food stocks would last. Over generations they developed a higher and higher tolerance.


What is the difference between local and global sequence alignments? There are a bunch of different alignment tools out there, and I don't want to get bogged down in the maths behind them as this not only between software but varies from software version to version.

There are two main divides in the programs; some use local alignments and others use global alignments. My question is threefold:

What are the fundamental differences between the two?
What are the advantages and disadvantages of each?
When should one use either a global or local sequence alignment?

The very basic difference between a local and a global alignments is that in a local alignment, you try to match your query with a substring (a portion) of your subject (reference). Whereas in a global alignment you perform an end to end alignment with the subject (and therefore as von mises said, you may end up with a lot of gaps in global alignment if the sizes of query and subject are dissimilar). You may have gaps in local alignment also.

Local Alignment

5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3'
             |||| |||||| |||||||||||||||
          5' TACTCACGGATGAGGTACTTTAGAGGC 3'

Global Alignment

5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3'
   |||||||||||    |||||||  |||||||||||||| |||||||
5' ACTACTAGATT----ACGGATC--GTACTTTAGAGGCTAGCAACCA 3'

I shall give the example of the well known dynamic programming algorithms.
In the Needleman-Wunsch (Global) algorithm, the score tracking is done from the (m,n) co-ordinate corresponding to the bottom right corner of the scoring matrix (i.e. the end of the aligned sequences) whereas in the Smith-Waterman (local), it is done from the element with highest score in the matrix (i.e. the end of the highest scoring pair). You can check these algorithms for details.

You can adopt any scoring schemes and there is no fixed rule for it.

Global alignments are usually done for comparing homologous genes whereas local alignment can be used to find homologous domains in otherwise non-homologous genes.


Are Protocadherin Gamma Cluster transcripts considered separate genes? The PDCH@ cluster of genes share exons and are therefore isoforms of each other.  However, they are considered separate genes, by both HUGO and Ensembl.

A "gene" is defined as "a locus of co-transcribed exons" (Venter 2001), and this locus clearly fits that definition with no ambiguity. So why are these transcripts considered separate genes?

I would say they are considered different genes because each isoform is under the control of its own promoter.


Predicting DNA nucleotide bases sequence from fully formed protein I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, given a sequence of such bases, produce a final protein (going through a simulation of the various processes that end up in a protein). However, are there any algorithms that allow to predict the opposite, i.e. the sequence of nucleotide bases that were the basis for the synthesis into a given protein?

It's trivial in principle, but remember that there are multiple codons that can produce a single amino acid, so reverse-translating a protein will either give you the most commonly-used codons for the protein, or will give you a large number of possible sequences.

Here and here are online programs that will give a single consensus, and here is one that considers ambiguities.


Is tongue rolling genetic? Is the ability to roll your tongue or not truly inherited or genetic? What I have gathered from school has been contradicting with evidence I found elsewhere.

I could only find fairly old literature on the subject, so take this with caution.

Some papers seem to indicate some sort of genetic component to tongue rolling, although the precise molecular basis are not really described (but, again, these are 30-40 years old papers...)

From: Inheritance of ear wax types, ear lobe attachment and tongue rolling ability. - Cruz-Gonzalez and Lisker - Acta Anthropogenet., 1982

  The mode of inheritance of ear wax type, ear lobe attachment and tongue rolling ability were studied in 77 families with a total of 293 children. The results clearly showed that the dry ear wax type and the attached ear lobe type represent the homozygous state for two pairs of autosomal recessive genes. The evidence for the same being true regarding the lack of ability to roll the tongue was less conclusive in our material, but this could be due to difficulties in communication between the examined individuals and the examiners.

Tongue-rolling phenotypes and geographical variation in the United Kingdom

  The distribution of tongue-rolling phenotypes in a sample (n = 477) of undergraduate students of the University College of Swansea (U.K.) was studied. The birthplaces of these students were also recorded. England was divided into six areas, and Wales was left as an area on its own. The data suggest that those students who come from north-east are more non-rollers, which may be due to mixture with Scandinavians.

Left-handedness and tongue-rolling ability.

  948 undergraduates at The Ohio State University were administered the 10-item Edinburgh Handedness Inventory and asked to indicate the extent to which they could turn up the sides of their tongues. Significantly fewer left-handers than right-handers (62.8% and 74.8%, respectively) reported being able to turn up either or both sides. Sex differences in tongue-rolling ability were also noted. Among the 403 men included in the final sample, 77.4% could roll their tongues, whereas only 69.7% of the 491 women could do so.

This paper, however says (luckily Google finds a PDF here... seriously it should be illegal to have papers from the 70s behind paywalls... but I digress):

No evidence for a genetic basis of tongue rolling or hand clasping - Martin, J Hered., 1975

  OCCASIONALLY one still finds in elementary genetics courses and elsewhere, the ability to roll the tongue and the manner of clasping the hands cited as examples of simply inherited human polymorphisms. This is despite extensive evidence to the contrary that has accumulated over several decades. Sturtevant T found that about 65 percent of persons studied were able to tum 1.JP the edges of the tongue and although some people were able to learn the ability, family data indicated that it was inherited as a simple dominant allele. However, Matlock reported 7 out of 33 monozygotic (MZ) twin pairs discordant for the ability, and Sturtevant concluded that there is sufficient nongenetic inftuence to make the character practically useless as a genetic marker. He confessed to being "still embarrassed to see it listed in some current works as an established Mendelian case."

The paper is also cited in the "Myths of Human Genetics" page of the University of Delaware.

So, all in all, it seems that there is evidence against a Mendelian transmission of this character, although these studies are quite old and some further analysis is warranted to exclude non Mendelian (read epigenetic) transmission of tongue rolling.


What is the motivation behind the CCA -> CCU modification between SARS-CoV-2 and the mRNA vaccine when encoding the signal peptide? The S glycoprotein signal peptide in SARS-CoV-2 and the mRNA vaccine is encoded by:
           3   3   3   3   3   3   3   3   3   3   3   3   3   3   3   3
Virus:   AUG UUU GUU UUU CUU GUU UUA UUG CCA CUA GUC UCU AGU CAG UGU GUU
Vaccine: AUG UUC GUG UUC CUG GUG CUG CUG CCU CUG GUG UCC AGC CAG UGU GUU
               !   !   !   !   ! ! ! !     !   !   !   !   !

What is the motivation behind the CCA -> CCU modification between the virus and the vaccine?

The other answer is a bit convoluted IMHO.
First note that as the article cited notes, that's not actually CCA -> CCU but CCA ->  CCΨ; they only used ASCII for convenience. Furthermore, these three all code for proline as the article also notes.
Second, Ψ stands for pseudouridine and it's the golden discovery of Kariko and colleagues (which made mRNA vaccines [more] practical) that you need to use as many pseudo-Us as possible to ensure that the exogenous mRNA doesn't get destroyed prematurely and/or triggers downregulation of transcription.
Third, that's not even pseudo-U that's actually used in the Pfizer vaccine but N1-methyl-pseudouridine (variously abbreviated as N1mΨ or m1Ψ), which is even more "potent" in these terms than even pseduo-U. (According to a book on RNA therapeutics, m1Ψ was actually discovered and is patented by Moderna circa 2012-2013, before any academic publications.) Actually a 2017 publication found that independently of reduced immunogenicity, m1Ψ seems to be more active "by increasing ribosome pausing and density on the mRNA":

We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.

And more research on the latter aspect (2019)

Global incorporation of different modified nucleotides often (but not always) markedly changed mRNA expression. This effect was seen across numerous synonymous coding variants of multiple proteins, in several different cell lines, and in vivo. m1Ψ generally gave higher expression than U or mo5U for the same sequence. Biophysical studies revealed that m1Ψ and mo5U have dramatically different and opposite effects compared to U (stabilizing and destabilizing, respectively) on overall mRNA folding, nearest-neighbor base-pairing thermodynamics, and secondary structure pattern as mapped by SHAPE.

There could be additional reasons, but these are probably marginal.
Now, canadianer asks an astute question below (which was not asked by the OP), whether it's (still) preferable to do UUU -> UUC (which normally it is) if m1Ψ is going to be globally substituted for U anyway. I don't actually know the answer to that; Pfizer or Moderna might have researched it, but I haven't found any publication on the trade-off.
The actual reason for the latter (especially since UUC is about 3 times as inefficient as UUU) might be that real goal is to slow down the protein folding there. The WHO doc does say that the protein is folded in a particular way "to ensure the S glycoprotein remains in an antigenically optimal pre-fusion conformation". In general, there's a trade-off between the speed of translation and accuracy of folding. (ΨUU is actually twice as efficient as UUU already, even with naturally occurring pseudouridine. In fact UUU is one of the most common places where one finds a naturally occurring pseudouridine.)


What is meant by a muscle fiber being glycerinated? I was popped this questions today, "what is a glycerinated muscle fiber, and what is required for its contraction," and had little idea. I'm assuming the question is "what's required for its contraction as compared to normal muscle tissue?"

There's a limited amount of information out there about this. It appears that it is a type of in vitro system requiring special preparation of typical muscle tissue. I was wondering if anyone here had a little more information. Is this something that's just used in teaching lab exercises?

From: http://www.acad.carleton.edu/curricular/BIOL/classes/bio126/Documents/Lab_5.pdf

  Glycerination disrupts the membranes of the muscle cells, ruptures mitochondria, and leaches out soluble constituents such as ATP and inorganic ions. However, glycerinated muscle retains the organized structural array of myosin thick filaments and actin thin filaments, actin-associated proteins like troponin and tropomyosin which regulate contraction, and the functional capacity for contraction.

I would expect that because the sample has lost ATP and inorganic ions, you would need to supply ATP (the source of energy), $Mg^{2+}$ (which is necessary for ATP hydrolysis) and $Ca^{2+}$ (to induce the contraction).


Relation between respiration and concentration of citric acid A and B are 2 reactions.

If there is an excess availability of citrate, then which of the above reactions will prevail?

I know that citric acid is formed when oxaloacetic acid reacts with acetyl coA. But how does concentration of citric acid influence the above reactions

This image is a bit misleading since both ways seem to be the reversion of each other, but in fact they are not (although the same metabolites are used).

Reaction A takes only place in gluconeogenesis which makes glucose from other metabolites (coming from the metabolism of fatty acids for example) and this pathway is only active when there is an abundance of energy present in the cell. Citrate activates the Fructose-1,6-bisphosphatase. The gluconeogenesis takes only place in liver and kidney.

Reaction B takes place in glycolysis and is the rate limiting for the whole pathway. It takes place when glucose is taken up and then used for the production of energy. The Phosphofructokinase (PFK) is inhibited by signals of excess energy as ATP (which is an allosteric inhibitor of PFK) as well as citrate and NADH/H+. While citrate is a weak allosteric inhibitor on its own, it acts as a strong inhibitor together with ATP. This makes sense since both molecules are indicators of free energy metabolites in the cell.
See these two publications for details:

"Allosteric regulatory properties of muscle phosphofructokinase."
Effect of citrate on the activities of 6-phosphofructokinase from
nervous and muscle tissues from different animals and its
relationships to the regulation of glycolysis.

If there is an excess of AMP/ADP then the enzyme is activated and phosphorylates Fructose-1-phosphate.


Why basement membrane thickens in diabetes mellitus? Untreated diabetes mellitus may lead to blindness and kidney failure because the basement membrane of small blood vessels in these organs thickens due to increased production of collagen and laminin.

My questions : why are these organs most susceptible ? Why will collagen and laminin production increase in diabetes mellitus ?

The endothelial cells in small blood vessels take in more glucose (as glucose levels in blood are high due to diabetes.) Thus they form surface glycoproteins which causes the basement membrane to become thicker yet less strong. This leads to blood and protein leakage from the blood stream in other tissues in the space between cells. Blood leakage alters cellular blood supply for all cells.

Less blood means less oxygen and less nutrients. As you probably know nervous tissue gets damaged fastest without oxygen thus explaining diabetic neuropathy. Also retina and kidney contain cells that get easily damaged when there is not enough blood.

Probably the worst complication is neuropathy, because the person suffering from it may suffer a heart attack (caused by the accelerated process of atherosclerosis in diabetes) and feel less pain (http://medlineplus.gov).

Collagen and laminin poduction increases as a result of the fibrosis process that takes place when a tissue gets less nutrients than it needs.

Diabetes affects all blood vessels, even the larger ones. See macroangiopaty.

From http://en.wikipedia.org/wiki/Microangiopathy


Do we get 1/4 of our genes from each grandparent? I know that we get half of our genes from each parent, but does it necessarily mean we get 1/4 of our genes from each grandparent? Or is it possible that we might get say 30% from one grandparent, 20% from other, 15% from another, 35% from another?

I have answered a similar question before: "How many genes do we share with our mother?".

It is not that you "get half your genes" from each parent, and thus a quarter from each grandparent, it is that you inherit the versions of the genes (we all have the 'same' genes).

The method that determines which traits are inherited from each parent by the offspring is known as homologous recombination, and this process is (essentially) random, and thus you end with ~50% of your traits (the alleles of the genes) from each parent, and ~25% from each grandparent, so you are right in this respect.

This is, however, a generalization; due to the chance nature of the recombination it is entirely plausible that you may inherit more traits from one grandparent in comparison to another, but this is unique to each individual (with the exception of course of genetically identical twins).


Is the human collarbone supposed to break? I've read it in a book and have heard people mention it, but I can't find any documentation about it. But the point being made is this:

  The human collarbone acts as a shock absorber for impact on the shoulder or stretched arm. If too much force is put on the shoulder (EG: during a fall), the collarbone is designed to break to prevent injury to the neck and/or head.

Is this actually true and if so, can anybody point me to some documentation about it?

This looks like a misinterpretation. Because collarbone is the only horizontal long bone of the human body [1], it is the first to fracture when falling on the shoulder.

Its fracture can affect many structures:

  The muscles involved in clavicle fractures include the deltoid, trapezius, subclavius, sternocleidomastoid, sternohyoid and pectoralis major muscles. The ligaments involved include the Conoid ligament and Trapezoid ligament [1].

It is indeed a shock absorber, but for the upper torso (some way or another any bone can be considered a shock absorber):

  The clavicle also serves as something of a "shock-absorber" for the upper torso. Physical contact from the side will be partially absorbed by the clavicle. Because of this function, the clavicle is a very commonly broken bone [2].

The fracture can lead to severe injuries:

  Displaced or comminuted clavicle fractures are associated with complications such as subclavian vessels injury, hemopneumothorax, brachial plexus paresis [...] [3]

References:

Wikipedia contributors, "Clavicle fracture," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Clavicle_fracture&oldid=615723256 (accessed July 30, 2014).
Erich Rosenberger M.D. Anatomy And Physiology (2009). Available from http://www.sciences360.com/index.php/anatomy-physiology-299-12859/ (accessed 30.07.2014)
George Mouzopoulos, Emmanuil Morakis, Michalis Stamatakos, Mathaios Tzurbakis. Complications Associated With Clavicular Fracture. Orthopaedic Nursing, October 2009, Volume 28, Number 5, Pages 217 - 224 - See more at: http://www.nursingcenter.com/lnc/cearticle?tid=938803#sthash.F09wonvJ.dpuf


What is the spacing between stop codon and transcription terminator? When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?

In general, there is no need for a spacing between stop codon and terminator. They can be right next to each other.

When transcribed, transcription terminator forms a hairpin-like structure which interacts with the RNA polymerase to stop the transcription. Usually, the upstream sequence will not interact with the terminator and it will be transcribed normally. In a rare case the coding sequence might contain sequences that extend the hairpin and might result in interrupted translation. This can be avoided by doing a thermodynamical inspection of the secondary mRNA structure, but this is usually unnecessary.


What is the life-span of the various organs in the human body? It is possible for a person to donate the harvestable organs (kidneys, eyes, and such) posthumously. Let's assume for a moment that the technology exists to kill rejection, and maintain the organ in excellent shape after it is harvested.

Could the organ/s ( e.g. Eye ) (assuming a decent life-style) travel for centuries from one donor to yet another donee? What is the typical life-span of the various organs in the human body assuming a healthy, and low stress life?

p.s. It's a curiosity question; my eyes even millenia after my death would continue to see.

Perhaps you can infer relative lifespan from the age at which organs start declining in someone of average health.

Skin, muscles, bones, eyes, and ears start to visibly decline around age 40.

Kidneys become smaller and their ability to filter blood starts to decline around age 30.

Brain function begins to decline around 70, even in the absence of neurodegenerative diseases such as Alzheimers.

I don't think any organs can be passed through people for centuries, since decline of virtually every organ is observed even in individuals in perfect health. There may be two exceptions: The digestive tract and liver seem to be the most long-lived and are very little affected in healthy elders, probably because they regenerate their cells.

Reference


Why the smell of sweat greatly varies across the body? Having only two types of sweat glands (eccrine, apocrine) I would expect the sweat odor "spectrum" to be very "narrow". However, the smell of sweat greatly varies between scalp, arms, armpits, groin and feet. Why is that?

Sweat is actually odorless regardless of what type of sweat gland it comes from, of which there are two types - apocrine and eccrine.

As suggested by canadianer, the odor comes from the mixture of bacteria and the resulting sweat. With regards to why your bacterial flora is so diverse is likely due to the different micro-environments found around your body.

In your armpits and feet (arguably where the strongest odor subsides), you'll find more anaerobic bacteria - bacteria that prefers low oxygen environments and sometimes, higher temperature, humid environments. Because they don't use oxygen to metabolize, their by-products in making energy are often organic acids, commonly lactic acid. Some anaerobic bacterias even have by-products containing sulfur.

Meanwhile, in less warm and damp environments on your body (i.e. face, hands), aerobic bacteria dominate. Oxygen is abundant and the temperature is just right for those strains of bacteria. Their by-products are much less putrid

EDIT: In addition, apocrine sweat is also high in the nutrients, such as lipids and proteins that bacteria can feed on. Once they metabolize the stuff in apocrine sweat, they start releasing the aforementioned by-products.


Metrics to analyze branch lengths in phylogenetic trees I'm interested know about some basic metrics that could be used to discriminate trees based on their branch lengths. I know of branch length unaware topological/tree shape-based methods such as Colless and Sackin's indices and am curious whether there are similar metrics that utilize branch length to discriminate. For example, the two trees below have an identical topology but are very different.

There are a variety of measures of tree similarity implemented in the TreeDist R package. (Your phylogenies appear to be from the R ape package, so hopefully you are somewhat familiar with R.)
Other tools include treedist from Joe Felsenstein, which computes Robinson-Foulds and the Branch Score Distance (which sounds closely related to your interests, described in this paper). You can see that software page for a lot more information.
For a practical description of the different tree comparison metrics you can see this article.
I would suggest taking a look at the manual and the multiple vignettes associated with the TreeDist package to learn more about how exactly those metrics work. There appear to be a wide variety of metrics in there that I have never heard of, such as clustering entropy or split entropy or Nye similarity.
This package also includes tools for making visualizations of differences, such as that shown below:


Why do adults lose hearing at high frequencies? Children and teens can hear high pitched sounds that adults can't hear anymore. Why do adults lose high-frequency hearing?

Hearing declines with age and, typically, high frequencies are affected first. Age-related hearing loss (or presbyacusis (Kujawa & Liberman, 2006)) is progressive and starts at the highest frequencies and as a person ages the lower frequencies are affected. The reduction in hearing sensitivity is caused by the loss of hair cells. Hair cells are sensory cells in the inner ear that convert acoustic vibrations into electrical signals. These signals are transmitted to the brain via the auditory nerve.

Because of the tonotopic organization of the inner ear (the cochlea) one can conclude that presbyacusis develops from the basal to apical region. The following schematic of the cochlea from Encyclopædia Britannica, Inc. nicely shows the cochlear tonotopy (i.e., high frequencies in the base, low frequencies in the apex);

As to your question why the basal region is more sensitive to aging - that is a very good and interesting question that has not been answered, as far as I am aware. What is known, however, is that the basal regions of the cochlea are also more sensitive to the damaging effects of ototoxic antibiotics such as kanamycin (Stronks et al., 2011) and other aminoglycosides, and some chemotherapeutics such as cisplatin (Schacht et al., 2012). In low doses these compounds specifically target the basal regions over the apical ones (at high doses the whole cochlea is affected).

Perhaps the specific anatomy and circulation causes the basal region to be affected more by these chemicals. For example, blood flow may be enhanced basally whereby environmental and food-based chemicals may enter the basal region more readily (educated guesses, I can dig up references of authors posing these possibilities if necessary). This scenario may also contribute to presbyacusis, since it is quite imaginable that years of exposure to various substances may cause accumulation damage specifically to the basal parts of the cochlea.

In addition, since high frequencies are coded in the basal region, and given that sound enters the cochlea in the basal region (see picture below), all sounds, including damaging loud low-frequency stimuli first travel to the base on their way to their point of processing.

Because sound is analyzed as a travelling wave, sound travel stops at that point where the frequency matches the cochlear characteristic frequency. There the wave quickly dies out due to cochlear filtering (Mather, 2006); see the first picture above. In effect, more apical parts of the cochlea are exposed less frequently to (damaging) sound stimuli, while the base of the cochlea is exposed to all sounds entering the inner ear.

Hence, chemical exposure and acoustic wear and tear may be more prominent in the cochlear base, which can explain why presbyacusis starts at the very high frequencies and progresses to low frequencies (upward in the cochlea) from there.

References
- Encyclopedia Brittanica* The-analysis-of-sound-frequencies-by-the-basilar-membrane
- Kujawa & Liberman, J Neurosci 2006; 26:2115-23
- Mather, Foundations of Perception, 2009
- Schacht et al, Anat Rec Hoboken 2013; 295:1837-50
- Stronks et al, Hear Res 2011; 272:95-107


How many molecules NADH are produced in the Krebs Cycle? I don't know which source i'm going to follow.

Some say its 3 molecules NADH per cycle → 2 cycles × (3 NADH) = 6 NADH

Some say its 4 molecules NADH per cycle instead?

This is slightly depending on which reaction you want to include into the cycle. I count four:

One when Pyruvate is converted to Acetyl-CoA,
one when Isocitrate is converted to α-Ketoglutarate,
one for the reaction of α-Ketoglutarate to Succinyl-CoA and
finally one for the reaction of Malate to Oxaloacetate.

If you see the reaction of Pyruvate as happening outside of the cycle, it's only the later three.
See this image (from here) for an overview:


Human ancestor reproduction after chromosome fusion I read somewhere that human chromosome 2 is the result of 2 primate chromosomes fusing together somewhere along our evolutionary journey. This is why we have 23 chromosomes while other primates have 24. My question is this: for the first ancestor whose chromosomes fused to have 23 chromosomes instead of 24, how did he reproduce? Don't offspring receive half of their genetic makeup from each parent, so if one parent has 23 chromosomes and the other has 24, how would that work? I know that there have been animals with different chromosome counts being bred together, but the offspring typically have issues and are sterile, so even if the difference in chromosome count was not a problem, wouldn't the offspring between an organism with 23 chromosomes and one with 24 be infertile, thus leading to the end of animals with 23 chromosomes? Would there have to be two organisms of different genders experiencing the same chromosome fusion at the same time in order to avoid this problem? I'm just a bit confused as to how this would work exactly.

Strangely enough we actually do have an answer for that.

There are a several examples of individuals who are born with two chromosomes fused together in all their cells.

We even have a few examples where these fused chromosome is in a diploid state, ie all instances of that chromosome are fused in the individual. Such individuals come from families in small isolated villages that are very inbred.

Chromosome number does not prevent fertility but it does reduce it in heterozygous state as it is now harder to get correct chromosome distribution during meiosis and thus fewer functional gametes are made. However in terms of function, as all genes are present in a somatic cell in the correct number, function is usually normal and the individual is alive.

If the population is inbred, it is possible to get an egg and a sperm that carry the same fused chromosome to meet. In which case you get a diploid individual with fused chromosomes. Fertility is now restored. And in an inbred population, a homozygote individual for the fused chromosome can meet another similar individual, and have offspring who are fully fertile.

AS you can imagine, over time there is a selection pressure for the population to separate. The homozygous state (be it fused or unfused chromosome) is more fertile that the heterozygous state.

So to put it short, chromosome fusion does not kill a cell. All gene are still present. However in the heterozygous state, where both fused and unfused chromosomes are present, fertility is dramatically reduced BUT is none zero. Fertility is restored in a homozygous state when an individual is diploid for either fused or unfused chromosomes. In small isolated populations, inbreeding allows for the emergence of diploid individuals which can reproduce with each other

http://genetics.thetech.org/original_news/news124


How are neurons selective towards specific stimuli? I've read several papers that mention that there are specific neurons that are activated for specific things (e.g. neuron A activate only when horizontal lines appear, neuron B activate when certain sound appear, etc).
How does this happen over time (unless the neurons are "born" with certain "affection" towards stimuli) and what is the mechanism that allow it? I understand that it's probably not some conformational change in proteins since the activity has to be really fast- so how can an electrical signal be selective?

Sensory receptors and neurons get their selectivity from physical processes and their position in space. For example, photoreceptor cells in the retina respond to light in a specific position in space because the lens and structure of the eye directs light incoming in a particular angle to a specific spot on the retina. Sensory receptors in the skin can sense touch in a particular place because that's where they are located. Hair cells in the cochlea respond to particular frequencies of sound because the membranes in the inner ear vibrate at different frequencies along the length.
For selectivity to lines of a particular orientation, neurons combine receptive fields of retinal cells, like this:

From https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Perception
The "LGN" (visual thalamus) cells pictured here have receptive fields that look a lot like the retinal ganglion cells that carry output from the retina. For simplicity, you can think like they are the same. These cells are excited by light in the center (red), and inhibited (indirectly) by their neighbors (blue) (there are also "off-center" cells that respond in the opposite way, preferring dark in the center and light in the surround).
If you add up a bunch in a row, you can make a cell in primary visual cortex (V1, the green cell) that responds to edges. If you summed up the receptive fields of cells in a different orientation you'd get selectivity to a different orientation of lines. The key feature to making selective receptive fields is which cells are connected to which.
These receptive fields are created in development by spontaneous activity in the retina and eventually by actual visual input when the eyes open. The process is pretty complex and occurs in multiple stages, but you can start with a review like this one:
Huberman, A. D., Feller, M. B., & Chapman, B. (2008). Mechanisms underlying development of visual maps and receptive fields. Annu. Rev. Neurosci., 31, 479-509.
Higher in the visual processing hierarchy you will find increasing complexity as receptive fields of different types are combined and recombined.


Are high sounds worse for your hearing than low sounds? From about 80 dB it is possible to suffer loss hearing after a couple of hours. But does it make a difference what frequencies those sound waves are or is it just the volume of the sound in dB that matters?

In your ear the first sounds you lose in case of hearing loss are the high sounds because they are at the beginning of your ear. So are high sounds also more dangerous?

Yes.  http://american-hearing.org/disorders/noise-induced-hearing-loss/#causes  Most of the discussion of noise-induced hearing loss talks about the loudness of the noise, only rarely mentioning that higher-pitched noise is more damaging.  Probably because it is much easier to measure the amount than the frequency.


Have there been attempts to identify Chomsky's "language mutation" in humans? I'm not versed in either biology or linguistics so please forgive any naiveties I may commit.

I've learned that Noam Chomsky thinks that language is a result of a single genetic mutation in humans. It would be a mutation allowing the human brain to conceive of natural numbers as I understand. Have there been any (even speculative) attempts by biologists to locate that mutation in the human genome and/or in time? Is it even feasible?

The anthropologist Svante Pääbo is more recently famous for trying to track down the 'language gene'.  There isn't a lot of reference to Chomsky in his work as I've noticed, but it is to me the same intriguing idea.

That being that the chimpanzee and the bonobo have 99+% identical to human genome sequences and we also have data from human variations as well from a few thousand individuals.  Using this data you could try to evaluate a small list of differences which might have led to the inborn trait human beings have to acquire language.

Pääbo's work focused on FOXP2, which leads to language disorders in humans when it is damaged in human beings.  On the other hand its also known that primates can learn to speak rather well if they are trained their entire lives by the right people.  They can even reflect on abstract ideas such as life after death.  This is a typical result when looking for a single gene that causes something- it rarely leads to a conclusive result as a phenotype like verbality, or even height or body mass is the result of the action and fine tuning of many genes acting in concert.

That is, if you introduced human FoxP2 into transgenic chimps its unlikely that they would be as verbal as human beings.  This current reference for instance talks about how important the slower development rate for human children is.  This is one of the most unusual thing about human beings - it takes 1/3 to 1/5 of the human lifetime before we are fully mature.  This phenotype is incredibly unlikely to be the result of FoxP2 alone, or any single gene.

There has been recent work published (2012) where the unique human FOXP2 gene was put into transgenic mice.  They seem to have different sort of personality tendencies and are said to vocalize differently - brain activity profiles are also different.  Kinda exciting, but not the Secret of NIMH yet....


In vitro transcription, contamination problem I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination.

Instead of perform the in vitro transcription again, I want to try to clean it with DNase treatment and LiCl precipitation afterwards. Do you think would that work?

And second thing, in vitro transcipted RNA is in different dilutions, so I have a little bit of stock (maybe 5 uL) which is around 200 ng/uL and I have other dilutions 1 and 0.1 ng/uL. I would like to clean all of them. Do you think if I just mix all of the dilutions with the stock and determine the concentration and do the rest? Is it appropriate?

Thanks!

DNase treatment is actually one of the optional steps if you want to get rid of the original DNA template: https://www.neb.com/protocols/2013/04/02/standard-rna-synthesis-e2050

If you know, your the contamination happened after the transcription, DNase treatment should obviously help.

Concerning the aliquots: your stock is 200 times more concentrated than the aliquots (so to get equal amounts of RNA as in 1 µl of the stock, you'd need to take 200 µl of the 1 ng/µl aliquot). I don't think it's worth mixing them (and the efficiency of RNA precipitation will likely be decreased), otherwise just make another transcription.


Genetics problem, test-crossed Image description: text reads "An $F_1$ x $F_1$ self gives a 15:1 phenotypic ratio in the F2. What phenotypic ratio would you expect if you test-crossed the F1?"

How do I find out the $F_1$ phenotypic ratio by using the given $F_2$ phenotypic ratio?
What method should I use to solve?

The 15:1 phenotypic ratio resulting from the self cross suggests duplicate dominant genes without cumulative effect.
In other words, two genes with complete dominance and dominant alleles producing the same phenotype, but independently, meaning that dominance at one locus ~ dominance at the other locus ~ dominance at both loci as far as phenotype is concerned.

So, in the self cross:
AaBb x AaBb =>
9 A_B_  double dominance = dominance
3 A_bb dominance from A
3 aaB_ dominance from B
1 aabb recessive
So that's where you get your 15:1 dominant:recessive phenotypic ratio.

Now, with a testcross, you were on the right track:
AaBb x aabb =>
1 AaBb
1 Aabb
1 aaBb
1 aabb
So, comparing this to the selfing results above, you'd get 3 dominant : 1 recessive for your phenotypic ratio.


Why are so many species reproducing late this year? Hope this question is OK for this site, couldn't see where else to ask it.
We've spent a few days out in the countryside recently, and have been very surprised at how many species appear to have very young offspring so late in the season. I was always under the impression that the vast majority of animals and fish produced young in the spring (March/April).
For example, we saw tadpoles, fluffy (ie obviously very young) coots and weeny minnows. I would have expected that all of these would have been born/laid a good 3 or 4 months ago, and so would be more mature by now.
Caveat: We didn't do a scientific study, this is just a strong impression we got from days out in north west England.

It's hard to say without more information, but one substantial possibility is that you are mistaken that species are reproducing late - that's a problem with anecdotal rather than scientific data!
Additionally, species you mention like the common coot can attempt multiple broods where the season is long enough. Wikipedia specifically mentions Britain:

Eurasian coots normally only have a single brood each year but in some areas such as Britain they will sometimes attempt a second brood

The same could be true for species of frogs/toads and fish, so without knowing specific species it can't be known whether these are species reproducing again or species reproducing late.


what snake is this and is it venomous? Found on my house on Khao Yai, Thailand

Looks like a common wolf snake, or house snake (Lycodon capucinus). Here another picture. I think they are not dangerous, but be sure to take precautions (I might have guessed wrong from just your photos).


Are pulp cells (in oranges) normal plant cells? Does a pulp cell contain all the elements that a 'normal' plant cell contains?

I've searched for an hour to find more information about this but couldn't find anything useful. Is the pulp cell the exception from the general size range of most eukaryotic plant cells, normally between 10 - 100 µm?

Please include link to a reputable website.

They are not individual cells. In fact, the "juice sacs" (as they are known) are actually specialized, multicellular hairs:

  Juice sacs originate as multicellular hairs in which the interior of the enlarged distal part breaks down and fills with liquid. The juice sacs constitute the fleshy, edible pulp of an orange and are the source of the sweet juice.

(Quote and image from Fruit Terminology, palomar.edu)

This is from a botany course; if for some reason that isn't reputable enough, check out the book Anatomy of Seed Plants by Katherine Esau (1960).


What are the animals in these pictures? I recently found some pictures of animals' skeletons. Does anyone know what species they are?

The top is some kind of seal (the flippers give it away) and the bottom is some kind of lemur (the long thin limbs and tail with the narrow skull) but that is the best I can do from just those photos. It might be a flying lemur but again from just the one photo without scale is difficult to say for certain.


Function of testosterone in women and estrogen in men I was recently surprised to find out that testosterone and estrogen are found in both men and women albeit in different amounts.
I know that testosterone is related to the development of facial, body and pubic hair, deepening of the voice, and muscle development in men.  And that estrogen helps in maintaining the condition of the vaginal lining and its elasticity, and in producing vaginal lubrication in women among other functions.
But what could be the function of testosterone in women or estrogen in men? A simple Google search could give me no good results except for here where it says:

  In men, estrogens have no known function. An unusually high level, however, may reduce sexual appetite, cause erectile difficulties, produce some breast enlargement, and result in the loss of body hair in some men.

and that

  Large deficiencies of testosterone may cause a drop in sexual desire, and excessive testosterone may heighten sexual interest in both sexes.

Does anyone have any further knowledge?

As you know by now, both males and females have testosterone and estradiol. Of course, their levels are different in each sex, but both hormones are important to males and females. A human male with zero blood concentration of estradiol or a human female with zero blood concentration of testosterone wouldn't be possible.

Here are some famous examples:

Role of testosterone in human females:

Increase libido1,2
Modulate physiology of vaginal tissue3

Role of estradiol in human males:

Help to regulate spermatogenesis4
Reduce bone loss5


Why are antibodies Y-shaped? I generally know how antibodies work by binding to antigens, but what is the specific purpose to being Y-shaped, as opposed to any other shape? Does this aid their function? Thank you.

Antibodies also known as immunoglobulins consists of two heavy chains and two light chains linked via disulfide bonds to form Y-shaped structure (as shown in figure below).
This Y-shaped structure bestows antibodies with two properties. Firstly, antigen-binding through the antigen binding fragment(Fab); and secondly, interaction with immune cells and proteins through fragment crystallizable region (Fc) to stimulate and regulate host immune defense mechanisms.
Fc and Fab portions of the antibody molecule are joined by flexible hinge region which enables antibodies to interact with the antibody-binding proteins and thus help in mediating immune effector mechanisms. So, this Y-shaped structure provide proper flexibility for binding to antigens and proteins/immune cells of immune system.

Reference
https://www.ncbi.nlm.nih.gov/books/NBK27144/
https://immense-immunology-insight.blogspot.com/2013/10/antibody-structure-simplified.html


What is the difference between a protein and a factor? In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors?

I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly the same function, but are named differently. For example,

Replication activator protein
Replication licensing factors
Replication protein A
Replication factor C
Transcriptional factor
Eukaryotic translation initiation factor

Short Answer

There is no agreed upon naming convention for proteins - there are some rough standards because in language people usually try to convey their ideas in a way others can understand, but that doesn't necessarily mean fixed rules.

Longer Answer

I think it's important to recognize the process for understanding what proteins do is not always straightforward. Most often, a protein's function is first understood by seeing what happens if that protein is absent (and sometimes overexpressed).

The terminology factor implies that a protein is either modulating a process or at least is not by itself sufficient for a process. That is, it is named because when it was omitted, some other measurable process changed. It  maybe implies something that has its main function by binding, rather than catalyzing a chemical reaction, or at least that the actual mechanism of action is not yet known at the time of naming.

You would not expect, for example, an enzyme with a known target to be called a factor: it's most likely to be named according to its target and the type of reaction being catalyzed.

However, it's possible for a name to stick from when there is less complete understanding. Something might be called a factor initially because of how it influences some process, but the actual contribution is only understood later. Just for an example, take Complement factor I. Initially named because it had some role in the complement system, now it's known that it enzymatically cleaves another protein.

Importantly, there isn't any pure terminology here or consistent naming convention: in most cases, it just goes back to however the first person to describe the protein discussed it. Some proteins are named (controversially, I'll add) things like Sonic hedgehog - related to the similarly named Hedgehog signalling pathway which is all named because of one person/group's creative description of a related fruit fly phenotype.

Naming something "protein" just identifies that it's a protein, little more.


Identification of a small mammal Could someone help with identification of this small mammal? Is it a possum? A dormouse?

It was photographed in Sukhumi botanical garden, in Abkhazia (west of Georgia, on the shores of the black sea).

This is not a marsupial such as an opossum, since no marsupials are native to the region. It looks to be a rodent of some kind, probably a species in the Muridae family.

Which species is it is exactly is hard to tell, since there are many species in Muridae which look quite similar, but my best guess is that this is a Tamarisk jird. It could also conceivably be an escaped domestic gerbil or some type of mouse. The one that you found has more pronounced light areas on its coat than the photographs I found, but is within reasonable limits of what variation can be expected.

Here are some of the few pictures I was able to find that I could verify were of this species.

Klaus Rudloff (source)

Klaus Rudloff (source)


Formula for number of divisions required to form x number of cells (Mitosis and Meiosis) In case of Mitotic Division, we say that if the total number of cells formed by mitotic divisions are $x$, then counting from the first cell onwards, we get $x-1$ divisions ($N$)

$N = x-1$

This is fairly logical to me

However, to find total number of meiotic divisions for $x$ cells, we use the formula
$x/4$ (In questions where we are supposed to find total number of divisions required for forming some number of seeds or pollen grains)

Shouldn't the formula be $N = (x-1)/3$ (Using the same logic as used for the mitosis formula)?

For a male, one primary spermatocyte produces two secondary spermatocytes through meiosis I, which in turn produce two spermatids each through meiosis II. So one primary spermatocyte produces four spermatids. That means that $x$ spermatids are produced after $x/4$ meiotic divisions consisting of once meiosis I and twice meiosis II.

However, we don't count the first cell here because a primary spermatocyte is fundamentally different form a spermatid. So in meiosis, the first cell isn't counted, and four new cells are produced.

In mitosis, we do count the first cell. Note that there are two cells produced form one, so there is only one new cell. Hence we get the formula $x-1$.


Sexually homologous traits When papers refer to traits as being sexually homologous do they refer to traits which are:

a) present in both sexes but can be dimorphic (e.g. body size is sexually homologous because both sexes have a measurable trait which has the same criteria in either sex, but this is frequently dimorphic)

Or

b) present in both sexes and not different between the sexes

I have always thought it is a, but I'm now using the term in a paper and want to check. I would have thought the latter would be "homologous homomorphic traits" or something like that.

If an answer could have an example of the use(s) which make it obvious from published work that would be great!

Your first definition is correct: a homologous trait is one that can be mapped unambiguously between two samples. What establishes the homologous relationship depends, of course, on the trait or feature being mapped.

For example, one way sexually homologous traits can be identified is by tracing the physical development of a male vs. a female organism. If precursor x becomes y in a developed male and z in a developed female, then y and z can be referred to as homologues.


Do taller people have larger somatosensory cortices than short people? When we assume that peripheral touch receptor densities are equal in tall and short people, then tall people should have more touch receptors than short people, given the larger amount of skin surface in the former. Hence my question:

Do taller people have larger somatosensory cortices than short people? And analogues to that, what about larger motor cortices in tall people? If tall people need larger somatosensory and motor areas, could this imply that they have less space devoted to other functions, like functions devoted to the prefrontal cortex?

I would say no.

Your question somehow implies that somatosensory cortex is equally distributed among the different sensory areas of the body, whereas in the reality this is the known "cortical homunculus" concept of how this distribution looks:

If you look at this representation you'll see that chest and legs take only about one third to one fourth of the cortex, thus the changes between short and tall people don't seem to have noticeable contribution to the overall cortex size.

If we just walk away from cortex size and discuss the amount of nerve cells in these areas I would say that these numbers should correlate with the number of peripherial receptor cells that provide input for them, and since there is no known changes in receptor density among different body sizes, even the amount of nerve cells seems to be more or less same.


Is it possible to have multiple stop codons in one exon? I would be very happy if someone can help me to find the answers for the following related questions.

Can one exon have many stop codons?
Can protein synthesis happen, if the stop codon is at the beginning of the exon?

An exon can have multiple stop codons but the first codon will terminate the ORF. The remainder of the exon will be a part of the 3'UTR.

However, there are some cases in which stop codon readthrough happens [1]. In these cases an internal stop codon does not terminate the translation and the ribosome reads through it. During this process an aminoacyl-tRNA successfully competes with the release factor. This is quite evident in the case of selenocysteine and pyrollysine- tRNAs which bind to the UAG (amber) stop codon in certain organisms [2,3] (this is also referred to as amber suppression). The exact mechanisms that affect stop codon readthrough are not elucidated but features in the mRNAs are likely to play a role in this. In case of amber suppression, the relative rarity of the UAG stop codon and lower concentrations of release factor-1, can be major factors.

I don't know what you mean by "beginning of the exon" but there are short ORFs (< 100 codons) which can code for small peptides [4]. Small peptide as small as 6 amino acid residues has been reported but most of the known small peptides are ~30-100 residues long.

References:
[1] Loughran, Gary, et al. "Evidence of efficient stop codon readthrough in four mammalian genes." Nucleic acids research 42.14 (2014): 8928-8938.
[2] Agafonov, Dmitry E., et al. "Efficient suppression of the amber codon in E. coli in vitro translation system." FEBS letters 579.10 (2005): 2156-2160.
[3] Wikipedia: Expanded genetic code
[4] Andrews, Shea J., and Joseph A. Rothnagel. "Emerging evidence for functional peptides encoded by short open reading frames." Nature Reviews Genetics 15.3 (2014): 193-204.


Do artificial light sources cause enough fatalities in light-attracted insect species to cause eventual extinction? There are various theories about how insects are drawn to light bulbs because of navigation mechanisms based on the sun and moon's position in the sky. It makes sense for that to work when the only major light source on Earth was high in the sky at a very slowly changing angle, but now that we have artificial lights it seems like that would severely interfere with the regular life cycle of insects. Being stuck buzzing around a light bulb for almost half of every day seems like it could be damaging to the life expectancy of each bug, and therefore damaging to the species as a whole.

But the reality is, most of the "livable" surface on Earth is not covered in cities, so most of the bugs aren't affected by these artificial lights.

So that leaves me wondering, if we expanded our cities to cover most of the earth livable surface, would we potentially kill off a large portion of the bugs on earth that are drawn to light or rely on bugs drawn to light as a food source?

That's sort of a hard question to answer though, because of so many factors, however I think the root of the question is a simpler one:

Do artificial light sources cause enough fatalities in light-attracted species to prevent them from successfully reproducing at the necessary rate for survival? (assuming the whole species were subjected to such light sources)

Short answer:
Yes, it is highly likely that artificial light sources may cause such high mortality that insects become (locally) extinct.

Long answer:
As you will understand, it is almost impossible to perform an experiment where lights cause extinction of a species. However, we have a lot of 'circumstantial evidence'; cases where it is clear that lights have dramatically decreased species richness (which means local extinction). If lights can cause local extinction, they can also cause global extinction if, as in your question, their entire population would be exposed to light.

Percentage of insects attracted/killed by light
Why insects are attracted to light remains unanswered, but that they do is clear. Also, it is known that insects that are attracted suffer an increased mortality, due to the light itself and due to predators actively hunting the blinded and inactive insects. The reported estimates of the number of insects that are attracted and killed by a light source differ and depend on the light source (color mainly), the background lighting (moon!) and other factors. A fair estimate is that about a third of the insects that are attracted by a light source are killed
A third is a very high mortality, that is off course added onto the other (natural and man-made) mortality insects suffer from. It is very likely that this would cause insect populations to become extinct, especially those already at risk.

Based on observations
Eisenbeis&Hänel give a number of examples that show that insects populations dramatically decline when exposed to lights:
- the number of insects drawn to the lights of newly build fuel stations is high in the first years, than rapidly declines.
- the butterfly fauna in remote Austrian valleys declines after introduction of lighting (for tourism).
- The number of caddisflies drawn to lights exceeds that of the number found in a stream.


Why is ATP the preferred choice for energy carriers? Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?

I really like this question as it is such a fundamental underpinning of all life on the planet, yet there is such sparsity of actual information on its origins and why selection rewarded ATP use over anything else. Here I am talking generally since no specific studies exist in ATP vs other candidates.
A lot of the below information is taken from a relatively old article mentioned in the comments by TomD that discusses: "Why nature chose phosphates." by Westheimer, 1987. The article is very influential and has been cited over a thousand times since publication. Another article that came out in the same year that this question was asked "Why nature really chose phosphate." by Kamerlin et al., 2013
Some of the below arguments are more convincing than others, but all of them should be thought of when attempting to answer this question.
Summary.

ATP has ancestral dominance. Most other reasons derive from this.

Alternative phosphate groups or other molecules may not provide enough energy.

Alternatives may be toxic.

Other molecules, particularly phosphates, are used for inefficient high energy bursts.

Pi is a "good" leaving group.

Phosphates are fundamentally able to be regulated through electrostatic manipulation.

ATP synthase can efficiently reattach the Pi to ADP.

Lots of Pi available to organisms because of it's ancestral dominance ("if it ain't broken, why fix it?" is at play).

ATP can provide more energy if needed; it's scalable to the situation. (ADP becomes AMP + Pi)

Easily usable by a variety of proteins.

Why ATP?
ATP is an efficient and relatively easily biosynthesised molecule that can fulfil multiple biochemical roles. Cells do have alternative energy carriers, some with more specialised roles, however, ATP is ubiquitous throughout our cells and inter-cellular spaces. There aren't a wealth of resources explaining why ATP is any better than other compounds, however, there is plenty of reasons why the phosphates are required.
Why not the alternatives?
Citric acids and their derivatives are a good candidate, with deductible groups and high bioavailability but they simply don't give enough energy to stabilise genetic material.
Another tribasic candidate is arsenic acid. This is a fundamentally toxic compound, though, which isn't particularly great for living things.
There are other phosphates too, and they are used in many organisms. In biology, they have specific functions, and not used as the general energy carrier. For example, creatine triphosphate provides a high energy phospho- anhydride bond, that is often used to quickly and anaerobically regenerate ATP, useful during high rate muscle activity for contraction.
GTP is structurally very similar to ATP. GTPases are used more to initiate cellular signalling pathways. It is sometimes used as an energy source. This is a good example of an alternative energy carrier.
Over the years, many proteins have specialised with a specific shape, and this chance is the primary reason behind ATP over GTP. In other words, the choice of ATP over GTP is primarily down to cellular preference of molecular shape. One of them had to emerge as being more widely used, and it was ATP that 'won'.
Efficiency and simplicity.
The reaction was once thought to be a relatively simple nucleophilic displacement. From the 2013 paper:

...this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalysed reactions.

Traditionally one will be taught that ATP is such a chemically efficient way of storing and transporting energy. This is due to the ATP->ADP & Pi hydrolysis reaction. The phosphate groups in ATP are full of negative charges and these are repelling one another. This means that the third phosphate is a great leaving group and breaking the phospho- anhydride bond is a favourable reaction. ...
...But the story is a lot more complicated than that. The above explanation isn't really satisfying because those same negative charge forces are repulsive of the nucleophile that is attempting to complete ATP->ADP & Pi. A more comprehensive explanation would go along the lines of 'although a negative charge repulsion exists between the nucleophile of the protein and the phosphate, that high energy barrier can be overcome by electrostatic manipulation'. This allows an "on-off switch" for the hydrolytic reaction by tweaking the electrostatic environment. This is another great regulatory tool that the phosphates provide. This regulatory feature is important for signal and metabolic/catabolic cascades.
When it comes to 'rebinding' the Pi to ADP, it is fairly easy since ADP seldom covalently binds to anything, which would require a lot of energy to recover the ADP. This also helps the bioavailability of free ADP to ATP synthase, an incredibly efficient enzyme, that uses membrane proton gradient to drive the production of ATP. Talking about actual numbers is difficult here as there is only data available from Rat hepatocytes. Who is to say mammals are representative of all organisms? The estimates of energy of hydrolysis range from ΔG˚ = -48 kJ mol-1 to -30.5 kJ mol-1. Note that these are considerable, but not exceptional values, so it's easy for many different proteins, that need not be very specialized, to break the bond all over the body. I couldn't even find the numbers for the synthase reaction per ATP, but a single ATP synthase can produce up to 600 ATP per minute.
The final point of this efficiency is that the elements in ATP are very abundant and established in the biosphere making it readily available. This makes the phosphates a convenient biomolecule.
Multi-functionality.
ATP is ubiquitous in the body, but in some cases more energy is needed than there are ATP available. In these times of need, ATP can be used to produce more energy, breaking another phosphoanhydride bond to become AMP+2Pi. AMP however is typically a signalling molecule.
With the low activation energy required to break the phosphoanhydride bond, a multitude of enzymes, far too many to list here, can make use of ATP in order to gain energy towards the activation energy for many other functions.


What software is there available for quantitative structure–activity relationship (QSAR) pharmacological studies? QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what software is available to assist me in doing these studies.

On the G6G Directory of OMICS and Intelligent software, I searched for "QSAR Analysis, and received two product abstracts:

1) SYBYL®-X Suite which contained:

3D QSAR: use the power of industry leading CoMFA in a new way to
generate novel ideas for R-groups - predict the level of biological
activity or potency based on structure-activity data, Not just yes/No
activity predictions;
Cheminformatics: produce highly focused queries that avoid false
positives using a rich set of 3D queries; on-the-fly conformational
searching means you only store a single conformation of your
molecules, keeping database size small and very transportable; and...

Link to this abstract:
http://g6g-softwaredirectory.com/bio/proteomics/structure-modeling/20710-Tripos-SYBYL-X-Suite.php

2) Fujitsu GhostMiner

GhostMiner can be employed in a number of business intelligence areas and the following areas:

Bioinformatics - genetics, proteomics, Quantitative Structure
Activity Relationship (QSAR) modeling...

Link to this abstract:
http://g6g-softwaredirectory.com/ai/neural-networks/20154-FQS-Poland-Fujitsu-GhostMiner.php

Perhaps the above will help.


How do I improve expression using the GAL1 promoter in S. cerevisiae above the "leaky" level I'm currently seeing? I am attempting to express GFP in S. cerevisiae using the GAL1 promoter.

I always grow an uninduced (in dextrose based SD medium) culture alongside my induced (in galactose based SD medium) culture. I see approximately the same very low level of fluoresence in both cultures, and also a band at 27kD on a PAGE gel. There is no overexpression of the GFP happening, the fluorescence is very weak by eye, and the cultures are not green in visible light, like E. coli cultures overexpressing GFP.

On the PAGE gel the amount of protein appears to be the same in both the uninduced and induced samples. I need to overexpress the protein, this leaky level of expression isn't acceptable. How do I go about fixing it? I am currently growing up a culture to do a plasmid prep to send for sequencing to make sure the promoter region of the plasmid is intact.

There are a couple of things that are strange here. First, you have low expression in the presence of galactose. The GAL1 promoter is really strong, so that strikes me as odd. Even if it was leaky, induced vs uninduced should be night and day. However, you should keep in mind you still may not be able to see it by eye. Second, it is weird that it would be leaky in the presence of glucose (or dextrose, in your case). The glucose should not only prevent the promoter from activating, but it should actually repress it.

A few potential fixes that come to mind:

1) Check your strain genotype. Some strains do not have gal4, the transcriptional activator of the GAL1 promoter, so if you don't have this, the system will not work in your strain. Likewise, you may not have an intact UAS, which would make the repression fail. Other issues may also arise which may make a strain unsuited for this system.

2) Sequence your promoter/gene. It is kind of a pain, but if you have a mutation in your Gal1 promoter, this could be the reason for all your problems. Also check the UAS, as this would create repression problems. Finally, check if the gene itself is inserted in the place you think it should be, if you got some recombination mishap this may be the problem. The appearance of an extra band at a low molecular weight makes me suspect this may be an issue.

3) On that note, try picking a different clone. Maybe you got unlucky and the colony you picked had a defect, and a different colony will be what you think it is.

4) If you haven't already, make fresh stocks of your galactose and glucose media. Maybe you got impurities or some other issue in your media, and therefore what you think you are giving the cells is not what you are giving the cells.

Anyway, that's all I got. Good luck!


Why are truncations in Receptor Tyrosine Kinases so sommon in transformations? Receptor Tyrosine Kinases (RTKs) present themselves on the surface of a cell as monomers until a ligand (such as a mitogen) binds and causes the formation of the active dimer. However I do not understand why truncations are so commonly seen in retrovirally delivered oncogenes or in oncogenic mutations. My confusion here is that if mitogen binding of RTKs facilitates the close proximity of two monomers, then simple overexpression should allow for increased transphosphorylation of monomers, and therefore be mitogenic (which it does). But then what advantage would a truncation that removes the extracellular portion of an RTK have in increasing transphosphorylation of monomer units?

As you said the simple overexpression can lead to transphosphorylation and activation of mitogenic signalling. This helps the cancerous cells to survive.

By truncation of the molecule the cell also gains a benefit, because it could prevent inhibition of the receptor from outside the cell.
The truncation furthermore could be induced by treating cancer with inhibitory antibodies against the receptor. For example a treatment with anti-EGFR antibodies could induce resistance by mutation and selection. One of this mutations could be the truncation of the receptor.


Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP? I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express.

Depending on the organism, there can be from 10 to 14 c-subunits in the c-ring of ATP synthase. For practicality/consistency's sake, let's assume 10.

Every c-subunit is protonated (from the cytoplasmic side of the mitochondrion) and rotated almost 360 degrees within the lipid membrane before it is ultimately deprotonated, which releases a proton into the matrix. Thus, since the c-ring is 10 subunits big (in this case), 10 protons are being introduced to the matrix every 360 degree turn, which mean that 1 proton = a 36 degree turn.

These protons allow for the gamma-subunit to be turned at the inside of the hexamer (of 3 alpha-subunits and 3 catalytic beta-subunits) found below the rotor. The b-subunits are thus located 120 degrees apart. Every 120 degrees precisely, that beta-subunit changes shape, dictated by the rotation of the gamma-subunit, and enters one of the three states that ultimately catalyze one ATP from ADP and inorganic phosphate (since only one of the three states actually forms ATP). Since the gamma-subunit catalyses the formation of 1 ATP every 120 degrees, a full 360 degree rotation would yield 3 ATPs.

This is where things go awry in my mind. Within 360 degrees, 10 protons and 3 ATPs are made. Thus, that makes (10/3) protons per ATP, or 3.33 protons/ATP. When the gamma-subunit receives a proton, it rotates 36 degrees, but ATP formation only happens at precisely 120 degrees, and the only common interval between 36 and 120 is 360 (when 3 as opposed to 1 ATPs are made)!

EDIT: The gamma-subunit must rotate in exactly 120 degree increments, because we observe it do so, as shown here.

  More detailed analysis in the presence of lower concentrations of ATP revealed that the γ subunit rotates in 120-degree increments, with each step corresponding to the hydrolysis of a single ATP molecule.

Logically, this shouldn't happen though, since the closest increments of 36 to 120 degrees are 108 and 144.

To summarize: How can 3.33 protons ultimately synthesize one, and only one ATP, knowing that a literal third of a proton doesn't exist (excluding quarks) and that increments of 36 degrees can never add up to exactly 120 degrees?

References

“A Proton Gradient Powers the Synthesis of ATP - Biochemistry - NCBI Bookshelf”, n.d. http://www.ncbi.nlm.nih.gov/books/NBK22388/.

I might be taking a bit of a simplistic view on this, but I'm not sure what the confusion is.

The ring of 10 c subunits constitute a motor which uses a proton gradient to drive the rotation of the FoFc synthase.

 (image reference is a nice lecture on ATP synthase).

The motor of c subunits has a 10 fold symmetry.  Each subunit releases a proton as it drives a 36 degree movement of the gamma subunit shaft.  The sixfold symmetry of the ATP FoF1 synthease is completely separate from this, and every 360 degree rotation, three ATPs are generated.  As long as the c motor keeps spinning more ATP is created.

This question is similar to asking why the gear ratios of a bicycle or a car are 3:2 or 5:3.   The symmetry of the synthase and the c subunit are independent except that the torque generated by the c subunit motor needs to be enough to drive the ATP synthase.  If the proton gradient were stronger it could well be 7 protons per full rotation and not 10. Think of the two as gears and you might get the picture?