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What does it mean for a protein to be dominant-negative?
I am reading this journal paper, which investigates the interaction of the NCAM protein and the Pak1 protein. In this paper I have come across the term "dominant-negative Pak1" and "constitutively active Pak1". I am not sure what exactly is meant by a protein being dominant-negative. I have searched online and found that dominant negative refers to a mutation whose gene product adversely affects the normal wild-type gene product within the same cell (with this occurring if the product can still interact with the same elements as the wild-type product, but block some aspect of its function).
Would I be correct in inferring that dominant-negative Pak1 is a mutated version of the wild-type Pak1 and interferes with the normal activity of wild-type Pak1 in cells? Any insights are appreciated.

You've got it. A DN not only doesn't have the desired catalytic activity, but it also binds to or otherwise inactivates WT enzymes, in effect "knocking out" that particular enzyme in the cells. The protein itself is still there, it just doesn't perform its normal function.


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What does γ mean before a gene name?
I am reading the following paper and I have come across the following statement:

It has been demonstrated that the phosphorylation of histone
H2AX-Ser139 to form γH2AX.

I am not sure what the γ before the gene name H2AX means. Is γ used to indicate that H2AX is phosphorylated? Any insights are appreciated.

Yes, in this context $\gamma$ indicates phosphorylation. See e.g. "The phosphorylated form of H2AX is called $\gamma$-H2AX [18, 19]." from here, and references therein.
I am unsure of the exact basis of this, but I believe that it is because the gamma phosphate group of a nucleotide triphosphate is the one that is generally used by kinases to phosphorylate other functional groups. SEE UPDATE for derivation.
Other notations such as the $p$ prefix are more readable to me, but the usage appears to be cultural and somewhat field-specific.
Update
In response to @MattDMO comment, I read further and found that the terminology derives from this paper. They don't directly explain the terminology, but in context it's pretty clear:

At the maximum, approximately 1% of the H2AX becomes $\gamma$-phosphorylated per Gy of ionizing radiation.

In mammals, the serine in this motif is residue 139, the site of γ-phosphorylation.

When mammalian cell cultures are exposed to ionizing radiation and the acid-soluble nuclear proteins are analyzed on two-dimensional AUT-AUC gels, novel components that will be referred to as $\gamma$ (Fig. 1, A and B) are found in the H2A region of these gels.

It appears that the name probably derives from an observation that was just "whatever in this 2-D gel is $\gamma$-P32 labeled when we induce DSBs when $\gamma$-P32 ATP is present."
@MattDMO also points out that the irradiation that induces the gamma component in this context is gamma radiation. So it's all a bit of a muddle, it could also be that.

I've never heard of $\gamma$ being used to denote phosphorylation except in the case of H2AX. I suspect the nomenclature derives from its discovery, probably as multiple isoforms by some sort of chromatography or gel electrophoresis, and the phosphorylated form was the third one named ($\gamma$ is the third letter of the Greek alphabet) or the third band/signal observed. This is just a guess, but an educated one. I don't think it has anything to do with the $\gamma-PO_4$ group.

@MattDMo Turns out we're both right- it is because of the $\gamma$ phosphate, but it is also H2AX-specific, if I read the paper that first described this correctly. Editing answer.

Thanks for the link to the paper, it's been helpful. After reading parts of it, especially the 4th paragraph of the results section, I think they called the novel components $\gamma$ because they appeared after ionizing $\gamma$ irradiation, which is the primary form of radiation emitted by $^{137}Cs$, which was the rad source used in these experiments. So, $\gamma$-H2AX is a phosphorylated form of H2AX observed after exposure to $\gamma$-irradiation. Actually, it's probably both $\gamma$ irradiation and $\gamma$-ATP.

Hm. a lot of gammas here...

Which is probably what the grad student doing the experiments thought when s/he was labeling the autoradiograms of their gels.

@MattDMo tNo i was wrong! P32 is a beta emitter. sigh of relief

You're correct: the gamma denotes phosphorylation, as explained and used in this paper's abstract

H2AX is a variant of the H2A protein family, which is a component of the histone octomer in nucleosomes. It is phosphorylated by kinases such as ataxia telangiectasia mutated (ATM) and ATM-Rad3-related (ATR) in the PI3K pathway. This newly phosphorylated protein, gamma-H2AX, is the first step in recruiting and localizing DNA repair proteins.

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Can a constitutively active kinase be highly regulated?
I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active kinase, meaning that it is always active and is not activated in response to a specific stimulus/condition. I have read that phosphorylation of GSK3 at specific tyrosine residues only enhances its activity, but the GSK3 itself is always active.
However, many of these papers also talk about the various mechanisms through which the activity of GSK3 is regulated (e.g. through phosphorylation at specific amino acid residues, subcellular localisation, protein complex formation). One paper states the following:

The many functions regulated by GSK3 (through its phosphorylation of
numerous substrates) suggests that the activity of GSK3 must be highly
regulated. Four key mechanisms have been identified that contribute to
regulating the actions of GSK3 in a substrate-specific manner. These include regulation by phosphorylation of GSK3 itself, the subcellular localization of GSK3, the formation of protein complexes containing GSK3, and the phosphorylation state of GSK3 substrates.

I am wondering how is it possible for a kinase to be constitutively active and be highly regulated at the same time? If it is constitutively active, doesn't this imply that it is always active? Any insights are appreciated.

Find a paper on GSK3 that explains precisely what is meant by describing it as “constitutive”. This appears to be yet another case of imprecise usage of English words for which there is no official definition in biology (because biology is not physics, as I have said previously). Only those who use the expression can tell you what they mean by it.

I think you have answered your own question, but yes, the nomenclature is confusing. When they say it is a constitutively active kinase, you are right, it plainly means the enzyme can always phosphorylate other molecules/proteins.
The regulation part is what you have in the review paper you cited. If the kinase is always on but localized in a compartment where there is nothing to phosphorylate, it could be considered "regulated". The same logic applies to the other regulation methods listed.

Welcome. I think you answered  the question, but it would be good to back up your claims by adding links to credible sources to allow other users to background read on your material.

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Why do you need to calculate the lane normalisation factor when doing western blot data analysis?
I am learning about western blot data quantification from some online resources. I have read about methods to normalise the data.
I have seen in a number of resources, such as this handbook and this video when normalising western blot data, they use a lane normalisation factor. For example, if using a total protein stain to normalise the integrated density of your target protein bands, they first obtain the integrated density of all the lanes stained with the total protein stain. Then they find the lane with the highest integrated density value. For each lane, its integrated density value is divided by the highest integrated density value - the resulting value being the normalisation factor of the lane.
Then when doing the normalisation, for each lane, the integrated density of the protein band of interest is divided by the lane normalisation factor.
However, I am not sure what is the reasoning behind calculating the lane normalisation factor. Why can you not just divide the integrated density of your protein band of interest by the integrated density of the total protein stain region for each lane?
Any insights are appreciated.

Read point 2 of your handbook: II.TheIdealWorldvsTheRealWorld.

Thank you, I think I understand now - it's to correct for variations in total protein signal between lanes.


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Is the phrase "transmembrane segment" equivalent to the transmembrane domain of a protein?
I am reading the Handbook of Neurochemistry and Molecular Neurobiology  and I am learning about the cell adhesion molecule NCAM2 and I have come across the following:

The overall structure of NCAM2 is similar to that of NCAM. Thus, NCAM2
consists of five Ig‐modules (supposedly of the C2‐type) followed by
two Fn3‐modules. The protein exists in a GPI‐anchored isoform and in a
transmembrane isoform that contains a 20–25 amino acid transmembrane
segment followed by a 106–119‐amino acid cytoplasmic tail (Alenius and
Bohm, 1997; Yoshihara et al., 1997).

I know that NCAM2 is located at the cell membrane and has an extracellular, transmembrane and intracellular domain. However, for the above statement: The protein exists in a GPI‐anchored isoform and in a transmembrane isoform that contains a 20–25 amino acid transmembrane segment followed by a 106–119‐amino acid cytoplasmic tail, is the term 'transmembrane segment' equivalent to the transmembrane domain? Further is the term 'cytoplasmic tail' equivalent to the intracellular domain? Any insights are appreciated.

Yes
I'll admit defeat in trying to find the section in the text you linked - if there's any one thing Google can't do, it's search.  But questions like this are better put to Uniprot, which gives quite a bit of information.  Following that link, you'll see they identify 21 AA of transmembrane topology from 698 to 718, with a cytoplasmic domain afterward.  So the cytoplasmic tail is the intracellular domain.
In a sense there is a second transmembrane domain - the signal peptide from 1-19 - but because it is cleaved little attention is paid to it.  The extracellular domain starts at 20, with an N terminus outside the cell.
To quote Wikipedia, a transmembrane domain "usually denotes a single alpha helix of a protein".  You should probably listen to them on such an issue because nobody is more fixated on semantics (it's a sort of vote).  Philosophically, you can picture that multiple transmembrane segments could operate as a functional unit - but each of these segments would be separated by some region of extracellular or intracellular sequence from the next.  A "domain" in a protein is a self-contained unit in the primary sequence, not just a series of helices that turn out to be near each other, so that wouldn't work.  And in fact if you look at a GPCR paper they speak in standard terms of seven transmembrane domains even while analyzing how they function together.


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In western blots, do loading controls have to be proteins that are in equal amounts in each lane?
I have recently done a Western Blot and I am doing data analysis on my blots. I am studying the protein GSK3, which is a phosphoprotein.
I have labelled my membrane against active GSK3 and inactive GSK3. I have also labelled the membrane against total GSK3. I have used Ponceau S as a loading control. From my Ponceau S staining I have seen that there are variations in the amounts of protein loaded per lane. So there are variations in the amounts of total GSK3 per lane (the intensities of the bands are not all equal).
I am wondering if the band intensities of total GSK3 are not consistent among lanes, in this case would using total GSK3 be a good loading control to normalize my data on? I have read for the case of phosphoproteins, you can normalise to the total protein (using an antibody that recognises all forms of the protein of interest).
I have read that loading controls are endogenous proteins that are unaffected by experimental conditions and used as an indicator of sample concentration. But if the amounts to total GSK3 vary between the lanes, how can this be a good loading control? Similarly, why do many researchers use Ponceau S as a loading control, if the band intensities among lanes vary (if you don't load equal amounts of sample)?
In other words, for a protein to be a loading control, does it have to be in equal amounts for all your samples/lanes?
Any insights are appreciated.

Can you clarify what you are loading? Purified GSK3, total protein, or something else.

I am loading 20 micrograms of brain lysates per lane (total protein that is present).

I'm aware that this question is over 3 years old at my time of writing this answer.
While @Minnow has one answer - it's not one that applies in your situation. That answer applies if you are using a defined standard protein detected by an antibody - usually something like B-actin or nucleolin, where you can compare intensity of bands relative to that single standard in each lane. However, even in this case you generally aim to have the same amount of protein loaded in each lane as it simplifies analysis and makes a more convincing story if aiming for publication of your research (as you should be doing...). The convincing story is important as people struggle to determine changes in target protein expression visually if the standards are not the same, which means reviewers will have a hard time and your analysis will be suspect.
In the case of something like Ponceau S staining, which is a non-specific stain for proteins, you do generally need same amounts of proteins in each lane so that you can compare the expression for the same reasons as outlined above. If you are doing densitometry analysis and using this to determine relative expression of the proteins in each lane, then you should choose one well-defined band on the Ponceau S stain in each lane and compare to that, not compare all lanes to a single band in one lane. Also be aware that this technique does not allow for inter-blot comparison!
Be aware that densitometry is an inexact science, so saying that bands are 1.1 increased expression relative to a control is problematic statistically (how did you choose the bands to determine as your reference? what if band areas are different sizes? was the image saturated at any point? What file format are you using for analysis (use raw or tif, not JPG - and you should know the difference and why not the last one!)?, while bigger differences might not be. Convincing reviewers of differences needs visual confirmation in the blot as well as a graphical representation.
There are whole websites (e.g. Retraction Watch) devoted to problematic/fraudulent results in papers, many of which are western blot results. Don't become one of the papers on there for dodgy analysis!

Controls do not need to loaded in equal amounts per say, but they do need to be expressed relatively equally between lanes. They need equal expression, such that controls can be used to normalize values of the experimental proteins.
It is common to use housekeeping genes, such as beta actin, which are usually expressed equally between treatments to control for loading.  Important to ensure treatments don't affect those proteins.
For examples and rationale, see:
https://www.abcam.com/primary-antibodies/loading-control-guide
https://www.bio-rad-antibodies.com/western-blot-loading-controls-antibodies.html
https://www.labome.com/method/Loading-Controls-for-Western-Blots.html


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What is meant by the steady-state activation of a receptor?
I am reading a journal paper about the insulin-like growth factor 1 receptor. In this paper, there is the following statement:

Finally, we show that the IGF-IR and the PI3K subunit p85 and Akt are
detected in cholesterol-rich membrane domains under conditions of
steady-state IGF-IR activation and that phosphorylated Akt and IGF-IR
are detected in CEMs with IGF-I stimulation.

I am not sure what is meant by the "steady-state activation" of the IGF-IR receptor. I have searched the definition of steady-state with regards to proteins and I have read the following:

The ‘steady state’ is defined by a zero net change of a parameter in a
system. For example, the abundance of a protein might not vary during
the time of observation because rates of translation and degradation
are balanced. The cell is said to be at the steady state with respect
to the concentration of this protein.

However, in the context of this paper, I don't this is what steady-state refers to since they are talking about the activation not levels of the receptor.
Does anyone know what is meant by the steady-state activation of a receptor? I think it refers to the activation that occurs without any exogenous stimulation (e.g. addition of insulin/IGF-1 to cells). Any advice is appreciated.

Did you read the Methods section of the paper? That's where you'd find this information. It's possible they mean what you guess, but I'd expect that to be called baseline or constitutive activity or something like that instead; still, the best source is the methods section.

As mentioned above, it is best to check with Method or a reference paper.
One method might be to introduce mutations in the kinase domain of IGF-1R, thereby constantly increasing kinase activity.
Other possible methods include overexpression of the IGF-1R gene to increase the number of IGF-1R receptors in the cell and enhance signaling, deletion of genes for inhibitor proteins that regulate IGF-1R or genes that negatively regulate signaling.


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Selective breeding fluorescent sheep - possible?
I got into a small argument :-)
Friends of mine try to draw fat line between "natural" selective breeding and applying molecular biology (CRISPR/Cas9) to put new traits in existing species. The line of their argument is "GMO is something different, because you can't (in reasonable timeframe, ~1000 years) breed a sheep that will glow in the dark.
Intuitively I think that doing so is possible even without molecular tools to "write" new genes, just using things like horizontal gene transfer and "standard" breeding (I reserve right to use all modern knowledge and tools to plan and monitor progress). I don't have much to substantiate this claim though.
In your enlightened opinion, who is correct?

We welcome new posters to SE Biology but ask them to read what sort of questions we encourage here, namely "questions about an actual problem you have faced", and those we don't, namely, questions the answers to which will be subjective. We are not here to arbitrate hypothetical arguments, even if we do have our own opinions, "enlightened" or otherwise.

Understood, and sorry if I did not adhere to guidelines - I can only say that is a community I trust to give me valid answers, hence I asked here.

Welcome to Bio.SE. Very interesting idea and I am definitely bringing this up at lunch! I think framing your question as a debate between GMO and selective breeding isn't clear. A more format friendly way of getting your answer would be "Has bioluminescence ever been selectively bred into animals or plants?" Remember to show evidence that you've attempted to answer the question yourself (maybe check google scholar).  Also, note that CRISPR is not the only way to introduce specific genetic changes into organisms.

Natural horizontal gene transfer in higher animals is possible, but still very rare.
If any transfer happens then it's usually from micro-organsims (viruses/bacteria) or parasites to the host animal (or the reverse). Transfer of genes from any other source to animals is almost unheard of, because the transfer needs to affect the germline (sperm / eggs) to last more than a single generation and anything that doesn't live inside an animal is unlikely to get there.
Therefore your example of getting GFP (or any other fluorescent gene) into a sheep is highly unlikely$^1$, even with a 1000 year timespan.
You'd need a virus or bacteria that has a fluorescent gene and naturally infects/lives in/on sheep. However, no natural bacteria or viruses have a fluorescent gene in the first place (they almost all come from corals or jellyfish). Another problem is that just having a fluorescent gene somewhere in the DNA, doesn't mean the any part of the organism is fluorescent; once its in the gene pool this should be achievable by breeding though.

You'd have to wait for HGT of a fluorescent gene from a source animal/life form to bacteria. (Time estimate is super hard, you can maybe house some of these jellyfish in a fish tank regularly sequence the bacteria that live with them to see if HGT happened.)
Then the genes needs to be transfered to a bacterial/virus strain native to sheep (This is relatively easy/fast, since bacteria are quite proficient at HGT between each other)
Lastly you need a 3rd round of HGT from the bacteria to the germline of the sheep. (Again this might take 'forever': most mammals don't like bacteria or viruses living in or near their reproductive organs. Also at least from this point on animal experiment laws will become a serious hurdle to your project).

1) This is a researchers highly unlikely: without trying this, its not correct to say impossible, but the chances are so low that for all practical purposes it might as well be impossible.

Great answer, thank you :-) I actually thought about using fluorescent bacteria to start with, but this only cuts time in half, not in orders of magnitude :D

Perhaps you can add that even if someone infects the animal with a bacteria/virus carrying a foreign gene, that is still artificial genetic modification (albeit an inefficient technique compared to CRISPR-Cas).


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Understanding genetic similarity in humans
I was reading "Blueprint" by Robert Plomin (online preview on webpage) and got stuck when I got to these two sentences in the prologue:
"We are the same as every other human being for more than 99 per cent of these 3 billion DNA steps, which is the blueprint for human nature." (page X)
"familiy members differ a lot genetically - you are 50 per cent similar genetically to your parents and siblings, but this means that you are also 50 per cent different." (page XI)
How does it fit together? Is he talking about different measures of similarity here?

If you search the site, I think you will find that this question has been asked before.

How can someone share 50% of their DNA with their parents yet all humans share 99.9%? is an even better duplicate.

Yes, these are different measures, and agreeably confusing. The "more than 99%" figure refers to pairwise distance. This figure (actually 99.9%) means that if you were to line up the 3 billion nucleotides of DNA from of any two people, on average, 1 in 1000 of these nucleotides would be different. Among siblings, this number would be even smaller. The 50% figure refers to the origin of DNA stands in a diploid organism: you get one exact copy of each of your genes from your mother, and an exact copy from your father. So half your DNA comes from each parent. But the DNA from each parent is still nearly identical. Siblings will get all their DNA from their parents, but for any particular section, they will get either their maternal grandmother's or grandfathers gene from their mother, and either their paternal grandfather's or grandmother's gene from their father.
For reference, you often hear that humans and chimps share 98% of our DNA. This is the not exactly a pairwise difference value, because it only counts changes in amino acids (http://humanorigins.si.edu/evidence/genetics). The amino acids between chimps and humans are about 98.8% identical to humans. The DNA across the whole genome is about 94% identical. There are about 50 genes present in humans that are absent in chimps https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level


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Did we evolve from Africans?
I learned about The Theory Of Evolution in middle school and our teachress told us that we evolved from African People. Is that true? How?

Did your teacher say that we came from africa or african people? There's a difference there.

Because you are young, you can see most simply from this list of images accompanied by the time in years, Ma means millions of years... https://en.wikipedia.org/wiki/List_of_human_evolution_fossils#Pleistocene Some of the people 's bones are at least 250,000 years old, if not older. If it takes 25 years for a generation of father to son, that means that we have skeletons from great-great-grandfather * 10,000 great.

Welcome to Biology.SE!

Did we evolve from Africans?

Who is "we" in your sentence?
Although, it might not have been your intent, you seem to exclude Africans (and people of recent African descent) from the "we" (which would be rather insulting)!
I will rephrase your question. I will pick "caucasians" (thinking that you might be caucasians and by "we" you may have had "Caucasians" in mind) to rephrase your question but I could have picked Han Chineese, Polynesians, Micronesians, Mongolian or any other (big or small) extant human lineages that currently lives mainly outside of Africa. I will rephrase your question as Did [caucasians] evolve from Africans?
What does "evolve from" mean?
No extant lineage is the ancestor of another lineage. An extant species of lizard is not the ancestor of an extant species of mammal, just like an extant species of mammals is not the ancestor of an extant species of lizard. The same hold true for any two extant lineages. Extant lineages share common ancestors. Their Most Recent Common Ancestor (MRCA) may have lived a long time ago or only relatively recently. This answer might help you to understand these concepts.
If you mean to ask Did [Caucasians] evolve from current Africans? as in Is Nelson Mendela the ancestor of Kurt Cobain, then the answer is (obviously) "No".
So, when you ask Did [Caucasians] evolve from Africans?, I am assuming, you meant Did [Caucasians] have descendants who lived in Africa?
Did Caucasians have ancestors who lived in Africa?
Yes. All modern humans (aka Homo sapiens or Homo sapiens sapiens) are descendent from first humans that lived in Africa. The MRCA of all modern humans lived in Africa.
To reiterate the above, this in no way suggests that modern Africans are "ancestors of" or "more primitive than" or "less evolved than" any other human lineage. However, interestingly, because early split among human lineages happened in Africa, the majority of genetic diversity among humans is found in Africa still today.

I learned about The Theory Of Evolution in middle school [..]

If you want to learn a bit more, you might want to have a look at a simple and very introductory source of information such as evo101 by UC Berkeley
EDIT
Comments shows that the OP did not quite get it yet. Here are some more info...
First, please have a look at this answer (already indicated under the section What does "evolve from" mean? above). Make sure to read it fully. Did you read it?
H. sapiens is a monophyletic group (for simplicity, I will make abstraction of horizontal gene transfer here). The MRCA of this group used to live in Africa. Some of the sub clades of this group have moved elsewhere in Africa, and some have moved elsewhere outside of Africa (there has been a fair amount of back and forth too and a fair amount of secondary contacts as there is no reproductive isolation among H. sapiens). That's all!
Your confusion comes from the fact that you call "Africans" both the MRCA and the current lineages that live in Africa. It may make you feel that people currently living in Africa and the MRCA of all humans who lived in Africa are somehow more related just because they live on the same continent but that would be wrong. All human lineages have evolved from this MRCA (who lived in Africa), whether the lineage you want to consider is currently living in Africa or not.

Or to reduce it to one sentence: All humans, including modern Africans, evolved from ancestors who lived in Africa.

Hmmm, interesting. If I understand your theory correctly, we evolved from the MRCA African People and NOT the extant African People because there is a difference between extant African People and the MRCA African People? We're two different lineages?

@Hierarchist I don't believe that's correct- properly speaking all the major lineages of humans are "African" lineages, which includes your "we". Some of these major lineages gave rise to people who left the African continent, but they still arose in the African continent. The MRCA of any group of people is different from the current people, was I believe what Remi.b was trying to communicate, so no one alive "evolved from" anyone else who's alive. More simply, the MRCA of "African people" is simply the MRCA of humans; all "non-African" humans are part of "African" lineages.

I'm trying to understand your theory: if the MRCA of us and African People is different from African People, then we're a different lineage from African People? Or are we the same lineage as African People because there's no difference between the MRCA of us and African People and African People? Moreover, you seemed to say that we split off from African People all the way back when we were Africans? I'd appreciate an explanation of your theory.

@Hierarchist Please see the Edit section which will hopefully clear things up for you.

@Hierarchist Please stop saying "we" when you mean "caucasians" (or something else). 1) it is unclear who is included in the term "we". 2) You clearly exclude current Africans from the "we" (which sounds rude) and for all you know I might be Nigerian and hence it would make the conversation very confusing.

Also, it there any reason you repeated your theory three times? It make it sound like you have an incorrect view of the legitimacy of the modern evolutionary synthesis (which is the name of what you call the theory of evolution). See the post Is evolution a fact? for more info.

@Hierarchist I think the issue is that the idea of a coherent group of humans different from "Africans" is not scientifically well-supported. Talking about people by their continental birthplace and/or physical appearance is, at best, misleading. "Non-Africans" are still "Africans" in that they are part of one lineage among many lineages that arose in the African continent. "Non-Africans" are quite closely related to many "Africans". A "non-African" person is much more closely related to many "African" people than randomly selected people of "African" descent are, on average.

"Did Caucasians have descendants who lived in Africa?" Do you mean "Did Caucasians have ancestors who lived in Africa?" few caucasians have african descendants, they all have african ancestors. A parent is an ancestor of their offspring a child is a descendant of their parents. you confuse the two several times.

@John Thanks for the correction. I fixed the error.

@John: Though if you want to get into linguistic confusion, there are a good many (several million, at least) Caucasians who have descendants who were born & live in Africa :-)

What you could do is to take a look at diagrams such as this one:
You can make a google image search for "Cavalli Sforza" and get a lot of similar diagrams. This diagram is using a concept known as genetic distance by fixation index. This is a way to measure how different different ethnic groups are genetically. From the diagram it is easy to see that there is a large genetic gap between the current sub-saharan Africans and the rest of humanity. The genetic distance between sub-saharan africans and any other ethnic group is almost twice as large as the distance between any two non-african ethnic groups. It is from measurements such as these that scientists are able to tell that humans first must have been living in Africa before we took off to the rest of the world.
The people who were living in Africa 50000-70000 years ago, before the "split", were probably on average very different from modern African people although they probably were adapted to the hot climate. I do not now if you are familiar with the so called "Bantu-Expansion" that occured in several waves in the last 4000 years? This is what wikipedia says about the populations in africa before the bantu-groups took over:

"Before the expansion of Bantu-speaking farmers, Central, Southern and
  Southeast Africa were populated by Pygmy foragers, Khoisan-speaking
  hunter-gatherers, Nilo-Saharan-speaking herders, and Cushitic-speaking
  pastoralists."

From very recent research we also know that all non-subsaharan groups are a result of interbreeding with Neanderthals/Denisovans. I think that current estimates says that people from western Eurasia has 2 percent of there genes from these groups, east asians has around 3 percent and people from Papua/New Guinea around 4 percent, but this is new research so those numbers might change.

Here are two other genetic distance by fixation index diagram, from this page, also based on the work of Cavalli-Sforza, more focused on how different ethnic groups in Africa are related:

There are also some more modern approaches that might not be so easy to comprehend, see for instance this article from Nature.

I find this figure somewhat misleading. Specifically, Cavalli-Sforza represents "Africans" as one clade, when in fact there are at least dozens if not hundreds of clades in that one leaf that are more distantly related than the other leaves are from each other. If you drew all those clades in, you'd see that all other clades are a rather tight group nested in the African clade.

You mean like this diagram on this page, which is also by Cavalli-Sforza, but I do not know if it is free of use, the other diagram was from wikipedia commons.

yes that one is better (URL is slightly broken)- it is still using the distance-based tree, which make it look like there are two clades, which we know isn't the case, but it is at least showing the huge diversity within the continent. From a cursory google, Figure 1 from this paper [https://www.nature.com/articles/srep29890] is much closer to the current scientific understanding.

On my current level of understanding the nature figure is a bit difficult to understand. The guy really just wanted to know why we think the "out of Africa" theory is true. Can you find some simple clues pointing in that direction in the Nature figure?

I think that OP had a somewhat different motivation for the question, though it's hard to be sure from his phrasing. We need to be very specific in this case because there is a lot of pseudoscience and bad stuff (racism, obviously) around human origins. The figure I linked is more accurate because it shows that "Africans" are not monophyletic. That is, there is not a common ancestor of "Africans" that is not also the common ancestor of "non-Africans", because "non-Africans" arose out of Africans. Cavalli-Sforza drew his figure to make the two groups look monophyletic, which is wrong.

@MaximilianPress, so we arose out of Africans? What's the difference between "around out of" and "evolved from"?

A couple things: 1) The people currently living in the continent of Africa and the people who lived there 100,000+ years ago are not the same people. This is why the term "Africans" is pretty meaningless in your question. You need to be more specific or your question is unanswerable. It's like thinking that Moctezuma I and Pancho Villa are the same person because they both had political power in Mexico (except 200+ times less accurate). 2) not saying what you mean by "we" is starting to look like trolling. 3) I don't know what you mean by "evolved from". Humans are all the same species.


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Are cells guaranteed to get at least one mitochondrion when they divide?
If mitochondria exist at random within a cell, isn't there a possibility that cell division will result in a daughter cell with no mitochondria?  If not, what is the process for guaranteeing at least one is present in each daughter cell?  If so, what happens to that cell?

Isn't there a possibility that cell division will result in a daughter
  cell with no mitochondria?

Yes, there is always the possibility. However, there must be a strong negative selection pressure against eukaryotic life that cannot achieve the proper partitioning of mitochondria, so you can imagine that there are mechanisms in place to prevent this case.
Mitochondria are both passively and actively partitioned to daughter cells. This is understood to occur through the cytoskeleton and with the control of mitochondrial fusion and fission at key stages of the cell cycle, prior to mitosis and cytokinesis!
Here is a great review from several years ago that addresses your question well.

The review is just 5 years old. If it's "several years old" then what would you say about the waiting time to be eligible for an academic job?

I’m not sure there needs to be any strong selective pressure for this whatsoever. Stochastically, it’s quite likely (actually, virtually assured) that both daughter cells end up with at least a few mitochondria and if not, well, then one of the daughter cells dies and the other one simply divides again. Little harm done, except in gametes. And gametes mis-segregate all the time. One more error in a centillion isn’t going to make a difference.

I thought about this too. But mitochondria are no ideal gas and do not follow such rules. Also, not all mitochondria-hosting life is multi-cellular and tolerant to such errors. I would agree with your randomness point, given the following suppositions: 1. mitochondria are randomly distributed in their host cells (untrue); 2. the number of mitochondria in the daughter cell is always unimportant (untrue); 3. cytokinesis is symmetrical (very often untrue); 4. cells without mitochondria are not selected against (which cannot be universally true in all ecological scenarios).

In addition to S Pr's excellent example, I wanted to point out that some very recent research describes some special behavior in oocyte development specifically related to mitochondria selection.
Here's a easy-to-read version:
https://www.sciencedaily.com/releases/2019/05/190515131741.htm
Here's the original version in Nature:
https://www.nature.com/articles/s41586-019-1213-4
Specifically, during meiosis, the oocyte specifically "puts the mitochondria to the test" by separating all of them (fragmentation) and having each of them operate independently.  (Typically mitochondria act in concert, each one potentially making up for deficiencies in their peers).  Any that do not "make the cut" are eliminated, and the result is an egg cell that has the best mitochondria to pass along to the next generation.

This is really interesting! I'd like to understand more about what "mitochondria act in concert" means. Perhaps one is better at one function while its "peer" is better at a different function? Or do you just mean that stronger ones make up for weaker ones that aren't "pulling their own weight"?

@uhoh Probably both. Mitochondria have many different functions, and they're very susceptible to genetic damage (since they store their genome in an oxygen-rich environment). Over the lifetime of an organism, many mitochondria fail to perform all or some of their functions, and one typical thing that happens with cancerous cells is that mitochondria replicate far more than usual. In the end, these rarely cause significant issues (beyond the effects of aging etc.) - with one major exception, which is the production of ova. There a single broken mitochondrion can "doom" the offspring.

Can you also cite the original research?

@WYSIWYG I added a link to the Nature article... Is that acceptable?  (I'm not sure how to find the link to the original research.)

A typical animal cell has 1000-2000 mitochondria.  From a statistical point of view, assuming a random distribution of the mitochondria and that the cell splits in half, the probability of having 0 mitochondria is (1/2)^1000 or 9e-302.  This makes it an impossibility for all practical purposes.
With enough mitochondria, a process to ensure the cell splits roughly in half and a somewhat random distribution of mitochondria would be sufficient to get at least one mitochondria in each daughter cell.
To address the assumptions:

Random distribution of mitochondria - assumed in the question
Cells split roughly in half - source on dividing assymetries "In somatic divisions, however, cell size asymmetry is mild and, only rarely, one daughter cell is more than double the size of the other."

I think both of your assumptions are highly suspect, unless you can cite research to back them up.

@Mike While I agree that some citation would increase the quality of this answer, I really like the perspective of it. Other answers regard the high evolutionary pressure on cells without mitochondria and refer to mechanisms to actively prevent that case by distributing mitochondria to the daughter cells. This one brings perspective to the importance of these mechanisms: It certainly is beneficial to actively control the mitochondria distribution, but is this a necessity or just a "nice to have" feature? The actual numbers certainly are not very representative, but I like the idea of it.

@NiklasMertsch Exactly.  I'm simply trying to demonstrate that in a certain class of cells, there are enough mitochondria that a random process will sufficiently guarantee distribution to the daughter cells; no active process necessary.


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Can the human body survive in a zero sugar diet strictly through gluconeogenesis?
I read an article a while back about athletes (I believe cyclists) being exposed to a 0 sugar diet and their blood sugar levels stayed relatively constant, which prompted the question whether people could survive strictly off a no sugar diet.


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What determines the duration of larval stage?
Why do insects have very long pre reproductive periods and very short reproductive periods? Is there a common characteristic that can indicate the duration of these stages or offer an explanation for the same?

I honestly find the question a bit too broad, since insects are a very diverse group that use a wide variety of substrates and environments. Is there a group of insects that you are particularly interested in? Generally, development time is often a function of food substrate quality (i.e. the food niche of the larvae) and temperature (especially for insects in a temperate environment). In the case of e.g. saproxylic (wood-living) beetles, development time is shorter for species that use the phloem of rather fresh wood and long for species that use dry core wood.

Also, in colder climates development times are longer due to shorter larval activity periods, so development times between individuals can differ e.g from 1-3 years depending on climate, location (open/sunny or closed) and substrate quality.

I actually see two different questions in your question. The first is "what determines the duration of the larval stage ?", the second is "why is this duration longer that the adult stage ?"
A) What determines the duration of developmental stages?

First, you must note that not all insects follow the same development process. Holometabolous insects (e.g. butterflies) have four life stages: egg, larva (with several instars), pupa and adult (or imago). On the other hand, hemimetabolous (e.g. bugs) only have three life stages, and some insects are ametabolous, i.e. no metamorphosis. Development time thus greatly depends on the mode of development. Of course, there can also be a huge variation within insects that have the same mode of development.
What else determines the duration of developmental stages ? (i.e. eggs/larva/pupa) A large combination of factors. Before they reach the adult stage, insects need to accumulate enough energy to undergo every developmental step and become mature. Resource quality and availability of course influence developmental "speed", but abiotic parameters such as temperature or humidity are also of prime importance. Actually, development time of many insects can be measured in degree days, which corresponds to the accumulation of temperature over time. For instance, larval-pupal development of the codling moth Cydia pomonella can go from 1 to about 6 months, according to temperature conditions.

B) Do insects have longer pre-reproductive periods that reproductive periods ?

It depends. There is a huge variation a) in the lifespan of all insect species, b) in the relative length of their developmental stages.
Some insects indeed have a very short adult life stage, relatively to their developmental stages. Mayflies are a classical example, but it's also true for many butterflies and moths of for mosquitoes, for instance.
On the other hand, it's not true for many other insects. Many Coleoptera (e.g. beetles, cockroaches) can have several-month long adult lives, sometimes way longer that their life as a larva. Bees are a more extreme example: bee queens need three weeks to become fertile, and can then reproduce during several years (same for ants).

C) Why do s̲o̲m̲e̲ insects have short reproductive periods ?

To my knowledge, the reasons are mainly ecological. Insects that have short adult lives are often fragile, flying insects that disperse a lot. They face an increased risk of predation as well as environmental fluctuations (weather, etc.) against which they are poorly protected. Besides their resources (e.g. sugar) may be scarce or poor-quality - some even do not have the ability to feed, e.g. mayflies.
What about evolutionary reasons? Developmental stages need some time because, as I said earlier, insects need to acquire a lot of energy to pass all developmental steps. I didn't even talk about metamorphosis, which is a complete cellular re-organization -that takes some time. On the other hand, adults just need to mate and/or lay all their eggs before they die. They don't need to live too long as they'll probably die soon anyway. Think about mayflies: they are less protected as free flying adults that as underwater-protected nymphae. And they'd better try to maximize egg laying in a reduced time.
Besides, note that there is a difference between potential lifespan and realized lifespan. For instance, parasitoid wasps can live up to 30 days in safe, food-abundant conditions - in the wild however, they often live just a few days.

References
https://www.terminix.com/blog/bug-facts/how-long-do-bugs-live/
Harvey, J. A., Cloutier, J., Visser, B., Ellers, J., Wäckers, F. L., & Gols, R. (2012). The effect of different dietary sugars and honey on longevity and fecundity in two hyperparasitoid wasps. Journal of insect physiology, 58(6), 816-823.
Müller, T., & Müller, C. (2015). Behavioural phenotypes over the lifetime of a holometabolous insect. Frontiers in Zoology, 12(1), S8.
Rafoss T, Saethre M-G (2003) Spatial and temporal distribution of bioclimatic potential for the codling moth and the Colorado potato beetle in Norway: model predictions versus climate and field data from the 1990s. Agric Forest Entomol 5:75–85


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Is evolution the reason why water is colourless for our eyes?
Liquid water is transparent to most of the visible spectra, whereas it absorbs infrared.
Similarly, the air is almost transparent to the visible spectra too.
Could these be the reasons why our eyes evolved to "see" the visible spectra, and not IR or UV?
(Also, are there other animal species for whom water is not colourless?)

Human eyes are too big to see UV. Animals that can see UV have eyes of a few millimeters. Frogs and snakes are vertebrates that can see IR using an enzyme related to vitamine A, althouth mammals mostly just see color. Sea mammals only see green. The most recent photoreceptor change in primates is the acquisition of red photoreceptors to see fruit in trees, so we can't say that changes in vision have co-incided with their investment in marine and riverine environments.


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Entropy during neuronal signaling
to begin with: I have some background in cognitive neuroscience, but have not intensely studied the biochemical background of neuronal signalling, so please correct me if my basic understanding is wrong.
As studying the generation of action potentials and EPSP/IPSP at synapses, I noticed that as those processes make use of the gradients, the actual signalling process works by resolving these gradients (i.e. the molecules flow without having a constant energy supply pushing them to do so). The big part of energy consumption during neural signalling is then actually needed for restoration of these gradients, transmitter reuptakes etc.
So if the above is correct, does that mean that the information "flow" in the brain is done by increase of entropy (which I intuitively understand as a increase of "unorderedness", but im not a physicist either...)? I have been told that biological systems actually want to resist the "natural" direction of entropy in that they want to keep themselves "ordered" to survive. I would have hence found it more intuitive if signalling would be acquired by an active decrease in entropy (followed by some sort of "passive" restoration). Is there any reason why that is not so? Are there other examples of signalling where that is the other way round?
Or am I just lacking understanding and messing up definitions?
Thanks for your help

In my view, thinking of entropy as something biological life has "wants" about is a bit mistaken. In general, entropy arguments regarding biology run into a major problem in that the interesting physical laws involving entropy required closed systems, and no biological system is closed, so it's a bit moot.
It makes more sense to think about what benefits "fighting against entropy" gives a biological organism, and I also think it makes more sense to think in terms of potential energy rather than entropy (even though they are of course related).
Neuronal signaling is best when it's rapid. By pumping ions against their gradient ahead of time, neurons establish a concentration gradient (which you can view as a decrease in entropy). This is indeed the active part. This also stores energy in the gradient, in that if a 'gate' were opened, the gradient would tend to equilibrate. Because the ions involved are charged, additional sensors in the membrane can respond to this changing electrical gradient.

I would have hence found it more intuitive if signalling would be acquired by an active decrease in entropy (followed by some sort of "passive" restoration)

I think you might be mixing up the "action" verbs here. Think about pushing a rock up a cliff or lighting a firework. If you want that rock to be a signal, it's going to be a much more dramatic signal falling down the cliff than it was pushing it up the cliff. It's going to be much more dramatic lighting off the firework rather than extracting the needed ingredients from various places and assembling them. Processes that release stored energy tend to be a lot more dramatic and "active" despite being "passive" in terms of needing to add energy (besides activation).


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How does the nucleophilic attack in DNA replication occur?

Hi there,
I am confused about how the nucleophilic attack occurs in DNA replication.I watched this video from a biology professor (https://www.youtube.com/watch?v=y4hKibS2fAo)
I watched this video which stated that during DNA replication, the hydroxl group forms a covalent bond with the phosphate and the two phosphorus groups are a leaving group.
I understand the basics of these kinds of reactions, but this one just seems confusing. I can see that the oxygen which was part of the hydroxl group forms a covalent bond with phosphorus. But what happens to the hydrogen? And why does the the double bond and position of the HO change position from the first picture to the second picture?
There are also some pictures which show water being produced. But the video states that the hydroxl group is forming a bond with the phosphate group. How does that work?
Thanks a lot

See Chemistry of phosphodiester bond formation by DNA polymerase and What makes/breaks the hydrogen bonds between DNA and RNA during transcription? for very related questions.

Also related: Is water released when a phosphodiester bond is made between two nucleotides during DNA replication?.

Polymerases uses a two-metal ion mechanism to carry out the addition of a new NTP to a growing RNA strand. Two Mg2+ ions are used in this process; metal ion A is involved in the formation of the nucleophile (O-) for the SN2 reaction to occur and metal ion B is involved in the stabilization of the transition state in the reaction. For the addition of a NTP to a RNA strand to occur, an activated 3’ hydroxyl group (O-) acts a nucleophile and attacks the alpha phosphate of the incoming NTP. The reaction is initiated by a deprotonation event. Metal ion A aids with this deprotonation as it reduces the pKa of the hydroxyl (so it is more acidic), making it easier to deprotonate and form the nucleophile, the proton is accepted by a nearby aspartate residue (not water) - doi: 10.1021/ja403842j. After the hydroxyl attack, the mechanism proceeds through a pentacovalent transition state like in a standard Sn2 reaction and the pyrophosphate group (PPi) is kicked out. The image is not mine but comes from this paper: https://doi.org/10.1038/34542, which is quite good, as is this paper: doi: 10.1074/jbc.274.25.17395 and this one https://doi.org/10.1016/j.molcel.2006.03.013

Perhaps you could properly cite the references you are using in case the links become broken in future.

I have included the doi's instead, hopefully this is better


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What is the outer boundary of oligodendrocyte myelination?
The sensory and motor neurons comprising the spinal cord and brain stem have the interesting property that different structural components belonging to the same neuron can occupy both the PNS and CNS.
Here are several examples:

Motor neurons' somas are in the CNS while the majority of their axonal projections are in the PNS
Sympathetic preganglionic neurons' somas are in the CNS while the majority of their axonal projections are in the PNS.
Pseuduniopolar sensory neurons' have part of their axons in the CNS, but their somas and other part of their axons are in the PNS.

The general dogma of myelinating cells states that Schwann cells myelinate the PNS axons while oligodendrocytes myelinate the CNS axons. However, I'd like to know which cells are responsible for myelinating the segments of axons that are just exiting or entering the spinal cord. Does there exist an abrupt demarcation point where the myelinating cells suddenly cease to operate / exist?
Referring to the provided picture below:
Does this picture reflect what is truly observed? Is there really a distinct "outer limit" of oligodendrocyte myelination?


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Time scale for cAMP-dependent pathway cascades
What is the time scale for cAMP-dependent pathway cascades that start at the level of ligand binding to a G-protein receptor and finish at the level of gene transcription regulation?
For example, when corticotropin releasing hormone binds to CRH receptor 1, a cAMP-dependent pathway cascade is initiated, which ultimately leads to an upregulation in the transcription of proopiomelanocortin (POMC) mRNA.
I recognize that this is a very broad question, that is likely highly case dependent (i.e. different from receptor-ligand pair to receptor-ligand pair). Nonetheless, are we looking at several hundred milliseconds? Several seconds? Several minutes?
In the case of CRH, how quickly does CRH-CRH receptor 1 binding lead to the upregulated transcription of POMC mRNA?
If there are any good sources to read about this, I would greatly appreciate it!


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What is meant by the stabilization of a receptor?
I am reading a journal paper, and have a question about the below statement:

PSD-95 is involved in the recruitment, trafficking and stabilization
of N-methyl-D-aspartic acid receptors (NMDARs) and
α-amino-3-hydroxy-5-methyl-4-isox-azoleproprionic acid receptors
(AMPARs) to the postsynaptic membrane during cortical development

What is meant by the stabilization of a receptor? Does stabilization refer to a receptor being protected from being degraded (e.g. lysosomal degradation)? Any advice is appreciated.

The key phrase is "to the postsynaptic membrane" which in that sentence modifies all of recruitment, trafficking, and stabilization.
Recruitment to the postsynaptic membrane means greater concentration of the receptor.
Trafficking to the postsynaptic membrane means externalization from vesicles to the actual external membrane.
Stabilization to the postsynaptic membrane means the receptors stay there and don't get re-internalized.
Though these may seem like they're all the same thing, the responsible machinery is different and the different processes can be measured separately. In the "leaky bucket" model it's the water level, water dripping in from a faucet, and water leaking out from a hole. To be clear, it's unlikely that PSD95 is actually doing all these entirely by itself, rather it's involved in signalling that has all these effects one way or another.


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Molecular Signaling: Why is it more difficult to study membrane-bound signaling molecules compared to soluble ones?
I am reading the textbook Neuroscience (6th ed.) by Dale Purves and colleagues. In one of the chapters (Chapter 7, Molecular Signaling within Neurons), I am reading about the different types of signaling molecules.
The book states that signaling molecules can be grouped into 3 classes: cell-impermeant, cell-permeant and cell-associated signaling molecules. Unlike the first 2 classes, cell-associated signaling molecules are membrane-found, found on the extracellular surface of the plasma mmebrane. Examples of such molecules are cell adhesion molecules such as the integrins and neural cell adhesion molecules (NCAMs).
There is something that the book says which I am unclear about. They say that "Membrane-bound signaling molecules are more difficult to study, but are clearly important in neuronal development and other circumstances where physical contact between cells provides information about cellular identities".
Why is it the case that membrane-bound molecules are more difficult to study compared to secreted/soluble molecules? Any advice is appreciated.

Secreted/soluble/extracellular signaling molecules you can synthesize/purify externally and dump them on some tissue or cells to see what they do.
You can't really do the same with signals that are membrane-bound - you'd need to manipulate their synthesis/trafficking/degradation.


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Is the kinase domain of a protein kinase the same as the catalytic domain?
I am learning about protein kinases and I have read that the protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. I am wondering whether the kinase domain is equivalent to the catalytic domain (the domain that contains the active site) of an enzyme? Any insights are appreciated.

What is a catalytic domain?
Catalysis is the acceleration of a rate of a chemical reaction.
The catalyst is the molecule responsible for catalysis.
A catalytic site is the exact place or region on the catalyst (e.g. enzyme or compound) that is resonsible for catalysis. These are the active sites on enzymes, for example.
A domain is a part of a protein - it may include a site, or it can also refer to the site itself, depending on the context. One can say catalytic domain to mean the exact part of the enzyme that performs the catalysis.
What is a kinase?
Kinases are enzymes that catalyze the transfer of a phosphate group. It's a specific biochemical reaction. In other words, they phosphorylate other molecules with the help of phosphate donor molecules (such as ATP). One part of the kinase is responsible for the catalysis of its phosphorylation reaction, and this part is called the kinase domain. It is, of course, a catalytic domain. More precisely, it is designated a kinase domain.

So, as you can see, now you should understand the following statements:

All kinase domains are catalytic domains. (Kinase enzymes catalyze phosphorylation!)
Not all catalytic domains are kinase domains. (Phosphorylation is not the only kind of catalysis!)


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What is meant by 4 –12% or 8% SDS-PAGE?
I am reading a journal paper and I am looking at the materials and methods section. Regarding the Western blot method in the paper, I have come across the following statement:

Proteins were separated by 4 –12% or 8% SDS-PAGE and electroblotted to
nitrocellulose transfer membrane.

I am not sure what is meant by '4-12% or 8% SDS-PAGE' in the above statement. Do the percentage values refer to the percentage of acrylamide in the gel? Any insights are appreciated.

Do the percentage values refer to the percentage of acrylamide in the gel?

Yes. The 8% gel is 8 g acrylamide per 100 mL. The “4-12%” gel is a gradient gel, which are useful for separating proteins over a large range of sizes. Read more about the uses and formulations of gradient gels here.


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What is meant by 'topologically continuous' in the context of cell compartmentalisation?
I am reading the textbook 'Molecular Biology of the Cell', and I am reading the chapter about the compartmentalisation of cells. I have come across the following statement:

The nucleus and the cytosol, which communicate with each other through
nuclear pore complexes and are topologically continuous (although
functionally distinct).

With regards to the above statement, what is meant by 'topologically continuous'? Any insights are appreciated.

Note that I think this type of question would be better for a language forum. ——— As far as I can see this sentence would mean the same thing with "topologically" removed and thus appears to represent an author adding unneeded words because it sounds more impressive.

The word is needed to distinguish from functional continuity. Imagine how ridiculous the sentence would be without those 2 words: "The nucleus and the cytosol, are (topologically) continuous, although (functionally) not continuous.

What "topologically continuous" appears to mean in this context is that materials can flow between them.
So far as I am aware, this is not a well-defined mathematical term, which is part of what makes this confusing. In topology, some spaces are continuous and others are not, but the meaning of "continuous" in topology is rather more general than the authors usage here.


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For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?
I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure to risk factor). Taking samples from college or university can help reduce time and money. Taking samples from hospital may take time (the hospital I have contact to, has small sample size?). Though both ways may have ethnic diversity, college students are of a given generation only. What to do. Please suggest with references to read.

I suggest this as a starting point.
Basically, if your aim is to determine the population frequency of the alleles, then you should sample from the population.
A possible problem with the university is the age stratification, but also possible different proportion of ethnic groups compared to general population. Also hospital might be biased, because you will have a higher prevalence of people with health issues.
The best thing is to randomly collect samples from the population (but I know it is very hard, especially because you can sample randomly, but the ratio of people willing to give you their blood will be biased!).
One thing that is commonly accepted is to retrieve data from healthy blood donors (which is not unbiased, but is accepted!).
You can give a look at a paper I published a lot of time ago. In that case, the estimation of haplotype frequency was performed on the bone marrow donors registry, and it was considered perfectly fine.
Good luck!


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Was there a first biological cell on earth? or a similar cell originated simultaneously around the world?
It logically follows that if life began on earth and life is cellular, then either that life began singularly or began simultaneously around the world?
What is the evidence or argument for either position?
Or is it both?

Welcome to SE Biology. On this site (for  biology researchers, academics, and students) we expect posters to conduct their own research before posting to try to answer the question themselves. You must have realized that this topic would have been raised and discussed before, and you may even find similar questions on this site. Have you looked?

@David Yes I knew this would have been thought of before however my only access to information is via the Internet and mainly Wikipedia I know there is a lot of information on the Web however it is just the Web and not an area where professional information is usually published. Not being a professional biologist I do not have access to biological papers so I thought this would be the best place where I could gather information that iam curious about. I will look through the posts on this site if you wanted to close the question.

or its a no one knows question.

The technical term for the origin of life from non-living matter is "abiogenesis". If you search this site with that term you will see a list of questions, including a very active one from ten years ago, entitled "Why did abiogenesis only happen once?". You might check this out.

@David Thanks for the referral. Having read the question that you suggested I look at. Do you think it would be possible to simulate the conditions however speculative they are, that life began with?

@David I have just looked and the question of a large scale simulated abiogenesis has been asked before.


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Linked genes outcomes in offspring
This question is from a genetics session in my university:
The test cross between a plant with smooth and yellow seeds and a plant with wrinkled and green seeds gives the following results: 140 plants with smooth and green seeds, and 142 plants with wrinkled and yellow seeds.
These results are consistent with which case of the following?

Linked genes
Epistatic genes
Genes with intermediate dominance
Genes with complete dominance and independent assortment

In my answer key the correct choice is linked genes.
What I know is that in the case of linked genes, the outcomes are: either all parental (complete linkage) or the majority of offspring have parental traits and we have few recombinants(partial linkage).
But here it seems like all offspring are recombinants?! How can this be? Is there a mistake in the question, in the answer, or in my information?
Any help is appreciated. Thank you.

There is nothing wrong with the question and it can be explained with not much more than mendelian genetics + linkage.
What do you think are the genotypes of parents?
First hint: If there is more than one phenotype (for the trait) of the offspring at least one of parents must be heterozygote. So the idea of pure lineages goes out of the window here.
Ok, there is at least one heterozygote for each color and smoothness of seeds. What is the genotype of the other parent?
Hint 2: Test cross is a term for cross between recessive homozygote and individual of unknown genome (with dominant phenotype). The test cross reveals genotype of the parent with unknown genome.
Hint 3: 1:1 ratio of phenotypes is typical of cross between a heterozygote and recessive homozygote.
Ok so we have heterozygote and recessive homozygote for both traits. Which traits are dominant and which are recessive?
Hint 4: This question seems to be inspired by original Mendel work. Feel free to read it here to find out which traits are recessive and which are dominant. It is quite a good read, clear in its presentation of evidence and conclusions and I recommend it to everyone.
However, this knowledge is not necessary to answer the question. How are dominant genes organized in parents? Principally we have two options:
(AaBb x aabb) or (Aabb x aaBb)
If we consider organization on chromosomes it expands to basically 3 options:
Option 1:
chr ---A---B---
chr ---a---b---
         X
chr ---a---b---
chr ---a---b---

Option 2:
chr ---A---b---
chr ---a---B---
         X
chr ---a---b---
chr ---a---b---

Option 3:
chr ---A---b---
chr ---a---b---
         X
chr ---a---B---
chr ---a---b---

I leave it to you to figure out which of the tree options leads to result offspring described in the question.

I aggree with you. I think there is a mistake in the question.
Note that the question does not specify whether the parental lineages are pure lineages (fully homozygotes) or not. In all cases, answer 'B' would not explain the observed pattern for the reason you explained. Such pattern would be possible with some complex epistatic interactions if the parental lineages were pure and with complete linkage.


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What does "~mitochondrial DNA ~bp linear DNA" means?
I'm surfing NCBI website -Nucleotide- to find some examples of real DNA sequences to use in my small homework project.
My question is related to the title of a DNA sequence below:

Sus scrofa mitochondrial DNA, D-loop region, isolate: Europeanwild boar 3
1,045 bp linear DNA

I thought a mitochondrial DNA is different than a linear/nuclear DNA, especially that a mitochondrial DNA is circular while a linear/nuclear DNA is linear. So what does the above title actually means (in simple terms)? Is it still linear or not?

Well, Mitochondrial DNA CAN be linear (in some organism), see the wikipedia page on this

In most multicellular organisms, the mtDNA - or mitogenome - is
  organized as a circular, covalently closed, double-stranded DNA. But
  in many unicellular (e.g. the ciliate Tetrahymena or the green alga
  Chlamydomonas reinhardtii) and in rare cases also in multicellular
  organisms (e.g. in some species of Cnidaria) the mtDNA is found as
  linearly organized DNA. Most of these linear mtDNAs possess telomerase
  independent telomeres (i.e. the ends of the linear DNA) with different
  modes of replication, which have made them interesting objects of
  research, as many of these unicellular organisms with linear mtDNA are
  known pathogens.[19]
For human mitochondrial DNA (and probably for that of metazoans in
  general), 100-10,000 separate copies of mtDNA are usually present per
  cell (egg and sperm cells are exceptions). In mammals, each
  double-stranded circular mtDNA molecule consists of 15,000-17,000[20]
  base pairs. The two strands of mtDNA are differentiated by their
  nucleotide content, with a guanine-rich strand referred to as the
  heavy strand (or H-strand) and a cytosine-rich strand referred to as
  the light strand (or L-strand). The heavy strand encodes 28 genes, and
  the light strand encodes 9 genes for a total of 37 genes. Of the 37
  genes, 13 are for proteins (polypeptides), 22 are for transfer RNA
  (tRNA) and two are for the small and large subunits of ribosomal RNA
  (rRNA). This pattern is also seen among most metazoans, although in
  some cases one or more of the 37 genes is absent and the mtDNA size
  range is greater. Even greater variation in mtDNA gene content and
  size exists among fungi and plants, although there appears to be a
  core subset of genes that are present in all eukaryotes (except for
  the few that have no mitochondria at all). Some plant species have
  enormous mtDNAs (as many as 2,500,000 base pairs per mtDNA molecule)
  but, surprisingly, even those huge mtDNAs contain the same number and
  kinds of genes as related plants with much smaller mtDNAs.[21]

https://en.wikipedia.org/wiki/Mitochondrial_DNA
In the case of your sequence, it only means that it has been entered in NCBI as a linear piece of DNA (it is usually the case when you sequence only a piece of a circular DNA for example)
It does not mean that within the organism it is linear !
I hope this answers your question !

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


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"Prime" structure of DNA Double Helix: Confusion
In this video on DNA replication, the diagram shows the unwound DNA as still being anti-parallel, but the first diagram in this post on Biology SE shows that the individual strands are 5'____5' and 3'_____3'. So my question is the following:
Does a single, unwound strand of DNA run as either 5'______3' or 3'_______5', or does it run either 5'______5' or 3'________3'?

DNA strands always have one 3' end and one 5' end (since each nucleotide has one of each and a strand is formed by connecting the 3' side of one nucleotide to the 5' side of another nucleotide).  In a double helix DNA molecule, the two strands run in opposite directions.
The Pearson Education diagram in the post you referenced has one pair of the strand ends mislabelled.  The lefthand-most labels 5' above the 3' should have been 3' above 5'.

In the SE post that OP mentions, the diagram is immediately preceded by a link to the source page of the diagram (via the word "schema"), and on that page there is a "Homework:" paragraph noting that the diagram is mislabeled.

Oh, didn't see that!

A single, unwound strand of DNA runs 5' to 3', the video is correct. When wound properly, the strands run in reverse directions, 5' to 3' for the first, 3' to 5' for the other. That diagram is not helpful, though the post itself is quite good.

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


text:
Pedigree Analysis: Problem
I'm struggling to arrive at the answer to the following question, which appeared on a pre-test of mine and which I am now using to study the material we've learned. According to this helpful video, I am assuming the possibilities for my question are also autosomal recessive, autosomal dominant, x-linked recessive, or x-linked dominant. I tried each approach as Mr. Douch did in the linked video, but I struggled to find a definitive answer. No matter which approach I picked, it seemed plausible that either the boy or the girl could have the trait, but it seems there's no guarantee that both the boy and the girl have to have the trait. During the pretest, I picked the first answer choice, both the boy and the girl, and got the answer correct by mere chance. But to say that the boy and girl are expected to have the trait would imply that there is a great deal of certainty that the trait will be passed on, right?

The pedigree below shows how a physical trait caused by a mitochondrial gene is passed from one generation to the next in a family.

Using this diagram, which children highlighted in yellow would you expect to have this trait?
(A) Both the son and the daughter -- correct, per answer key
(B) Neither the son nor the daughter
(C) The daughter only
(D) The son only

Please let me know what I am doing wrong or if I am not understanding the question wording correctly. Does it have to do with the fact that it's a mitochondrial gene? Thanks.

The key here is that it is a question about mitochondrial DNA. mtDNA in humans is inherited maternally (from the mother). Both sons and daughters inherit mtDNA, but only the daughters will pass it on to the next generation.
A child's mtDNA has to come from his or her mother, and all of a person's mitochondria are genetically identical. Therefore, children of an affected female will almost certainly have the abnormal trait, while children of an affected male will not.


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What is this frog?
(Man, there's a lot of 'What is this X?' questions here...)

I saw this while walking in Cyprus in early April. It was at about 100m altitude, in woodlands, sitting in the sun on a concrete step beside a muddy ditch; it's about 3cm long.
There appear to be three four types of frog in Cyprus, one of which is actually a toad, and this doesn't really look like any of them --- the closest is the Middle Eastern tree frog (http://en.wikipedia.org/wiki/Middle_East_tree_frog) but the colouring doesn't match and my frog is much more wrinkly and chunky-looking.
So what is it?

Looks to be a pretty good match for middle east tree frog... http://en.wikipedia.org/wiki/List_of_amphibians_of_Cyprus what specifically makes you think it is not that? remember that the wiki picture might not represent the variation that occurs in colouration and patterns etc

The mottled white patches on its back, the colour and shape of the waterline mark (although that could just be because it's in a different posture from the METF pictures I found), and the skin texture. The colour of the throat skin doesn't match either, although I don't have a good view of it here. I'm quite willing to believe it's a METF variation; I just don't know enough about frogs to know for sure, which is why I'm asking.

...I've discovered that most tree frogs look pretty similar.

Hyla arborea?

Since, frogs from the Hyla genus, look near enough exactly the same, it's fairly improbable to get an %100 accurate answer from a single picture. Not to mention, they change colour depending on their present surroundings and environmental conditions, making some of the more bold, distinguishable features in relation to visual appearance, that you could use as part of classification, no longer valid. However, the region of the frog helps in the process of elimination.
The frog and toad species with the greatest populations in Cyprus are; bufotes viridis; Hyla Savigyni; Pelophylax bedriagae. The toad Pelophylax cypriensis, is present too just not in as great populations.
In my opinion this frog in particular shows the greatest affinity to a mature Hyla Savigyni (Audouin) (shown below):

The frog in the picture you posted shares characteristics with the Pelophylax bedriagae, also found in cyprus:

More specifically, the dorsal spot distribution (although they're black in this picture); the dissolving white/cream border to lateral band and position; white "patches" on the legs etc. Notably, the nodules are of different size too; amongst the many other differences.
The size of the two species differs largely, as well.

You stated how the frog you captured in the image above had a rougher texture than the those you've seen. This could be due to the factuality that in some genus's, the males have rougher skin than the females. As well as the skin texture, sometimes male frogs have "thicker" and more muscular front limbs than their female counterpart! Considering this, you may now be able to spot one of the reasons towards the theory, of why female frogs are larger in overall size, than males. During mating, the male has to fully mount the female which, obviously would cause strain and possible injury. You can relate this to us as humans: if you were to mount (like a frog) your partner and you weigh more than her there's an increasing probability that she will get hurt; unless it's Ronda Roussey -  it would be you getting hurt. Incoherently, there are many variables to consider for example, muscle mass of "the one taking the weight".  This could be used to explain how some male mammals are more adapted to mating, by having a longer penis (male sex organ) e.g. a Horse.
Hence, the general rule: the larger the objects mass, the greater the resolved downwards force. To put it briefly. Providing you're on earth, and the force of gravity is equal to, 9.80665 NM, that is.

Presumably you used flash to capture the image on the camera, and this sometimes affects identification of the species since, it alters colours slightly and the appearance of certain features. Diverting the direction of the flash on your camera using a device can help avoid this - likewise with an attachment that alters the flash-effect. I have no idea what they're called, to be honest. Hopefully you know what I mean!

Despite my conclusion, I still have doubts. Did the frog make any noises that you can remember? That would help differentiate between members of the same genus.

This patchy frog looks similar to one of the Gastrotheca species:
for example -
Gastrotheca pseustes -

It does looik similar --- thanks! But I suspect it's probably not, given that Gastrotheca appears to come from South America and I was in Cyprus. Unless it was very lost.

@DavidGiven Do you have other images of this frog?

@DavidGiven Perhaps an escaped pet?  Although the skin texture is quite different between the two pictures.


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Why a continuous supply of energy is needed to support a weight?
What motivates this question is the apparent discrepancy between the concept of Work in physics and in physiology.
Work in physics is defined as the dot product of the force applied to move a certain object by its displacement:
$W = \vec{F} \cdot \vec{d}$
$\text{ Work  =  (Force) $\cdot$ (Displacement)}$
Where $\vec{F}$ is the force vector, and $\vec{d}$ is the displacement vector.
Now if there is some weight lying on a table, it takes no Work at all to maintain its present configuration, since both $\vec{F}$ and $\vec{d}=0$, As a result $W=0$. In other words, this weight-table system does not need to be provided with energy at all, for the table to be able to support the weight, because it takes no energy to support it.
What about an identical case but with a human hand supporting a weight(at a constant height) at this time? Although according to the above reasoning one should expect that it does not need any energy to support the weight, this is not what we observe in everyday life, because when I hold the weight, it takes a tremendous amount of effort to support and maintain its position.
When I looked up the reason behind this, I found out that it has to do with the fact that the muscles of the arm are skeletal muscles not a smooth one.
If the arm were made out of smooth muscles, then it would take no effort or energy at all to support any weight at a fixed height.On the other hand, the muscle fibers that contract to support the weight in Skeletal muscles has to be continuously provided with energy to be able to support it, and hence although no mechanical work is applied on the weight so $W=0$, nevertheless energy is wasted in the form of heat in this process, and hence we get tired after holding an object for some time.
So what is the mechanism by which Skeletal muscles support certain weight? Why it needs continuous supply of energy while holding an object? How is this energy supplied( my guess is:some component of a cell breaking down molecules so as to transfer chemical energy to mechanical contraction of muscle fibers)?And how it differs from smooth muscles?

Welcome to Biology and thanks for your question. I think the big difference with a table and a human arm is the presence of joints. Even if holding a weight straight in the air, it is sill a balancing act that needs continuous muscle strain.

Do you have a reference for your statement about smooth muscle? It seems implausible to me.

@Rolan the Feynman lectures on physics : "The smooth muscles work very slowly, but they can hold a “set”; that is to say, if the clam tries to close its shell in a certain position, it will hold that position, even if there is a very great force trying to change it. It will hold a position under load for hours and hours without getting tired because it is very much like a table holding up a weight, it “sets” into a certain position, and the molecules just lock there temporarily with no work being done, no effort being generated by the clam."

"Smooth muscle would be much more effective for holding up weights because you could just stand there and it would lock in; there would be no work involved and no energy would be required. However, it has the disadvantage that it is very slow-operating."

@OmarNagib You should note that even in pure mechanical examples, the energy consumed may not be equal to work done because some energy is also used up in countering the frictional force.

I think there are too many questions in here ! I answer on the most novel one (smooth muscles vs skeletal ones). For the basics of muscle contraction, I believe you can easily find answers online (look for myosin and ATP cycle)

For skeletal muscles, you'll find a discussion in the Physics SE: https://physics.stackexchange.com/questions/1984/why-does-holding-something-up-cost-energy-while-no-work-is-being-done
To make things short: while holding a position, muscles need to maintain a given length. However, internally, the muscle looks like a collapsible array of filaments, with myosin heads acting as crossbridges between them. Even when the muscle is not contracting, myosin heads unbind and rebind at some rate and would let the muscle relax -- unless you input more energy to compensate this with a further contraction.
For smooth muscle, according to this article, the rate of unbinding can be very slow:

Once the contraction has occurred, the cross bridge attachments need
  to be released in order that the muscle can relax. Although less is
  known about this phenomenon, it appears to be related to
  dephosphorylation of MLC20. In some situations, the dephosphory- lated
  MLC20 is very slow to allow detachment of the actin from the myosin
  cross bridge, resulting in a prolonged contraction. This has been
  referred to as a ‘latch-bridge’ (Hai and Murphy, 1988). This
  phenomenon may be of great value especially for tonically active SM
  beds as it would allow them to maintain basal tone through holding in
  an isometric state without a great energy cost.

So as the muscle is not relaxing, no input of energy is needed to adjust its length to the desired one. I assume a disadvantage of that is that the reaction time of the muscle is slower.

@BenCrowell: well, in fact it is there. "myosin heads unbind and rebind at some rate and [would] let the muscle relax" : so in the absence of input, muscle yields to the load slightly, until "you input more energy to compensate this with a further contraction" : so at a small scale, you can picture it as cycles of yielding and bringing back load to previous position.

You should note that even in pure mechanical examples, the energy consumed may not be equal to work done because some energy is also used up in countering the frictional force.
In your example you consider an object kept on a wooden table and in this case the weight is balanced by the reaction force by the table. You have not considered the material properties of the table. The reaction force would be equal to weight only if the weight does not cause any distortion to the object that it is resting on. When distortion happens; for e.g. the if wooden plank bends, the resting object comes closer to ground with a reduction in its potential energy. Now the weight is balanced by the reaction force which is basically the force exerted on the plank to get back to its original position (analogous to the spring; $F=-kx$). Even in this case the material property of the wood is, more or less, invariant.
Getting back to biology. Muscles consume energy in order to maintain their material properties, even if they do not perform work. Muscles can be thought of as dynamic materials because their material properties can change.
When you are holding a dumbbell in your hand with your arm poised at an angle then your biceps need energy to keep maintaining that tension (a temporary material property). The energy is supplied in the form of ATP.
I won't discuss the case of smooth muscles. You should read more about what they exactly do.


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X linked traits expression in females
We all know that females have an inactivated X chromosome (Most of its genes are inactivated).
Consider a female who is a heterozygous carrier of an X linked abnormality,
If the inactivated X was that carrying the normal gene, shouldn't the abnormality be expressed in this female? Why is it not expressed even though the other X is inactivated?

Because in different cells different copies of the X chromosome might be inactivated.
So, in (approximately) 50% of the cells you will have the X carrying the normal gene activated, and in the remaining 50% you will have the other.
You might start reading something here, and then go in further detail to understand. A nice article is here


text:
What renders a cytoplasm basophilic?
I know that being basophilic or acidophilic corresponds to affinity to certain dyes used in microscopy.
What i want to know is what characteristics of the cytoplasm can we infer from its basophilic property? Does it give us any idea about its different compartments relative abundance, or practical features of the cell? Can we predict how acidophilic and basophilic cells differ in their life and roles?
Thanks for help.


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What is background signal in a Western blot?
I have done a western blot and I want to remove the background signal when doing densitometry analysis of my protein bands of interest. I have read some articles online such as this one regarding high background in western blots. I have learnt that there are many factors that can contribute to high background in a western blot. However, I am still not sure what exactly is defined as background. Does it refer to non-specific antibody binding on the membrane, or can it also refer to regions on the membrane where there is no binding to any protein?
Any insights are appreciated.

In this context (and many others), the terms "background signal" and "noise" can almost be used interchangeably, if that helps.
Generally speaking, noise or background refers to any signal that isn't coming from the thing you're trying to detect (typically in reference to how that signal might interfere or be confused with your "true" signal). So non-specific binding could qualify as background, but it can also refer to regions of the membrane that shouldn't have any protein binding (with any number of causes). One exception I can think of in practice is if you have a specific non-target band that consistently shows up, that might technically fit the definition (sensu stricto) of "noise", but a molecular biologist will more likely refer to it as a "technical artifact" rather than "background".
That said, there are still a number of different kinds of "noise" or "background" that may show up on western blots, and the article you referenced does a pretty good job of describing them, but it could benefit from including some images. Here's a similar guide with more images and links to other Western troubleshooting guides. Hope it helps.


text:
What is mitochondrial run length?
I am reading the following journal paper and I have come across the following statement:

Overexpression of GSK-3β significantly increases motile mitochondria
in a Tau protein-dependent manner. However, GSK-3β does not alter
mitochondrial velocity or mitochondrial run length.

I understand what mitochondrial velocity is but I am not sure what exactly is meant by mitochondrial run length. Any insights are appreciated.

Run length means how far the mitochondria move, each time they move.
The article this references is:
"GSK3β Is Involved in the Relief of Mitochondria Pausing in a Tau-Dependent Manner".
This article has a figure showing the distances in micrometers, although I have trouble working out interpreting the error bars on the graph to see if the distances ("run length") are really different.


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What is a proximal deletion breakpoint?
I am reading a journal paper about the relationship between NCAM2 and autism. I have come across the following statement in the paper:

Based on analysis utilizing the UCSC Genome Browser (hg18, build 36),
there are a total of 19 genes deleted (Table I). The proximal deletion
breakpoint falls within the NCAM2 gene, deleting 17 out of 18 exons,
and the distal deletion involves 16 out of 17 exons of the GRIK1 gene.

I am not sure what is meant by a 'proximal deletion breakpoint'. I have tried searching for the definition online but I have not found anything useful. Any insights are appreciated.

Just break it down: look up "breakpoint" for chromosomes, look up "deletion" if you have to, and look up "proximal" and "distal".

This paper is not very helpful with understanding the role of NCAM2 in Austism, as the patient had chromosomal translocations in addition to the deletion.

Let's break down the phrase as one of the commenters mentioned:

"proximal": in the context of chromosomal position, this means closer to centromere, whereas "distal" means further from the centromere (the middle part of the chromosome).
"deletion": referring to the genes that were deleted as a result of the chunk of the 21st chromosome being missing.
"breakpoint": points at which the chromosomes was broken leading to the deletion.

Putting it all together, this says that the deletion breakpoint closer to the centromere falls within the NCAM2 gene, whereas the deletion breakpoint further from the centromere falls within the GRIK1 gene, with the other 17/19 genes falling between the two.
To verify this interpretation, we can use the USCS Genome Browser as mentioned. We can see that if we compare the position of the NCAM2 gene and the GRIK1 gene on the 21st chromosome, the former is closer to the centromere than the latter. We can also do a spot check to verify that ADAMTS1 one of the other 19 deleted genes, lies between the two of them.


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Is colocalisation of a protein with a presynaptic marker sufficient evidence to say that the protein is a component of axon terminals?
I am reading journal papers about the subcellular localisation of the insulin receptor (IR) in neurons.
I have read a paper stating that IR is highly enriched at synapses, localising to both the presynaptic axon terminal and the postsynaptic density compartments.
The above statement saying that IR localises to presynaptic axon terminals comes from immunofluorescence images of cultured neurons where IR colocalises with synaptophysin puncta.

^ https://pubmed.ncbi.nlm.nih.gov/16978790/
In contrast, another paper showed via subcellular fractionation of the rat brain that IR is enriched in the post-synaptic density (PSD) fraction (through analysing the IR levels in the PSD fraction via Western blotting).
I think this is stronger evidence compared to immunocytochemistry.
To say that a protein is a component of the presynaptic terminal is colocalisation with a presynaptic marker (e.g. synaptophysin) sufficient evidence? Or should there be other forms of evidence to back this statement up?

Colocalization of a protein with another structure is necessary but not sufficient to say that the protein is a component of that structure.
Mixed into the concept of a structure's existence is the concept of an observational timescale. A presynaptic terminal is a structure that exists over specific timescales; all of its constitutive (and identity-conferring) components must colocalize with it, over all of its lifetime. Otherwise it would be more apt to specify something which colocalizes over more limited timescales to be cofunctional structures with the presynaptic terminal.
Experimental techniques tend to probe specific timescales. For example,  immunostaining is based on the assumption that the dissociation rate constant for a specifically bound state is small compared to nonspecific bound states (allowing for the 'washing' steps to have sufficient efficacy). So, in general, spatial correlation of two molecular structures, based on a single observational approach, is insufficient evidence to qualify the structures as parts of a whole.

Empirical science is not based on proof, but on evidence.
No one study is the final word on anything. "Sufficient evidence" is entirely up to the person operating on the evidence and what they plan to do with it. Sufficient for further study? Certainly. Sufficient for using insulin injections to cure every mental/cognitive issue? Of course not.
I think I'd focus less here on the different measurement techniques and more on the model systems used, in addition to Ryan's points about timescales.


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Is there a chemical compound, element or something else that could color the eye lens in purple?
I hope this is a right place to ask this question. I'm writing scifi book, and looking for information whether it is possible for any element, chemical compound, radiation or something else to color the human eye lens (and or freckles) to purple.

slightly related: Could being exposed to excess UV in the arctic lead to a human eye color change? If so, what is the mechanism?

You meant the iris by writing the lens? Colored lens would lead to partial blindness in chosen part of the spectrum.

If it's for a sci-fi book, how about genetically engineered (designer baby kind of thing) humans where the humans have a genes inserted to express purple chromophores in their lens or on their skin in melanocytes? It wouldn't be awfully straightforward, but hey, if you can cause organized fibrillation of lysozyme (a protein normally found in bodily fluids), you can get purple pigment! Also, a purple lens would mean that your purple-lensed character would be impaired in seeing purple.