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What are "primary amino acids and secondary amino acids"? Context: analysis of amino acid content using reversed-phase HPLC
In a Russian document I'm translating, an HPLC system is used to analyse the amino acid content of a substance.

The detector wavelength is set at 262 nm for "secondary amino acids" and 338 nm for "primary amino acids". But what are those?
I googled and found a lot of mentions with exactly these wavelengths being used, but I haven't been able to quickly understand how a "primary" amino acid differs from a "secondary" one. Is it that the secondary amino acids are the products of the destruction of the primary amino acids (those that initially existed in the substance)?
What is the difference between a "primary amino acid" and a "secondary amino acid"?

You might be interested in this.

@another'Homosapien' - thank you, I'll read it.

@tomd - in my paper, they do 'hydrolyse' the substance, but they don't use OPA. But the term 'secondary' must apply whatever chemical you use to break the bonds. I'll abstain from disclosing too much from my paper.

@tomd - I should have looked further in the document. They do use OPA and FMOC. So the 'secondary amino acids' must be amino acids affected by derivatization.

Could someone — tomd or the poster — make this into an answer when they are satisfied it is correct. Then the question can be marked as answered.

I would guess that 'secondary' refers to amino acids that have been derivatized in some way, possibly by reacting with o-phthalaldehyde. (To measure the fluorescence of an OPA-derivatized amino acid, you excite at 340 nm, so I presume the derivative will absorb at this wavelength?).

Based on the reference I read for my biochem exam, secondary amino acids are those which are made of primary amino acids by adding some materials to them for ex :

hydroxylysine is made by hydroxilation of lysine
cystine is made by integrating two cysteins so cysteine is primary but cystine is secondary
etc but in other references the explanation maybe different :)


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Does Ox or Bull Semen have Taurine?
Numerous skeptical communities have debunked the claim that Red Bull has bull semen (including Snopes, and Skeptics.StackExchange. But, none have said whether or not it is even possible.
Taurine, according to Wikipedia, is "widely distributed in animal tissues." But, does it get excreted through semen, and has anyone found it in bull semen?

I'm unsure as to why this question is about to be closed as unclear. I don't think it could possibly be any more clear.

Taurine is widely found in meats and fish. It was named from the Latin word for bull (taurus) because it was first discovered in ox bile.
From http://www.frontresearch.com/news/china-taurine-market-is-fluctuating/

In recent years, the global Taurine consumption has kept growing with an GAGR of 5.5%, more than 50 kilotons in 2014.

I have no idea how much taurine is in bull semen but even if it contains a great deal, do you really think Red Bull will be using that as a source? Can you actually imagine a way of getting bull semen to extract it? The ratio of bulls to cows or steers is very small. The only reason a farmer or breeder keeps a bull is for breeding and many cows are artificially insemination from a limited number (relatively speaking) of bulls with the desired qualities.
All this is to explain to you that your question is  completely inane and pointless. I can't believe anybody would actually think it could happen.

I found a few papers about the function/concentration/localization of taurine/hypotaurine in the male reproductive system of various species:
The taurine and hypotaurine content of human semen:

Hypotaurine, an antioxidant, may play an important role in protecting sperm from reactive oxygen species.

Protective effect of taurine from osmotic stress on chimpanzee spermatozoa:

These results suggest that taurine plays an osmoregulatory role in chimpanzee spermatozoa, which possibly involves stabilization of the cell membrane.

Taurine maintains and stimulates motility of hamster sperm during capacitation in vitro:

These results suggest that in addition to its importance for motility taurine might stimulate capacitation. The mechanism through which taurine supports and stimulates motility is not yet known, but its use results in the first relatively “defined” in vitro capacitation medium for hamster sperm.

Hypotaurine in spermatozoa and genital secretions and its production by oviduct epithelial cells in vitro:

Taurine and/or hypotaurine are necessary compounds for sperm capacitation, fertilization and embryo development. Hypotaurine has a protective role against peroxidative damage... Hypotaurine and taurine were quantified in spermatozoa and seminal and tubal fluid of various species, and in secretions by oviduct epithelial cell layers in vitro. Significant amounts of taurine and hypotaurine were identified.

These are but a few papers I found in a cursory search. You can also see this article for what seems to be a comprehensive overview of the "physiological actions of taurine". Even though I haven't found any direct measurements of bulls, it seems safe to say that, given its function and ubiquitous nature, bull semen contains taurine.

I too don't doubt bull semen contains taurine. As you mention, it's ubiquious, found in most animal tissue. All members of Felidae require taurine in their diet as they're unable to synthesize it as most mammals can. But I can't imagine felines, even a Siberian tiger, relying on bull semen for their source. When I read the OP's question, a mental picture of people trying to collect bull semen came to mind. :D

@Jude Ha! I just read the question as whether or not bull semen contains taurine; the stuff about Red Bull seems ancillary. I only posted this answer because I found that article with a quick search but, truly, I know about as little as is possible about this topic.

Which is why I told him in my answer that his question was both inane and pointless. I was doing my best as being polite as is fitting for a fellow Canadian.

Inanity is quite common in questions here.

I'm beginning to notice that! There are some but much less on Gardening SE and Seasoned Advice SE as people ask for advice or to honestly learn how to do something, for the most part.

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Elements that make action potential to conduct quicker?
The texts, online materials describe the velocity of conduction of action potential depends on axon's length and cross sectional area e.g. short length and large diameter decreases the resistance. Myelin sheath increases the speed of conductivity as well.

Can someone explain why chemical synapses allow quicker conduction than regular arrangement of sodium fast channels along the axon? Can regular arrangement of Na channels help in propagation of AP (I guess it's referring to the nodes of Ranvier)? What's the difference between fast sodium channel and a 'normal' sodium channel?
The question is: Of the following, which allows action potentials to conduct quicker?
1. Chemical synapses
2. Regular arrangement of sodium fast channels along the axon
3. Small axon diameter
4. Depolarisation suppression through the majority of the axon's length
I picked 2, but the answer is 1. I want to know the reason behind me being wrong and that being correct. 1 doesn't make sense at all to me. Come to think of it, I see that 4 could be the most relevant.

"Can someone explain why chemical synapses allow quicker conduction than regular arrangement of sodium fast channels along the axon?" - This part of your question doesn't make any sense to me. Chemical synapses are for communication between cells. Do you mean nodes of Ranvier and saltatory conduction?

Also what do you mean by "an regularity or irregularity help in propagation of AP"? As far as fast vs "normal" sodium channels...I don't know what you mean there either. Different voltage gated channels can have slightly different speeds, but in general all voltage gated sodium channels are pretty fast. At the level you are learning at there is no reason to distinguish between faster and slower sodium channels, unless you talk about hypotheticals like "what would happen if sodium channels were faster/slower?"

@BryanKrause that's precisely my confusion as well. This was a test paper question not homework. Let me type the question exactly as it is, perhaps you may get a better grasp of the context than I do. Also not a duplicate at all. Because I am really not concern about the myelinated or unmyelinated factor of the axon. It is obvious which is stated in my question. I added the image from wiki (which just happened to be referring to saltatory conduction), I am eager to know the general, main concept of AP conduction on any neuron.

1 is definitely wrong, it is a nonsense answer in this context - your confusion is understandable. None of those answers make much sense to me actually...2 is the closest, but that's not what allows an action potential to conduct "quicker" it's what allows it to conduct "at all."

My only guess as to why (1) is supposed to be correct is that an electrical synapse would make an axon electrotonically longer (this is a bit hand wavy in my mind). But honestly, your Prof did a terrible job writing that question.

Agreed, the question asks about action potentials, strictly speaking, chemical synapses have nothing to do with "conduction" of action potentials, only the transfer of information (initiation/suppression of AP's in the postsynaptic cell). 4. i.e. myelination looks the most likely to me to.

@OliverHouston and the rest here, could you please clarify this a bit?depolarisation suppression through.... I understand the basic concept of how myelinated sheath supports the AP propagation. However I do not get the suppression bit. So for my own learning and knowledge, if you could elaborate or point to a comprehensible resource (to 1st year Bio level) : that would be great.

Basically, the myelin sheath prevents AP's in coated areas, as there's no sodium channels. Therefore action potentials only occur at the nodes of ranvier... Ions diffuse along the axon from one node to the next, depolarising the next node of ranvier enough to trigger an AP, more sodium floods in and diffuses along and so on. It's not well covered, the wikipedia description is OK, but the idea of hopping? I think it's a bit outdated and oversimplified by professors.

@OliverHouston a lot of articles is referring to Depolarisation induced suppression. After this discussion and thanks to you all, as a take away I want to understand depolarisation suppression. Perhaps the jargon is strangling me a little.

@DevonRyan I really wish it was my Prof who wrote it. It is from a national test paper... actually international - sample revision paper. I shall take the rest of the 120 questions with a pinch of salt...

One note about "depolarisation suppression" is that it's not even correct. You don't need depolarisation, you just need current moving (e.g., a chloride shunt) to change the electrotonic structure.

@bonCodigo Eek, good luck with that then!

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Why is EcoRI supplied with a unique buffer when it is allegedly 100% active in universal buffers?
Thermo packages a unique buffer with EcoRI:

50 mM Tris-HCl (pH 7.5)
10 mM MgCl2
100 mM NaCl
0.02% Triton X-100
0.1 mg/mL BSA

However, they also list their EcoRI enzyme as 100% active in Buffer O with no indicated star activity:

50 mM Tris-HCl (pH 7.5 at 37°C)
10 mM MgCl2
100 mM NaCl
0.1 mg/ml BSA

The same is true of 2X Tango:

66 mM Tris-acetate (pH 7.9 at 37°C)
20 mM magnesium acetate
132 mM potassium acetate
0.2 mg/ml BSA

Is there a reason one would preferably use the unique buffer over a universal one? Given that buffer compatibility is a major selling point for restriction enzymes, why would they continue to supply a unique buffer?

I look forward to the explanation for why this is a homework question...

Me too. I think this is a legitimate question. And an interesting one, too.

Interestingly for the Fast Digest system an universal buffer (green) is recommended.

@Chris Thanks. Are the Fast Digest enzymes engineered? I know NEB offers two EcoRI enzymes: regular and high fidelity. The latter is engineered for high activity in universal buffers. For Thermo, their "regular" EcoRI is apparently active in multiple universal buffers and is actually supplied with the unique buffer and Tango universal.

The composition of the fast digest buffers is not disclosed...I found one paper, which links the presence of Triton X-100 to a lower star activity, but they use much higher concentration, see here.

I have a suspicion that the unique buffer might be technically the best but the enzyme is also almost fully active in the universal buffers and displays neglible star activity so they just list it as 100% active for simplicity's sake. I may write their technical support a short email to see if they can clarify.

If you do, please let us know when you get an answer that tells us anything (although I doubt it).

@Chris I will do.

I'd +1 your thought to ask their technical support; they probably have more technical data than most users would, most users are probably just going to say "oh yeah it worked fine for me in _____ buffer" without having a quantitative comparison to a dozen buffer compositions. I don't use restriction enzymes in my work but I'm guessing they might supply it with the Triton X to get it into solution when it could be adhered to the supplying vessel. The other buffers might work fine but with a little Triton X they are confident it will all be in solution and therefore results more reliable.

@canadianer I expect that you get 100% of the listed units as activity in all buffers, but that you can get more activity if you use the unique buffer. Who might need this? No clue...

@Chris In case you're interested, I contacted tech support and updated the answer below. Apparently it may show star activity in the universal buffers despite this not being listed.

@canadianer Cool thanks. I find this interesting, and the suspicion it might have to do with star activity is right.

Activity toward the desired substrate sequence is not the only concern in evaluating a restriction enzyme buffer system. In addition, you need to be concerned about so-called "star activity", or activity of the enzyme toward other, non-desired nucleotide sequences.
For example, NEB supplies an enzyme-specific buffer for it's standard EcoRI, even though it lists 100% activity in buffer #2 of NEB's standard buffer series. But at the very bottom of the page, there's this note: "May exhibit star activity in NEBuffer 2.1 or CutSmart Buffer."
Promega has a similar warning about it's "MULTI-CORE" buffer - even though EcoRI has 100% activity in that buffer. The MULTI-CORE buffer is not recommended due to star activity - cleavage at non-standard sites.
It's a little hidden on the product data sheet, but Thermo Scientific does have a mention of star activity in the standard "Tango" buffer, and mentions star activity with overdigestion in the standard "R" buffer. There's no warning about buffer "O", but given EcoRI's propensity toward star activity, I'm guessing this is part of why they recommend a unique buffer for routine usage. Given how frequently EcoRI is used in molecular biology, it's worth using a custom buffer to get the star activity as low as possible.

From canadianer: I contacted Thermo's technical support. Despite the fact that star activity is not listed as a concern for either 2X Tango or Buffer O in the product data for EcoRI, they say that it may actually show some star activity in these universal buffers which is why they continue to supply the unique buffer for this enzyme.

Thanks for your answer. I should've clarified in my question that Thermo does not indicate star activity for both Buffer O and 2X Tango. As I mentioned in the comments, I suspect you may be right that star activity is minimized in the unique buffer whereas there may be some higher degree (negligible?) in the universal buffers.


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Why does increasing the space constant increase conduction velocity in myelinated neurons if nodes of Ranvier are constantly spaced?
If depolarisation at one node of Ranvier triggers, by passive conduction, an action potential at the next node of Ranvier, why does increasing the space constant increase conduction velocity? Surely the locations of each action potential are pre-determined by the sites of the nodes of Ranvier? Is it simply the rate of the passive conduction that changes?

I think the simplest answer to your question is that you're correct in thinking passive flow would be what changes, but the reason behind it is important to understand.
I'd recommend looking at UT Health's neuroscience online resource where they break down action potential propagation in an understandable way. The main takeaway is that the space constant is determined by a number of different physical characteristics of the neuron/axon. You can find these characteristics at the link I provided, but the three parameters that define the length constant are diameter of the axon (d), membrane resistance (Rm), and axial resistance (Ra).
Starting with Rm (because you allude to myelin in the question), this is dramatically affected by myelination. An internode (the myelinated portion of an axon in between nodes of Ranvier) has an excessively high Rm, which just means that current doesn't readily flow across the membrane, so current doesn't "leak out" while it's passively flowing down the axon here. Therefore, increasing Rm by lengthening internodes would help increase the distance across which current can passively flow in the axon (which increases the space constant). Shortening internodes would have the opposite effect. However, you seem to be asking "All things with myelin remaining the same, why would a higher space constant increase conduction velocity?"  That's where d and Ra come in. I explain these below:
The values of d and Ra are somewhat linked. Basically, a high the value of d allows passive current to flow more easily along the axon, meaning it has a low value of Ra. So in the context of your question, if you had an axon and theoretically doubled the axon diameter (so from d to 2d), Ra is cut in half (so from Ra to Ra/2) and passive conduction can speed up. This would increase the space constant by its effect on passive conduction. The converse is true if you shrink the axon diameter. However, it's important to realize that Ra can also be affected by other factors like the contents of the cytoplasm in the axon. That is why both are used to calculate the space constant even though they relate to one another.

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Why is arterial pO2 normal in carbon monoxide poisoning?
Arterial blood gas measurements often show that pO2 is 'normal' even though haemoglobin is bound to carbon monoxide with high affinity.
Is this because there is still oxygen bound to some subunits of the haemoglobin? Surely the CO will displace at least some oxygen, reducing the pO2? As oxygen solubility in plasma is very low, where would oxygen be in the blood if not bound to haemoglobin if there was still high  pO2?

First, let's think about what pO2 means:
pO2 is not the same as "oxygen concentration." pO2 is the partial pressure of oxygen, you can think of it as proportional to the "number of oxygen molecules per unit area leaving the solution" (or colliding with the side of the container). There is also pO2 for the atmosphere, which is going to be approximately 21% * 760mmHg = about 160 mmHg. Partial pressures are often a convenient way to measure gas concentrations, but that only works when there aren't any other interactions happening, so it's not valid for blood.
When blood comes in contact with inspired air, there are >100 mmHg of oxygen molecules hitting the solution and <100 mmHg of oxygen leaving, so there is a net diffusion of oxygen from the inspired air to the blood. If the gas in the alveoli and the blood in the lung capillaries have the same partial pressure of oxygen, there is no more net transfer of oxygen, they are at equilibrium.
Hemoglobin can't do anything to cause the blood to carry more "partial pressure" of oxygen. What hemoglobin does is to "hold on" to oxygen molecules. These "held" molecules can't leave the solution, so they don't "count" as much towards the partial pressure. Hemoglobin instead allows for a higher concentration of oxygen at the same partial pressure of oxygen. Another special thing hemoglobin does is to change its affinity for oxygen in the acidic environment of metabolically active tissue, releasing O2 at a higher partial pressure than it was initially dissolved at.
If you pumped plain saline through the lungs, it would get to about the same partial pressure of oxygen, but it wouldn't have as many oxygen molecules.
If not enough fresh air is entering the lungs, or if the air entering the lungs is low in oxygen, you would expect the blood pO2 to drop, but this isn't what happens in CO poisoning.
There is also the issue that what actually happens in CO poisoning is that affinity of hemoglobin for oxygen increases, but this is actually irrelevant to the pO2 question. The oxygen tightly bound to carboxyhemoglobin (CO-poisoned hemoglobin) doesn't "count" towards the pO2.

Nicely done. I added an answer with some more structure around how we measure and think about total oxygen content that may complement this.

@Bryan's answer is good. I'd like to add a little structure around what seems to be the primary confusion in your question.
There are three important measurements here:

$P_{aO_2}$
$O_2$ saturation
Hemoglobin concentration

$P_{aO_2}$
Arterial $P_{O2}$ ($P_{aO_2}$) is typically expressed in mm Hg. It is very specifically a measurement of the concentration of oxygen dissolved in arterial blood and NOT bound to hemoglobin. Low $P_{aO_2}$ is called hypoxemia.
$O_2$ saturation
$O_2$ saturation is a measurement of the percentage of Hemoglobin binding sites occupied by oxygen. It is expressed as a percentage, e.g., 98%.
Hemoglobin concentration
Hemoglobin concentration is a measurement of the concentration of hemoglobin protein in blood. It is typically expressed in the U.S. in g/dL.
Total oxygen content
Together, these three measurements ($P_{aO_2}$, $O_2$ saturation, and Hb concentration) determine the total oxygen content of arterial blood. Any one or any combination of these three measurements can result in hypoxia (inadequate oxygenation of tissue).
Carbon monoxide poisoning in an otherwise healthy individual is a specific cause of hypoxia that has a characteristic pattern: normal $P_{aO_2}$, normal Hemoglobin concentration, and low $O_2$ saturation. Because there is no problem breathing in oxygen or having it cross the blood gas barrier, there is a normal level of oxygen dissolved in arterial blood. $P_{aO_2}$ is normal. There is no anemia, so Hb concentration is normal. The problem is strictly a matter of $O_2$ saturation.
In many cases of hypoxia, the picture is mixed, but $CO$ poisoning is a classic example where the problem is exclusively one of $O_2$ binding. Anemia is another example. In anemia, $P_{aO_2}$ is normal, $O_2$ saturation is normal, but total oxygen content remains low because there is not enough Hemoglobin.
These are fairly complicated concepts, but covered quite well in West Respiratory Physiology, Ch. 6. The following table may be helpful. Note the footnote for $O_2$ saturation in the row for CO poisoning. Saturation is normal when calculated for Hemoglobin not bound to CO, in other words, there is nothing wrong with the Hb molecule itself. It is simply bound to something else. This is why administration of 100% $O_2$ is a useful treatment.

I like the inclusion of other clinically relevant measures in your answer, +1. I think mine got to be a bit more of a ramble than I intended. Physiology is one of those things that only makes sense once you get it - and then it all clicks. I'm all for trying various ways to getting to the get it step. I'm curious about the O2 saturation measure in the presence of CO... my understanding is that arterial O2 saturation would seem normal in typical CO poisoning, because of high affinity of CO-bound hemoglobin for oxygen.

@BryanKrause the typical bedside measurement is actually not useful in many specific cases, so this is more a physiology teaching concept. I honestly have never seen a CO poisoning patient myself, but in theory you'd have a suggestive history, normal arterial PO2 and normal Hb, and need to have some index of suspicion. Interestingly, another classic teaching about CO poisoning is that you see a cherry red complexion. It turns out, that only happens post mortem, and since we were all taught by pathologists, we passed it along for a number of years.

That last anecdote is both an entertaining and terrifying one.

@DeNovo thank you. I am slightly confused when you say PaO2 is "very specifically a measurement of the concentration of oxygen dissolved in arterial blood". My understanding was that oxygen is relatively insoluble in blood (0.0031 mL / mmHg of oxygen / dL of blood), hence the need for haemoglobin. How can PaO2 therefore reach 100mmHg? Is the /mmHg term in this solubility that of the alveolar air it is exposed to that supplies the oxygen dissolving?

@pincushion44 partial pressure is independent of solubility. Partial pressure in a liquid reflects the amount of gas dissolved in a liquid at equilibrium with a gas at that partial pressure. That's a little confusing, so perhaps it would help to think of it this way: Oxygen is more soluble in freshwater than seawater. Imagine a body of fresh water next to the sea.  More molecules of oxygen will be in a liter of fresh water than a liter of seawater, but both would have the same partial pressure of oxygen, because both are in equilibrium with the same partial pressure of oxygen.

@pincushion44 we use partial pressure to reflect the concentration of oxygen in blood instead of mass or moles per volume because we're not interested in the mass or number of moles dissolved in arterial blood. As you understand, it is not much relative to what is bound to Hb, but O2 dissolves in blood first, before it can bind to Hb. It is important to be able to see if there is a problem getting O2 from the alveoli to the blood, or from the blood to Hb.

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Adult Bugs in Low Humidity House Heated With Wood?
I have a home heated with wood. The humidity is currently around 30% but I'm guessing these bugs have reproduced when the humidity was higher. They really have a hard time when I see them in the basement.
I do have some wood that was a little punky. They seem to come out as soon as I start a fire in the stove, probably due to the heat?

Approx 3cm long
Located in the eastern townships of Quebec, Canada. Any suggestion on what this is and how to treat them?

Welcome to Biology.SE! Please edit your post to add an estimate for the size of this insect as that can be a helpful clue for identifications. ——— You may also want to take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

@tyersome Thanks. I modified the question with the length of the insect. I'm starting to think this may be a Sirex Woodwasp?

Great, thanks for updating — looks like you got a good answer as well!

The pictures are not entirely clear, but I’m relatively certain that it is a wood wasp of the genus Xiphydria (family Xiphydriidae). Traits that point to this is e.g. 2 pair of wings (i.e. a wasp and not a fly), narrow slender antenna, elongated body, the shape of the head sitting on a relatively long “neck”, often with light/white markings on the top and or the back of the head (which can be seen on picture 2) and often white markings along the side of the abdomen (which your insect has) The second picture also shows the relatively robust ovipositor (used to inject eggs into wood).
They also lay eggs into dead wood (usually deciduous wood) and are not uncommon to find in houses, hatched from fire wood.
The species is very hard to determine though, but X. mellipes could be one bet. This species also seem to be found in Canada, see zoology.ubc.ca/entomology. It is also similar to Xiphydria camelus which is common here in Sweden, but I’m sure if it is also found in Canada.

(Xiphydria mellipes from wikimedia commons
Pictures of some species can be seen at bugguide.net).
These insects are not dangerous to find inside, and they only attack dead wood in standing or fallen trees, not construction wood. They are not uncommon to find indoors (along with longhorn beetles and other wood insects) if you bring in mixed fire wood, especially if the wood wasn’t processed and dried quickly after felling. An interesting feature of these insects is that many (all?) inoculate the wood with particular fungi spores, and the fungi later function as the food for the larvae.

Excellent. Thank you, I think you're right with that picture; it really looks like it. White stripes on its head and abdomen. How dangerous is this to my house and what could I do to treat it? I've been searching every log in the pile but it's quite difficult. Do they rather punky wood?

It’s not dangerous at all. The adults have hatched from wood taken inside. They will try to escape outside or die inside the building. They only attack moist dead wood or strongly weakened trees. It is common to get these inside (along with eg long horn beetles) when you bring wood indoors.

You should be able to find round exit holes in one of the logs. From wat I know, all wood wasps have round holes. The other option is that they hid under loose bark but that is less likely, especially if you find several of them.

Thanks a lot! Very appreciated.

I think that is a soldier fly.
https://animals.howstuffworks.com/insects/will-black-soldier-fly-maggots-save-humanity.htm

The adults do not eat or sting, only mate, lay eggs and die.  The maggots are very large and awesome devourers of rotten fruit.  They alternate with worms in my worm bin depending on season.
I have no idea what they are doing in your house!

thanks for the well-written answer, but (-1) because this doesn't appear to be the correct insect. for example, look at the difference in shape of antenna, color of legs, wing characteristics, ecology (soldier flies don't burrow in wood to my knowledge), etc.


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What is tissue patterning?
This term gets thrown around sometimes in biology articles, and I have a rough idea of what it is: during embryonic development, the tissue differentiates in a certain spatial configuration. Wikipedia also mentions that its two main mechanisms are regional specification and cell differentiation. However, I would really enjoy a thorough definition of the term (either in the form of an answer or a reference).

I would guess that the term "tissue patterning" could be an umbrella term for multiple different developmental processes. In precise (more modern) developmental terms it could be a old synonym or sub-type for "Regional differentiation"
https://en.wikipedia.org/wiki/Regional_differentiation
It also fits to the concept of X-inactivation in female mammals, but this phenomenon can not be observed by the bald eye.
https://en.wikipedia.org/wiki/X-inactivation
It is quite possible the term originated from pigmentation biology an early genetic discipline. The underlying mechanism are the Pibald mutations , which result in dysfunction in dorso-ventral melanoblast migration , a dominant mutation, that is a source of white spots and patches in many mammals.

These mutations are almost omnipresent in domesticated furry mammals (cows, dogs, cats rats,horses) as well as some wild species where it gives an evolutionary advantage.
You can also check out cat coat genetics its a lot of fun and relative easy classical genetics.
https://en.wikipedia.org/wiki/Cat_coat_genetics

Excurse biological definitions:
Many biological terms originated in the first years of biology as a science (<1820 ) when genetics, microbiology, evolution and developmental biology where not discovered as disciplines yet (Mendel, Pasteur, Darwin&Wallace where born later, Boviery, Speemann even later), so people (zoologists, botanists) just named the thing they observed, without knowing what the underlying mechanism was. So since they did not have the concept of mendelian inheritance, nor embryonic development, they just called it in layman's therms: "patterning".
Nowadays with the term "tissue patterning" is not totally clear anymore what an author means, if it has no proper context, in my opinion. We have clearer defined terms.

The historical explanation at the end is pretty cool, after reading up a bit more on it and consulting your links, I tend to agree that regional differentiation is close to what is meant by tissue patterning.


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Can one mouse gene have multiple human orthologs?
I was trying to map a mouse gene: Arfgap1 to it's human ortholog. Uniprot shows there are two human orthologs of this gene:
https://www.uniprot.org/uniprot/?query=yourlist:M2021081292C7BAECDB1C5C413EE0E0348724B68210A46CH&sort=yourlist:M2021081292C7BAECDB1C5C413EE0E0348724B68210A46CH&columns=yourlist(M2021081292C7BAECDB1C5C413EE0E0348724B68210A46CH),id,entry%20name,protein%20names,genes,organism,length,reviewed
The two human genes are: ARFGAP1 and ARFGAP3 (it says ARFGAP3 is a synonym of ARFGAP1)
When I tried to find the human homolog in the Mouse Genome Informatics (MGI) database: http://www.informatics.jax.org/downloads/reports/index.html#homology
I found that mouse gene, Arfgap1 only maps to human gene ARFGAP1. What could be a possible explanation for this? Is it possible for a mouse gene to have multiple human orthologs?
Edit: This is just one example. I have encountered mouse genes that have four human orthologs.

ARFGAP1 and ARFGAP3 are distinct proteins.  I think the "synonym" deal is that the two proteins were both referred to as ARFGAP1 in early literature, and one had to be renamed.  So, if you're searching for ARFGAP3 literature and want early literature, you may also need to search for the term 'ARFGAP1'.

Yes.
If duplication of the human gene happened after the speciation event, we have multiple orthologues. This is shown in the following diagram from Ensembl as one-to-many orthologue (ortholog_one2many). In the example from the figure, one human gene has two mouse orthologues, but it could be vice-versa as in your case.

This is an answer to your general question about orthologues. I haven't looked into details about your particular gene (ARFGAP1).


text:
Can the knowledge about torsion angles alone be sufficient for specifying secondary structures of protein?
I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the information about how much of these structures are present in the protein. But, it seems intuitively unreasonable. I can't convince myself "why there can't be other structures with the same torsion angles as alpha helices or beta sheets". Am I missing something?

Perhaps you are missing time with a suitable text book. Try Dickerson and Geis. Long out of print but you might pick up one second-hand if it isn’t in your university library. And this list can hardly respond to your intuition, other than to suggest you do not put too much trust in it.

There is some information on Ramachandran Plots that you may find useful in an answer I posted to another question.

The problem with your question is that you do not quote a source, so it is impossible to know what is meant by Ramachandran plots being used to identify secondary structure of proteins. Why? Because a Ramachandran plot made up of all the amino acids in a protein requires knowledge of the dihedral angles of each amino acid, and so can only be plotted for a protein if its 3D structure is known — in which case the secondary structure is evident as it is defined in terms of repeating dihedral angles. So what do you mean? Some kind of blind recognition quiz? You need to clarify your question.

Its not true that the Ramachandran plot will determine the secondary structure of an amino acid.
Ramachandran plots show the sterically allowed phi/psi angles of an amino acid.  As such nearly all non-glycine amino acids are in alpha/beta spaces.  Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense orders. (alpha/beta/beta/alpha/alpha and etc)
The dihedral angles repeated in a pattern over a several consecutive amino acids create secondary structure (N>4 or 7 for helices - strands need other strands forming sheets).

So, is it possible for two amino acids to have the same sterically allowed phi/psi angles ?

all the amino acids except for glycine have pretty much the same allowed phi/psi angles :) . glycine, having a hydrogen on the alpha carbon rotates much more freely. IN a polypeptide the allowed angles will change depending on the rest of the peptide... this is not as predictable..


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Can the word "Strain" be used to describe plants or is it used only for microorganisms?
I am trying to determine if I can use the word strain correctly as it is presented in the dictionary as "a variety of plant occurring naturally or developed by breeding" or should strain be used only to refer to subtypes of microorganisms such as a virus or bacteria. More specifically, would I be correct if using "strain" to refer to naturally occurring variety in plants?

I don't know whether it's "correct" or not - who's the judge of correctness here? - but it is commonly used to describe varieties of garden plants in catalogs & gardening books.

Yes, you would be correct in referring to a strain of a cannabis plant.
I have seen the term mostly applied to plants and microorganisms but it can also be used to describe genetically identical animals in experimental studies. Check out the Wikipedia article for strain and some of the sources in it where the term is used:

A strain is a low-level taxonomic rank used at the intraspecific level
  (within a species). Strains are often seen as inherently artificial
  concepts, characterized by a specific intent for genetic isolation.1
  This is most easily observed in microbiology where strains are derived
  from a single cell colony and are typically quarantined by the
  physical constraints of a Petri dish. Strains are also commonly
  referred to within virology, botany, and with rodents used in
  experimental studies.

More specifically, see this article about cannabis where the term 'strain' is used consistently:
https://www.biorxiv.org/content/10.1101/592725v1.full

I should mention the source of this question is a debate in the cannabis farmer community as to whether or not "strain" can be used to refer to naturally occurring variety in plants, so using a cannabis article for my purpose is too meta.

Your question is asking directly whether 'strain' is a term applied to plants. It is :) The idea is that the word 'strain' describes genetically similar organisms, regardless of whether they occur naturally or in a lab (also naturally after all).

@Hasselhoff It seems like you've run into an XY problem. In the future, it's much better to ask about your actual problem. In this case, your question could have been about whether "strain" can be used to refer to naturally occurring variety in plants - that isn't what you asked originally.

Fair enough.  Will edit the question.  pawelek zzz comment to JohnHadish's answer sbelow is also very helpful.  I would upvote and accept that comment as an answer if I could.

The word "strain" is colloquially used to describe cannabis, but is usually not used to describe other plants. The following are common terms for differentiating plant sub-species groups which are used by horticulturists, gardeners, evolutionary scientists and farmers.
"Breeding stock" is a breeding term used to identify genetic stocks in a breeding program. Breeding stock names are typically not ones that someone outside the breeding program would be able to identify, as they are used primarily for tracking hundreds to thousands of plants. Think of these as barcodes used to keep track of plants. Examples would be names like "WA38" and "WW_2019_7"
"Cultivar" is used to describe plants that have been released from a breeding program to the used in agriculture. These are typically hybrid plants, or plants with an interesting trait that the breeder selected for.
"Variety" is a tricky term. It is  used to describe breeding material once it is released to farmers in the case of most grain crops, and some major horticulture crops, but is also used to describe naturally occurring sub-species populations of plants (see below). In the case of grain, not all breeding material become varieties. To be released as a variety, the breeding stock must exhibit a trait that is desirable and unique from other already released varieties (i.e. different flavor, resistance to disease, drought tolerance, etc.).
A good example of varieties at the store would be apples. There are many varieties (Cosmic Crisp, Honey Crisp, Gala, Granny Smith, etc.) but they all still belong to the same species.
"Sub-population" is typically used to describe plant sub-species in the wild. This is a term that you may see in plant evolution papers. If a population of a species of plants becomes separated for a long enough time (we are talking evolutionary time here, i.e. 10's of thousands to millions of years) they may begin to develop novel characteristics. For example, the "Rocky mountain white fur" and the "California white fur" are the same species (meaning they can mate and have viable offspring), but they have traits unique to them. These are also often referred to as varieties.
The above descriptions, while useful, are often imprecise. All describe variation within a species, but the threshold for these designation is often based on easily observable phenotypic traits (i.e. flower color, height, leaf shape, flavor) rather than actually genetic evidence. It also does not help that these words are often interchanged (sub-populations are often referred to as varieties, varieties is sometimes interchanged with cultivar). This makes these terms tricky, and you must know the context they are presented in.
For your use, you can use "strain" and people will know what you are talking about.
For other plants you might find in a garden, you can usually refer to them as "cultivar" or "variety" and people will still know what you are talking about.
These terms have developed colloquial meanings as our understanding of plants and genetics has progressed. They are imprecise by their very nature, as they are attempting to describe differences in species at the sub-species level, and are arguably only describing variation that is interesting to humans. These terms are most useful within the context of a specific discipline, where their meaning is usually more constrained.
Sources:
http://kansasfarmfoodconnection.org/blog/2017/11/29/what-are-the-different-types-of-wheat
https://hortnews.extension.iastate.edu/2008/2-6/CultivarOrVariety.html
https://extension.unl.edu/statewide/buffalo/Yard/Cultivar%20vs%20Variety%2001-30-2016.pdf
Conifers of the Pacific Slope by Michael Edward Kauffmann

The word strain has been widely used in scientific publications to refer to identically genetic varieties of a specific plant species and is not restricted to cannabis. See this and this publications from late 90s related to Arabidopsis, common model organism for plants. And if you check in biorxiv for recent publications in Plant Biology you will see that it is still actively used (for many plant species, not only for Cannabis).

I usually have seen Arabidopsis referred to "accessions"/"ecotype" (for example, Col-0) and "lines" (for specific T-DNA insertions, or point mutations). This is the nomenclature that the salk institute uses: http://signal.salk.edu/tdna_FAQs.html
I was not aware that some people use the word strain, that is interesting.


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Making new antibodies
Is there a model of how the B-cell-antibody pool in the lymphoid organ evolves during the first two weeks of infection by a new virus ? With a model I mean something like this

At first we have $10^6$ different antibodies binding weakly to 4-5 amino acid  motives and through somatic hypermutation and selection the pool converges to a few dozen of antibodies binding strongly and specifically to some 8-10 amino acid  motives in the most numerous antigens presented by T cells (mostly motives found in the viral protein sequence since they must be in the peptide presented by antigen presenting cells).

This is what would make sense from the algorithmic point of view, which is often valid in biology, but not always. I have a few refs 1 2 3 but they stay elusive on that point.
If there is no such model then please make a few expert guesses.

There are plenty of papers with models for this. For instance, check a few hundred here.
Edit: I'm not an expert in modeling these particular processes. However, I do know about mathematical models in biology more generally. The OP asked if there is "a model" of how the B-cell antibody pool matures ('evolves'). The short answer is 'no'. There is not 'a model', because anyone can make their own model, with their own assumptions, parameters, methods, etc. The 'algorithmic point of view' is not something that is valid on itself, it is only useful (sometimes). It is the job of the modeler to navigate the nuances of her/his own model so that it ends up being useful for some particular purpose or question at hand. Thus, there is no simple answer to this question, or any other modeling question (take, for instance, all the talk about epidemic models in the COVID-19 case: even experts differ about the relevance of some particular details/assumptions). This is my long answer.

Tks, most of them are a little too specialized or hard to read, if you are an expert in this field, can you choose one and enumerate the 3 or 4 concepts you find relevant to the low affinity of the antibody pool at first and how (TCR-antigen engulf?) leads to increasing affinity and specificity, finally recognizing a few dozen of AA motives ?

@reuns check out my answer edit. In short, you are asking a hard question, because whether a model is useful or not, depends on many things, including the purpose of the model. If you want me to ennumerate '3 or 4 concepts', I could do that, but why would these be the relevant ones? No one knows but me. You need to decide by yourself, because there is no absolute truth here. You asked if there is 'a model', and I can say, in short: there are as many 'models' as you can imagine. Find one (or build one) that is useful for you. Good luck!


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Recombinations between Distant coronaviruses
With recombination I mean long ones, say > 1000 nucleotides, so that the two parents must be coronaviruses and the two pieces of genomes must have compatible genomic coordinates for the recombinant to be viable.
Though co-infection by distant CoVs (for example SARS-related with HKU2-related) are often found in nature, most recombinations occur between closely related coronaviruses.
One thing preventing distant recombination is the TRS (a small motif causing most sub-genomic mRNA junctions) which must be compatible when the 5' part of an ORF is included in the transferred piece of genome. Another one is the complicated interactions between the host and viral proteins and RNA.
However, some rare distant recombinations might occur.

An example is Deltacoronavirus which is a distant genus except in the spike where it falls into Alphacoronavirus (though a bit distant to others).

There are also two Alphacoronaviruses: HKU2 (a normal one) and Wencheng shrew CoV (a distant one) that form a separate "genus" in the spike.

Swine enteric coronavirus (SeCoV) is a near perfect recombinant between two distant alphacoronaviruses, PEDV and TGEV (both responsible of enteric swine diseases).

Are there other examples of recombination between distant Coronaviruses? Note that I mentioned one proven and three putatives recombinations, ie. we often don't have the triplet [major parent, minor parent, recombinant] as it is the case with SeCoV.
Discussing related lab experiments might be interesting as well (of note replacing VSV's G protein by various attachment&fusion proteins often produce viable chimera).

In every case recombinations are rare as not many were found in the 2 million SARS-CoV-2 sequences, but they end being common when looking at the long-term evolutionary history of a given lineage.

Recombination between distant viruses is less likely to produce a viable virus, which is why is rarely observed (recombination rate in a cell may be nearly as high as for similar viruses).


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Can Meiosis 2 be called as mitosis?
I know Meoisis involves a reductional division and an equational division.Say if I am asked a question to find the no. of divisions an egg mother cell undergoes in a Polygonum type division to form the 7 celled 8 nucleate stage, would the Meoisis2 be counted as a mitosis?
Then would it be said to have undergone 1 reduction division and 2 equational division(1Meoisis +2Mitosis).
Or is it just 1Meoisis +1Mitosis ?

Meiosis 2 can not be called mitosis.
You correctly recognized there are similarities between Meiosis 2 and mitosis. In other contexts, however, there are further differences. For instance Mitosis usually does not recombine genetic material (https://en.wikipedia.org/wiki/Meiosis), and the molecules that regulate Meiosis 2 and Mitosis are different. Calling "Meiosis 2" "mitosis" could lead to miscommunication.

But  there aint any recombination in meoisis 2.And are the enzymes mediating Meoisis 2 different from Mitosis even if both are equational divisions?

In mitosis (usually) no crossovers have to be resolved - which contrasts meiosis 2; The results of mitosis and meiosis 2 are also different in terms of chromosome copy number; mitosis entry is regulated by the cell-cycle machinery whereas meiosis 2 is not. The resulting cells have distinct biological functions too - for instance in meiosis 2 the resulting cells will be gametes


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Dopamine receptor count: Role and Measurement
Can the Dopamine (DA) receptor count take a significant drop over the course of life or does it stay constant? I read that low D2 (Dopamine receptor type 2) receptor count does not cause Parkinson's Disease (PD) and has some interesting effects instead, but what abut low D1 (Dopamine receptor type 1) receptor count? What are its effects? All I found is this. Is D1 receptor only related to motor activities?
I found some research papers on how to measure the DA receptor count, but are those tests publicly available and affordable? Is there any indirect way to determine D1 & D2 receptor count?
Disclaimer: This is not a self-help question, and PD is not my focus. I am trying to form a theory that requires easy way to measure DA level plus D1 and D2 receptor count, but sadly I am not part of any university with biology department to go seek advice from.

Welcome to BiologySE! Your question, for me, is a bit unclear. You could help people that are not experts in the field (but may still be willing and capable to help you with your question!) by (i) giving full name of abbreviations before using abbreviations and (ii) providing references (Wikipedia articles are sufficient for basic concepts) to both the major actors in your system (e.g. the receptors) and some claims. If you mention something like 'I found some research papers', people will definitively want to know which, so please provide the reference to these papers.

Sorry for the poor accessibility. I have edited the question. I am not allowed to most more than two links. So here is one link I wanted to post: Effect of low D2 receptor count: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871784/.


text:
Why doesn't submersion in water kill fungi?
I have read that fungi cannot live without air. Does a couple of minutes in a swimming pool full of chlorinated water kill them as it would a mammal? I've never heard this suggested. Will they survive by enjoying trapped air? Or by "holding their breath" for a long time?

Is oxygen soluble in water?

So would they die if submerged in halon or carbon monoxide?

Mammals have a brain, heart and other vital organs that consume a lot of energy (and therefore oxygen). Fungi don't need that kinda stuff and therefore don't need a lot of oxygen (they can hold their 'breath' for a very long time).

Is your question why chlorinated water doesn't kill fungi, or why they don't drown when submerged like mammals and many other animals would. In the case of either, are you sure that the premise is true?

@HarrisWeinstein   Good question. Let me revise my question...

There is a lot of anecdotal evidence that frequent visits to the pool help with fungal infections. Surely, someone from the scientific community must have noticed too, right? So why don't we frequently hear people suggesting to go swimming to treat these infections?
Because scientific results suggest the opposite!
Incidence of occult athlete's foot in swimmers

In our results, 22 swimmers had positive cultures (15%), 8 of these cases had no lesions (36%). They included 7 infections with Trichophyton mentagrophytes (87.5%) and one with T. rubrum (12.5%). We observed one case with a dual infection. Only one sample from the inanimate environment was positive. This study showed a significant incidence of occult athlete's foot in swimmers. To control this endemic problem, adequate preventive measures must be taken.

Foot Infections in Swimming Baths

A 10% random sample of all bathers at a public swimming bath were examined for tinea pedis and verruca.
The overall incidence of tinea pedis was 8·5% and of verruca 4·8%. The incidence of tinea pedis in 205 male adults was 21·5%, in 288 boys 6·3%, in 60 adult females 3·3%, and in 220 girls 0·9%. The incidence of verruca in juveniles ranged from 4·2% in boys to 10·5% in girls.
It was clear that both infections spread within the baths, and since a relatively small proportion of users admitted to taking precautions to avoid contracting or developing infections it seems advisable that more publicity about recommendations on foot care should be provided.

Onychomycosis in Icelandic Swimmers

The prevalence of
culture-positive onychomycosis was 15% in women and 26% in
men. Our results suggest that onychomycosis of the toenails is
at least 3 times more prevalent in swimmers than in the rest of
the population.

Does this mean that not only is going to the swimming pool not a cure of fungal infections, but it is actually the cause? Well, maybe not. While the articles show that there is a larger incidence of fungal infections among swimmers, they only show correlation, not causality. People who partake in sports activities have a bigger chance of having these infections than the general public. These are also the people who are more likely to go swimming.
To settle the matter for good, we need an article named "Prevalence of fungal infections among occasionally swimming couch potatoes" :-)


text:
What is the science behind talent?
So some people are better at doing stuff than others of the same age..in other words, they have talent.
So I am asking, what is the science behind talent? What is different in their brains than others which give them an advantage?
By talent I mean excelling in physical performances like sports and mental abilities like IQ

This is far too broad. What kind of traits/talents are you most interested in? IQ, social skills, physical performances etc? All traits differ to what extent they are determined by genetics, environment and gene/environment interactions, and our knowledge about different traits also differ dramatically.

I agree with @fileunderwater , this question is way too broad and shows no research effort whatsoever. There is plenty of literature available on this subject. One just needs to search for it (hint, hint)..

i DID search it but couldn't find very satisfying answers. And sorry for the broad question, I narrowed it down..

Excellent. Would you perhaps care to add some of the sources to your question? I mean the ones that you came across and found unsatisfactory. It always helps to create a better understanding.


text:
Is there a type of amnesia that separately affects long-term memory?
Is there a medical condition that affects the long term memory, but leaves the short-term and working memories totally or fairly intact?


text:
Retrieve all predicted cds from NCBI
Please apologies if this has been answered somewhere else, but I couldn't find an answer to this problem.
I would like to retrieve all the predicted coding sequences on the NCBI ftp for a given species. Let's say my interest species today is Stegastes partitus and that I go here. I know how to get all the predicted mRNAs (./RNA/Gnomon_mRNA.fsa) or all the predicted proteins (./protein/protein.fa) but I cannot find how to get the CDS... if ever it's possible? This can be done on the Ensembl FTP.
Thanks for any insight!

EDIT: The output would ideally be a multifasta file like this:
>Stegastes_partitus_gene1_cds
ATG(.................................)TAA
>Stegastes_partitus_gene2_cds
ATG(.............................)TGA
>Stegastes_partitus_gene3_cds
...

One QA site, which specializes on detailed bioinformatics questions is biostars.org

I'm downvoting because the readme file already tells you that the GNOMON folder should contain the files you want.

The GNOMON and the GFF folder. As per as the text mining goes, you can use excel and awk...awk is more of a stackoverflow question...but I don't think you are on linux.

@Koustav Pal So you're downvoting because you know the answer? You could at least provide a proper answer ;) Thanks anyway! PS: I'm on Linux, which does not mean I know everything of text mining -- hence my question.

My point is, read the readme. I didn't even read the readme, I only did a ctrl+F for CDS and found out that they were inside the GNOMON and GFF folders

The GNOMON and GFF folder contains the files you want, the GNOMON if you check the README relates to the GNOMON gene predictor and the GFF I think links back to the same file. I think the file you want is ref_Stegastes_partitus-1.0.2_scaffolds.gff3.gz which contains the coordinates on the scaffolds.
And as you stated you are on linux, so the best and geeky way to go is awk.
awk '!/#/{if($3=="CDS")print}' ref_Stegastes_partitus-1.0.2_scaffolds.gff3 > SomeFile.gff3

UPDATE

This part is from python. With reference to the previous user's answer if you fetch the GBK file, rna.gbk, this should allow you to fetch CDS using biopython
You should also check out Peter cook's tutorial on handling genbank files in python
from Bio import SeqIO
from __future__ import print_function

Genome = SeqIO.parse("Examples/rna.gbk","genbank")
handle = open("Examples/rna.faa","w")
for genes in Genome:
    i=1
    for Feature in genes.features:
        if Feature.type=="CDS":
            FASTA=Feature.extract(genes.seq)
            print(">"+genes.id+"_CDS_"+str(i),file=handle)
            print(FASTA,file=handle)
            i += 1

I would recommend that you install anaconda, it is a package management software, which when installed installs its own python version and alongside it installs some 400 different packages. Instructions are available on the link. So these packages should come with the link.
After you have installed anaconda, put all that code from up there into a Myfile.py and execute on the command line with python Myfile.py.

I cannot upvote (not enough rep), but +1 anyway. "I would like to retrieve all the predicted coding sequences on the NCBI ftp for a species." --> we're getting closer! :)

do you mean any species?

Yes, for instance this one (Stegastes partitus). (See my edit)

CDS are a bit different, because this particular annotation is provided with GFF files on the genomic coordinates. And the genomes themselves have many versions in different stages of assembly primarily contig, scaffold, assembled chromosome with unknown chromosomes, but the files should be inside ./GFF/ and the name will change according to version and stage of assembly of the genome the gff file relates to

Ahh so you want the sequences!

Yes! Apologies if this was not clear.

check the edits

Brilliant! Many thanks :) And indeed, Peter Cock's webpage is really helpful, I'll keep this in mind.

The RNA folder of your link provides several annotated file formats. These include reference to the CDS for every transcript.
Stegastes_partitus/RNA/
Download and unzip the rna.gbk.gz file and open it.  You will see CDS location information for every entry.

Yes but this does not provide an "easy" access (such as a multifasta file) to all the cds of this species.

No, true. That would require some text mining skills, but would be pretty easy for someone that has that expertise, if you had them or knew someone that did. I'm just a hack.

A web-based way of getting this data:

Go to the NCBI Assembly page: https://www.ncbi.nlm.nih.gov/assembly and search for the species of your interest. Here, the query would be something like "Stegastes partitus"[Organism] which would return only one hit that is the latest reference version of the assembly. Since there is only one hit, you are directed to the 'Full Report' page by default. Click on the link at the top left corner and change the 'Full Report' format to 'Summary'
At this point, you will see a 'Download Assemblies' button. Click on that, choose the data source as RefSeq and file type as 'CDS from genomic' and you are good to go!


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Merge NCBI and Ensembl data
Apologies if this is a really naive question, but I cannot figure out how to do this easily. Here is a related post regarding the best method to find orthologous genes of a species.

Let's say I have a protein alignment downloaded from Ensembl (coming, for instance, from this Ensembl tree).
This gene is present in some other "NCBI species" that I would like to include in my tree (for instance, Stegastes partitus, with available genome and present in the NCBI database but NOT in the Ensembl database). Indeed, if I manually blastp asip protein sequence of D. rerio (extracted from my Ensembl multifasta protein alignment) onto nr database parsed for S. partitus, I find this sequence, corresponding to the first blast hit. Perfect! And I can manually append it to my initial protein tree.
Where the problem starts is that I don't have one gene and one NCBI species but many of them (let's say p genes and n NCBI species). I already have an Ensembl protein multifasta file for each of my p genes.
My question is: is there an easy way to append to each of my p multifasta files the corresponding homologous protein sequence(s) for the n "NCBI species"?
Thanks for any insight!


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Difference between Premature Atrial Contraction and Atrial Fibrillation
what is the difference between Premature Atrial Contraction and Atrial Fibrillation. I know that both have irregular heart beat but have normal QRS complex. Both have abnormal or absence P waves but a normal T waves.
Can PAC be considered as an isolated event? and AFib be considered as chronic event?

Atrial Fibrillation is a dysrhythmia while PAC is an early depolarization coming from the atria. An occasional PAC can be normal for some people. In that case their heart rhythm would be a sinus arrhythmia instead of a normal sinus rhythm.
In AF, the atrias don’t contract/pump at all, but they quiver/twitch due to the many simultaneous ectopic foci that are being discharged from random cells; similar concept to Ventricular Fibrillation. Due to the atrias not fully depolarizing, you won’t see any P waves on the EKG. If/when an electrical discharge reaches the AV node, it goes through the normal electrical condition system from there, forming a narrow QRS complex. AF is the only irregularly irregular rhythm, meaning that the QRS complexes have no regularity at all, and have no pattern to their irregularity.
Video example of AF.
Rhythm Strip

As for PACs, the atrias depolarize earlier than expected creating what looks like an early beat. The next beat though will be later than expected. The pacemaker cells “reset”, returning to their pattern after this early beat.

Both AF and PACs can be acute or chronic depending on the person.

i see~ thanks for the response!

another question, so does it mean you cannot have PAC in two consecutive peaks right? because otherwise clinically how would you know the atria depolarized earlier or just because the patient's heart rate is increasing

You can have what’s called a run of PACs(PJCs and PVCs as well). Remember that what is seen on the EKG is the electrical activity, not the actual contractions. On the cardiac monitor the HR will increase a bit. There is a debate on whether to count premature beats as part of the heart rate or not. You can tell if someone has a premature beat by feeling the pulse, but to know the type of premature beat, you’ll need an EKG. Clinically, premature beats are not an immediate life threat because they can be caused by something as simple as stress. A run of PVCs (aka run of V Tach) is dangerous.

I hope this answered your question, as I was a bit confused about the second part.

Not quite haha. So you know there are bigeminy and trigeminy for PVC, because you can have consecutive premature ventricular contraction. But my question can you have consecutive "premature atrial contraction"? Because wouldn't it be difficult to distinguish a consecutive PAC and an increased heart rate?

Yes you can have bigeminy/trigeminy PACs, but I don’t understand your point on increased heart rate. Any time you have a premature beat, your heart rate on the cardiac monitor will increase by a couple of beats because the monitor calculates approximately how many beats per minute your heart will beat based on how often it senses electrical activity. This is not clinically important as you might be thinking it is. You can always manually calculate the pulse rate or use a 6 second strip to calculate the heart rate accurately.

With irregular rhythms, it’s more important to know the range of the heart rate rather than the actual number. For example, Atria fibrillation will always have different numbers displayed on the monitor, but as if the range of it is in the 70-85 range, then you know it’s a stable rhythm (if the patient normally has AF).


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Growth of Axons
Does anybody know a paper in which the growth of axons, i. e. their length in dependence of time was measured? I did some literature mining myself, but couldn' t find any results.
I'm looking for a graph that shows the length of an axon in dependence of time.

Can you add where and what you searched for? It will help others know what to avoid in duplicating your efforts.

There are many papers on that topic. Please clarify what exactly do you want and what have you already looked for. Also, please add a [tag:reference-request] tag addressing all the necessary requirements mentioned in its tag-wiki.

I've looked already for the topic "growth of an axon", but I couldn't find the results I wanted.

http://www.google.com/search?q=axon+growth+dynamics


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Correlation between genome size and mutation rate?
Martin Nowak in his book "Evolutionary Dynamics" talks about a given correlation between genome size and mutation rate.
What correlation does exactly exist between these two concepts?

Is it a linear correlation?
What is the coefficient of correlation?
Does this correlation exist in many different taxa?

One will need to make whether we talk about mutation rate per base per generation or for the whole genome.
Some references to accompany claims are welcome!

Could you provide a reference for the first sentence of the question, or is it an opinion? And what are the units of mutation rate- is it mutations per bp per generation? Or are we talking somatic mutations?

I read about this correlation in Nowak's book "evolutionary dynamics". I am sorry I don't have a better reference right now. Good point! Yes I meant mutation rate per base pair per generation. And generation time is correlated with genome size. Let me rephrase completely my question in order to not assume this correlation.

@AlanBoyd I'll ask the "why" part of my question in another post depending on the answer to this post.

its probably not a linear relationship to genome size because larger genomes don't necessarily have

Drake proposed an inverse correlation between genome size and mutation rate A constant rate of spontaneous mutation in DNA-based microbes.. His rule seems to be true for DNA viruses (this is probably also interesting for the other thread on this). The paper has some kind of a follow-up for higher organisms (I have so far only read the abstract):"The mutation rate and cancer."

I missed this question somehow. Well, when comparing mutation rates many more hidden variables come into picture- general biochemistry, habitat etc. Also, eukaryotes should not be compared to prokaryotes.

Bradwell et al. report RNA viruses with the smallest genome may have particularly high mutation rates. A particular bug was shown to have about 1.4 x $10^{-4}$ substitutions per nucleotide per round of copying (high for viruses generally) and the authors suggest this is to optimize adaptibility. Correlation Between Mutation Rate and Genome Size in Riboviruses: Mutation Rate of Bacteriophage $Q \beta$, Genetics, vol.195 no. 1 243-51 (2013).
Cuevas et al. report a phage with 1.0 x $10^{-6}$ mutations per base per round of copying (m/b/r), which conforms (they state) to Drake's rule of 0.003 mutations per genome per round of copying in DNA-based microorganisms. They indicate that DNA-based microorganisms range between $10^{-10}$ to $10^{-6}$ m/b/r. They state that RNA viruses vary between $10^{-6}$ and $10^{-4}$ m/b/r, consistent with the result above. Point Mutation Rate of Bacteriophage $\Phi X174,$ Genetics, vol. 183 no 2 (2009).
Drake's paper often-cited paper (one of them) is available at this link.
He has a remarkable graph on p. 7163 of this paper in which based on his observation of seven microorganisms with a wide range of genome size (bp) he plots the log of the mutation rate per base pair against the log of genome size (bp). The resulting (fitted) line has a slope of roughly negative one.
In a nutshell, Drake shows that over a wide range of genome size, as the genome size climbs exponentially the mutations per base per round of copying drops exponentially. This relationship is roughly log-log linear.
In his discussion he says that the factors influencing mutation rates (in either direction) are so general that they seem to have imposed a small range of variation of mutation rate per genome in microbes that have a large range in genome size and mutation rate per base pair.
As for more complex organisms, I have read very little. There is a recent review article in Nature about a report that a hypothesized inverse correlation between genome size and mutation rates in certain plants (angiosperms) is untrue. Genome size is positively correlated with genome size. Plants with the larger genomes have higher mutation rates than those with smaller than average genomes. I don't have access to this pay-walled article or the methods involved so I am quoting the abstract. Tasci, Nature Reviews Genetics 13, 148 (March 2012).
As usual an expert in this area could correct/expand these few details I've found but it's an interesting question. Drake's paper gives a remarkable result.
As for the question about correlation coefficient, I think that Drake's graph suggests a strong correlation between linearized functions over a certain range.
I suppose we could attach a number to that...

I'd clarify the above that the mutation rate is probably linear with the number of bases in the cell, since they are caused by random collision with ionizing radiation most of the time.
The number of mutations retained will vary though by organism which may reflect the trend that @daniel is describing.  Certainly larger prokaryotes will start to have more DNA and mutation repair genes when they have larger genomes, on the average.
Eukaryotes, including metazoans will have more elaborate selection mechanisms such as diploid recombination and social selection to throw out mutations for many of the genes.  This may explain the additional dropoffs for even larger genomes, who tend to be eukaryotes.
As an example of the points above, take a look at Deinococcus radiodurans, a prokaryote found in cans irradiated with gamma radiation as a means of sterilizing and preserving the food.  This bacterium can withstand a half million rad of gamma radiation - one thousand times the human lethal dose.  D radiodurans has multiple copies of its genome and several times the number of DNA repair pathways, and probably all the tricks in the book to keep its DNA intact and break/mutation resistant.  It would be way off the mean slope in your chart.

The plant article seems to support your idea. I think Drake's finding is interesting in part because it is counterintuitive. The info on Deinococcus sort of reinforces that the niceness of Drake's result is due in part to the narrow range of bugs involved (although I think he mentioned a couple of outliers).+1

thanks @daniel!  Its always important to remember the underlying assumptions and a constant mutation rate from the environment is important.  viruses also have their own requirements - they favor variation because they have no replication genes to protect and it helps them evade immune systems - its not entirely a matter of size.


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Why did translation develop a specific codon for initiation?
The translation of mRNA is initiated by a specific methionine-accepting tRNA at a specific initiation codon, usually AUG (complementary to the tRNA anticodon). However translation at suitable (albeit unphysiological) conditions in vitro does not require a specific initiation codon or a specific amino acid, so it is not difficult to envisage an earlier stage in the evolution of the translation apparatus in which this specific initiation system was absent. Instead there might have been random initiation or initiation from the 5′ end of the mRNA.
A specific initiation codon puts constraints on the sequence of the mRNA and adds an unnecessary amino acid to the N-terminus — one that is sometimes unwanted and needs to be removed.

What advantages can one envisage for initiation at a specific internal
  site, rather than at, say, the 5′ end of the mRNA?

I appreciate it is impossible to prove which factor was actually responsible during evolution, but by soliciting concrete explanations I trust that this question is as valid as the original from which it is derived (see Footnote).
FOOTNOTE
This question has been expanded from one part of a three-part question posted some time ago on “Why is AUG the Initiation Codon?”. This recently resurfaced, and as nobody had answered this particular part, and as it is site policy to ask one question at a time, I decided to remove it from the original and repost it here so it could be considered on its own merits, without the distraction of other questions such as the choice of codon or of methionine over other amino acids. I shall contribute an answer with some thoughts of my own, but, of course, anyone can join in.

It could simply be to prevent random fragmentary RNA from being transcribed,  they are fairly common in the cell afterall.

@John — Thanks for your comment. I can include it in my answer if you are not going to answer yourself. One thing — do you have a reference to support your statement that random fragments of RNA are fairly common?

There are many things like ribosomes that are made of RNA, ribonucleases (which are also made of RNA) is one of the many ribozymes which could be transcribed. It is also one of several mechanisms that cut RNA into smaller pieces. https://www.sciencedirect.com/science/article/pii/S0092867409000671

@John — Thanks. I've included your point in my answer.

It is not clear to me where initiation took place in the translation of artificial polynucleotides such as (UC)n which Khorana used in experiments that, following up the work of Nirenberg and Matthaii, helped decipher the genetic code. It may well have occurred at random positions rather than the 5′ end. Such a mode of translation would obviously have been wasteful if it occurred during early evolution as a mixture of products would be formed, many of which would be inactive and might even compete with the active species. If this were the original situation,  it is easy to see how a change to initiation at a specific point would be advantageous.
But why not start at the 5′ end? Contemporary eukaryotic initiation complexes recognize the 5′ end of the mRNA, even though they then scan further to find a specific initiation codon that will respond to the initiator tRNA. As there is no physical separation of  genes on a chromosome, it is obvious why transcription needs to start at a specific point within the DNA, but the need not be true for the translation of individual mRNA transcripts.
I can see two ways of approaching this question.
The first is from the standpoint of the contemporary ‘DNA World’. The arguments one can make  include:

In a general sense 5′-end initiation may be regarded as restrictive
in that it would not allow the 5’ end of mRNA to provide other
functions such as forming a secondary structure to regulate the ease
of translation.
5′-end initiation would preclude the polycistronic mRNAs we see in
contemporary bacteria.
In 5′-end initiation it might have been difficult to distinguish the
ends of mRNAs from other RNAs before the modification of bases that
we see in contemporary eukaryotic mRNAs had developed.
Likewise, as suggested by @John in a comment on the question, 5′-end initiation might have caused translation of fragments of RNA as they degraded.
The selection of a specific codon was secondary to the need for a
single initiator tRNA, which has been discussed in relation to
another SE question, although the arguments there relate to more recent stages in evolution.

However there is another approach which considers the situation in a putative ‘RNA World’.
The difference here is that — like some contemporary RNA viruses and bacteriophages — the genome might also have been the mRNA but without a system to produce many copies of the ‘plus’ strand for translation. Translation may have been on the genomic RNA.

To translate several proteins it would have been advantageous to have
several initiation sites on what would have been a polycistronic
messenger (rather synthesize a polyprotein like poliovirus).
The 5′-end of the RNA may not, in any case, have been available for
encoding protein as it might have another (e.g. replicative)
function, and it is also possible that part of what in contemporary
systems is a separate part of the translation apparatus was
physically incorporated into the genome.


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Can Covid-19 (similarly to HIV) infect T-Cells?
I'm interested in better understanding this Nature publication, discussing the potential for Covid to infect t-cells.
After describing the results they conclude:
"Based on the results of pseudovirus and live virus infection, here we proved that (1) SARS-CoV-2 could infect T cells, (2) SARS-CoV-2 infected T cells through receptor-dependent, S protein-mediated membrane fusion, and (3) infection could be inhibited by EK1 peptide."
Is this big news? I am not an expert but I believe that HIV's special trait is it's ability to infect CD4+ T cells. If this virus has this ability, does it mean it will have long-term effects like lymphocytopenia, which occurs in HIV?

Cell-cell fusion means it can probably infect and even replicate inside any kind of cell? But this is probably a minor target compared to type II cells. In the paper they obtained significant virus entry and cell-cell fusion but not significant replication inside their T-cell line. It might explain partially some of the pathogenic effect in particular if the virus induces apoptosis or just cytokine release in immunity cells.

As referenced the publication you shared, other human corona viruses also infect, but do not replicate in T cells, so it's not "Big News" in the sense of being a novel or unexpected finding. This also differs from HIV, which actively replicates in CD4+ T Cells. However, it does seem like CoV-2 patients have reduced T-cells after recovery, and that reduced lymphocyte levels during infection are associated with greater risk of mortality from COVID-19.
It doesn't seem like there's any evidence in the literature for long-term lymphocytopenia in recovered SARS and MERS patients, but it's still too early make any strong conclusions about long-term effects from the current outbreak.

So, the T-Cell is susceptible, but not permissive?

Now 20 months later are there any newer results?


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Does animal based food contain molecules that behave like dietary fiber for humans?
I have read that dietary fiber is beneficial to human health in many ways, for example that it can help to reduce risk of colorectal cancer. However, when I look at nutrition labels on food it seems that only plant based food contains fiber; animal based food (meat) contains none.
What exactly is meant by fiber? I looked it up and found that there are actually a variety of definitions. The CODEX Alimentarius Commission has recently come up with an updated definition described in a paper by Jones. The definition states that “dietary fiber means carbohydrate (CHO) polymers with ten or more monomeric units, which are not hydrolyzed by the endogenous enzymes in the small intestine (SI) of humans”. Further more their definition "includes resistant oligosaccharides, resistant starch and resistant maltodextrins" when a footnote of the definition is included.
Jones points out that some definitions of dietary fiber do not explicitly rule out dietary fiber from animal sources. So does meat or animal based food contain any carbohydrate (CHO) polymers that are not hydrolyzed by the endogenous enzymes of the small intestine in humans?
An earlier version of this question was posted in my blog.

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). In particular, your question is based on an assumption — I suggest you find references that support that assumption, which will almost certainly lead you to an answer for this question. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. Thanks!

Definitely prior research needed.  For instance, why would digestibility by humans matter to microbes?  It would mean they would just have to get to (some of) the human-digestable stuff before the human uses it.  Also, I think the idea of dietary fiber is that it is not digested by either humans or gut microbes, and thus adds bulk to the stool,

Thanks @jamesqf for your feedback. I overhauled the question and provided a reference for my assumption. I focused only on the definition of dietary fiber, and left off the discussion about gut bacteria since that was just confusing things.


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Protein denaturation and edible toxins
As a protein denatured, it may lose its functions.
So theoretically if I heat some type of biological toxins like poisonous mushroom to 100 oC or higher temperature, will I able to eat it? (I know peoples still death after eat them even boiled to 100 oC, but why?)
Is there anyway to make them edible?
Update: i know some protein can survive in high temperature, for example: taq polymerase. Can i destroy it functions by boil it to higher temperature like 140-160 oC at higher atmosphere pressure and then return back to normal temperature?
Update2 : i found some information on the internet by searching keyword "toxin destroyed by heat" : http://aggie-horticulture.tamu.edu/food-technology/bacterial-food-poisoning/

The botulinum toxin is destroyed by boiling the food for 10 minutes.*
.
So it's depend on the type of protein, the heat and time.

So is there any way/formula to predict the temperature and time to destroy a protein? Or is there any absolute temperature and time to kill most type of protein ?

Why people still die after eat them even boiled to 100 oC, but why?

Well not all toxins are protein based. Some are just small molecules that fit into some vital protein in your body, causing  it to stop and death not long later. Some are cyclic peptides and are not denatured by heat. The peptide is simple, and has many carbon bonds to stablize its structure (it is a ring and has carbon bonds linking internally) https://en.wikipedia.org/wiki/%CE%91-amanitin

Or is there any absolute temperature and time to kill most type of protein ?

Autoclaving.. 134 °C (274 °F) for 18 minutes in a pressurized steam can destroy prions. And prions pretty tough. https://en.wikipedia.org/wiki/Prion

then you have things like amatoxin which is a tiny little ring protein so it is highly resistant to heat. It survives normal cooking just fine.

Prions are not alive. A prion is protein with a specific folding pattern. And when it meets another protein of the appropriate kind, it can cause the normal protein to be refolded into the pattern it has. In this way a prion propagates. It is not a protein replicating but a folding pattern that is spreading. And the folding pattern of a prion is very stable, perhaps the most stable folding patterns known to man. Because prior to the understanding of what prions were, autoclaving at 121 C, for 17 min steam was considered sufficient to denature and sterilize everything.


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Can I grow unlimited stem cells from limited embryonic stem cells?
If I theoretically extract a few embryonic stem cells from the embryo and cultured in vitro with enough nutrient to grow more cells. How many maximum of stem cells can I get?  Do I need to add any compound to inhibit the differentiation progress?

Culturing stem cells (especially embryonic ones) is very tricky - that's why its so hard to clone mammals. Without a lot of care your cells will not survive or differentiate for that matter.

@Nicolai hi! thank you for your reply. If you know anything about this, could you please tell me about the parameters? What do I need to take care? The temperature, nutrients or anything else? Since I'm an engineer, I will create a robot with several sensors to monitor them for me.

Like I said in my comment stem cell culture is a very difficult process, and while people have been doing research on this for about two decades there is still a lot we don't know about stem cells. Additionally working with (human) stem cells can cause a lot of ethic problems and is therefore under strict regulations in most countries.
In principle stem cells will continue to divide until they get a signal o differentiate. In normal embryo development some cells start producing these signals at different stages, and the complete interaction of different signals allows the formation of the organism.
In cell culture one has to make sure that exactly the right signals (which are mostly growth factors) are present in the culture medium, since stem cells can easily die if they do not get any signals.
I don't have any detailed experience or knowledge in working stem cells, but a quick literature search turned up these two papers, which should provide you a good starting point. There's likely a lot more research out there you can look for.

Hi! Thank you for those information. As a first glance at the article you provided and other information that I've found on the internet, it seems possible to grow a lot of stem cells. I still waiting for some answer from experienced researcher in stem cells to give me some more advice and information, thank you again!


text:
Join a linear plasmid just using a primer (without ligase enzyme)
Can I use just a primer and PCR to join the cutted plasmid like this ? without using any further enzyme like ligase.

After the linear dsDNA plasmid annealed into 2 ssDNA, primer will bind to middle. And Taq Polymerase will bind to the 3' and start extend the DNA to join the plasmid. So I don't need a ligase enzyme, is that possible?
Edit: I think the plasmid will be nicked at 2 position with this method but will this plasmid still work in e.coli cell?

Your diagram shows two single-stranded pieces of DNA that are annealed together to form two short regions of dsDNA, but in your description you mention linear dsDNA (which is not shown here).  Assuming that you intend to denature the linear dsDNA, and then add the shorter primer, then yes, adding a suitable DNA polymerase enzyme, proper buffer and reaction conditions, and dNTP substrates, will yield some relaxed (nicked) circular DNA molecules.  If there is a selectable marker on the plasmid then you should be able to transform competent E. coli cells.  NOTE: There is no PCR involved.

@mdperry In all protocol I found. They usually use some extra enzyme. For example Ligase, or exonuclease (Gibsom Assembly), or T4 polymerase. Is there anyway I can use only Taq Polymerase?

It is not clear to me which protocols you are referring to. T4 DNA ligase, Exonuclease (type unspecified), and T4 DNA polymerase are three distinctly different enzymes (and could not be substituted for each other).  The main difference between Taq polymerase and T4 polymerase is the temperature of the reaction.  So I think they can easily be substituted if you change the reaction temperature.  It is quite clear that a dsDNA plasmid does not need to be covalently closed in order to transform E. coli. The cells will repair the nicks after they take up the DNA.

@mdperry "The exonuclease activity of T4 phage DNA polymerase will create overhangs at the ends of your PCR product and within the homologous site of your destination vector, thus allowing your PCR product and vectors to anneal to create a final cloned piece of DNA" - I found it on "Method : Sequence and Ligase Independent Cloning (SLIC)".  I may though like you too but I can't find any evidence on the internet, so it still uncertainty to me.

Okay, yes, that is true, IF: you add T4 DNA polymerase IN THE ABSENCE OF dNTPs then there is a 3’ -> 5’ exonuclease activity that we used to use to turn a 3’-overhang into a blunt end.  As I recall, this is not a very processive activity, and difficult to control, but maybe there are newer applications I a, not aware of.  Anyway, you don’t need it for the picture you drew above.  What you described is if you have the same short sequence on both ends of the two blunt fragments (based on the quotation).

Anyway, bottom line: what are you afraid of? Just try it (denature, anneal, extend, transform).  You could even compare +/- ligase to see for yourself if it makes a difference.  What’s the big deal? Don’t you have somebody local to bounce your ideas off of?

@mdperry Thank you very much, May be I will try. I just want to know if someone tried it before so we can save time and cost for doing other things.


text:
Can proteins/peptides pass through the intestine?
I've heard somewhere said that :

Stomach cells do not absorb anything larger than single amino acids.

Is that wrong?
How do biological toxins (peptides/proteins) from mushroom or bacteria like Botulinum come to our blood and affect our body after we eat them?
Update: In fact, i want to know if we drink milk, is there anyway IGF-1 protein from milk can pass through the intestine and affect our body. Because I see some arguments/debates about the IGF protein in milk can cause acne.

Related (duplicate?): http://biology.stackexchange.com/questions/36050/how-does-botulinum-toxin-enter-the-blood-stream-from-the-digestive-tract

Entire proteins can be transported across the epithelial cells of the digestive system.https://en.wikipedia.org/wiki/Transcytosis
This is common in neonatal infants aiding in immunity passed via proteins in mother's milk. It is much less common as you age. http://www.vivo.colostate.edu/hbooks/pathphys/digestion/smallgut/absorb_aacids.html
The process is termed "transcytosis" if you wish to search for whether this occurs for a particular substance. One such goup of proteins entering the body in this manner are prions. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5004172/

And viruses can pass through epithelial cells in this manner.


text:
Does some form of self organizing map exist in the brain?
Self organizing maps (SOM's) are an extremely interesting and powerful tool in the field of artificial neural networks. My question is: Does something similar exist in the brain? Or are these systems completely "man made"?
Also, if there are such things in the brain, how do they work?

These are great questions.  The SOM was absolutely biologically inspired.  Sure, there are many examples.
Examples of self-organizing topographical feature maps in the human brain include the the sensory homunculus, retinotopic maps, and the entorhinal cortex.  There are even maps such as these in the midbrain auditory nucleus of the barn owl as well as the auditory cortex of the mustache bat.
As to how they work and organize in nature, that is still an active area of research, and it seems like there are no experimental conclusions that suggest the existence of  universal rules for self-organization of sensory maps in the brain.  As far as I know, however, Kohonen's theory that these maps organize via a combination of lateral inhibition and Hebbian learning has not yet been displaced by a more modern idea.