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Evolutionary Cell Structuring
I'm a total novice when it comes to biology, and I'm really just looking for an answer to a question that has been posed to me by people who deny evolution fervently.
Evolution dictates that we've gone from simple, single cell organisms to complex, multicellular organisms. If we consider the hand, for example, the hand is made up of various cells. Those cells are created according to DNA, which acts like a cell-level instruction manual.
Where are the "instructions" for where those cells go? I.e Where are the instructions that state that various cells have to line up in a thin, long, appendage structure to form a finger, or hand.
This isn't a particularly difficult question, I imagine. If it's been asked before, apologies. I don't know any of the technical terminology; this is just something that I would like to learn about.

I am afraid you would expect a simple answer but the subject is actually very broad. It is called Developmental biology or Ontogeny. This wikipedia article might give an introduction into this subject. Or maybe one wants to smake a summary this field. Or do you want specific details on the regulatory genes, signaling cascade, transcription factors, gradient of signaling molecule, mechanism of apoptosis and other things allowing to develop a hand?

Well, and I know this might be wildly ignorant, I was hoping for some sort of biological governing principle that will explain how cells behave in this way. If you could give me an answer to my question (even if it's complex, I'm pretty good at understanding stuff) that would be cool. I'm kind of just looking for an explanation of what happens to produce this effect (in this case, the hand).

Ok, I am not able to make this precise answer for the hand, but I'm sure someone will ;) I just wanted to give you the wikipedia links and to let you realize how this field is called and how big it is.

@ChrisCooney I would recommend the book "Endless forms most beautiful" by Sean B Carrol. I think it will give the best answer to your question in a simple, non technical language.

The main governing principle is very simple and one of the most elegant mechanisms in biology. It is based on concentration gradients.
Briefly, certain cells secrete signaling molecules (called morphogens) that are detected by other cells. These molecules then activate the transcription of genes in the target cells. Since the molecules in question are produced by a subset of cells, their concentration varies according to the distance between the receiving cell and the producing cells. Different concentrations of the signalling molecules have different effects and this allows the formation of really quite complex patterns.
This can be illustrated very well using Wolpert's classic French Flag Model:

So, different concentration thresholds of the morphogen result in different patterns of gene expression. This simple system can give extremely complex results (such as yourself, for example). It gets more complex when there are multiple morphogens acting in tandem. Say morphogen1 is produced by cells on the left and morphogen2 by cells on the right, cells in the middle will have varying concentrations of both morphogens and will react accordingly:

Just about every pattern formation during development boils down to differential concentrations of diffusing morphogen molecules, it really is a wonderful example of how simple systems can give rise to extremely complex results.

On an unrelated note, this has absolutely nothing to do with evolution. At least no more so than any other biological process. If your friends do not accept evolution, I don't see how they can use this as an argument. Even if a god created humanity in his or her image as these people tend to believe, babies are still born and they still develop in the womb. As far as I know, even the most fundamentalist Christians do not believe in a mechanic god that puts babies together in the womb from some kind of IKEA kit. Even if humans sprung fully formed from the hands of this god, individual infants are still formed out of multiple cells. There is therefore a need for a mechanism that can coordinate this process, whether this mechanism evolved or was designed is irrelevant, it is still there and extremely easily observable (images taken from here):

The image above shows the locations and concentrations of various morphogens in a fruit fly embryo. You can see the concentration gradients clearly.

Just to explicitly answer "Where are the instructions?", they are in the DNA of the cells (which tell them to secrete and respond to the morphogens that terdon speaks of).  [And note terdon's point that this is just from studying cells as they exist here and now, and not related to how the cells got here.]

Wow, thanks for the detailed answer. So, if I have understood this correctly; a single cell produces these Morphogens. Morphogens are chemicals that, depending on their concentration, cause varying behaviour in surrounding cells and causes the cells to change and form different patterns. Because of the huge variations in concentration, this allows for a huge range of patterns. Is it also these Morphogens that cause the cells to bind together in the way that forms "the hand"?

@ChrisCooney Well, it's not a single cell that produces the morphogens but various groups of cells. You might want to look up Spemann's organiser for example. The rest of your analysis is pretty much correct, as for binding, that's a different issue but that too will be affected by morphogens, yes. It is the morphogens' concentration that causes one group of cells to form an index finger and another to a pinky for example.


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I don't wash my hands and never get sick. Any theories?
I have only been sick a few times in my life(I'm 21 and probably 3-4 times) and even when I am sick I don't feel that bad and I am over it within a day or two. My family has always given me slack for never washing my hands but I see no point unless they physically look dirty. Unlike me though my family gets sick around the same amount as other people(a couple times a year).
I have this theory that since my body is always exposed to germs and other bacteria that it is stronger and able to fight off most colds before they ever happen. This theory obviously contradicts popular opinion and what doctors recommend but I have always felt fine not washing.
What do you guys think?

it's well known that exposure to germs at a low level improves the immune system, but not washing your hands also increases the risk of exposure to doses of germs large enough to cause sickness.

You may very well be strengthening your immune system, but there are microorganisms that you don't want to get, which can have longer term health consequences. For example, there seems to be a significant increase in developing MS if you've ever had the Epstein-Barr virus. But this is just one case. You also don't want Salmonella, tape worms, etc.
So there may be a price to pay for a stronger immune system: namely higher probability of exposing yourself to the more dangerous things out there.

That is a minor fear of mine but the way I see it a lot of these diseases/infections are spread many other ways than through just being picked up on your hand. eg breathing them in/eating them etc. In which case a stronger immune system would be beneficial in fighting things off that may have nothing to do with washing your hands.

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There aren't any animals like hornets that hunt large prey (like a rabbit, or even up to a deer), right? Why not?
There aren't any eusocial animals (hives of wasps, ants, termites, etc) that hunt large prey, are there?
I'm thinking prey in the size range of, say, a rabbit, or even a deer.
I can't see a rabbit or a deer having any real effective way to defend against a swarm of hornets, especially if you supposed that the hornets' venom could easily be adapted to be particularly effective against such prey.
Intuitively, this seems like it would be a lucrative little niche.
Like:

A swarm could bring down a kill without risking losing too many members.
The return seems like it could be very high.
There shouldn't be too much of a risk of losing much of the kill to scavengers or whatever.
And after starting down the evolutionary pathway into such a niche, they could easily develop methods of preserving meat (I'm imagining a horrifying hive full of natural ham, here).
Protecting this ham-hive wouldn't be any more difficult than protecting a honey-hive from bears etc.

And such a niche doesn't seem that evolutionarily distant from where hornets already are.
Like:

They already do seriously hurt or even kill large animals that they perceive as threatening their hive.
They already do scavenge large animals they find dead, and even steal the occasional chunk of flesh from living animals.

But as far as I know, nothing like this exists, right?
Why not?
(And, like... maybe the most important question: How can we make sure it never comes into existence?)

Army ants regularly kill and eat birds (although they primarily hunt insects). Dorylus, or siafu ants consume rats and are considered a menace to humans with restricted mobility. And [invasive] bees do kill humans although we are not prey.

@Luigi Yeah, that kind of stuff is essentially what I meant about them already being pretty close to that niche. That is, those are examples of eusocial insects with behaviors on the edge of the "ham-hornet"-like niche. My question is, why haven't any species fallen right smack-dab into the middle of it? Ya know what I mean?

I wonder whether hornets &c can effectively sting through fur?  Then there's the sheer number of stings that it would take to kill a non-allergic animal.

@jamesqf In case you think sting victims who die only die of allergy reaction (anaphylactic shock), some species of hornets actually have a sting that contains neurotoxins, and some can cause kidney failure. E.g.: the Asian giant hornet

They're not fast enough
A hornet has a top speed of around 40 kph, while a rabbit is only a touch faster, a deer can hit 75 kph (all figures from Wikipedia). In order to act as hunting insects they need to match the speed of these large animals in large enough numbers to surround and overpower them but these animals could easily match their speed or outpace them. Let's suppose they can overcome that limitation somehow and bring the prey down. They've now bagged a big lump of protein but it's a long way from the hive because they've had to chase it down first. That means that a long round trip is required every time they visit the kill and thus reduces the energy yield as well as increasing the chance of losing it to scavengers.
Against this you have the simpler option of eating smaller, easier to catch, prey as they do now.

Alright, that's the first idea that feels like a potentially satisfying answer, thanks! :D So in order to wander into this niche, they'd need to at least start by hunting animals that can't accelerate away as quickly, but those seem like they'd be less common (so it'd be less lucrative) and/or much more massive (so they'd need to also happen to have stronger venom). Of course, it might also work if the hornets were able to sneak up and surprise animals, but those kind of stalking behaviors are complex and not very close to their current behaviors...

Alright, yeah, I'm starting to feel like I'm getting a sense of the kind of barriers that prevent a species from simply wandering into this "ham-hornet" niche. Thanks again! :D Think I should mark this as accepted? Do you have any other ideas to add?

Like, to be clear, I'm not convinced this is definitely the reason, and I still overall feel like I should be surprised that ham-hornets don't exist. It's not intuitively obvious to me that the net number of calories transported back to the hive per hornet per meter flown would be lower than that for honey bees. But your answer at least starts to suggest models you could actually test!

Moreover they have to masticate the prey to feed the larvae. It would not be feasible with big animals.

@Owen_R: The comparison between honey bees and hornets is moot; the comparison which is evolutionarily relevant is to investing their energy in hunting small prey as they do now. In order to start hunting large prey they need to get a benefit from ineffectually hunting these prey since they have not yet adapted to do it well.

While it is true that rabbits and deers run faster than hornets can fly, I'm not entirely convinced that speed is really a problem. All the hypothetical hornets/wasps need to do is to gather around the rabbit without disturbing the rabbit, and then go all in at the same time, before the rabbit has time to react.

@Kal: Do you really think that a swarm of hornets would be undetectable to a rabbit? Remember, as well, that even if this strategy would work first it has to evolve and for that you need to have functional, beneficial, intermediate steps - what do you think they could be?

I'd argue that it's not so much they aren't fast enough movers, more that they are not fast enough killers. The note below about the army ants killing a worm... that's a worm, not known for its ability to sprint, and it got 3m or about 10ft. They then butchered it in situ, rather than carrying it back in one piece.
For a flying hunter, you have better range, but still... I suspect that most large animals, being attacked by killer bees, will run away far further than is feasible to recover their flesh, and will also do what they can to harm the bees, rolling etc. Sounds maladaptive.

Why not the turquoise?

@JackAidley It's actually quite possible for the wasps to swarm and remain undetectable to a rabbit. The rabbit's hearing range is about 360 Hz to 42 kHz. Meanwhile, wasps beat their wings at around 200 Hz, so the sound of their flight would probably be undetectable to the rabbit. As far as sight goes, wasps are small and they can easily hide in foliage. Behaviour-wise, wasps and bees are known to have already evolved coordinated attacks against intruders, so it shouldn't be hard to evolve into a hunting strategy as long as there is an actual advantage.

They do exist. Many such examples can be found. Such as the most terrifying one, being social groups formed by Spiders, Anelosimus eximius documented here.
Colonies of upto 9000 individuals have been documented by the scientists in their report.
Also let's not forget Piranhas, another group of social animals, which take down much larger prey due to their larger colony size.
This particular phenomenon is concisely explained in this article in wikipedia under Cooperative Hunting
As the models explain and I also think the same, that the only reason a social aggregation would seem necessary to any animal is because it provides increased fitness or survival. This particular phenomenon can be viewed from the perspective of Human society as well. I given an income source X, would always choose to rent a private space for myself. If my income does not allow me such an option my best option is to cooperate with another in a shared system.
So the same can be said for Insects if availability of prey which can be candidates of solo hunting goes down, the only option left for the species to survive is to either compete if that is the only available source of food, or if larger prey is available for group hunting where individuals don't come into direct conflict, then to go for the option which provides the greatest fitness to the species as a whole. Obviously, in such a case you go for aggregation and not competition such as those seen in ant colonies.
Many more such systems exist I am sure, but I am no evolutionary biologist only a humble genomics guy. They will be able to provide much more comprehensive answers.

Well, that's interesting, but it seems like kinda a non-sequitur to my question. Eusocial insects seem like they'd be really effective in a niche focused around cooperative hunting, especially if they bring down prey hundreds or thousands of times more massive than an individual member of the swarm, and then store the meat in their hive. But apparently they don't do that. My question is, why not? These spiders aren't eusocial, and they're not cooperating to catch prey that much more massive than the individual spider.

I would disagree on the point of eusociality as this study states http://rd.springer.com/article/10.1007%2FBF00300005. Can they bring down something which is a hundred or thousands to times larger than them? No I do not think so, but as the investigative group notes in the answer, they do not really catch the same number of prey. Rather, they catch a much smaller number of prey of increased biomass culminating ultimately towards more biomass per spider than they would have gotten individually.

Hmmm... still, I think my question could basically be summed up as: "Why don't ham-hornets exist?" Do you think the case of these spiders really seems like the same thing I was asking about? Or does it just seem similar in a few factors?

I mean, it's definitely not the answer: "Yes, actually, ham-hornets do exist", so how does it help to shed light on the question of why they don't?

It is similar in the fact that the creatures are as eusocial as a non-eusocial species can get. This species being the most social ones among spiders, an organism generally considered as a solitary animal. But to answer the question why don't they hoard food? I would have to say that because the needs of the few outweight the amount of food available. A leopard will never get caught in the web, it will generally be smaller animals which the entire colony can devour.

But as far as hoarding goes, this article documents hoarding in spiders

Hm, yeah, everyone knows that the stereotypical individual spider "wraps up flies for later", even. But still, do you really think this is actually a direct answer to my question? Or just interesting, potentially related information? It makes sense to me as the latter, but not the former.

While piranhas can take down very large prey, such as cattle, that is not their ordinary behavior by far, and actually quite unusual. Attacks on large animals and humans are typically non-fatal, with some nips and bites taken, but the victim usually can escape. Fatal attacks occur with children, impaired or disabled adults (such as drunkenness), and at the peak of the dry season when water levels are very low and food is scarce. Studies have actually shown that they are rather timid fish, using their teeth primarily for defense.

Your giant spider colony example completely misses the point. Yes, they exist in large colonies, and larger webs can catch somewhat larger prey "several times their body size" (from your link), but they do not hunt much larger species like the OP is looking for. I don't think s/he doubts cooperative hunting exists, they're just looking for examples of individual predators being orders of magnitude smaller than their intended prey.

Unfortunately for you, such animals do exist (O'Donnell et al. 2005).
This is a direct field observation of a swarm of army ants attacking and consuming a 60cm long earthworm, as well as consuming a 10cm long snake.
From the linked article:

We collected workers from two Cheliomyrmex andicola foraging raids.
  During raid 1 on 26 September 2003 at 1030 h, we encountered a large
  C. andicola raid column in primary terra firme forest, exiting from soil-covered foraging trails that the ants had constructed on a slope.
  The sky was clear, and ground surface temperature was 25.9°C. Beneath
  the raised tunnel of soil particles that the ants had constructed, we
  found the partially consumed carcass of a snake (1 cm in diameter and
  10 cm long). Most of the snake's scales and skin had been removed.
  Cheliomyrmex andicola workers were observed chewing on the snake and carrying away bits of flesh in their mandibles. As we dug near the
  carcass, the ant workers responded by biting and stinging our hands.
  The workers clung to our skin, and we noted that their stings were
  more painful than those of other army ants from the site (e.g.,
  Eciton burchellii and Eciton hamatum). We collected ant workers and samples of snake flesh into 70 percent ethanol. During raid 2 on 1
  October 2003 at 1205 h, during a brief rain shower, our attention was
  drawn by rustling sounds in the leaf litter on a slope in a partially
  cleared area of terra firme forest adjacent to the station buildings.
  A subterranean column of C. andicola workers erupted from the soil
  in pursuit of a fleeing giant earthworm (possibly a species in the
  genus Martiodrilus: Zicsi 1990). Several hundred ant workers emerged
  from the soil and ran over the leaf litter in the direction taken by
  the worm. Five C. andicola workers mounted the worm and were biting
  and apparently stinging its body. After the worm crawled for a
  distance of 3 m down slope from where it exited the soil, its body
  contracted from over 40 cm in length to approximately 20 cm in length.
  The worm abruptly stopped moving and became rigid on the soil surface
  within 10 sec of exiting the soil, and was then unresponsive to human
  touch. We assumed that the worm was either paralyzed or dead. We
  lifted the worm to examine it, and we collected ant workers from its
  body and from the raid column as it arrived where the worm came to
  rest. Workers collected from both raids had no prey (other than snake
  flesh at raid 1) in their mandibles.

However, most army ants are (fortunately) not predators of large animals. This appeared to be the only unambiguous literature reference of predation of large animals by eusocial insects that I could find in a brief literature search.

Sigh. Okay yeah, that sounds like what I was expecting. No hornet ham-hives, though? I guess the obvious follow-up question is: How can we kill them all? I guess we should really just migrate into space and then nuke the entire horrible planet to be sure.... Do we have enough nukes? Do we need more nukes? Maybe we could just fling it into the sun, to be sure...

@Owen_R Actually, despite the fact that they can prey on animals much larger than themselves, many army ants are themselves preyed upon. For example, driver ants are often eaten by chimpanzees

That joking aside, though, I still feel like it should be surprising that this isn't a more prevalent strategy. The lack of ham-hornets seems like it needs an explanation, ya know?

Also, I find myself focusing in more and more now on this idea of "ham-hornets", and I think there are actually good theoretical reasons to focus on it. Flying hornets would be particularly effective at attacking a rabbit~deer, since they can attack from all directions and are so individually manoeuvrable. That is, it's a lot easier to imagine escaping from a swarm of ants crawling up your leg than a swarm of hornets flying all around you. So it seems like it should be additionally surprising that we have reports of ants acting like that but not hornets. What might be preventing ham-hornets?

Army ants have been reported to kill and butcher animals that were unable to get away - babies in cradles, tied up goats, etc. Speed of killing really does seem to be the issue here.
Japanese tiger hornets are huge, have a potent venom, and inject a lot of it, which kills dozens of humans every year... eventually. But because it's slow-acting, they don't use their sting for hunting, just for defense. For hunting, they use their mandibles, and bite the heads off stuff.
Some hunter wasps can paralyze smaller prey, which would give more time for killing, but they can't paralyze anything big.

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What is the distribution of the number of heterozygotes in finite populations?
Consider a bi-allelic locus with alleles A and a. We denote the frequency of the A allele by $p$. Assuming absence of selection and panmixia, the expected number of heterozygotes is $2p(1-p)N$, where $N$ is the population size. We can also calculate the expected number of AA and aa individuals.
What is the joint probability distribution of the number of AA, Aa and aa individuals?

The distribution would be binomial.

Thank you. I developed my question a little bit to improve it. I am looking for the joint distribution for each possible genotype. Probably some joint binomial distribution. If you know the answer, please make it an answer.

It is a multinomial (trinomial) distribution with $N$ trials, $p_{AA}=p^2$, $p_{Aa}=2p(1-p)$, and $p_{aa}=(1-p)^2$. The probability to get exactly $n_{AA}$ AA genotypes, $n_{Aa}$ Aa genotypes and $n_{aa}=N-n_{AA}-n_{Aa}$ aa genotypes is
$$P\left(N_{AA} = n_{AA}, N_{Aa} = n_{Aa}\right) = \frac{N!}{n_{AA}!n_{Aa}!n_{aa}!}p^{2n_{AA}}\left(2p(1-p)\right)^{n_{Aa}}(1-p)^{2n_{aa}}.$$

Thank you! I edited your answer to write out the actual distribution (let me know if I made a mistake). +1


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Mathematical periodic turns in DNA
Today our college professor gave us a mathematical biological challenge in DNA. He challenged us to find the pattern in which DNA follows the following equation in its periodic turn. How can we crack this? Also,  forgive me if I have gone against community guidelines; it’s my first time posting a question.
Here is the equation:
$$2 \sum_{n=0}^\infty \frac{(-1)^n}{(2n+1)^2}$$

Welcome to Biology StackExchange! Can you please elaborate more on the context of your question? What is the overall topic in which you've encountered this expression? Was it DNA sequencing, X-ray crystallography ...? What is a "periodic turn in DNA"?

A hint is that you don't have an equation, you have an expression. So you could rephrase your question as, what does this expression equal to, in the context of DNA structural biology? (I say it's a hint but to be clear; I haven't figured out the answer. Is it actually related to sequencing as you tag?)

My personal opinion is that we'd need a bit more context for this to be on-topic here; we're not after solving riddles and puzzles but about understanding biology. So, if you want to understand why a particular expression is used in some particular biological context, that would be very much on topic.

Thank you, @Domen, The topic at the instance was DNA sequencing; that is why I tagged DNA- sequencing, though the challenge is out of unit course work, as the college professor indicated. It is an expression. I have rephrased the question to English as a secondary language. At that instance, he described how a mathematical transformation can describe the turn from a set of base pair nucleotides to another and inverse periodically; he talked about a sinusoidal wave pattern as an example; he wrote the expression.

I would start by plotting the expression as a function of n if you don't have an intrinsic intuition of what it would look like. Then I'd check your language and terminology carefully, it seems like a lot is being lost in the translation. Phrases I'd check carefully would include "in its periodic turn" and "DNA follows".

If it's of any help $(-1)^n$ will flip-flop between $+1$ and $-1$. Is there anything in DNA that cycles back and forth like that? $-1 \leq \sin \theta \leq +1$. The denominator has $2n + 1$ which always evaluates to an odd number. The first term in the series is $1$. The second is $-1/9$. The third is $1/25$. The fourth is $-1/49$. We're, it seems, converging to "something".

To anyone wondering, the value of the expression is $2K\approx 1.832$, where $K$ is the Catalan's constant.

@Domen, while researching the Catalan’s constant I found out that it is used in calculating of volume of the complement of the Borromean rings. where else physical instances of the Borromean rings have been made from linked DNA molecules.

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What effect does L-cysteine have in a growth medium on Lactobacillus and Bombilactobacillus found in bee species?
To cultivate Lactobacillus and Bombilactobacillus species we used MRS supplemented with 2% fructose in both aerobic and anaerobic conditions and also MRS supplemented with 2% fructose and 0.1% L-cysteine. The second medium showed significantly better growth in both conditions therefore we attributed this effect to L-cysteine. Could anyone explain why exactly this would have made a difference?

Welcome to the Biology Stack Exchange. Please take the [tour] and visit the [help] for more information on this site. Please also note the homework requirement, as this question sounds very much like easily answerable homework.

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Understanding DNA Fingerprinting
I am a high-school student learning about DNA fingerprinting. I know that satellite DNA is non-coding DNA and has a lot of repetitive sequences, and the length of each repeat can be either short or small.
The procedure of carrying out DNA fingerprinting I was reading about says that after doing gel electrophoresis, we hybridize the DNA fragments with VNTR probes and then we can identify the DNA.
My question is that how do I have the VNTR probe sequence ready from before?
What I thought is that all of us have the same SEQUENCE of the repeating DNA but the only thing that differs is the number of continuous repeats due to mutations. Am I thinking right?
So I am saying that me and the person reading this question have repetitive DNA with same sequence say (AGGTTCC) but the thing that differs is the number of continuous repeats. And in the lab, we have the radioactive probe (TCCAAGG) ready which we can hybridize and then check.

I have tidied your question up a bit — having "question" in the title is clearly redundant on a Q&A site, and if you come onto a site for students and professionals of biology it's rude to "shout" that you are only a high-school student. However there were two points I couldn't deal with because they didn't make sense to me. What do you mean by "How do I have the VNTR probe sequence ready from before?" ? This isn't English and I honestly can't guess what it's supposed to mean. And what does continuous mean in "continuous repeats"? If they repeat they must be separate, not continuous.

On this site you do not make statements like “if you don’t understand it’s not my problem”. They are considered unfriendly and condescending and I would normally flag to the moderators to remove them. However it IS your problem because you are the poster and your message is unclear to me, and being a molecular biologist of some standing I know that if I don’t understand you half the people reading this message will not. Try googling “continuous  repeats”. You won’t find anything because it is not a term that is used. “Tandem repeat” is.

Please refrain from using harsh language; our central theme here is 'be nice'; such language doesn't fit here and can result in a site ban.

Several things going on here. Briefly, yes, you are thinking right about what a VNTR is but there are several small points of clarification.

VNTRs are not satellites in the normal sense as they are quite short sequences and satellites are usually longer. Many such "microsatellite" or "short tandem repeat" (STR) sequences can be in genes and expressed into proteins.
The preferred method these days for fingerprinting would not be probing with radioactive probes (Southern blot) but rather PCR. PCR or similar lets you visually discriminate between alleles on a gel, and determine their lengths based on making many copies of a small DNA region. It works by leveraging the constant non-VNTR sequences immediately flanking the VNTR. It's much easier and less radioactive. See this illustrative figure from wikipedia:

You then don't need any such probe. PCR is much more quantitative than trying to hybridize a probe against the repeat unit and guess copy number. I am actually not sure how the probing approach that you suggest would work, you would probably instead probe a nearby non-repetitive sequence and see how different its size is on the gel (which would change based on VNTR copy number).

Actually our syllabus only includes a very minimal portion of basics of DNA fingerprinting (just definitions of satellite DNA and probes and all), that's why I was trying to understand that, using PCR to do it is also interesting, anyway i just needed a basic understanding of its working and as you said i was thinking correctly, i am clear now


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How to download transcripts with certain words in description in the ENSEMBL. description?
I want to download all human tumor transcripts (in FASTA and GTF format) in ENSEMBL and I have a skim on Customize your download and Fetch data programmatically, but none of them mentioned how to download the transcripts when the keyword appeared in description.
It seems that I have to obtain all the transcript_id so that I can get the transcripts. What if, how I achieve these id?

This doesn't seem to be a biology question, but an administrative one. Shouldn't you be contacting customer services at ensembl.org?


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Production of plant derivatives using genetic engineered micro-organisms
I saw a Thought Emporium video where spider silk was produced by genetically modifying yeast. I have also read about companies making vanillin (vanilla flavour) using this technique.
I am curious to know if plant derivatives like saffron (or its flavour), rubber, or even substances like quinine, tetrahydrocannabinol and cocaine, can also be produced by this same technique. From the information I have found, it seems that some plant derivatives are being manufactured in genetic engineered micro-organisms, but most are not.
Some of these derivatives are very expensive, so I would imagine such techniques could be used to mass-produce them more cheaply. If so, what is stopping industry from doing it? If not, what is the problem?

@tyersome While this question is high-level, I think it's entirely reasonable and readily answerable.

Are you asking what we can theoretically do or what is we can currently capable of?

@tyersome I have very little knowledge of advanced biology and I come from an electrical engineering background. So to 'show an attempt' or to research would mean reading all the basic biology books, which defeats the purpose of having a site like stackexchange.

@John I am mainly concerned about what we are capable of today.

@electronikor You don't need an advanced degree in biology to show you have researched a question before asking it here. The model here is to help people who have shown prior effort at understanding a relevant question - the purpose of SE.biology isn't to spoon-feed people who don't fancy spending time researching a question for themselves.

@user438383 'Research' is a broad term and what qualifies as 'prior research' and what isnt is some esoteric subjective knowledge that only the mods can lay claim to. Also, I would like to point out I have put in enough prior effort to search and even reach out to some PhD scholar on twitter and I didn't get convincing answers anywhere. It would be helpful if the terms could also mention the procedure to 'show' this prior effort. Perhaps attach screenshots of all the searches and results?

@electronikor if you've done your prior research then that's great - just say what you did in the original question (i.e. - I read these papers / articles / asked these people / did whatever and still couldn't find the answer). You don't have to write a whole essay detailing everything you did, but just show enough to signal to the community that you have spent some time trying to find an answer before posting and you'll find people here are very receptive.

@jakebeal — The question is vague and as written the answer is "yes", but that is trivial. The OP has "no knowledge of biology or genetics" and so is unlikely to be able to understand your (or any) non-trivial answer without taking the time to gain some background. If they take that time, the answer should become obvious — if they don't I expect that your answer is wasted effort. ——— That being said, since you spent the time to write a good answer maybe you could edit the OP's post so that it is a good question for this site?

@tyersome I've attempted some minor cleanup and improvement; I actually found it a pretty cogent question to begin with.

@jakebeal thanks a lot!

General Considerations
The question asks specifically why certain plant products are not produced commercially in genetically modified micro-organisms. There are some general reasons, illustrated in some of the examples mentioned:

The product is actually a complex mixture, rather than a single compound. This is the case for saffron, preparations of which contain protein, fat, fibre, sugars and gums, in addition to the the bioactive components — thought to be crocin, crocetin, picrocrocin and safranal (see this review).
It is much easier and cheaper to obtain the product by growing the plant. Although saffron is expensive because it is obtained by hand from crocus blossoms, other plant products do not have this problem, e.g. cotton, mentioned in another answer.
The overall market may not justify the effort. Ignoring other considerations the worldwide consumption of saffron, for example, is small, whereas that for vanillin is huge.
Highly developed chemical production methods may already exist. This is the case for rubber, the chemical production of varieties of which was stimulated by the development of tyred vehicles, and subsequently by war-time demands. Natural rubber is actually a mixed polymer, and specific polymers have been used to develop types of synthetic rubber with individual desirable properties.

Production of Secondary Metabolites
The question mentions “quinine, tetrahydrocannabinol and cocaine” — specific secondary metabolites of plant metabolism which may be of value in medicine, but the complex structure of which renders them difficult to synthesize chemically, much less on a commercial scale. This seems the most pertinent area to consider, especially as the question mentions the successful production in bacteria of another secondary metabolite, vanillin.
I shall take a single example of the successful synthesis in yeast of a pair of secondary metabolites — tropane alkaloids — hyoscyamine and scopolamine. These two compounds (hyoscyamine is shown) have much more complex structures than vanillin:

This is reflected in the fact that their synthesis entails 26 enzymes, compared to the 15 use in the engineered synthesis of vanillin. The synthesis of these more complex secondary metabolites illustrates some problems encountered in the production of such compounds from plant genes cloned into micro-organisms not encountered with vanillin, and not fully covered in other answers thus far:

Identifying the genes for all the enzymes involved in a uncommon biosynthetic pathway
Modularizating the pathway between different organelles to mimic the separation that occurs in plants
Maintaining concentrations of precursors and intermediates that might be removed by the yeast cell’s own metabolism

The example to be described was published in an article in Nature in 2020 by Srinivasan and Smolke, and reports the synthesis of the medicinal alkaloids hyoscyamine and scopolamine starting from simple sugars and amino acids. These compounds occurs in plants of the families nightshade (Solanaceae), coca (Erythroxylaceae) and bindweed (Convolvulaceae), and currently they are produced commercially by extraction from crops grown in tropical and sub-tropical countries.
Identifying the Genes
In many biosynthetic pathways the genes responsible for individual steps can be identified by homology of the predicted protein products to those of known genes. In addition, the genes for biosynthetic pathways are often clustered. However, plants which produce useful products may be relatively obscure and their genomes poorly characterized. In the case of the synthesis of hyoscyamine in the nightshades, Solanaceae, the enzyme responsible for catalysing the final step of the 26 step pathway was unknown. Srinivasan and Smolke had to identify candidate genes from gene-expression patterns under different conditions and then, for the 12 candidates identified, express their gene products and assay for the required hyoscyamine dehydrogenase that catalyses this step.
Modularizing the Pathway
In plants the synthetic pathway does not take place in a single location, but is compartmented between different organelles and, indeed, different tissues. The latter is, of course, not possible in yeast, but was mimicked by directing the products of these 26 genes to six different subcellular locations by engineering appropriate targeting signals onto them. These were the cytosolic fluid, the mitochondrion, the peroxisome, the vacuole, the endoplasmic reticulum, and the vacuolar membranes. This is one reason why yeast rather than bacteria (which lack subcellular organelles) were used in this work.

The purpose of this is explained in a Nature News & Views piece from which the diagram above is taken:

“Subcellular compartmentalization of enzymes can improve product
biosynthesis by enabling proper enzymatic activity and isolating
metabolic intermediates to reduce their toxicity and loss to competing
pathways. By restricting space, compartmentalization also increases
local interactions between the enzymes and their targets. …so each
step can be separately optimized to maximize productivity.”

Maintaining concentrations of precursors and intermediates
Expression (in fact over-expression) of the enzymes of a pathway is not enough to ensure adequate production of the end-product. The precursors for the pathway (here glucose and phenylalanine) must be continually available at a suitable concentration, and reactions which consume key intermediates must be supressed. To this end eight other genes were disrupted in the work in question.
Coda
The example described is a major tour de force, showing the power of recombinant molecular genetics to express genes in micro-organisms for production of secondary metabolites. Possible it is, but routine it certainly is not. In addition to overcoming the types of problems described, there remains the task of obtaining an efficiency of production that it commercially viable. The authors of this work write:

“Process improvements to increase productivities from titres reported
here (around 30 to 80 μg per litre)… to commercial production
(approximately 5 g per litre)…we anticipate would take 1–2 years of
focused effort by a professional team.”

In principle, any biological product should be able to be developed through microbial synthesis, with the appropriate choice of chassis. Indeed, this was the goal of the DARPA "1000 Molecules" program, which did indeed demonstrate it was possible to rapidly engineer new pathways for production of new biomolecules.
In practice, however, some products are far more difficult to achieve than others.
A (very) rough sorting from easiest to hardest:

Small-molecule chemicals that are "near" to an existing metabolite already being produced by the organism, requiring only small number of modifications to the organism.
Proteins, polymers, and small molecules requiring more extensive or difficult synthesis
Materials with a homogeneous structure
Materials with a highly heterogeneous structure

Basically, the more you have to manipulate the cells, the harder it is, and if you need the cells to coordinate with each other to make a material it gets much harder yet. Even some simple everyday materials, such as cotton, are actually fantastically complex and would be extremely difficult to synthetically generate, since even a single cotton fiber has a carefully controlled multilayer structure far larger than any microbe.
Finally, just because something can be produced doesn't mean it will be produced efficiently. Getting from a proof-of-principle to something that operated effectively at industrial scale is a massive challenge, and while this is likely to become easier in the future we just aren't there yet.
Something to keep an eye on, however, is BioMADE, a major government funded venture just kicking off with the aim of making such production much more feasible.
In short: in the near term, expect to see mostly high-value products with relatively simple routes to synthesis, but over the long term a much broader range of materials can in principle be produced.

Thanks a lot.Its a very lucid answer. I was mainly awestruck by The Thought Emporium's video on making spider silk with yeast. I thought if something that is produced by a complex organism like a spider can be made by yeast modification. Then why not something the ester(s) that gives saffron its fragrance?

@electronikor It's a good thought; it just happens that some things, like silk, happen to be much more accessible than others due to the nature of the substance being fabricated.

@electronikor  — saffron is not a good example as it is a mixture of substances, the bioactive components of which are thought to be crocin, crocetin, picrocrocin and safranal, although the preparations used contain protein, fat, fibre, sugars and gums. The synthesis of the bioactive components is hardly likely to be the limiting factor in the lack of a replacement for preparation of saffron from flowers.

Not all can be produced.
Getting the correct glycosylation on proteins hasn't been systematically worked out. For example, to make human-compatible antibodies.
Many of the proteins are modified by multiple enzymes after production - this could require massive amounts of research to replicate.
Some biological products are just unknown mixtures.

Is glycosylation an issue for any current plant products?

@jakebeal — the compartmentalization of the steps of secondary metabolism in the example I consider in my answer suggests it, or some other post-translational modification, might be, but I have not researched the details. The case of human-compatible antibodies is, of course, irrelevant to the question which asks about products of plant metabolism.


text:
Is there a family equivalent to "congener"?
Is there an equivalent word to "congener" but for species in the same family (family in the sense of the taxonomic rank)?
"confamer"? "confamiler"???
I know I can just say "species X and other taxa in the same family" but I thought a nice one-worder would be better if anybody uses such a word.

Confamilial is the term for same family, it has even been used in print.

Congenerics were twice as likely to fight as conspecifics, and confamilial competitors were three times as likely to fight as conspecifics.

I just found "confamilial" as well in a different paper.


text:
Why is mRNA needed in the Protein translation?
The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't there be a similar chemical molecule like tRNA which can directly read from DNA and exclude the mRNA intermediate. Also is the current translation process optimal in the sense that can there be a system which does not need mRNA or a similar intermediate altogether. Or is the presence of an intermediate a necessary requirement.

Although this does not directly answer the question, I think you could take the inverse point of view and rather ask why/when is DNA needed for the replication of an organism.

One reason is that an intermediate like mRNA allows for higher amounts of protein expression. You can have multiple mRNA molecules that are translated simultaneously. If you read directly from DNA you can have at most two translations in parallel.
I'm not sure about this, but I would imagine that having to unwind the DNA double strand every time for translation could be a drawback to directly reading from DNA as well. The mRNA is also subject to various forms of regulation, which might be an advantage as well for the added intermediary.

Beat me by 15 seconds because I thought I could find more references.

"If you read directly from DNA you can have at most two translations in parallel." - upvoted, but this is not true, you can have many parallel translation in series right after each other in one or many codon distance - depending on the space necessary between them. I think a more accurate explanation, that accessibility would limit the translation speed.

Is there data on how fast translation and transcription happen? If translation is slower than transcription (which it might be due to the larger tRNAs diffusing more slowly, having 20 amino acids vs 4 nucleotides, etc), then there would probably be an advantage to quickly transcribe the mRNA from DNA, then pass the mRNA on to ribosomes for the slower translation. Might still be able to do multiple transcriptions at once like inf3rno mentions.

@inf3rno I was thinking about including the fact that multiple ribosomes can read the same mRNA at the same time, but decided to skip that to avoid making it more complicated than necessary. And one codon distance is certainly not possible, the ribosome is quite large.

@user137 you can perform many translations from a single mRNA. So you don't need to transcribe the DNA into mRNA as often as you translate the mRNA into protein.

@MadScientist Right, but there might still be a speed difference between the two, and I suspect translation is the slower one, even if it doesn't need to be. I might be wrong, transcribing a gene of length N needs N ribonucleotides, while translating that mRNA only needs at most N/3 amino acids (splicing out introns would reduce the length, untranslated regions don't need amino acids, etc) so that the reduced material cost compensates for slower speed.

I don't have a lot of references for this, but it's too long for a comment.
Separating the roles of RNA and DNA helps to better control protein production and gene replication. If ribosomes worked directly on DNA, it would probably be very hard to replicate that DNA, as the DNA polymerases would collide with the ribosomes. You'd have to stop protein production and move the ribosomes out of the way before you could copy the DNA. Keeping mRNA separate allows the ribosomes to keep making protein while the DNA is being replicated.
However, transcription of DNA would be similar, where the DNA replication could collide with the transcription machinery. I can't find anything about that situation so I don't know how its regulated or how often it happens.
Additionally, having mRNA allows amplification and further regulation. Every mRNA copy can make several protein copies, so the amount of protein produced from a single round of transcription can be higher than if the DNA were read directly by a ribosome. mRNA also has many binding sites for miRNA and other regulatory RNAs. If DNA were read directly, that wouldn't be possible.
There are also some cases where mRNA is stored and used later, such as immediately after fertilization, or in platelets and erythrocytes where translation can happen even after transcription stops due to loss of the nucleus.

In lay man terms you need your DNA to remain intact and protected. so instead of shipping it to the cytoplasm where a lot can happen to it, the cell makes an intermediate mRNA. if anything does wrong with mRNA, the cell can discard it and make another copy and after translation the copy of mRNA is also discarded.You also have the amplification; instead of making one protein from one gene on a DNA strand, and then one more and the another, we can just make a bunch of copies of mRNA and send them to the nucleus where we can make as many proteins as we need. by doing this there is minimal manipulation of the original DNA strand and the cell get a lot of product over a short period.

"instead of shipping it to the cytoplasm where a lot can happen to it"..... Doesn't apply in case of prokaryotes

yes thanks for that i was mainly focusing on eukaryotes


text:
Confusion regarding the meaning of the coding strand of DNA

I am having problems getting the ‘correct’ answer for the above question.
I am assuming that mRNA uses the template strand (not the coding strand) for protein synthesis. So:
         ---------[DNA]  -  [mRNA]  - [Amino Acid]

Original A T A -> U A U -> tyrosine
Mutated  T C T -> A G A -> Arginine
What is my mistake?

Welcome to the site. Please visit the [help] and take a [tour]. One of the requirements for questions on this site is that they demonstrate that they have done the research to look for the answer themselves. Think about what the question is asking and what the word coding means...

Look up "coding strand" in wikipedia.

The problem here is the misleading nature of the term “coding strand”.
I have previously posted on this topic making the point that mRNA — which is what the genetic code relates to — should be the basis of nomenclature, and that the best and least ambiguous terminology is sense (the way the code is read from the mRNA) and antisense (its reverse complement). To quote myself:

The idea seems to me clear that when you read the string of codons
that encode the amino acid sequence from this strand they ‘make
sense’. (Anti-sense is used in preference to non-sense, as ‘nonsense’
was the term used historically for mutations that converted amino acid
codons into stop codons.) It can also be extended to non-protein
coding genes (e.g. for tRNA), where ‘sense’ correlates with the
sequence of the gene product.

Thus, if you consider the two strands of DNA, the one that is transcribed by RNA polymerase into DNA is the anti-sense strand, and the other (which is the one humans may read after a DNA sequencing experiment) is the sense strand.
My main objection to the use of coding and non-coding for DNA strands (apart from logic — how does one code and the other not?) is ambiguity:

As the anti-sense strand is the template for RNA polymerase, one might
make the mental association between this and ‘coding’, whereas it is
the sense strand that is meant [by coding] in this (admittedly common) usage.

So in my opinion the question is to blame, although this is very common. But, to answer the question, one presumably should assume that the strand with the asterisk is the sense strand, and any changes in it are reflected directly (apart from T to U) in the mRNA.
Footnote
It is ironic that the genetic code provided in this question is unlikely to be correct, although the organism is not specified. For example, in vertebrates the following applies:
 AGA    Stop (not Arg)
 AGG    Stop (not Arg)
 AUA    Met  (not Ile)
 UGA    Trp  (not Stop)

[https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi]


text:
Relationship between an Integrin-binding peptide and the Collagen type that it models
Recently, I have been investigating whether collagen can interact with integrin α2 (the product of human gene ITGA2). There is a structure in the protein data bank (PDB ID: 4BJ3) in which an integrin domain is bound to what appears to be a peptide fragment of human collagen type XXVI (gene COL26A1). However, the sequence of this peptide differs from that in UniProt (Q96A83) for this collagen, which raises the questions:

Why are the sequences in the PDB file different from the sequences in UniProt?
Even though there are differences between the sequences, can I still assume that chain C/D/E in 4BJ3 represents the protein translated from COL26A1 and that COL26A1 can interact with integrin α2?

The PDB structure contains 4-hydroxyproline, a post-translational modification of proline commonly found in collagen. This is not a standard amino acid and doesn’t have a one letter code, which is why it is designated as “X” in your alignment. In the PDB file it’s called HYP. In the paper reporting the structure, it’s designated “O”. Note that it aligns with proline in the UniProt entry.

I have edited the title to make it a little shorter and more focussed on the biology. I have revised my answer after having done some work on the problem. The timeline shows how the synthetic peptide evolved from work with larger collagen fragments. In fact the methodology of studying binding was affinity purification, but I cannot locate the paper that mentioned this — too many already.

Summary
The entry for 4BJ3 on the web pages of RCS Protein Data Bank contains information regarding a “collagen-like, GFOGER peptide” (authors’ words) that is at the best misleading and at the worst incorrect. This peptide is totally artificial, designed to have the integrin binding motif, GFOGER, flanked by model collagen GPP repeats so that it adopts a triple helical structure. The web page editors (I presume) have presented it as a mutated form of the α1 chain of collagen type XXVI, presumably because it scored highest in a sequence alignment. However the alignment is clearly on the basis of the GPP repeats, and this collagen has two mismatches in the key integrin GFOGER motif, specifically in the functionally important F and E residues. It is clear from the literature that the peptide was designed to study the interaction occurring in the integrin-binding collagens type I, II and IV — indeed collagen type XXVI was unknown at the time of design.
Collagen type XXVI completely lacks the GFOGER motif or any similar motif that has been shown to bind integrins. Although the possibility cannot be excluded without experimental evidence, the assumption would be that collagen type XXVI does not bind integrin α2.
The GFOGER peptide is not derived from collagen type XXVI
The PDB structure 4BJ3 is described in a file that can be downloaded from the RCS Protein Data Bank, and in the associated publication. According to these sources it consists of domain I of integrin α2 (residues 171–368) in a complex with a triple-helical “collagen-like, GFOGER peptide” of  sequence [GPO]2GFOGER[GPO]3, where O represents hydroxyproline.
The web page for this structure at the RCS Protein Data Bank allows one to view the protein, and contains additional information, prepared by the site curators and web editors. This includes a “Protein Feature View” in which the GFOGER peptide is aligned to Uniprot entry Q96A83, the conceptual translation of the α1 chain of collagen type XXVI:
This is the section that the poster appears to have found, and from which he has produced an alignment that includes X, which is actually the hydroproline in the synthetic peptide. Here this is replaced by P.

I have annotated the alignment to emphasize the GFOGER region and the differences (broken circles). Of the three mismatches, two are in the crucial GFOGER region which is the basis of the interaction between collagen and integrin, and both (‘F’ and ‘E’) are at critical positions.
It is clear that the choice of alignment with collagen type XXVI is not based on anything originating from the authors and makes no biological sense. How did it arise?
I have conducted Blast searches with the sequence of the synthetic peptide and found no exact hit. The highest scoring hit is with type XXVI, even though an intelligent scoring system would have demanded perfect alignment with the GFOGER motif. I assume that a person with an informatics background, but unfamiliar with the biology, accepted this.
It is misleading and wrong!
What is the GFOGER peptide derived from?
To answer this question I tracked back through the literature, following the references in the Introduction or Methods sections, starting from the 2013 paper and ending in 1986. To summarize:

1986: Collagens Type I, II and IV bind to a platelet membrane adhesion protein (Cell 46, 913-920) — Subsequently this was designated VLA-2 and later integrin α2β1.
1994: Artificial collagen-like peptide crystalized, confirming the triple-helix that had been proposed in the 1950s (Science 266, 75–81).
1994: Domain I of integrin α2β1 shown to contain binding site(s) for collagen.
1997: Domain I of integrin α2β1 crystalized (J.Biol.Chem.  272, 28512–28517). Molecular modelling suggested that a glutamic acid side chain (E) from collagen could coordinate to the integrin through a metal ion'
2000: Crystal structure of a complex between domain I of integrin α2β1 and the “GFOGER peptide” (Cell, 101, 47–56). The rationale for the synthesis of this peptide is clearly stated: “…We therefore designed the shortest peptide that would fold into a stable triple helix and that had the glutamate at its center. We synthesized a 21-residue peptide with the sequence [Ac-(GPO)2GFOGER(GPO)3-NH2]
and showed that it folds into a triple helix…”

There are further papers that could be cited, but this makes the provenance of the peptide clear, as also its relationship to collagens I, II and IV. The date of 2000 for the description of this peptide is also significant given the fact that collagen XXVI was not reported until 2002 (J.Biol.Chem. 277, 37678–37684).
Nevertheless could collagen XXVI still bind integrins?
I know of no direct experiments on this topic. What I have done is to perform Blast searches with those hexapeptides that have been shown to interact with integrin, with or without activation of the later. The results were:

Peptide
Integrin

GFOGER
Type I     (α1

GFOGER
Type II (α1)

GFOGER
Type IV (α3,α4,α5)

GFOGER
Type VII (α1)

GFOGER
Type XI  (α1, α2)

GLOGER
Type I (α1,α2)

GLOGER
Type II (α1)

GLOGER
Type VII (α1)

GASGER
Type I     (α1)

GASGER
Type XXIII (α1)

GMOGER
Type I (α1)

GMOGER
Type II (α1)

GMOGER
Type III (α1)

GMOGER
Type IV (α6)

GMOGER
Type V (α2)

GMOGER
Type IX (α3)

GLOGEN
Type III (α1)

GLOGEN
Type XXII (α1)

GLOGEA
Type II (α1)

It is evident that collagen type XXVI does not contain any of these motifs. Thus, in answer to the poster’s question:

Although one cannot exclude that it possesses a hitherto unidentified integrin-binding motif, there is currently no justification for assuming that collagen type XXVI will bind integrin.

Advice to anyone using the RCS Protein Data Bank
Read the documentation on the actual structure file, and the paper in which the structure is reported.

Thank you for sharing your informative answer and your advice.
Using genes to refer to proteins is a practice that I learned from some literature 123.This seems likely to impose an extra burden on people unfamiliar with the genetic symbols.
I have revised the question accordingly.

@WanNIE — Using gene names to refer to proteins is convenient (a) where the name of the gene product is not known (b) when tabulating data with space limitations (c) where their is ambiguity in protein nomenclature (although this may also be true of gene names.   Point (b) is probably the major factor in the paper you cite. Otherwise only collagen researchers would know what COL26A1 and COL11A2 are (I would have no idea), and it is bad practice to use these without the names of their products. The authors of the paper make no reference to any gene in their paper.

@WanNIE — Before I amend my answer could you clarify whether you wish to know whether the collagen human collagen type XXVI interacts with integrin, or whether the peptide GPOGPR does?

Sure, I want to know whether the collagen human collagen type XXVI (COL26A1) interacts with integrin and especially with the alpha2 subunit.

By the way, this paper states that the Wnt/Beta-catenin pathway can regulate the expression of genes in extracellular matrix (ECM)-receptor interaction, including COL11A1 (Collagen alpha-1(XI)), COL26A1 (Collagen alpha-1(XXVI)), LAMC3 (Laminin, gamma 3), and ITGA2 (Integrin, alpha 2). Does this implicitly suggest that there is a high possibility of an interaction between COL26A1 and ITGA2?

@WanNIE — No, co-expression says nothing about interaction. I think you are approaching this from the wrong end. You need to go back into the last century and see what studies had been done that relate directly to the interaction of these two proteins: antibody co-precipitation, electron microscopy or whatever. It would only have been on the basis of this sort of evidence that anyone would prepare a library of peptides to find what part of the collagen interact. But it may be that only certain collagens interact, so you need to read about the characteristics of individual types.

I checked ENSEMBL and the reason is not due to known alternative splicing but still allows for the possibility that they investigate a different sequence/allele due to mutations.
Importantly, in the (open source) paper, you can read that ..

GFOGER constitutes a high-affinity motif for all the collagen-binding
integrins reported to date [12]–[14].

Therefore, I would highly doubt that you can assume that COL26A1, if it does not posses that sequence, would be bound equivalently. Also, this quite frankly indicates that you are wrong with your premise, that the PDB shows COL26A1.

I agree, and have given you credit for this. And human collagen type XXVI alpha 1 does not contain this sequence as a sequence comparison or a Blast search with the peptide GFPGER will demonstrate.


text:
Does Rough ER (RER) produce phospholipids?
I have found out that rough endoplasmic reticulum (RER) produces membranes. Therefore it has to produce phospholipids, but I thought that the smooth ER was where the synthesis of lipids occurs.
What specific part of the ER produce phospholipids?

Could you substantiate your statement about the site of synthesis of phospholipids with a reference to your source of the information. I'm not sure that many of us are experts in that area, but our experience may help us to assess it. Also, please, one question at a time. Your general question about the functions of rough and smooth ER is a separate question and should not be included here. I imagine you can find that by reading, so I have edited it out. You can roll back the edit if you wish, but it won't help you get an answer to your main concern.

The endoplasmic reticulum (ER) is one of the largest continuous membrane bound organelle of the cell.
The rough ER and smooth ER share the same membrane and some membrane proteins can diffuse between them. At the same time there are specific markers for ER sheets (rough ER) and ER tubules (smooth ER). The terminology of rough and smooth come from early electron microscopy and biochemical work where large amount of ribosomes (polyribosomes) were found on the rough endoplasmic reticulum membrane, and less on the smooth. These membranes can be biochemically separated one being more heavy (RER because of attached polyribosomes) than the other.
In general the ER has several functions: protein synthesis, calcium storage, entry of the secretory pathway and lipid synthesis. It can not only produce phospholipids but also a large array of precursors for steroids and neutral lipids.
This is a topic of research itself but it is general thought/accepted that the smooth ER is the one responsible for the synthesis of phospholipids.
In reality, there are multiple ways to produce phospholipids (from recycled membranes, from lipid droplet stores, etc) and there are multiple possible pathways for producing lipids and lipids precursors (de novo synthesis). This also implies that there are multiple enzymes involve in this process. Now these enzymes are often ER membrane proteins and they can but do not always specifically localize particularly to one part of the ER.


text:
What is the purpose of centrioles and the centrosomal matrix?
In centrosomes, the gamma-tubulin ring complexes (gamma-TuRCs) located on the surface act as an essential nucleation site for the growth (with polarity) of microtubules.
However, there is also a centriole composed of two centriole units in a T-shape structure and a centrosomal matrix. According to the article in Wikipedia, cells can still function normally and grow without centrioles, and I have been unable to find information regarding the purpose of centrioles and the centrosomal matrix.
My question is therefore:

What is the function of centrioles and the centrosomal matrix?

If it were possible to construct a synthetic sphere with many gamma-TuRCs on its surface would the cell be able to perform a normal cell cycle?


text:
How can good Shine–Dalgarno or Kozak sequences enhance translation?
In prokaryotes the Shine-Dalgarno sequence, a polypurine consensus sequence near the initiation codon (usually AUG), is required for the mRNA to bind to the small ribosomal subunit, allowing initiation of translation.
In eukaryotes, the ribosome binds to the 5′ cap of the mRNA, and then moves along it until it finds an initiation codon — usually the first initiation codon — for initiation of translation (the Kozak ‘scanning’ model). In some cases the first initiation codon is skipped, and this appears to because the sequence context of the mRNA — sometimes called the Kozak sequence is in some way unfavourable.

I have read that either a Shine–Dalgarno or Kozak sequence that is
optimal for recognition by the small subunit will greatly enhance
translation. However I cannot understand why this should be so, as the
actual insertion of amino acids only occurs in response to base
triplets 3′ of these sequences.

In addition, for eukaryotes, it would seem that the scanning ribosomal
subunit is skipping the first AUG it encounters if a second or
subsequent one is in a ‘better’ sequence environment. If this is the
case, what mechanism enables such a selection to occur.

While this is a good question with plenty of detail, it's often helpful to cite sources (e.g. links to journal articles, textbooks, wikipedia, or other resources) to maximize clarity and reliability.

As what I regarded as a poor question has resurfaced with an answer, I have edited it to remedy its scientific deficiencies (other than in the logic).

I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions.
At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes happening at a single molecule. Thus, what changes with different sequences is a rate at which some step occurs (e.g. rate of ribosome assembly, rate of translation initiation, rate of start recognition); none of these steps will occur with 100% probability on every mRNA molecule.
What this means is that you can write down equations for kinetic models of translation, allowing us to apply principles of mass action and rates of reaction from elementary chemistry. Having a higher rate of ribosome affinity for a sequence is therefore similar in effect to just having more mRNA, in the sense that in both cases you will do more translation and make more protein.
Thus, it might be easier to use the terminology of "strong" and "weak" SD/Kozak sequences. A strong sequence has a high rate of reaction and a weak sequence has a low rate of reaction. Here, the "reaction" in question is ribosome binding, or translation initiation, or whatever process we're currently studying.
Now, as to the specific questions:

Sequences alter the rate at which downstream processes occur. So, e.g. a weak Kozak sequence will often simply not initiate translation, and the ribosome will fall off without translating anything. This will almost never happen with a strong Kozak sequence, so a strong Kozak is more "efficient" in the sense of more reliably leading to translation. A strong Shine-Dalgarno sequence increases the rate at which ribosome binding occurs.

Both ribosome binding and translation initiation are necessary for protein production, so if you increase the rate at which these processes occur, you increase translational efficiency in each case.

There is no "foreseeing". Think about this mechanistically. The ribosome scans 3' along the mRNA, starting at the point of attachment. Also, each ribosome attachment to an mRNA can only start one translation event. Once a ribosome stops scanning and starts translating, it does not recognize subsequent Kozaks.

Thus, if there is a strong Kozak sequence, then translation will almost always start at the strong sequence, and will never have the opportunity to start at a sequence further 3'. It is mostly only when a 5' Kozak is weak that further Kozaks get recognized at all ("leaky scanning"):

The first start codon closest to the 5′ end of the strand is not always recognized if it is not contained in a Kozak-like sequence. Lmx1b is an example of a gene with a weak Kozak consensus sequence.[22] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. Exceptions to the first AUG rule may occur if it is not contained in a Kozak-like sequence. This is called leaky scanning and could be a potential way to control translation through initiation.[23] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. (Wikipedia)

So it's not that Kozaks are required, necessarily. You just need some set of circumstances which increase the probability that the ribosome starts translating next to a start codon. The Kozak simply happens to be an efficient way to get a ribosome to start translating. The closer a sequence is to the consensus Kozak sequence, the more efficient it is, because the probability of translation initiation is higher.

Oh thanks! So to clear my understanding, for q1: 'efficiency' means how strong are the interactions between the ribosome and the SD sequence. If it is stronger, the ribosome will less likely to detach during translation (i.e. higher processibility), hence a better efficiency? (i.e. higher efficiency = stronger ribosome binding)

for q2: when the ribosome slides to a strong Kozak sequence, it will start translation there no matter if there are even stronger Kozaks downstream? But sometimes when the first Kozak is too weak, leak scanning occurs i.e. subseuent Kozaks are selected?

@Questions comment 1: I would say that "efficiency" is a very high-level term that just means "how much protein do I make for a fixed concentration of all reactants". I would agree that higher affinity of sequence for the ribosome (what you seem to call "interaction") does lead to higher efficiency, but efficiency is a much larger outcome, really the product of (ribosome affinity of mRNA) * (strength of translation start site/kozak) * (ability to recruit co-translational helper complexes) * (...a lot of other stuff). A sequence on its own is not "efficient", it doesn't do anything.

@Questions comment 2: I believe that is approximately correct. There is always a small chance that the ribosome fails to start translation, and therefore downstream Kozaks get a chance. Likely there is some weird mechanism by which a downstream Kozak can conformationally constrain upstream Kozaks; for example viral translation is weird and there are often internal ribosome entry sites (IRES) and weird stuff like that. But for normal canonical translation, I think that a strong first Kozak dominates everything else. Though I could be wrong in some detail, biology is weird!

@Maxiilian Press Thanks a lot for the clear explanation :)

The argument regarding the insertion of amino acids in response to a section of the mRNA 3′ to the (usually) AUG initiation codon — an argument only applicable to eukaryotic translation — is easily refuted. If the ribosome isn’t associated with the mRNA it can’t translate it. This represents the extreme case — translation or no translation. However if there are factors that have an effect on the efficiency of this association, they will have a graded effect on the rate of translation. It is conceivable that different mRNAs may be translated at different rates or in different physiological circumstances.
It is important to realize that the mechanism of attachment of mRNA to the small ribosomal subunit is quite different in prokaryotes and eukaryotes, so each must be considered separately. This is important because the first unique step in any biochemical process is the step at which control can be exerted most efficiently†.
In prokaryotes the first step in initiation is the attachment of the mRNA to the small ribosomal subunit by base-pairing between the Shine-Dalgarno sequence in the mRNA and a complementary sequence in the 16S rRNA§. This positions the AUG for interaction with the initiating fMet-tRNA. A perfect base-pairing with the rRNA is not required, and Shine and Dalgarno sequences differ in the number of base-pairs, and hence the strength of interaction. If binding of the mRNA to the ribosome is rate-limiting, this provides a potential mechanism for regulating the rate of translation of different mRNAs. There are some examples of poorly expressed mRNAs with poor Shine and Dalgarno sequences, as well as mutational experiments, that provide support for such regulation.
In eukaryotes the first step in initiation is the attachment of the mRNA to the small ribosomal subunit by  binding the 5′ cap. This is a complex process involving many initiation factors and is a logical point for regulation to occur. In fact this is the case, the activity of cap-binding initiation factor 4E being regulated by the phosphorylation of a protein that binds to it. In contrast, it is difficult to see how the ‘goodness’ of the subsequently encountered environment of the first AUG could have a regulatory effect — either the ribosome stops and the met-tRNA it is carrying at this stage interacts with the initiation codon, or it continues to the next.
And, of course, it is incorrect to suppose that in the scanning model a mechanism exists for ribosomes to reject the first AUG in an otherwise satisfactory environment because the environment of a subsequent one is better. All that might happen is that a portion of the ribosomes skip the first AUG in a marginal environment and initiate at a subsequent one, producing an alternative protein — a different sort of regulation.

§This sequence is absent from the eukaryotic 18SrRNA subunit, so the Kozak consensus sequence is in no way analogous to the Shine-Dalgarno sequence. The mode of action of the Kozak sequence is, as far as I am aware unknown.
†It is recognized that other factors can regulate initiation. The tertiary structure of the mRNA can affect access of ribosomes to Shine–Dalgarno sequences in polycistronic prokaryotic mRNAs, and the phosphorylation of eIF2 (the initiation tRNA binding factor) can also regulate initiation of eukaryotic translation at a stage later than 40S ribosome binding.


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Does neuroeconomics study the brain or study economics?
I'm trying to understand what neuroeconomics is. There are two possibilities for what it might mean. (1) The study of cognitive processes in the brain by applying basic principles of economic theory like concepts of utility, decision making, etc. (2) The study of how a human behaves in an economic setting, somewhat like game theory and so on, which is more economics than brain science.
Which one is it?

Neuroeconomics is the study of the neural basis of economic behavior.

You should consider asking this question on the cognitive sciences stackexchange, which specializes in neuroscience and related fields.

As @Kyle beautifully summed-up,

Neuroeconomics is the study of the neural basis of economic behavior.

The terms applies to studies concerning the appeal of new logos for marketing purposes to the understanding of the neural correlate of subjective value. The term neuroeconomics has been subject to some debate which made it sometimes unclear. In particular, the term is ambiguous with regards to its applications.
Are the theories that are built upon these studies used for marketing purposes (some would say "to optimize brain washing you in the necessity of buying a 7 blade razor") or for the sake of knowing how the brain may be better understood and to the therapeutical applications of these new theories.
My answer would therefore be this:

the brain is a complex system for which science often used analogies to make progress. It has been compared as steam machines in the 1800s, electricity in the 1900s, or to computers in the this century.
The complex interactions present in an economic system -as studied by game theory for instance- present a powerful analogy to understand the brain.
Of course, it thus impacts our knowledge on economics as these are often based on our knowledge of decision making. Thus, your two options are (1) and (2) are interconnected.

My initial reaction is that (1) is preposterous, because there is no economics of the brain, as it is not made up of rational actors who trade or manage resources as individuals. Therefore it must be (2).
Also, I happen to know from experience that there is much said and written about (2) and less about (1).
Here is some evidence supporting this:

Duke University's Center for Neuroeconomic Studies states that they apply "the techniques of cognitive and systems neuroscience – along with computational modeling – to understand economic decision making and related behavior".
The IISDM at NYU (who have a program in neuroeconomics) says their goal is to "better understand the mechanisms, predict the impacts, and shape the policies that will define the study of decision-making tomorrow (...) by developing novel research infrastructures to support the propagation of neurobiological insights about the human animal into the policy domain"..
The Society for Neuroeconomics says their mission is to "foster research on the foundations of economic behavior by promoting collaboration and discussion among scholars from the psychological, economic, and neural sciences".
The most highly cited result on Google Scholar for "neuroeconomics" is titled "Neuroeconomics: How Neuroscience
Can Inform Economics". The third hit's abstract says "Economics, psychology, and neuroscience are [aiming to provide] a single, general theory of human behavior. This is the emerging field of neuroeconomics (...) The goal of this discipline is thus to understand the processes that connect sensation and action by revealing the neurobiological mechanisms by which decisions are made."

So I would conclude from this that neuroeconomics is the study of human decision making, by application of neuroscience.
Granted, at this point I feel compelled to admit that perhaps I was too quick in my initial reaction: Is it really possible to isolate the study of the human brain from the study of human decision making? There is just so much overlap that even a "pure" neuroscientist will inevitably generate research which bears much relevance to economics. And with economics, the only way to "escape" neuroscience is to assume that all actors are perfectly rational, which is almost certainly at least a little bit untrue (although a staple of classical economics). It's probably a bit of loop, and I'd favor NYU's emphasis on it being interdisciplinary field rather than "field X applied to field Y". That said, indeed, most neuroeconomics studies appear to be interested in solving economics problems, and not neuroscience problems.


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Do low light levels during development affect the distribution of rods and cones in the retina?
I just can't seem to find any retinal development experiments that have been done using low light conditions. I am very interested in knowing if raising an animal in such conditions leads to a different distribution of rods and cones in the retina. Perhaps it would lead to a more uniform distribution that the skewed distribution that is normally found?
Any thoughts or pointers to resources would be appreciated!

I found a few studies in fish that showed constant light exposure changing rod density. First one in goldfish:
Raymond PA, Bassi CJ, Powers MK.
Lighting conditions and retinal development in goldfish: photoreceptor number and structure.
Invest Ophthalmol Vis Sci. 1988 Jan;29(1):27-36.
http://www.ncbi.nlm.nih.gov/pubmed/3335431

The retinas of 63 goldfish were examined after varying durations of exposure to one of three environmental lighting conditions beginning before hatching: constant light (340 lux), cyclic light (12 hr 320 lux, 12 hr dark) and constant dark. Up to 8 months, no effects of constant light or dark on photoreceptor numbers or structure were apparent. Densities of rod and cone nuclei were normal and all retinal layers appeared normal by light microscopy. Exposure to constant light for 12 months or longer resulted in a reduction in rod density by 37%. Cone numbers were unaffected by constant light, even with exposures of 3 yr, and rod and cone outer segments were normal in length at 11-20 months under all environmental conditions. Due to poor survival, only one animal was available for quantitative examination from the group reared in constant dark 12 months or longer. Photoreceptor size and number in this retina were similar to those in the constant light condition. The results suggest that the formation and maturation of rods and cones in goldfish retina is unaffected by rearing in constant light. However, long-term exposure (greater than or equal to 12 months) may disrupt maintenance of differentiated rods.

See also http://www.vision-in-cichlids.com/fenotypic_plasticity.htm where they say rod density changes in early retina development of Tilapia leucosticta.


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How do developing neurons become tuned to fire only on receiving specific inputs?
Research has uncovered neurons that seem to "listen" for specific inputs and fire only when these inputs are received. For example, neurons in the visual cortex may fire at a higher rate when visual stimuli of a particular orientation is presented, and may not fire for stimuli of other orientations.
Are there any good models on how neurons develop this tuning for specific inputs? Could anyone provide links to good papers or other resources?

The only "good model" I know of is hebbian plasticity* or hebbian theory, here's a link: https://en.wikipedia.org/wiki/Hebbian_theory
Usually what we mean by neurons "listen for" or are "tuned for" or even "like" a particular stimulus is that spiking activity in those neurons is significantly increased (or decreased) in the presence of that stimulus as compared to equal amount of time in the absence of it.
*Plasticity refers to the capacity of the brain to change both the strength of connection as well as number and configuration of connections.


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What is different between the pigment of giraffes and the pigment of flowers?
I saw this video created by Derek Muller and he says there that it is very unusual to evolutionary develop the colour of the skin without the pigment. That sounds reasonable but if so, what nutrients have to get animals with pigment to get colored? Is it an active job of the cells or skin cells are just full of colorful minerals?
In case of giraffes: How does skin correct the shape of the spots? (For instance in cause of zebras it is clear according to this video)
And what about purposely colorful flowers? What nutrients do they need?
Thank you very much.

Pigmentation in most animals which is between black, brown, red, yellow and which is made up by the mixture of two pigments: Eumelanin (yellow to red) and Pheomelanin (black to brown). The ratio between these two makes a color. These are pigmental colors which are made by a special kind of cells in the skin, in mammals they are called melanocytes (and I will only look into mammals here, as this is already complicated enough). Additionally there are other colors, especially in fish and insects iridescent color play an important role.
This pigmentation is made by a cascade of enzymes from the oxidation and polymerization of the amino acid tyrosinase. So there are no minerals involved in the process. See here for more details.
For the pattern: As far as I know the literature, these pattern by x-inactivation are only present in cats. Here one of the enyzmes which is important for the generation of the dark pigment is encoded on the x-chromosome of the animals. Gene defects on this chromosome then lead to pigmentory defects.
Pigmentation patterns can be explained by a model which was formulated by Alan Turing and which is called "Reaction Diffusion Model". You can find an interesting article about this in reference 1.
Basically two different morphogens (different pigment cells) influence each other with positive and negative signals. If these signals would occur independently, than only relative incomplex two-dimensional colorations would be possible. See the figure from reference 2:

References:

How the zebra got its stripes, with Alan Turing
Reaction-Diffusion Model as a Framework for Understanding Biological
Pattern Formation

Ok,thank you but how do flowers create their pigment without their partner´s chromozome?

I'll add a section on it later.


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Why do herring have fine bones
Most fish have largish bones which support the core muscles.  Around the abdomen, they act as a sort of framework protecting the organs.  With herring, the bones are really fine: almost thread like and there are lots of them: more than on any other fish I've eaten.  I would like to know why herring have such fine bones.

Most likely to assist in maintaining neutral buoyancy. Many fish have reduced weight of heavy structures (evolutionary wise)like bone to assist in maintaining nuetral buoyancy. The swimbladder struggles to maintain  buoyancy near the surface for some herring
https://www.researchgate.net/publication/231918276_The_herring_swimbladder_Loss_and_gain_of_gas/amp

I've changed your link to the actual link


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Why does IUCN classify pistachio as a "Near Threatened" species?
When reading the Wikipedia entry on pistachio, I noticed that IUCN has classified the plant under "Near Threatened". On looking up its entry at IUCN, I see that its population is trending downwards, and it is "threatened by fruit collection, livestock grazing and cutting". The treat seems to have nothing to do with the often reported fungus. Looking up the yearly yields at Administrative Committee for Pistachios, I see that 2010 and 2012 were bumper years, but otherwise, I see no real trend of a decrease. Quite the contrary, I get the impression that the yearly yield is increasing. It's not as if the tree is difficult to grow, and we rely on trees growing in the wild; these trees are grown in orchards.
So, what's going on? Why would IUCN say that pistachio is Near Threatened?

You cited the reason already yourself: "Threatened by fruit collection, livestock grazing and cutting". Obviously conservationists see this as a big enough threat to raise some alarm.

@Chris: What I wrote after that invalidates that reason: unflagging and even bumper yields.

@prash It is near threatened and not endangered. I guess the IUCN sees this plant as going to face problems in the future due to a variety of reasons to which I would like to add habitat loss and temperature changes from changing weather patterns too.

@Chris You should post your comment as an answer.

Short answer: They were talking about the wild species.
Using the presentation by a Farm Advisor and a Pomologist, Pistachio Cultivars as a rough indication of the state of the species, we see that the commercial crop does not have much diversity.

Probably 97% or more of the pistachio acreage in California is planted to the Pistacia vera female cultivar called ‘Kerman’ and a P. vera male called
‘Peters’.

The presentation mentions that other geographic regions prefer other cultivars. But generally, the the entire commercial population of pistachio seems to be limited to a few tens of cultivars.
The IUCN Red List that I cited in the question is rather poor on the details. However, the publication, Geneflow '06, included a report on Uzbekistan's pistachio:

Saving Central Asia’s pistachio diversity
For three millennia, pistachio trees were used in metallurgy and mining in Central Asia due to their accessibility and the highly calorific charcoal they produce. The result was a major depopulation of wild pistachio in the region. During the Stone Age, pistachio trees in Central Asia covered approximately 2 million hectares, compared with only 300 000 hectares today.
The loss of wild pistachio diversity in Central Asia has major implications for pistachio growers in the region and beyond. Most of the pistachio gene pool is to be found here, where it is needed to underpin the continued availability of the tasty nut.

All the reasons they cited as factors for threatening the species likely refers to the wild trees.

Pistachio populations don't appear to be decreasing from your research because you are looking at  yields, not population level trends. Yield is not directly indicative of species health and is also not likely to immediately decrease with a population level decrease because farmers replant after loss.
The IUCN Red List Website lists declines in number of mature individuals, number of subpopulations, number of individuals in subpopulations, and number of individuals in the largest subpopulation. Other characteristics contributing to the "Near Threatened" classification are that the overall population is severely fragmented and both the overall population and subpopulations have been experiencing extreme fluctuations.
The IUCN lists the threats to the species as: "Natural stands have been impacted by overgrazing and are considered unproductive (Trees and Shrubs Online 2020), which may impact their management. Wild trees are also under threat from cutting and fruit collecting (Eastwood et al. 2009), while historically, the wild population has been reduced due to trees being felled for timber (Khanazarov et al. 2009). Human development has also led to habitat loss in some regions, though the extent of the impacts these actions have had across the species range are not clear."
Source: https://www.iucnredlist.org/species/63497/61526633#population
I also imagine that there is concern about species diversity. According to https://www.gbif.org/species/3190585 Pistacia vera is dominating the gene pool and population, which makes makes the sustainability of the Species unstable. If a pathogen were to target Pistacia vera, the impact on the Species could be devastating.

It's not clear what the sources "Trees and Shrubs Online 2020", "Eastwood et al. 2009", or "Khanazarov et al. 2009" refer to: more information is needed, like a DOI or URL, a title, a journal/book, etc.


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Estimation of tissue-partition coefficients and clearance for liposomic nanoparticles
I am working on developing a PBPK model for liposomic nanoparticles used to deliver drugs to fells in the bloodstream. However, I do not have any in vivo data or in vitro data. Given only chemical and physical properties like pKa or the octanol-water partition coefficient, how can a get a relatively accurate estimate of the tissue:blood partition coefficient, as well as the renal & metabolic clearance?

What is your overall goal or research question that you would like to answer?  We could collaborate on a research project.

@Polymania that would be great! How can I contact you? This has to do with modeling liposomic nanoparticles binding to cells that flow through the blooddtream. I want to estimate thr concentration of the cell-lipsosome complex in various compartments of the body, so I am trying to model the systems seperately for now. However, there is not much in vivo sata for both the cells and the nanoparticles, although I do have a little data on the cells. Hence, I need to estimate these parameters. I am new to PBPK modeling so i am not sure if this approach is suitable for my project.

@Polymania I have saved your email. I will send an email as soon as possible.

Regarding the tissue partition coefficient, Li et al. said:  "By using such a parameter, it is assumed that there is the same transfer kinetics of nanoparticles from blood into tissues as from tissues back into blood circulation, and an equilibrium of concentrations between blood and tissue exists. These assumptions may not be appropriate for nanoparticles."

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

However if you are set on using a tissue:blood partition coefficient (Kp), Yun and Edginton have done a review of 6 in silico methods for determining Kp for small molecules.  You may be able to extrapolate to nanoparticles.

Yun, Y.E., Cotton, C.A. & Edginton, A.N. J Pharmacokinet Pharmacodyn (2014) 41: 1. doi:10.1007/s10928-013-9342-0

Finally, if you are looking for data to help determine a partition coefficient, there is an excellent review of liposomal doxorubicin pharmacokinetic data in animals and humans here.

Gabizon, A., Shmeeda, H. & Barenholz, Y. Clin Pharmacokinet (2003) 42: 419. doi:10.2165/00003088-200342050-00002

Do you work with PBPK models of liposomes?


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white blood cells and cancer cells transport through lymphatic vessels
It is a well-known fact that both of these cells can reach the lymphatic vessels from interstitial space. How does it do so physically? Are there any mathematical models describing this process? It seems like there are endothelial cells along the lymphatic vessels that act like valves, so I would assume that these "valves" open, the cancer cells/WBCs would fit through to reach the lumen?
This question is also a reference request. I am looking for papers that describes the process of intravasation of WBCs and cancer cells into the lymphatic capillaries? Mathematical models are preferable but this is such a niche topic that probably there are no mathematical models.

good question +1 specially on the cancer cell part.looking forward to an answer.

The "valves" are basically one way valves that just prevent backflow of interstitial fluid from the lymph into the interstitial space, so they do not specifically affect the flux of WBCs, cancer cells, etc. into the lymph vessels. In terms of a mathematical model of flux into the lymph vessels, you could use Poiseuille's law to determine the flow rate of interstitial fluid through the "valves", then multiply by the concentration of WBCs, etc. in the interstitial fluid to get the flux of the given cells into the lymph vessels. Of course, that is just one possible model for one parameter (cell flux).

I am looking for more of a biomechanical/fluid dynamics model. Also, you haven't explained how the WBCs/ cancer cells go through the valves...