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Usage and mechanism of the Bastien protocol to treat amanitin poisoning
In 1971, 1974 and 1984 a French doctor Pierre Bastien (frwiki) voluntarily poisoned himself by ingestion of Amanita phalloides mushrooms in order to popularise his method of treatment of such poisoning. This method seems to have consisted of vitamin B and C injections and dosages of Abiocine and Nifuroxazide. Is this method still being practiced or has it been discouraged? What would be the mechanism of this protocol?

More medical than biology, and very much a continental European thing, but I thought it would be amusing to search the internet. (You could have done this yourself.)

@David I have obviously done that, but the number of publicly available sources is limited (and you have demonstrated that yourself by using two paid resources in your answer). Anyway, thank you for looking into this.

Apologies. Having access to many journals through my university I am sometimes unsure whether papers are open access or not. I'll modify my introduction slightly.

I know nothing about this subject, except that I can recognize edible and poisonous fungi, to the extent that it concerns me in a practical sense. However, as I have access to a range of journals through my university I thought I would see if there was anything ‘out there’ on the topic.
A recent paper entitled Amanita phalloides poisoning: Mechanisms of toxicity and treatment by J. Garcia et al. in Food and Chemical Toxicology 86 (2015) 41–55 contains a table listing the drug therapy used in a range of countries. There is no reference to Bastien in this paper and the most frequently used therapies are benzylpenicillin and silybin.
Abiocine is another name for dihydrostreptomycin and nifuoxazide is nifuroxazide is an oral nitrofuran of questionable efficiacy. So they are not identical to the agents mentioned and Bastien’s protocol does not appear to be in current use.
The impression I get from the article is that the agents used for treatment are not strict antidotes, but rather part of a strategy to treat the general effects of the poison. To eliminate the poison activated charcoal is often used.
If Bastien’s protocol really had an effect I imagine it may have acted in a similar manner to the current agents, although I have no idea what the vitamins might have been doing (if anything). Incidentally it was the subject of a letter (in English) to Lancet in 1981 (subscription required), in response to scepticism expressed in a previous editorial.

I'd forgotten I'd even written this answer, but it seems that I did better than the deleted effort of ChatGPT (hidden post) which declares that abiocine is phosphatidyl serine. Numerous sources including the US National Institutes of Health support it being dihydrostreptomycin. Somebody's obviously been halucinating again.


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Why does an Enzyme-Substrate Complex have slightly less energy than the substrate alone?
In some books the graph of the change in free energy during an enzyme-catalysed reaction is depicted as shown below, where S = substrate, E = enzyme, P = product, and T* represents the transition state.

In this depiction the free energy of the enzyme–substrate complex (ES) is shown as having a slightly lower free energy than the substrate (S).
What is the explanation of this?

Welcome to SE Biology. I have tidied your question up a bit, decreasing the graphic to a more reasonable size, improving the presentation, indicating that the type of graph is only found in some depictions (where did you find it? You should say) and defining the terms. Is this question an assignment of some sort? If so you should state this and present your attempt to find the answer yourself. See our Homework policy.

The diagram presented in the question is only one of many variations found in text books and the like. It is unsatisfactory to the extent that it shows one of the intermediates (ES) in the catalysis, but not the other (EP), and that it does not label the species present at each stage. Such energy diagrams are considered in a paper by Aledo et al. in Biochemical and Molecular Biology Education, from which I reproduce their favoured example, below.

Explanation: A simple first order reaction in which a single substrate (S) is converted to a product (P) is shown with intermediates, ES and EP. The transition states between the various conversions in the sub-reactions are shown in red, and that for the uncatalysed reaction (E + S≠) in dark blue. (I am not sure why the E is included in this, except to allow use of a unified diagram.) ΔG is the overall free energy change of the reaction and ΔGUC≠ and ΔGC≠ are the free energy changes to reach the transition state in the uncatalysed and enzyme-catalysed reactions, respectively.
This diagram reflects the key point made by the authors of the paper:

“For an enzyme-catalyzed reaction, it should be stressed that, under conditions where the overall reaction is spontaneous, each elementary step must exhibit a negative free energy change, and this must be properly reflected in the progression profile of the reaction.”

So, to answer the poster’s specific question, for the reaction to proceed not only must the overall free energy change from E+S → E+P be negative, but that of the intermediate stage, E+S → ES must also be negative, i.e. the free energy of ES is lower than that of S — or E+S, to be precise.
(And the free energy of E+P must be less than that of EP, the violation of which principle is apparently a common failing of many diagrams.)

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Does spinal cord have pain receptors?
I understand that the brain itself does not have pain receptors, so when the brain is damaged or cut, there is no experience of pain. For example, surgeons can operate on the brain while a patient is awake without causing pain.
How about the spinal cord? Are there pain receptors in the spinal cord? Will damaging the cord itself cause a feeling of pain?

I'm voting to close this question as off-topic because it's the same as this question https://biology.stackexchange.com/q/81524/107

@kmm that question has no upvotes or accepted answers. This question is slightly better worded than the one you linked. I think this one should be left open.

That question should be edited and thus proposed for reopening, not posed as a new question.

This is a difficult and subtle question for many reasons. The primary issue here is that there is a difference between "does the parenchyma of this central nervous system structure have nociceptors (or, in fact, any peripheral receptors)" and "can the parenchyma of this central nervous system structure detect direct stimulus". There is also the issue that pain is not a sensation, so much as an associative cortical event. So this is a hard question to answer completely, as it is phrased, but it is also difficult to expect someone to understand this after, even a few hours of undirected research

tl;dr
Like the brain, the receptors commonly called 'pain' receptors aren't in the spinal cord itself, but they are present in the meninges around the cord, and damage to the cord can be perceived as pain in particular because it can increase activity in the pathways carrying 'pain' information to the brain.
Details
Nociceptors, often called pain receptors, are peripheral structures that sense and transmit noxious stimuli to the central nervous system. The cell bodies of afferents from these receptors are found in the dorsal root or trigeminal ganglion. The receptor structures themselves (the afferent terminal of these neurons) are not found in the parenchyma of any central structure, though they do innervate the meninges of both the brain and spinal cord. Despite the lack of peripheral receptors of nociception, damage to the spinal cord is often associated with increased activity in the tracts that carry nociceptive information.
This may be beyond the question you're asking, but I would note that the IASP defines pain as:

a sensory and emotional experience associated with actual or potential tissue damage or described in terms of such damage.

Pain is probably best understood less as a sense that nicely maps the external environment to a conscious representation of that environment, and more as an emotional need state, like hunger. Many different receptor structures and nerves can transmit a signal that can eventually be interpreted as pain, and in fact pain can be experienced without any physical peripheral input at all (as the IASP definition attests). This is one of the reasons nociceptors are typically not called pain receptors by people who treat or study pain.

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Is PrEP used for anything other than HIV?
In the field of HIV prevention, PrEP is an abbreviation of pre-exposure prophylaxis. This is a very generic term. Are any diseases other than HIV prevented using a similar approach? Do they use the same name?

Prophylaxis is typically prior to exposure. Condoms, for example, were historically referred to as prophylactics, in that they prevent pregnancy and many STIs. The reason the pre-exposure bit is given special attention in this context is that it refers to use of drugs with substantial risk of harm. Because of their associated risk, these drugs were previously only used for post exposure prophylaxis. Similar to rabies vaccination after an animal bite, this strategy involves preventative treatment given after exposure but before a critical point in the progress of an infection.
To more directly answer your questions

Are any diseases other than HIV prevented using pre-exposure prophylaxis?

Many, many, many diseases. Vaccines are a good example of prophylactic treatment, typically given prior to exposure. Malaria prophylaxis is another example, where a medication (with non insignificant risk of harm) is given to healthy people traveling to an endemic area.

Do they use a different term?

In most cases, as you can see by searching for the words used in the linked references, the term is simply prophylaxis, rather than pre-exposure prophylaxis.

Yes, I'd wondered about the semantics. I assume vaccines aren't classed as PrEP because of the different mechanism by which they work?

@ChrisW vaccines are treatment prior to exposure, intended to prevent infection. And so they are pre exposure prophylaxis*, but they are typically just referred to as prophylaxis. The special terminology for HIV PrEP is, as I indicated, to distinguish use of ARV prior to exposure from use of ARV post exposure, which has been done for about 25 years.

Sorry, I meant the difference in that vaccines are typically an injection of the virus, (immune response) rather than a continual drug to prevent the disease if you come into contact with it (pharmacological response) - I hadn't realised that both were technically PrEP.

@ChrisW condoms are technically pre-exposure prophylaxis as well.


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Can an organism exist as a single cell but come together as multi-cellular during certain times?
I am trying to remember a particular segment from a BBC special, about a single celled species. However, at certain times all the individual cells came together to form a structure, not unlike a mushroom, to scatter something like spores into the wind. Afterward, the individual cells separated and continued on as individuals.
Am I remembering this incorrectly? Is this even possible?

Welcome to Biology StackExchange.

Am I remembering this incorrectly?

No, you're remembering it correctly.
I think you're talking about slime molds. You'll find more information on the wiki page
Is this the video you saw? These images are pretty cool.

Is this even possible?

Yes (given that it exists). There is no way to correctly answer this question as it really is an open-ended question. But here are a few words that may push you writing further posts.
Just a few words on the evolution of altruism
The main interest behind this life-cycle is that not all individuals reproduce. Some individuals form the stalk while others go through meiosis (see below on the life-cycle).

How unfair does it seem to those who form the stalk! Why would those individuals forming the stalk spend energy to help other individuals to reproduce?
Kin selection
Let's think about us, vertebrates, "real multicellular" organisms. The cell that is in your eye is never going to reproduce. Although it is spending all its energy into helping your ovules/spermatozoids to fuse. Why would this cell in the eye make such an effort? The genes in the spermatozoids/ovules are essentially the same as those in the "eye cell". Therefore, by helping your spermatozoids/ovules the eye cell is actually contributing to spreading copies of the genes that it is carrying. This is referred to as kin selection.
Slime molds and altruism
Now, the story is not exactly the same for the slime molds. The cells in the stalk can be quite different from those that are undergoing meiosis. Altruism can exist in a variety of different mechanisms and it would take several books to go over the literature about the evolution of altruism. Without knowing the literature specific to the slime molds reproduction, I just want to notice that the cell in the stalk will die anyway, whether or not it spend energy helping other cells reproducing. There is, therefore, no fitness cost into construction a stalk. Little population structure (causing higher relatedness within deme than among demes) could be enough to allow this behaviour to evolve.
Just a paper (that I haven't read) on the subject
Hudson et al. 2002
Genetics of the fruiting body
Interestingly, similar genes are being used in Dictyostelium discoideum (slime mold) to create this fruiting body than what is used in multicellular eukaryotes (ref.). Thanks to @Tim Cutts for this info.

The interesting thing about /dictyostelium discoidium/ and similar slime moulds is that the mechanisms they use to form their multicellular fruiting body use related genes to those used in development of true multicellular organisms. They are thus very instructive as to how multicellular development works, and show that these mechanisms evolved very early

"Kin selection" - also why the traits for being (perhaps) a celibate priest or (on more solid evidential ground) a worker bee are not ruthlessly selected against :-)

I would add two other examples: biofilms and Myxococcus xanthus fruiting bodies.

Fun fact : Slime molds have been used by artists to make some really great works ! I remember seeing a TED talk on it.

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can one be infected with Naegleria fowleri by taking Steam?
will Naegleria fowleri be present in the steam molecules.
Many people take steam from hot water to get relief from sinus.
I read somewhere that Naegleria fowleri gets killed over 70 C. So steam will also kill it?

N. fowleri infection can occur after nasal and sinus irrigation, swimming and other exposures to contaminated water. The infectious agent in this case is the trophozoite, not the cyst. Boiling water contaminated with this amoebae kills it, preventing infection. Though it does thrive in warm water (37 C), it doesn't survive in steam (100 C).
Despommier's Parasitic Diseases Ch. 14 discusses N. fowleri in some detail. It's also covered in Murray Medical Microbiology Ch. 82, and Cecil medicine Ch. 360. There's also useful study in The Laryngoscope on the viability of various pathogens in contaminated water after sterilization methods.

To see how these data compare with those obtained in the semiquantitative tests, the ex- posure times for a 99.9% cyst destruction were extrapolated from the survival curves in Fig. 2 and came out as 65, 26, 17, and 3 min at 55, 57, 60, and 65C, respectively.. 3 minutes in 65 degree water might be more severe than 100 degree steam. Note that if the habitat of the bacteria surpasses 65 degrees, the sinus area also is hotter than 65 degrees for 3 minutes.

Ah, this does consider the cyst though, not the trophozoite. My point about inserting boiling hot water/heating your ear up to 65 degree remains valid though.


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Can a cancerous cell from outside cause cancer in a healthy person?
If a cancerous cell enters the body of a healthy person from someone else's blood or something, will that healthy person get cancer? In human beings.

Yes it can.  See https://www.livescience.com/63596-organ-donation-transmitted-breast-cancer.html

@sterid those case involve immunosuppressed patients with end organ failure. This question is about what happens when a healthy person is exposed to cancerous cells

Can a cancer cells from someone else's body cause cancer in a healthy person?

No. Cancer cells from another person cannot cause cancer in a healthy person. The rare cases of transmissible tumors all involve unhealthy or not yet developed persons.
Transmission of tumor cells from one individual to another happens, but is quite rare, and in all cases involves some compromise or reduced development of the immune system. Though tumor cells do metastasize in an individual, when this occurs, tumor seeds must be able to evade the immune system and find an environment suitable for adhesion and replication. Tumor associated cells (non cancerous cells that regulate the microenvironment to make it favorable for growth and replication) are discussed in this seminal paper on cancer biology by Hannahan and Weinberg.  There are similarities to infectious processes, but cancer is not measles. Tumor cells don't shed in comparable numbers, aren't adapted for immune escape in a separate host, and don't express appropriate adhesion proteins for portals of entry on a new host or readily induce tumor associated niches in a new host. The cases where person-to-person transmission of cancer via tumor cell inoculation does occur seem to demonstrate more how cancer cells are not infectious agents.

Donor-related tumors in transplant patients occur in immunosuppressed patients, but are still rare. The low frequency of transmission seems to be due, in part, to screening. The fact that we see this at all demonstrates the significance of transmission route and immune escape.
Maternal-fetal, and in utero twin-twin seem to be exceedingly rare, but have occurred, again, demonstrating the existence, but poor efficiency of transmission. Here, the fetus has an undeveloped immune system. I would not consider this case to be cancer cells causing cancer in a healthy person.
Inoculation of volunteers with tumor cells in a problematic series of experiments at Sloan Kettering in the 50s, transplantation of tumor cells into patients with other cancers, resulted in growth, recurrence after excision, and death in some cases. Transplantation into healthy volunteers (yes, they did this) resulted in nodules that spontaneously regressed. This experiment has since been interpreted as evidence for immune system control of transplanted tumor system in healthy individuals, as compared to growth and progression in a receptive niche in a cancer patient.

So person-to-person transmission of cancer cells is rare and requires an immunosuppressed or undeveloped host, or a host who already has cancer. There are no documented cases of person-to-person transmission to a healthy individual, and documented cases of failed transmission despite a surgical attempt. This is because, unlike an infectious microbe, in a healthy individual, there is not a suitable receptor for adhesion at an exposed or accessible site, a suitable environment for replication, and adaptations for immune escape by tumor cells in the original host are not effective in a new host.
As a side note, there are contagious cancers in other species, but this doesn't seem to be particularly relevant to a question about whether cancer can be transmitted between two humans. Many cancers have transmissible risk factors (e.g., human herpesvirus-8, hepatitis B and C viruses, human papilloma virus 16 and 18, and others)

@Chris I don't believe I have that privilege (moving other people's comments to chat). Feel free to move the whole series of comments to chat if you think they belong there.

Comments are not for extended discussion; this conversation has been moved to chat.

I thought about you guys moving to chat. Anyway, the chat link is above.

The last sentence in this answer seems to refute the others.  If the introduced cancer cell contains a cancer-causing virus then the answer is 'yes', my cancer cell could give you cancer.

@aml good instinct, but that doesn't happen to be the way it works. The virus is the risk factor, not the cancer. If you want to ask a separate question about that, I'd be happy to answer in detail. I'll just give you an example here: blood exposure could, for example, expose someone to HBV, and they might develop cancer 30 years later, but it would be the extracellular HBV, not any cancerous cell that was responsible. The foreign cancerous cell would be rapidly killed by the healthy host's immune system.

@Chris Actually the system gives an Option for the OP or others commenting to move it to chat when it gets quite long. When they do not, I think mods are notified.

@DeNovo Yes, IIRC if there are 7-8 comments between two users within quick succession, it prompts......

If I recall, only one in around 10,000 cancer cells that break off from their primary tumor and get sucked into the lymphatic system survive the trip to the subclavian veins. It's likely that far fewer cancerous cells would survive if they carried significantly more non-self antigens as would be the case with foreign cancer cells.

Before OP edited his/her question, it was a little unclear whether the question was only about humans. The following answer is more general than asked as it also considers cancers in non-humans

Most cancers are not transmissible but some are. We call them (clonally) transmissible cancers.
Transmissible cancers
The most famous case of transmissible cancer is the Devil facial tumour disease in Tazmanian devils. Other cases of transmissible cancers exist in Syrian hamsters, dogs (CTVT), and some bivalves. No such transmissible cancer is known to exist in humans.
Transmission of viruses inducing cancers
There are cases of cancer caused by viruses. Those viruses are transmissible and hence it looks like the cancer itself is transmissible. In humans, this is for example the case of Kaposi's sarcoma-associated herpesvirus.
Transmission via transplant
Finally, there are cases of cancer that can be transmitted to a new person via a tissue transplant. In humans, Kaposi's sarcoma is (again) an example.

Kaposi's sarcoma is not a transmissible cancer. It has a transmissible risk factor, HHV-8, but this is definitely not an example of cancer cells from one person causing cancer in another person. The cancer cells are not the transmissible agent (unlike the transmissible cancers in nonhuman animals). The special cases of Kaposi sarcoma transmission after transplant definitely don't involve healthy recipients. These patients are immunosuppressed, and the cells are, well, transplanted.

@DeNovo You're right. I actually made reference to transmission of Kaposi's sarcoma indirectly via the transmission of a herpesvirus. I clarified that. Thanks. I added the idea of transmission via transplant. If I am not mistaken Kaposi's sarcoma is known to be "transmissible" via both transplant and virus transmission. Please correct me if I am wrong.

Thanks for editing. I'm removing the downvote. I'm not going to upvote because I don't think this directly addresses the question about what happens when cancerous cells enter the body of a healthy person.

The answer states that different cancer types may be transmissible but I think this is wrong, or at the very least misleading. In reality the transmissibility mostly isn't a function of the cancer, it's a function of the host organism. Tasmanien devils have transmissible cancer due to a recent population bottleneck that reduced genetic (and thus immune factor) diversity. Same for transmissible dog cancer cases.

@KonradRudolph both the immune characteristics of the animal and the cellular behavior and genetic characteristics of the neoplasm are important here. I think it is correct to say that only a few types of cancers are transmissible. Tasmanian devils have a wide variety of neoplasms, but only DFT is transmissible.

The answer is no.
From molecular/mechanistic point of view cancer cell itself is not a self-maintaining and independent creature. Even assuming its infinite potential to renew and grow, it still needs constant nutrients supply and tailored microenvironment to survive. Therefore, there is a growing number of attempts to therapeutically target tumour cells niche, see: Joyce JA, Cancer Cell, 7(6), P513-520, 2005 and Belli C. et al., Cancer Treat Rev. 2018 Apr;65:22-32. To overcome this limitations, Cells can undergo epithelial-mesenchymal transition, which allows for migration outside the primary location and is crucial to initiate metastases.
Another important issue is the major histocompatibility complex, which allows to identify and eliminate cells, that contains foreign antigenes. Also, constant immune surveillance in immunocompetent individuals leads to elimination of potential cancerogenous cells. Therefore, patients with immunodeficiencies (eg. with AIDS or on prolonged pharmacological immunosuppression) have significantly higher risk of developing infection-related cancers, such as cervical cancer (HPV) or Kaposi Sarcoma (HHV-8).


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Why is there such a large evening rise of temperature and night sweats in certain diseases like TB, lymphoma etc?
I've heard that it's got to do something with the levels of cortisol which usually dampens the effects of IL-1, but when it's night time the cortisol levels are usually low so IL-1 response is exaggerated.
But why does it occur to a greater extent in diseases like TB and lymphoma? Why is the interleukin 1 effect during night so much greater in these diseases than in case of other viral and bacterial infections?

Where are you getting the idea that temperature doesn't tend to increase at night with other illnesses?

@BryanKrause night sweats are a typical, and at times dramatic symptom characteristic (but not diagnostic) of TB, endocarditis, and certain cancers. I'm not aware of data on the how the mechanism is different from typical fever produced by IL-1 myself. I would say this is a good question.

Of note, there are other instances where fever has a periodicity to it. The quotidian fever of malaria comes to mind, but if I recall, that's associated with the life cycle of the parasite.

@DeNovo But isnt body temperature itself also circadian, with fevers from just about every cause following this cycle (exceptions being anything with an onset or resolution too fast to see it)?

@BryanKrause you're right, body temperature is circadian. I remember a 4th year medical student asking me if a regular increase in temperature by 0.5 C every night meant his patient might have malaria. It didn't. The difference is a matter of degree, but it's a significant degree. Drenching night sweats will make any good clinician immediately suspicious of some specific causes. As to the periodicity of fevers in malaria, the pattern is an increase of 3-4C at regular intervals (the specific interval depends on the species).

@DeNovo I don't doubt that malaria, TB, or lymphoma could have a particularly strong periodicity, but my understanding is that fever of all cause follows a circadian rhythm (again, excluding cases where pyrogen levels are either increasing so rapidly or dispersing quickly, in which case that time course would overwhelm a circadian rhythm, I'm referring to cases where fever is persisting on the order of at least days), whereas OP suggests that this is limited to TB and lymphoma, which seems to be a similar misconception shared by your med student.

OP, I've edited this question to focus on why the nightly increase in temperature is exaggerated in these particular disease (rather than why it occurs at all, since you seem to already have a handle on why it occurs in the general case). @BryanKrause I see your point. I've edited to make it a better question.

I beleive sweating is a sign of Fall in temperature and not Rise?? Am I wrong?

As for some parasitic infections like Wucheria, filarial worms were shed during night, so fever at night. In certain other conditions, temperature outside in daytime is already hot, so body does not need to rise core temperature to kill virus/org ,but need to do say at nights.


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Infant immunization
I know that polio vaccine consists of small dose of polio virus itself, which activates body's immunity against the disease. An infant is given a no of vaccines including chickenpox, tetanus, diptheria etc, see here for details. Does all these vaccine work on same principle ie they contain small dose of respective virus/bacteria to activate hosts immunity?

There are a wide variety of different kinds of vaccines. The basic principle is that the human (and more generally, jawed vertebrate) immune system can identify invaders by recognizing and responding to portions of macromolecules on those invaders called antigens. Vaccines use this principle by exposing the immune system to specific antigens ahead of time, so the immune system is prepared for them. There are, of course, many more details about why that is helpful, but I think they're beyond the scope of this question.

polio vaccine consists of small dose of polio virus itself

Vaccines generally don't involve a small amount of the pathogen itself. Current poliovirus vaccines include an inactivated virus (killed with formaldehyde) that cannot reproduce, and several live attenuated viruses, that is different strains of viruses that can replicate, but do not cause disease. The inactivated virus is used in the united states, but the attenuated virus is used in some other countries.
There are several types of vaccines, and none of them involve small doses of the pathogen itself. The key here is exposing the immune system to the antigen, not the pathogen. As with polio, the major groups are live attenuated or inactivated vaccines. There are many kinds of inactivated vaccines. They can be whole killed viruses or bacteria, or just the important parts. Some vaccines are a just subset of key proteins or polysaccharides.
You can read about all these details in the CDC pink book. Chapter 1 discusses the principles and the different types of vaccines. Chapter 18 discusses polio virus.

Small dose of either killed or live attenuated (they are grown in other animals, so they evolve to better infect that animal, making them slower to infect humans) pathogen...yes, that is the general idea behind all vaccination.


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Concentration dependent cellular processes
Are there any famous biological processes that depend strongly on a chemical concentration reaching a particular value, like some sort of switch?
E.g. if concentration of chemical x reaches concentration y at cell location z (membrane, organelle etc) then a particular biological process will occur?
Thanks

Related: http://biology.stackexchange.com/q/50517/3340

There are several, but I guess the most well known is the neuron action potential, where the concentrations of Na+, K+, and Cl- ions determine the membrane potential of the cell. When the potential reaches a certain level, it triggers the action potential. You can read about this in much more detail on wikipedia, https://en.wikipedia.org/wiki/Action_potential .
But to be pedantic about it, almost every cellular process is concentration dependent.

thanks that helps. I was also thinking along the lines of "everytime a cut off value is reached, this physiological process occurs" something like cell death, or signalling or repair....

"But to be pedantic about it, almost every cellular process is concentration dependent." Do you think that I could find a proper source on that, like a review paper or something - I need to be able to justify this to my supervisor!

What you are basically asking is if there are cellular processes that are thresholded (ultrasensitive). Yes; there are many examples and it would be difficult to list them all.
There are different mechanisms by which such a switch like behaviour can be implemented. Positive feedback loops and co-operativity (in transcription factor binding or enzyme-ligand binding) are common mechanisms by which such switches can be implemented. Have a look at this wikipedia page. For more details you can refer to a book on enzyme kinetics and non-linear dynamics. If you search co-operativity and postitive feedback loops then you will find studies on specific examples.
But as already pointed in the other answer, almost all cellular processes are concentration dependent. There are a very few examples where you can actually observe zero order kinetics.

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What is range of the number of individual organelles in cells
What is the range of the number of individual organelles in a cell?
I am not a biologist but I understand that there's one nucleus and sometimes lots of mitochondria, so I am after the total number.
I understand that different types of cell will have a different number of Organelles in them, (e.g. there might be some very simple cells with 10 but there might be some with many more than that) but I am after the range with some examples. (I need references)
This is for a computational model.
Thanks very much

This varies enormously between species, between eukaryotes and prokaryotes, plants and animals and within the cells of the same species. Also, what organelles are you interested in? Mitochondria? Chloroplasts? Lysosomes? Golgi? Vacuoles? Proteasomes? The list goes on... Have a look at http://en.wikipedia.org/wiki/Organelle

Yes @terdon definitely has a point. In fact, organelle concentration is very different even in different parts of a single cell. E.g. the axon terminals of neurons contain a lof ot mitochondria to provide ATP for continuous firing, while the cell soma (the main body, which can be more than 1m away) contains much fewer of them. Another case, most cells only have one nucleus. Certain cell types like skeletal and cardiac muscle or the placental trophoblasts however fuse and form multinucleated cells.

@terdon I am aware that there are many different types of organelle. I am interested in the range of the total number of organelle (from the simplest cell to the most complex)

BioNumbers is a database that contains exactly this sort of stuff.
For example, I took this from this site:
Number of mitochondria per cell:
Yeast Cryptococcus neoformans cell: ~34
Human HELA cell: ~6000
Mouse L cell: ~1000

that is a cool site!


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Structure and reactions of the cofactors of oxidoreductases such as ferredoxin
I have seen the word flavoprotein being used in place of ferredoxin in few places and vice-versa. I have not found any source that mentions them both together and explains the relation between them.
Examples I have found are:
FAD-Flavin Adenine Dinucleotide/Ferrodoxin Adenine Dinucleotide
FNR-Flavo protein NADP Reductase/ Ferredoxin NADP reductase
Is there any relation between the two? Are they the same or do they serve the same purpose?

Have you tried searching for each of these terms on Wikipedia or the like? You need to search for flavoprotein, ferredoxin (not ferrodoxin), flavodoxin, FAD, FMN, NAD and iron–sulphur clusters. In addition, make sure you know what a protein is and what a prosthetic group or cofactor is. Although it appears from the tags you have used that you have encountered ferredoxin in photosynthesis, it is better to first consider these molecules in their general roles in oxidation and reduction reactions. Then tell us what you have found and any remaining difficulties.

i will try to but at max what i have found(and understood) is that they both are have Fe-S in it. i will do using the keywords provided and get back.

i searched using the keywords you have provided and found that the serve the same purpose as oxidants/reductants. so mainly they take up electrons and then release them. am i right? and the iron sulphur clusters also are co factors in this process. so basically they are present wherever there is a need to move electrons?

I have now provided a more general answer for which I modified the title of the question. I dealt with FNR briefly at the end.

Summary
Enzymes catalysing oxido-reductive reactions (oxidoreductases) do so with the aid of non-protein molecules (prosthetic groups or cofactors) at their active sites. The three main types of such prosthetic groups or cofactors are iron–sulphur clusters, derivatives of flavin (FAD and FMN) and nucleotide derivatives of nicotinamide (NAD and NADP). The groups of proteins incorporating these type of cofactors are often referred to by the general terms ferredoxins (also iron-sulphur proteins), flavoproteins, and NAD(P)-linked oxidoreductases, respectively.
Introduction
The vast majority of enzymes are proteins, linear polypeptide chains folded into specific but irregular spheroidal shapes. In addition to interacting with the reaction substrates, the amino acid side-chains of the polypeptide chains participate in the actual reactions catalysed by many enzymes, and in many cases are sufficient for the catalytic properties of enzymes. However for the catalysis of some sophisticated reactions, additional non-protein molecules are required — metal ions or organic molecules — known generally as ‘co-factors’, ‘co-enzymes’ or ‘prosthetic groups’. This is the case for the various enzymes termed oxidoreductases, which catalyse oxidation/reduction reactions, involving the transfer of electrons.
Nucleotide derivatives of nicotinamide in NAD(P)-linked oxidoreductases
The cofactors found most frequently in oxidoreductases are nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP). The pyridine ring of the cofactor is the electron acceptor, and the oxidized and reduced forms are termed NAD+ and NADH, respectively.

[Own diagram]
Proteins with bound NAD or NADP (non-covalently) are the most common type involved in oxido-reductions, and have systematic names composed of the cofactor, substrate and ‘oxidoreductase’. e.g.
Systematic Name: lactate:NAD+ oxidoreductase
Common Name: lactate dehydrogenase)
Flavin Nucleotides in Flavoproteins
The other common cofactors in oxidoreductases are flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The isoalloxazine ring is the electron acceptor, and the oxidized and reduced forms are termed FAD (FMN) and FADH2 (FMNH2), respectively.

[Adapted from section 14.3 of Berg et al.]
Proteins containing FAD or FMN are called flavoproteins, and are less abundant than NAD(P)-linked oxidoreductases, and a few of them actually perform non-redox reactions. Example of nomenclature:
Systemic name:  short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
Common name: short-chain acyl-CoA dehydrogenase
Iron–Sulphur Clusters in Ferredoxins
Whereas the above two oxidoreductases are common in intermediary metabolism, those containing iron–sulphur clusters (some of which are known as ferredoxins) tend to be involved in more specialized and ancient reactions, such as photosynthesis, tagged in the question. The diagram  shows one particular type (2Fe–2S) of iron–sulphur cluster and its covalent attachment to the ferredoxin through cysteine residues. 4Fe–4S stoichiometries are also found, as well as some others.
The electron transfer involves changes in the oxidation state — Fe(II)/Fe(III) — of the iron.

[Adapted from section 19.3.3 of Berg et al.]
The figure also provides a good illustration of the relationship between a co-factor and the protein in which it resides.
Example of nomenclature:
Systematic name: hydrogen:ferredoxin oxidoreductase
Common name: ferredoxin hydrogenase
The situation here is complicated by the fact that iron–sulphur clusters are found in other proteins besides those termed ferredoxin, including some specialized oxidoreductases involved in the electron-transport chain, and in nitrogenases. The term ferredoxin is historical rather than systematic.
Differences between these oxidoreductase cofactors
The specific roles played by these three cofactors in oxidoreductases is a topic of its own. However, it should be mentioned that an important difference is their standard reduction potentials, the biochemical background to which can be found in Section 18.2.1 of Berg et al., available online.
Ferredoxin-NADP+ reductase (FNR)
Electron transport occurs between the different cofactors in certain circumstances, one of which is photosynthesis where electrons are transferred from ferredoxin to NADP+. The enzyme catalysing this — Ferredoxin-NADP+ reductase — uses the third type of cofactor — FAD!


text:
How to identify the GPD gene when the sequence varies between organisms?
I'm reading a paper on genetic transformation of a fungi and the plasmid used in the paper uses two forms of the same GPD (glyceraldehyde3-phosphate dehydrogenase) promoter to drive a GFP gene, one from Agaricus bisporus and one from Lentinula edodes (GenBank: GQ457137.1).
However, I noticed that the sequences for the aforementioned GPD promoters do not match the reference sequence in GenBank (NC_007251.2) which itself is derived from another organism.
Why are there different sequences for the same promoter? Furthermore, how would I identify the GPD gene in another organism if I'm unable to compare it to a known sequence?
The organism I wish to transform has had it's complete genome sequenced and my transformation would be much more effective if I could use a native promoter like GPD.

I think in general you are looking for a more general answer about finding homologous sequences or analogous sequences. There is a lot of discussion about how you define a homolog/analog and whether it is a sequence homolog or a functional homolog/analog. This question gives a good answer about potential tools to use. You might also be inte

Nice synthetic biology question; want to support the SynBio SE proposal? https://area51.stackexchange.com/proposals/125068/synthetic-biology?referrer=NDY5ZDU3MWM0Mzc2NmU5OWNjMmZjYjRlYzRmOWJhNzRiYjhmNzIzNjAxYTFkYmE5NmZjMjMxZjY2MTkzMzM2MSlXfcGon_KIsoktWMGcYchcm3KOxHLit6rYuYwj6cmN0

@jakebeal Supported!

@doremi Thank you!

I might be misunderstanding you here, but I take from your links above that you want to match the GPD promoter regions from two (distantly related) fungi Agaricus bisporus and Lentinula edodes, to the GPD promoter of Leishmania major, which belongs to a completely different Kingdom!
Promoter regions tend to be relatively poorly conserved between species compared with protein coding regions, even for closely related species. Given the evolutionary distance between the species you are mentioning, the chance you will find any homology between their promoter regions is probably zero.

Furthermore, how would I identify the GPD gene in another organism if I'm unable to compare it to a known sequence?

What I would do is to take the translated GPD protein sequence, which for Lentinula edodes would be GenBank BAA83550.1. I would then use that to search for protein matches using blastp, specifically subsetting for Leishmania major; and use the result to locate the coding gene in the genome. You can also do this in one single step with tblastn, which looks for matches in a translated nucleotide database (see this tblastn example query).
You can then simply take the 1000 bp or so upstream of the coding region to represent your GPD promoter.

This might be an ignorant question, but how can completely different sequences produce the same GPD dehydrogenase? In the blastp, for example, even the translated proteins only have 40% homology in some cases.

As an added example, the GPD protein sequences for KT067727.1 and KM273235.1 are both from the same species (the one I'm transforming), but they vary wildly. How am I to know which one I can use?

This section is not a good place to answer your first question, but in short: not all residues are equally important for an enzyme's activity. See this Wikipedia article on active sites for some intuition.

The two proteins are probably paralogs. Which promoter to choose depends on your experiment and what you might know about each gene's expression. Compare for example the GPD equivalents in budding yeast: TDH1, TDH2, and TDH3. The latter two are expressed in exponentially growing cells, whereas TDH1 is apparently only found in stationary phase.

Related to this question, I want to replace the gpdA promoter from that plasmid with the GPD promoter from KT067727.1 or KM273235.1 (my target organism). If I have the organism in-hand, how am I supposed to design a primer to clone the promoter if the seq varies even within the same species? If I just had it synthesized, how would I decide which accession to use?

To get a comprehensive answer to this you will want to post a separate question where you explain in detail what it is that you want to do. But you cannot expect to use the same primers to clone two different promoters, even if these code for proteins with the same function - same species or not.

I want to clone the same promoter, but am stumped as to why it differs within the same organism. I'll post a clarifying question shortly.

As promised, link to the follow-up question.


text:
What is meant by “unique ligand” on the RCSB Protein Data Bank website?
I went to the https://www.rcsb.org/ site, and searched for some proteins. For each entry, “unique ligands” are listed.
I understand a ligand is a molecule or ion that binds to a metal atom. I don’t understand what a unique ligand is. Why is this important? What can we do with this information?

It is usually helpful to search the documentation of the site in question: https://www.rcsb.org/docs/general-help/identifiers-in-pdb (section "Small molecule Instance ID"). If the documentation doesn't answer your question, then you can post here and explain what is still confusing. Ideally, you would get in touch with the administrators of the database in question to ask about their database-specific terminology. (This term is only for their database, it is not a biological concept.)

@Maximilian Press , it doesnt mention "unique" ligand. I thought it was a biological concept hence my post.

"Small molecules such as ligands, ions, drugs, inhibitors, and individual residues (amino acids, nucleotides etc.) are found in PDB structures... For example, all ligands, water molecules, etc. nearest protein chain A will also be assigned to chain A, though each of these small molecules will have unique residue numbers. So all ligands, waters etc. near a protein with chain ID A will be assigned the same chain ID. However, each of these small molecules and ligands can be specifically located by using unique residue numbers.

Your understanding is incorrect. A ligand at its most basic is a molecule that binds to another molecule. There is no requirement for metal atoms whatsoever. In the context of RCSB (home of the Protein Data Bank) we are only concerned with ligands that bind to macromolecules, the structures of which are presented there — usually proteins. The following definition is in the Glossary on the RCSB site.

ligand - A molecule that binds specifically to another molecule (usually a protein or nucleic acid) to form a complex. A ligand can be another protein, but is often a small molecule.

I’ll assume a protein here.
Original Answer
Unfortunately that Glossary doesn’t explain their usage of “unique” in this context, perhaps because it may be a recent modification. However what it would appear to me to be is an aid to distinguishing those molecules that bind in a biologically significant manner to a protein, from those molecules — metal ions and molecules like glycerol — that only bind to the protein because they are present at a high concentration in the crystallization or other preparation medium. Such molecules are likely to be present in more than one copy, i.e. not unique.
Why not just say “biological ligand” rather than “unique ligand”? The fact that only a single molecule is present doesn’t prove it is biologically significant, and this information would seem generally to be absent from submission information (in my experience). The job of the curators of PDB is to describe rather than interpret.
Edit: 17 June 2021
After inspecting several entries it became evident that my original interpretation of “unique ligand” as “individual ligand” (with a suggestion of biological relevance is incorrect. There are examples of non-biological molecules, molecules present several times, and molecules occurring in different numbers in different identical subunits all listed as “unique ligands” (@canadianer also commented on this.) The bromide ions in protein 2RC3.pdb provides an example.
I wrote to support at RCSB Protein Data Bank and I would summarize the situation as:

Any non-polymer, non-water molecule in the structure is designated in
the RCSB interface (but not in the mmCIF data format) as a “unique
ligand”.

The support at RCSB tacitly acknowledged the unsatisfactory nature of this and stated in their reply that “We will re-visit the use of this term.”.
As the reply was from support, I feel that it is reasonable to quote from it, but thought it better to exclude the name of the actual contact.
In short, “unique ligand” means: each of the distinct small molecule entities present in the PDB entry (i.e. a “non-polymer entity” in mmCIF nomenclature).
The word “unique” is our attempt to describe what an entity means in a brief way.  We will re-visit the use of this term.
Please note that the data is very well described in mmCIF format (https://mmcif.wwpdb.org/; https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity.id.html).
For example, here is an excerpt of the mmCIF file for the 2RC3 entry:
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer     man 'CBS domain'                      15169.631 4   ? ? ? ?
2 non-polymer syn 'BROMIDE ION'                     79.904    39  ? ? ? ?
3 non-polymer syn NICOTINAMIDE-ADENINE-DINUCLEOTIDE 663.425   4   ? ? ? ?
4 water       nat water                             18.015    710 ? ? ? ?
Lines 12 and 13 correspond to the 2 “unique ligands” shown on the structure summary page.

and then is a second message:
To clarify, entity is a chemically distinct part of an mmCIF entry.
For example, looking at entry 4hhb (https://www.rcsb.org/structure/4HHB), there are 2 "unique" protein chains OR 2 protein entities.  There are 2 copies of the alpha subunit (chains A and C; one entity) and 2 copies of the beta subunit (chains B and D; a second entity).

thank you so much for your explanation David. I have been searching everywhere since this post, read so much about ligands . but unique ligands yielded no results.

You are welcome. "Unique ligands" is not a set phrase, which is why you didn't find it — the PDB was just using "unique" as an adjective. Some years ago I looked through the PDB entries for 400 proteins to find ligands and had a terrible job finding which were "real" in the biological sense. Often you have to go to the original paper, and even then it may not be clear.

Any chance you can also explain what a unique branched monosaccharide is refering to? That yields no search results either :(

@HarshDua Again it sounds merely as if it is being used as a descriptive adjective. You need to provide context. Write a separate question, quoting the sentence in which it occurs, the source (name of the book or web link) and what you think it might mean. Then you will have played by the rules and I or someone else will surely be able to provide an answer.

But non-biologically significant “ligands” like glycerol are still listed in RCSB as unique ligands. I think unique ligands in this context is a list of all the small molecules that appear in the structure, but does not include multiple entries for multiple occurrences of the same molecule. This applies to both molecules that have a biological interaction with the protein and molecules which interact only as a result of the experiment.

@canadianer You are right that the situation is not as simple as I stated. Earlier today I was working on the PDB site and took a random protein with two “unique ligands” to post as an example. But… So I have contacted their support for clarification and will update my post when I hear back from them.

I have now (17.06.21) posted an edit to my original answer following correspondence with RCSB.


text:
In what reaction of mitochondrial respiration is hydrogen peroxide an anomalous product?
I understand that hydrogen peroxide is produced in an anomalous manner during mitochondrial respiration, which also produces other by-products or free radicals. Does anyone know the details of the specific reaction in which hydrogen peroxide is formed and what is the normal product(s) of the reaction?

The normal product of mitochondrial respiration is water. Perhaps "incomplete reduction" would be a better phrase than "unpaired reduction".

Perhaps rare, but I think that's exactly what cytochrome c oxidase does.

I found your question unclear, which is why I have voted to close it. I do not think merely asking about the product is sufficient to justify it so I have changed it to ask for the details of the reaction (which will include the product).

I'm sorry but I have modified the question to make it more comprehensive. If you can expand your answer, with links to supporting references, please do so.


text:
Is blood regarded as an organ?
It consist approximately 7 percent of body weight.
By definition organ is composed of multiple tissues. Blood is a fluid, a circulating tissue.
Therefore can we call this fluid system a liquid organ?

I think , blood is an organ due to the composed of different tissues

Hmm... Blood(a connective tissue) in my own opinion qualifies to be called an organ, if we are going by the definition which states that " Organ is a group of different tissues coming together to perform a specific function".
And we know tissue is basically a group of similar cells performing one function. So group of red blood cells in the blood is one tissue, group of white blood cells in there is another tissue,etc. So I think with these two different tissues coming together (with others) to make up the blood, automatically makes the blood an Organ.

Blood is considered a type of connective tissue (sometimes). However, an organ is formed of multiple different tissues. Thus, blood is a tissue, not an organ.

Would it be fair to say that a counter to blood not being an organ is that blood has multiple cell types? But what is key to remember is that tissues are organised structures of different tissues. Blood has very little organisation due to its fluidity.

@Good Gravy I suspect that the fact that blood lacks structure is a reason why not everyone considers it to be a tissue. As far as I know, the multiple cell types themselves are not considered to be separate tissues by anyone (for instance, we don't consider blood to be composed of red blood cell tissue and white blood cell tissue), but then again this is not my area of expertise so I wouldn't be able to say for sure

organs have to be solid or gelatinous to be organs OR tissues in my opinion. otherwise, they are just juices. blood is not a tissue, it is a juice! tissues are called tissues because they are meaty. your brain is tissue. your blood is merely liquid.

While organs are generally considered to have a single, specified function (or perhaps a group of closely-related functions), blood (the fluid inside the vessels, not the vessels themselves) has many different functions:

deliver $O_2$ from lungs to cells
remove waste $CO_2$ from cells to lungs
respond to injury by clotting
carry multiple different types of nutrients by multiple different means (free-floating, carrier protein-associated, lipid particles, etc.)
provide transport for the immune system, which in itself has diverse functions
transport waste products to liver and kidneys
move regulatory molecules around the body (hormones, chemokines, cytokines, antibodies, etc.)
regulate heat in the body
maintain $pH$ and $H_2O$ balance
and probably more I haven't thought of

So, I don't think blood should be classified as an organ, just because of its multitude of uses. Instead, it is vital for the proper functioning of pretty much all the organs in the body, and allows for connections among them.

Any reason for the downvote?

Sorry for the late update. I don't think multitude of functionality is an criterion of being an organ or not. Organs like the liver also have a multitude of uses which are not necessarily related. One could also argue that the functions you listed are also a group of closely related functions (transport and dissipation).


text:
How do cats shed their fur?
Dogs shed their fur twice a year, so I assume this is the same with cats.
What is the mechanism whereby the change in temperature (assuming this is what causes the shedding) leads to the falling off of fur? Is it the same mechanism as balding?

Basic reasons as to why cats shed fur can be found in this link and this link.
An elaborate understanding of shedding in animals including cats can be obtained from this link. Hope that helps.

It would be extra helpful if you could summarize the content of the links in your response. :)

I would suggest that he read and get the info he needs and put in any queries later on. I prefer guiding rather than making it too easy

I would agree if it were only for OP. But what about all the other people who come to Bio.SE to get an answer to this question? For the health of this community, I think having a tiny bit more detail would be a good thing.


text:
Is it possible to condition the body to reduce bruising?
I do combat sports, and in these sports there are a lot of hits that can cause bruising.
I've found that, over time, physical conditioning can reduce and/or eliminate the bruising to the point where even after hard impacts, there is no residual bruising.
However, I was under the impression that it is not possible to "condition" for reduced bruising since bruising is the result of ruptured capillaries, and you can't condition to not rupture blood vessels.
Can someone offer an explanation to why, with conditioning, it is possible to reduce/eliminate bruising?

Hi Leonardo. Thanks. What causes the increased capacity for repair? Is it increased blood flow?

healing, esp speed of repair would be dependent upon your genetics as well as your nutrition

Shigeta, genetics and nutrition has nothing to do with this topic. Please read the question.

@me2 nutrition has a lot to do with healing better actually as I have pointed out in my answer

Bruises are a type of hematoma of tissue in which capillaries and sometimes venules are damaged by trauma, allowing blood to seep, hemorrhage, or extravasate into the surrounding interstitial tissues (reference).  From what I read there seems to be two reasons why you notice a reduction in bruising.
The first would be because there is a deadening of nerve cells where they get used to the pain and eventually less sensitive. There could also be the development of some scar tissue from the bruising which has irregularly developed nerve endings leading to lesser stimulation. (reference 1 and reference 2)
The second reason could be because you yourself get stronger. The Wolff's law states that:

Bone in a healthy person or animal will adapt to the loads under which
  it is placed.1 If loading on a particular bone increases, the bone
  will remodel itself over time to become stronger to resist that sort
  of loading.2 The internal architecture of the trabeculae undergoes
  adaptive changes, followed by secondary changes to the external
  cortical portion of the bone,3 perhaps becoming thicker as a result (reference).

So, repeated stress on the bones of your face/hands should be make them stronger. I don't think your body can adapt to heal faster in an area from repeated bruising as most likely scar tissue will develop from repeated stress on the skin. You can however improve your nutrition and diet to help your body heal better (reference).


text:
Measuring sugar content of a tree
I would like to grow mushrooms on oak trees I can harvest from my property.  I've read that the best results will be when the sap is rising but the tree hasn't budded yet.  The mycelium feeds on the sugars in the logs.
I would love to be able to measure the sugar content so I could accurately asses the sugar content.  Here in Southern Oregon the winters are mild and the leafing out of the oaks varies quite a bit from year to year.
How can I measure sugar content of the sap in a tree?

Interesting, +1. If you don't get any answers here after a few days, try Chemistry.SE.

The soluble carbohydrate can get the mushrooms off to a good start, but it is the cellulose that will be most important for production. Another reason people innoculate logs in winter is because there are fewer spores from competitors in the air, and less work to be done in the field (for farmers).

Yes, @Abe, an excellent point. Also many fungi can degrade lignin so this would also be a carbon source.

@alan even if lignin degraders breakdown lignin and can utilize some of the products, I don't think the lignin itself results in a net benefit to the fungus (because ligninases are so costly to build) it is the cellulose inside the lignin matrix that they are after.

@Abe - I didn't know that - any references?

@AlanBoyd Moorhead and Sinsabaugh 2006 "Theoretical Model of Litter Decay and Microbial Interaction" gives a good summary (see Part 2: Lignin x
cellulose controls).

The difficult step will be getting samples of sap: have a look at the WP page for maple syrup for ideas about methods of tapping into the xylem of your trees.
You will then need to assay sucrose in the sample of sap. There are many commercial assay kits available (Google: sucrose assay), which rely on an enzyme, invertase, to convert the sucrose to glucose + fructose. The released glucose is then measured by a glucose oxidase assay. You would need some kind of colorimeter/spectrophotometer for quantitative results but there is a visible color change, so you could probably get a rough idea of what is going on by visual comparison with a set of glucose standards.
Supplementary
An alternative would be to measure sugar concentration by refractometry: see here and here.

Is sucrose the most common disaccharide in sap?

I can't say for certain. Here is a reference for pedunculate oak: http://onlinelibrary.wiley.com/doi/10.1055/s-2001-12898/abstract Sucrose is 2x more soluble than glucose or maltose, so may be the best choice for transport in aqueous solution. The assay would, of course, pick up glucose.

Seems as if you can collect sap from cutting the end of a twig.  http://tywkiwdbi.blogspot.com/2011/04/adventure-with-birch-water-birch-sap.html  I wonder if, for my purposes, I can just monitor the quantity of sap production?  I'm guessing that when the tree is producing the most sap would be the time that the most sugar will be in the logs I harvest.

A spectrophotometer is a great idea!  http://spectralworkbench.org/sets/show/207 shows spectrograms for various stages of reducing maple sap to syrup.  I'm guessing that a season of collecting and analyzing samples would show me whether sugar concentration varies over the course of the sap run.

Ah, yes, the refractometer looks like the way to go!


text:
Do Acyl Carrier Proteins and Conenzyme A have similar reactivity?
In terms of the reactions they undergo are they roughly equivalent groups?

The acyl groups ligated to CoA and to acyl carrier proteins are actually attached to the same group (a phosphopantetheine group) as shown below, and so have very similar reactivities (i.e. group transfer potentials).


text:
Are there disadvantages to using Rhizobium rhizogenes for genetic transformation?
Rhizobium rhizogenes causes hairy roots, which are transgentic. Are the transgentic roots able to eventually grow normal roots or will they always be hairy in the transgenic organism?

After integration and expression, in vitro or under natural
  conditions, the hairy root phenotype is observed, which typically
  includes overdevelopment of a root system that is not completely
  geotropic, and altered (wrinkled) leaf morphology, if leaves are
  present.  - Cardarelli M, Mariotti D, Pomponi M, Spanò L, Capone I,
  Costantino P. 1987. "Agrobacterium rhizogenes T-DNA genes capable of
  inducing hairy root phenotype". Molecular and General Genetics
  209(3):475-480.

Is this permanent or temporary?


text:
Why is thymine rather than uracil used in DNA?
What is the advantage gained by the substitution of thymine for uracil in DNA?  I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of DNA, which seems fine in theory, but why does the addition of a simple methyl group make the base more well protected?

I have now posted the original question, "Why is uracil, rather than thymine, used in RNA?" separately, as promised.

One major problem with using uracil as a base is that cytosine can be deaminated, which converts it into uracil. This is not a rare reaction; it happens around 100 times per cell, per day. This is no major problem when using thymine, as the cell can easily recognize that the uracil doesn't belong there and can repair it by substituting it by a cytosine again.

There is an enzyme, uracil DNA glycosylase, that does exactly that; it excises uracil bases from double-stranded DNA. It can safely do that as uracil is not supposed to be present in the DNA and has to be the result of a base modification.
Now, if we would use uracil in DNA it would not be so easy to decide how to repair that error. It would prevent the usage of this important repair pathway.
The inability to repair such damage doesn't matter for RNA as the mRNA is comparatively short-lived and any potential errors don't lead to any lasting damage. It matters a lot for DNA as the errors are continued through every replication. Now, this explains why there is an advantage to using thymine in DNA, it doesn't explain why RNA uses uracil. I'd guess it just evolved that way and there was no significant drawback that could be selected against, but there might be a better reason (more difficult biosynthesis of thymine, maybe?).
You'll find a bit more information on that in "Molecular Biology of the Cell" from Bruce Alberts et al. in the chapter about DNA repair (from page 267 on in the 4th edition).

@fredsbend the 2'OH of the ribose and the methyl group of thymine are pretty far away from each other, there is no obvious way they would affect each other.

@user338907 either I don't understand how evolution works, or that paper doesn't (assuming you paraphrased it accurately). As far as I know evolution doesn't need to "see" any future possibility, it simple rolls the dice and whatever works get passed on.

I think it's justified and relevant, I'm just surprised to see that claim from professionals. I'm a layperson when it comes to biology so I'm sure they know better than I do. I would have though the U-T mutations could have occured, perhaps been useless and benign but persisting to some offspring, and then later the offspring developed the advantageous UNG enzyme and both mutations then propagated through the population. I suppose I don't see how some future knowledge of the advantageous result is required.

The existence of thymine in DNA instead of uracil is apparently due to evolution process which made DNA more stable.
Thymine has greater resistance to photochemical mutation, making the genetic message more stable. A rough explanation of why thymine is more protected then uracil, can be found in the article

Arthur M, L., Why does DNA contain thymine and RNA uracil? Journal of Theoretical Biology, 1969. 22(3): p. 537-540.

which gives three major reasons for it to happen:

"Excitation  energy  in  DNA  is  mobile,  and  is  eventually  transferred  to
thymine  residues,  which  are  the  sites  of  radiation  damage."
"Uracil but not thymine forms a stable photohydration product. The dimerization of thymine can be partially photoreversed by irradiation at relatively longer wavelengths, while this process is less effective for uracil dimers because of the competing photohydration reaction"
"Photochemical  mutation  is,  or  at  least  was  at  one  time,  a  serious
problem,  since  there  exists  a  series  of  enzymes  to  repair  radiation  damage.  Therefore  resistance  to  radiation  damage  was  an  important selective  advantage."

Thymine has a greater resistance to photochemical mutation, making the genetic message more stable. This offers a rough explanation of why thymine is more protected then uracil.
However, the real question is: Why does thymine replace uracil in DNA? The important thing to notice is that while uracil exists as both uridine (U) and deoxy-uridine (dU), thymine only exists as deoxy-thymidine (dT). So the question becomes: Why do cells go to the trouble of methylating uracil to thymine before it can be used in DNA? and the easy answer is: methylation protects the DNA.
Besides using dT instead of dU, most organisms also use various enzymes to modify DNA after it has been synthesized. Two such enzymes, dam and dcm methylate adenines and cytosines, respectively, along the entire DNA strand. This methylation makes the DNA unrecognizable to many nucleases (enzymes which break down DNA and RNA), so that it cannot be easily attacked by invaders, like viruses or certain bacteria. Obviously, methylating the nucleotides before they are incorporated ensures that the entire strand of DNA is protected.
Thymine also protects the DNA in another way. If you look at the components of nucleic acids, phosphates, sugars, and bases, you see that they are all very hydrophilic (water soluble). Obviously, adding a hydrophobic (water insoluble) methyl group to part of the DNA is going to change the characteristics of the molecule. The major effect is that the methyl group will be repelled by the rest of the DNA, moving it to a fixed position in the major groove of the helix. This solves an important problem with uracil - though it prefers adenine, uracil can base-pair with almost any other base, including itself, depending on how it situates itself in the helix. By tacking it down to a single conformation, the methyl group restricts uracil (thymine) to pairing only with adenine. This greatly improves the efficiency of DNA replication, by reducing the rate of mismatches, and thus mutations.


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Reaction mechanism and substrate interaction of dopamine beta-hydroxylase
The reaction in which dopamine beta-hydroxylase catalyses the conversion of dopamine to norepinephrine is shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves structural biology?
Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else. I'm really wondering what in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. In other words, what is the structural mechanism behind substrate specificity?

Maybe I'm misunderstanding, but the product obviously has to be epinephrine, so the enzyme will add the OH to that specific place that results in the right product. If you're asking how the enzyme does that, you might want to be more specific about which parts of the mechanism you're interested in.

Evolutionarily speaking - yes - the enzyme has evolved to add OH to that specific place. I'm really wondering what in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. I'll just edit the question to include that now.

It's still not clear what you're asking. At the moment, I would answer: "The enzyme has evolved to do that and the body has evolved to use that molecule. That's just how it is, for some reason that exact molecule was convenient." Or are you asking about the reaction mechanism of the active site? In that case you should say that.

Okay I changed it to say that.

I think he is asking about what is the structural mechanism behind substrate specificity.

May be a good start is at BRENDA database http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.17.1

Dopamine beta hydroxylase is not really substrate specific, it will affect many different compounds.

There are various studies on the mechanism of action of dopamine beta-hydroxylase (DBH).
This review (sorry, non-free article) by Kaufman and Friedman was written less than 10 years after the discovery of the reaction of conversion of tyrosine into [nor]adrenaline in the adrenal gland:
DOPAMINE BETA-HYDROXYLASE - Kaufman S., Friedman S. - Pharmacol Rev. 1965 Jun;17:71-100.
It makes for an interesting read, as they start detailing the history of our knowledge on adrenaline synthesis (well, at least at that point in time!), the various hypotheses and models that were thought of, experiments with radioactive labeled precursors and so on.
They then procede to talk about the mechanism of the enzyme. Without going too much in detail, they report experiments showing that oxygen, ATP and Mg++ stimulate dopamine beta-hydroxylase enzymatic activity, with the following note on Mg++:

[...] Mg++ is required for the uptake of catecholamines by the adrenal vesicles. EDTA inhibits the uptake of the precursor, hydroxytyramine, but does not inhibit the enzymatic conversion to norepinephrine if the vesicles are intact.

They also list the requirement for two cofactors: ascorbate and copper

The first indication that Dopamine-beta-hydroxylase is a mixed-function oxidase was the demonstration of a requirement for ascorbate. It was found that this reducing agent
could stimulate the hydroxylation reaction even in adrenal particles, and the requirement for ascorbate became more pronounced as the enzyme was purified.

Bringing to the reaction:

Dopamine + ascorbate + O2 → L-norepinephrine + dehydroascorbate + H2O

For the Cu:

Only recently, however, was the enzyme obtained in a pure state and the metal characterized by direct analysis. The metal is copper and it is present in a concentration of 0.65 to 1.0 ug per mg enzyme (4 to 7 moles of copper per mole of protein). It can be removed by treatment with concentrated potassium cyanide. This copper-free enzyme is inactive but can be reactivated by addition of Cu<sup++.

They then proceed to detail some basic mechanism of action, which I will not report here for briefness.
A few years later, researchers from the same group authored a book chapter for the American Chemical Society entitled:
The Mechanism of Action of Dopamine β-Hydroxylase - Kaufman S., Bridgers W.F., Baron J - in Oxidation of Organic Compounds, Chapter 73, pp 172–176, 1968 - Chapter DOI: 10.1021/ba-1968-0077.ch073
From the abstract (I do not have access to the full text of this):

Dopamine β-hydroxylase catalyzes the side-chain hydroxylation of dopamine and other phenylethylamine derivatives. Ascorbic acid serves as a specific electron-donating cofactor. The enzyme from bovine adrenal glands contains Cu2+ and a smaller amount of Cu+. When the enzyme oxidizes ascorbate to dehydroascorbate, most of the Cu2+ is reduced to Cu+. Added substrate is hydroxylated, and Cu+ is reoxidized to Cu2+.

To get to some more recent years...
In this review
New insights into copper monooxygenases and peptide amidation: structure, mechanism and function. - Prigge ST, Mains RE, Eipper BA, Amzel LM. - Cell Mol Life Sci. 2000 Aug;57(8-9):1236-59.
A mechanism for Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3) is proposed, and

Since PHM is homologous in sequence and mechanism to dopamine beta-monooxygenase (DBM; EC 1.14.17.1), the enzyme that converts dopamine to norepinephrine during catecholamine biosynthesis, these structural and mechanistic insights are extended to DBM.

A structure of PHM along with a modeling of DBH is shown in Fig 14. You can see the two catalytic copper atoms and the possible binding of dopamine to the site.

They also show a mechanism of action for PHM. Essentially, through the oxydation of ascorbate the Cu++ becomes Cu+ and can then bind an oxygen molecule that will be used to hydroxylate the product:

Finally, a detailed computational model of the enzyme, and its active site is shown in this paper:
Structural Insight of Dopamine β-Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms - Kapoor A, Shandilya M, Kundu S - PLoS One. 2011;6(10):e26509. Epub 2011 Oct 20.
The active site is shown in Fig. 7, where you can clearly see the two copper atoms in purple and green, the most important aminoacids at the active site and two water molecules in red:

(source: plosone.org
Figure 10C shows the interaction of dopamine with the aa of the active site (Fig 10A and B show superposition between rat and human enzymes and Fig 10D shows the interaction of a drug with the enzyme):

(source: plosone.org)

Finally, a remark on your question. You say:

Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else.

As I said somewhere else: not everything has an evolutionary explication, and evolution is not finalistic. This specific enzyme structure appeared at some point and it was evidently working fairly well, and at the time the rest of the pathway may or may not have been like it is at present, but the important thing is that the enzymatic network managed to work together. It could had well evolved to hydroxylate another position, but probably in that case we would have different enzymes downstream. The important thing to remember is that the enzyme did NOT evolve with the finality of oxidizing the beta carbon.

great answer nico, and excellent fair-use quoting to help those without access to the article.

As an aside, I think it's crazy that copyright covers scientific articles for this long - I think copyright expiry should be much shorter for papers.

@Richard Smith: that is very true, and it makes life very difficult for researchers sometimes... (anyway, luckily the last two articles I quoted are free, the last one is under CC license).

The likely catalytic mechanism of dopamine β-hydroxylase, based on molecular modelling and the actual structure of peptidylglycine α-hydroxylating mono-oxygenase, was presented ten years ago in the extensive answer of @nico. The key point is that two copper ions are almost certainly involved in the chemical oxidation mechanism.
However the crux of the question, removing the reference to evolution is:

…the enzyme … add(s) OH to the beta-carbon rather than somewhere else.
I'm really wondering what in the enzyme’s shape makes the OH added to
the beta carbon, rather than somewhere else. In other words, what is
the structural mechanism behind substrate specificity?

which can be stated more succinctly as:
What structural factors in the enzyme determine the position in dopamine where the hydroxyl group is added?
The answer from @nico does not  address this point, and, indeed he appears to dismiss this in a comment in which he writes:

Dopamine beta hydroxylase is not really substrate specific, it will
affect many different compounds.

This, I maintain, is quite misleading: whatever other substrates it may oxidize, dopamine β-hydroxylase is absolutely specific for a single carbon atom when dopamine is a substrate.
So how does the substrate interact with the enzyme?
Ever since the analogy of enzymes and substrates fitting like lock and key, the idea was that the amino acids at the enzymes active site bound the substrate in such a way that the appropriate atoms on the substrate were brought into proximity to the catalytic components of the enzyme, amino acid residues or non-protein co-factors. This has been borne out by the countless protein structures that have been determined subsequently and, indeed, in this respect the question appears rather naïve, despite its chemical sophistication.
Obviously, the interest in this case is in identifying which residues of the enzyme interact with dopamine — perhaps binding the hydroxyl and amino groups and interacting with the aromatic ring. At present we do not know the answer as the single experimental structure available for dopamine β-hydroxylase does not include a substrate or substrate analogue. In this respect the most that comes out of this study (published in Science Advances in 2016 — i.e. since @nico posted his answer) is identification of the active site cleft where Cu is located and which is presumed to bind dopamine, and the modelling of the substrate, as shown below. This is from Fig. 6 of that paper, with the Cu ions shown in blue and the modelled substrate in yellow.

No apologies for posting 10 years after the question first appeared. It was bumped up recently for some reason and I felt it worth providing a different viewpoint and some more up-to-date info.


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

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

I would argue that the "answer" you quoted is exactly the sort unresearched speculation this site is intended to avoid. ——— Codons "code" for amino acids not peptides. Peptides are composed of multiple amino acids — these terms are not synonyms! In addition, codon usage tables for humans are readily available and don't support the idea that use of CCU is strongly favored over CCA (1.75% vs 1.69%).

@tyersome thank you for the feedback, great to know! (This is why such an answer should be posted as a separate answer and not within the question, so that people could vote on it.)

Please re-read the tour and the Help. A question is a question. An answer is an answer. If the poster of a question thinks a particular answer is correct he can accept it. He may be right or wrong but he has made his judgment clear. Posting an answer as an appendix to a question completely negates the SE Model, which is why I have deleted it.

@David Thanks for removing it from the question. Franck originally posted it as an answer, but as it was comprised entirely of a quote from one source, with no original content, it was outside the referencing guidelines here: https://biology.stackexchange.com/help/referencing therefore I deleted it. Better to write your own answer, Franck, using your own words, referring to other content by reference rather than duplicating.

@David -> No answer on my SE question, posted it somewhere else, got an answer there: what should I do?.

@tyersome: true, but that's not actually U being used there in the vaccines (the quote is incomplete/misleading) but m1Ψ.

The article mentioned says:

Why would you do that? As noted above, our immune system takes a very dim view of ‘exogenous’ RNA, RNA code coming from outside the cell. To evade detection, the ‘U’ in the RNA was already replaced by a Ψ.

However, it turns out that RNA with a higher amount of Gs and Cs is also converted more efficiently into proteins,
And this has been achieved in the vaccine RNA by replacing many characters with Gs and Cs wherever this was possible."
So codon optimisation - as Canadianer suggests.
RNA structural reasons
I expect the sequence was also put through a folding analyser (for the mRNA that is) and that may be why not all the codons were optimised to C and G, and why there is an A → U change as well.
If someone wants to use an online tool to show the folding differences, please feel free to add the graphics output to this answer.
It is also possible the designers didn't want the final sequence to exactly match the output of popular optimisation software, to reduce legal arguments about whether the software was used.
Differentiating between vaccine and viral sequences.
Even though the vaccine uses a different base instead of uridine, when researchers check the sequences of mRNA in the future the base differences will make it easy to tell the source.
Why?

In case the mRNA keeps being found in someone's cells long term.
Testing for contamination in the production facility or research lab.
Testing efficacy in cell cultures exposed to virus.
Adding messages such as patent info.

Some of your speculations sounds quite plausible — would you please edit in some supporting references? Does psuedouridine really help the exogenous RNA evade detection? Also note that the question is about CCA->CCU so increased GC isn't relevant, but if you want to include it please put in supporting references.

"reduce legal arguments about whether the software was used" why is that an issue?

A software company making optimisation software might make trouble, even if their software wasn't used. A bit like making sure your returned homework is very different from what you expect your classmates homework to be.

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

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

And more research on the latter aspect (2019)

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

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

Then why change UUU->UUC,  GUU->GUG, etc?

@canadianer: Frankly that one is even more mysterious because "The proofreading ratio of the UUC programmed ribosomes is one-third that of their UUU programmed relatives. From these results ribosomes programmed with UUC are apparently more prone to errors than those programmed with UUU" https://www.pnas.org/content/pnas/86/18/6888.full.pdf

I raised the question because all of the substitutions made in the coding sequence for the signal peptide are towards the most frequently used codons and tend to result in less methyl-pseudouridine in the final product, which seems to contradict your answer with respect to this specific sequence. I don’t know how they selected codons for the entire mRNA, but I wonder if for this sequence their selection was simply based on codon usage rather than trying to incorporate methyl-pseudouridine. Regardless, I found your answer quite informative.

The modification "to ensure the S glycoprotein remains in an antigenically optimal pre-fusion conformation" is the 2P modification of 2 amino acids, not due to codon synonym optimization (that I'm aware of)


text:
Are differing shapes of the acromion congenital or acquired?
In the human body, the acromion is located here:

There exist different shapes of acromion, at least 3:

The frequency varies according to the acromion type:

Some clinicians consider that there exist more than 3 types of acromion:

Are differing shapes of the acromion are congenital or acquired?
{1} says:

Debate continues as to whether the differing shapes of the acromion are congenital or acquired. […] We conclude that the different shapes of acromion are, therefore, acquired as a response to traction forces applied via the coracoacromial ligament and are not congenital in origin.

However, this study was published 16 years ago. What is the current scientific consensus, if any, regarding whether differing shapes of the acromion are congenital or acquired?

References:

{1} Shah, Nirav N., N. C. Bayliss, and Archie Malcolm. "Shape of the acromion: congenital or acquired—a macroscopic, radiographic, and microscopic study of acromion." Journal of Shoulder and Elbow Surgery 10, no. 4 (2001): 309-316. https://scholar.google.com/scholar?cluster=2046701264133216154&hl=en&as_sdt=0,22 ; http://doi.org/10.1067/mse.2001.114681; http://sci-hub.cc/10.1067/mse.2001.114681


text:
Why do raw prawns turn red after sitting in vinegar?
Yesterday morning I put some raw prawns (shell removed) into vinegar (more specific this one), and put them in fridge. When I came back at night all of them turned red, which looks cooked, except those not covered by vinegar.
Why do the raw prawns change colour?

Heat and Acids denature proteins.

To me, this should be more suitable for Chemisty-SE.

The way I understood lobsters was that their shells have molecules of many different colors, giving them a mottled green-brown appearance. When cooked, the non-red molecules are destroyed, leaving only the red color. Vinegar may do something similar to the non-red molecules by being acidic, maybe the pigments are like pH indicators. I know shrimp aren't lobsters, but are probably close enough.

The prawn has proteins (meat, muscles).
Beef is red because the muscle proteins in it have a molecule that binds oxygen called myoglobin (whereas our red blood cells have hemoglobin that allows them to carry oxygen better).
In fish you know the meat is white because there is no myoglobin present (in the muscle proteins), but another molecule that still binds oxygen but doesn't look red.
When you add heat or acids (vinegar) to the meat, the proteins get denatured, change their shape and their colour too. You get red shrimps by heating the proteins in them.
Hope this helps

@Him , please let me know if you understood my answer and if you found it helpful please mark the question as checked


text:
Short, concise, practical manual for doing experimental biology
I am am physical scientist working in biology, and have recently started doing experiments. I would like a manual akin to "Numerical Recipes", but for the lab: straight forward, easy instructions on how to do the (100) most basic biology experiments - PCR, cloning, etc. I realize that a lot of these depend on kits, and specific equipment, but it seems like there still should be something that would give you the outline of how to do these experiments. Does anyone know of a resource like this?

Kits are often a good way to do a basic procedure, but don't use them as black boxes, and learn how to make the buffers and buy the reagents individually because you can often save money doing it that way instead of buying more kits. Also allows you to modify the procedure to fit your research.

Molecular Cloning is updated and in its 4th edition.  Every lab used to have it.  Its comprehensive, but really no book could be complete.

Along with @shigeta's answer, I'd highly recommend Springer/Humana Press's series Methods in Molecular Biology, which started out as just a single collection of protocols (as I recall...) and is now a series of 1208 books, published between 1984 and 2015. There are a ton of protocols available online at places like Springer Protocols and Cold Spring Harbor Protocols, as well as at many locations across the 'net, with varying degrees of accuracy, reproducibility, and clarity. As you mentioned, you can do just about every molbio assay with a kit nowadays, and the manufacturer's websites (like Qiagen's) are often great resources, and frequently (but not always) include some scientific background as well, if you want to go back to the literature. There are also sites (some independent, some sponsored) that cater to specialized areas of research. For example, I work in immunology, and the Human Immunology Portal is a pretty good resource for basic and advanced protocols and assays.
So, there are quite a number of digital resources available, which I actually prefer because there is a greater chance that they are kept up-to-date, and will have new technological advances much more quickly than they are likely to show up in a revised edition of a book. Best of all, most of the online resources are free, and if you have academic access through your institution, you may be able to access some of the pay sites as well, such as the archives area from Cold Spring Harbor.


text:
What does phasing mean?
What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually means?

This refers to haplotype phase (aka gametic phase). This essentially means knowing which allele belongs to which copy of the chromosome, or alternatively, which alleles appear together on the same chromosome.
In short-read sequencing, for example, it is difficult to resolve the haplotype of two heterozygous SNPs if they have not been covered by the same read. If you observe A/a and B/b, you do not know whether you have AB + ab or aB + Ab. So you would say you do not know the phasing.
See the Wikipedia links for more information.

Can you shed some light on why this process is called phasing? It reminds of phase as in waves which makes no sense.

phasing is the relationship between adjacent alleles on the same chromosome i.e. if they are in cis or trans configuration. In other words, weather two alleles are indeed on the same chromosome or on different chromosome. One of the reason alleles get shuffled is by process called recombination where chromosome exchange happens. Majority of current methods infer the phase using linkage disequilibrium principle however with advent of whole chromosome sequencing it's possible to determine empirically the phase from related samples. i.e. father, mother, son


text:
Do snail shells increase the number of rounds with age?
Do snail shells increase the number of rounds with snail age?

I think my answer to this question can help

Yes. Once secreted the shell cannot increase in size, so that the growth of the body is accompanied by continuous growth of the shell, i.e. by the gradual increase in the number of the whorls.
This also means that the topmost whorls are the oldest and the aperture marks the front of the new shell.