text:
The colors blue and golden (yellow-orange) and the human eye / brain
Many years ago I read a review in an article about why we love for example Lapis Lazuli so much. The article stated that there are two specific colors, yellow as golden (when it glows or shines) and a very certain type of blue (the one of Lapis Lazuli) or also a shiny dark blue. I think we are not talking about the way those are absorbed in the eye but rather which color has the biggest impact on our eyes. Like often we say red is a warning color and we see red as most 'aggresive' color this article stated that in fact this type of blue and gold is the one that causes the strongest respond in the human brain. They also added a chart back then where you could see this 'response' for each wavelenght.
I was unabled however to find anything related. I don't think it has to do with the absorption peaks of the human eye, the graph looked a bit different. Has anyone heard about this before?


text:
Could plasmids and conjugation mechanisms be used against antibiotic-resistant bacteria?
I'm surprised no one has mentioned something like this.
Plasmids are often exchanged between bacteria, sometimes through conjugation. In particular, conjugation could be considered an "open-port" vulnerability.
Intuitively, there are several schemes that exploit plasmids and bacterial conjugation that could form alternatives to antibiotics:
1: Pwnage by Conjugation
A specially engineered nanoscale capsule or specially rigged bacterial cell is programmed to call out to target bacteria for conjugation. When the conjugation tunnel is opened, the capsule or rigged bacterial cell floods the target bacterium with toxins or malicious RNA designed to sabotage it.
2: Fake Conjugation
A specially designed novel antibiotic contains a conjugation-signaling structure. When a bacterium docks with the antibiotic molecule, the antibiotic irreversibly latches on and tears a massive hole in the bacterium from the inside.
3: Backdoor Plasmids
Plasmids that confer significant advantages are isolated from naturally-occuring bacteria and a special "crash gene" is added to the plasmids. The modified plasmids are implanted back into bacteria that are known to spread them around.
The crash gene's promoter listens for a small set of chemical cues. If it detects a certain threshold of 1 of these cues, it becomes active and sabotages the bacterium. The gene could code for a toxin that specifically damages bacteria. Alternately the promoter could be specifically designed so it never releases the chemical cue, forcing the bacterium to repeatedly produce a garbage produce and waste its resources.
4: Bad Neighbor Plasmid
This might be more difficult to build. A synthetic plasmid encodes 2 products: The first confers a significant benefit to prevent bacteria from discontinuing it through natural selection. The other product is periodically ("randomly") transcribed and vandalizes other plasmids, causing large numbers of nonsense mutations. A set of special markers on the synthetic plasmid protects it from vandalism by its own product. This could silently remove antibiotic resistance from bacterial populations and the bacteria have no way of "knowing" they've been sabotaged until it's too late.

What is the question?

If we assume all of these things could be practically done at least at some point in the future, here are the problems I see with the suggestions, and why they might not work (others may spot additional ones).
1 Translocation of a sabotaging 'agent' via the conjugation apparatus.
This basically already exists, look up the various secretion systems of bacteria. In particular, the Type 6 Secretion System does exactly this (though with a somewhat limited target range).
The first paragraph on wiki summarises:

The type VI secretion system (T6SS) is molecular machine used by a wide range of Gram-negative bacterial species to transport proteins from the interior (cytoplasm or cytosol) of a bacterial cell across the cellular envelope into an adjacent target cell.

The reason this wouldn't work is that bacteria have already evolved to deal with such mechanisms, and one we engineer is unlikely to fare much differently.
You can take it from me (as my PhD concerns exactly this!) that changing what the secretion systems translocate, while possible, is very difficult.
2 Phony conjugation
Antibiotics tend to be small molecules. They bind and dock with enzymes or substrates in order to inhibit some kind of activity typically, e.g. cell wall synthesis in the case of Beta-lactam antibiotics such as penicillin. I'm not sure how you imagine it would "tear a hole in the bacterium" really?
Related to the T6SS, are R-type Pyocins, which are co-opted bacteriophages that sort of do this. It requires no conjugation, and the currently proposed mechanism is that they either deliver a payload of toxins or molecules in to the cell by puncturing the exterior, or they simple create a pore in the membrane causing cellular depolarisation and death. As with phage and antibiotics however, these mechanisms can have resistance evolved against them.

As an additional point, unless you could somehow guarantee that the conjugations were sabotaged or ineffectual in some way, promoting conjugation artificially is almost certainly going to aid the spread of resistance and virulence determinants, actually worsening the situation.

3 A suicide plasmid
It is not trivial to 'confer significant advantages' on a cell. Most plasmids are maintained by amelorating a significant disadvantage that is often supplied artificially, e.g. auxotrophy or antibiotic selection. Given the 'choice' bacteria tend to kick out the plasmids unless they simply cannot afford to live without it. Maintaining the replicon is an expensive process in terms of cellular metabolism and resource utilisation.
'In the wild' the weaponised plasmid would likely not persist long enough to be translocated in to any target of interest in a significant enough proportion to have a real effect. The key is that and of these ideas mentioned cannot simply kill a single target cell, as they will not have an appreciable effect on the population. The bacteria will recombine or straight up remove the plasmid if it's in any way deleterious or even neutral to them, until they've 'corrected' the problem.
Addiction modules and toxin-antitoxin systems are common to see in natural plasmids, as with the other ideas mentioned. Bacteria can recombine out the 'poison' though, and eventually over time lose the plasmids. If the toxin is encoded on the chromosome, it's a little more robust.
4 Bad plasmids
See addiction modules and toxin-antitoxin systems above.
I'm afraid in general I think you're underestimating evolution!

On #2: If enough phony/dangerous conjugation agents were present (such that conjugation is much more likely to be lethal than helpful), that would promote the growth of bacteria that avoid conjugation and slow the spread of plasmids. Another effective approach might include lysogenic (conditionally nonlethal) bacteriophages that only sabotage their host cell on the presence of any of a small set of synthetic signals.

While you may be right in your first point (I don't have any facts to say the dynamics wouldn't work like that, though I'm dubious), conjugation is not the only way bacteria obtain plasmids, so I'd say it's still very unlikely to be viable. On your second point, about triggering lysogeny of bacteriophages, that is both feasible, and practical - and we are actually doing just that (or a slightly modified but similar idea) in my lab presently.

Could plasmids and conjugation mechanisms be used against antibiotic-resistant bacteria?
Apparently yes. At least, it's plausible. The study is very new and, even though it was conducted in vivo, it was still under artificial conditions. We'll have to see what comes out of it.

Most important modern antibiotic resistance genes spread between such species on self-transmissible (conjugative) plasmids. These plasmids are traditionally grouped on the basis of replicon incompatibility (Inc), which prevents coexistence of related plasmids in the same cell. These plasmids also use post-segregational killing (‘addiction’) systems, which poison any bacterial cells that lose the addictive plasmid, to guarantee their own survival. This study demonstrates that plasmid incompatibilities and addiction systems can be exploited to achieve the safe and complete eradication of antibiotic resistance from bacteria in vitro and in the mouse gut. Conjugative ‘interference plasmids’ were constructed by specifically deleting toxin and antibiotic resistance genes from target plasmids. These interference plasmids efficiently cured the corresponding antibiotic resistant target plasmid from different Enterobacteriaceae in vitro and restored antibiotic susceptibility in vivo to all bacterial populations into which plasmid-mediated resistance had spread. This approach might allow eradication of emergent or established populations of resistance plasmids in individuals at risk of severe sepsis, enabling subsequent use of less toxic and/or more effective antibiotics than would otherwise be possible, if sepsis develops. The generalisability of this approach and its potential applications in bioremediation of animal and environmental microbiomes should now be systematically explored.

The idea is that a natural, addictive plasmid conferring antibiotic resistance is displaced from a bacterial community by an incompatible plasmid expressing the appropriate antitoxin for the addiction system, and tetracycline resistance.

Replicon (solid circle), antitoxin and toxin genes (arrowhead, arrow) and antibiotic resistance genes (CTXR, orange and TETR, black solid blocks). Interference plasmid not excluded by entry exclusion system (EES) is incompatible (INC) with resident CTXR plasmid and is selected by TET.

In the top pathway, conjugation has not occurred and the bacterium retains the original plasmid. Tetracycline kills this population. In the bottom pathway, conjugation has occurred and, because of the incompatibility between the natural plasmid and the interfering plasmid, binary fission results in asymmetric segregation of them. Again, the natural addiction system is bypassed because the interfering plasmid expresses the antitoxin. The population containing the original plasmid is killed by tetracycline but that containing the interfering plasmid is resistant. However, because the this plasmid doesn't have the complete addiction system, it is lost over time in the absence of selection. Thus the resulting bacterial population is antibiotic susceptible.
You may ask why not just use tetracycline to kill all the cells in the first place. That's not the point! This is a proof of concept.

Purifying selection using antibiotics is not ideal, both because of the effects of the drug on other cells and because effective antibiotics for this purpose may be increasingly hard to identify in future. TETR bacteria are not uncommon in the human gut but TETR (or FOSR) populations that arise by plasmid acquisition will not only lose their TETR or FOSR plasmids spontaneously but are made immediately vulnerable to other commonly used antibiotics (e.g. GEN, CTX) in the process. A target plasmid that acquires FOSR by recombination with the interference plasmid will likely acquire the immediately adjacent antitoxin. An important future challenge is to develop interference plasmids with non-antibiotic selection but the inclusion of fosA3 also means that plasmid eradication is compatible with existing use of fosfomycin as a ‘rescue’ therapy of last resort.

This was in 2017, have further developments occurred here? I think de-antibiotic-resisting bacteria would probably be an incredibly useful technology to have

Your ideas are not bad, but in all cases there are a few reasons that make them pretty much unusable in a real world (medical) application. Also none of your approaches solve the problem of resistance: bacteria can just become resistant to this new type of treatment (the bacteria using slightly different conjugation methods are immune and will have an evolutionary advantage).
1) This could work - but not today.
You either need some sort of nanobots or very advanced genetic engineering to pull it off. While the technology to make such advanced 'killer machines' should be available within the next few centuries, the ethical question of 'letting them loose' into a human body or the environment will always remain very tricky.
2) I think this is too complicated.
Antibiotic drugs are very small chemical molecules whereas the bacterial conjugation machinery is very large biological complex. Trying to make something bind the machinery and then make it able to kill the bacteria is superfluous - you could just make antibodies against the bacteria in the first place (they can also be coupled with effectors). Also it does in now solve the problem of evolving resistance
3/4) The added level of complexity does not help.
Trying to trick bacteria with 'trojan horse' plasmids won't work. First of all evolution will work against the whole plasmid and just because it has one favourable gene does not been bacteria can't just get rid of it, if it would kill them otherwise. Secondary, mutations can act on the genes on the plasmid indecently so the bacteria can just shut down the part that's supposed to kill them and keep the rest.

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What is the difference between a response element and a enhancer?
I have been confused as to the difference between a response element and an enhancer.
Wikipedia has the definition of response element as the following:

Response elements are short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes.

Wikipedia's definition of enhancers:

In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.[1][2] These proteins are usually referred to as transcription factors.

They seem almost the same. What are the main differences?
The only difference I can see is that response elements can both halt transcription or allow for it. While enhancers only promote transcription if the transcription factor is present.
Is this the difference between the two, or is there something else that differentiates them?

Enhancers specifically bind transcription factors in an effort to obtain robust rates of transcription, in a very general fashion and may be upstream or downstream of a promoter. Remember that you don't need to receive a signal to produce housekeeping genes, regulated by general transcription factors, because they're always needed (in part). A response element can enhance or repress transcription depending on the stimulus.
Vitamin D response element (VDRE) is a fair example: In response to your extracellular calcitriol or 1,25(OH)2D, the vitamin D receptor will complex with a number of proteins that bind at the VDRE, controlling transcription of various vitamin D-controlled gene targets.

Vitamin D activity is mediated through binding of 1,25(OH)2D3 to the vitamin D receptor (VDR), which can regulate transcription of other genes involved in cell regulation, growth, and immunity. VDR modulates the expression of genes by forming a heterodimer complex with retinoid-X-receptors (RXR).

Source: http://www.wikipathways.org/index.php/Pathway:WP1531
And just as well, other promoters such as that for pro-parathyroid hormone contain VDRE sequences that suppress it's transcription (ref).

I had the notion that transcription factors binding to enhancers can also have a ligand binding domain. Which would mean that it would be activating depending on a stimulus. If my notion is correct, what then differentiates them?

Essentially your RE is always in the promoter, and the action can be bidirectional, either activating or silencing, based on the same stimulus across genes that contain that RE. You enhancer can be anywhere and always up-regulates in response to any number of variables that site reacts to.

You know it just cant be miles away from the TSS because it still needs to interact, so when I say anywhere I mean not just in the promoter.

A response element is a DNA sequence that binds with a set of one or more transcription factors/cofactors/factors  in order to regulate transcription. A response element is usually specific to a given stimulus that a cell needs to respond to.
A promoter is a sequence of DNA located nearby a gene and contains one or multiple response elements and up-regulates transcription
Once a promoter’s response element is binding with factors and is beginning to be set up for its role in transcriptional up-regulation of the nearby gene, the response element of another, second sequence of DNA (typically farther away from the gene than the promoter) has its own response element that in turn begins to bind with its own factors.
The factors of this other, second sequence interact directly or indirectly with the promoter’s factors to enhance the promoter’s transcriptional up-regulation to the gene. This other, second sequence is called an enhancer.

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Assay for Glycosyltransferase
I want to do an assay to see, if an ordered enzyme is active or not. It's a glucosyltransferase from S. mutans which hydrolyses sucrose into fructose and glucose. It then connects the glucose-monomers to dextran. Our idea is to detect the free fructose. There are many tests for this, for example the Fehling-Test or the Tollen-Test. The trouble is, that they have to be heated on a waterbath - I think that's very suitable for microwell-plates. Maybe someone here has a better idea how to measure the enzyme's activity?

If you've access to a PCR machine or a heating plate with a microplate with a heating block you can use that

There are indirect enzymatic assays to detect fructose based on NADH production by glycolytic enzymes.

Yes, true, but they are very expensive (about 400 Euro).
Thanks for the answers, but we now sticked in to a new method with 3,5-dinitrosalicylic acid (photometrically), which also detects free fructose.

What about this kit? http://www.sigmaaldrich.com/catalog/product/sigma/fa20


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What is the distinction between deoxyribonucleases and restriction enzymes?
Both deoxyribonucleases (DNases) and restriction enzymes are endonucleases (some DNases can be exonucleases).
They both break the bonds between nucleotides. Therefore, what is the difference between the two?
My original thought was that restriction enzymes, unlike DNases, cut at specific sequences of DNA. Then this raises the question of whether restriction enzymes are just a category of DNases, but I have found no sources to back that up. Also, according to this Wikipedia article:

There are more than 900 restriction enzymes, some sequence specific and some not...

This further erodes the distinction I had created between the two types of nucleases.

You already mentioned that all restriction enzymes are endonucleases but DNases may be endonuclease or exonuclease

...so could u be a bit more specific.

This paragraph from Lehninger's Principles of Biochemistry (in my opinion the best textbook on biochemistry) is very didactic:

 DNA Is Degraded by Nucleases
To explain the enzymology of DNA replication, we first introduce the enzymes that degrade DNA rather than synthesize it. These enzymes are known as nucleases, or DNases if they are specific for DNA rather than RNA. Every cell contains several different nucleases, belonging to two broad classes: exonucleases and endonucleases. Exonucleases degrade nucleic acids from one end of the molecule. Many operate in only the 5'→3' or the 3'→5' direction, removing nucleotides only from the 5' or the 3' end, respectively, of one strand of a double stranded nucleic acid or of a single-stranded DNA. Endonucleases can begin to degrade at specific internal sites in a nucleic acid strand or molecule, reducing it to smaller and smaller fragments. A few exonucleases and endonucleases degrade only single-stranded DNA. There are a few important classes of endonucleases that cleave only at specific nucleotide sequences (such as the restriction endonucleases that are so important in biotechnology; see Chapter 9, Fig. 9–3).

We can conclude that restriction endonucleases (or restriction enzymes) are a type of endonuclease, and that endonucleases are a type of DNAse. So, all restriction enzymes are DNAses, but not all DNAses are restriction enzymes.
Besides that, we can conclude that your initial statement ("Both deoxyribonucleases (DNases) and restriction enzymes are endonucleases") is wrong.
For a more complete table have a look at Molecular Biology of Nucleases, page 18.
Sources:

Lehninger, A., Nelson, D. and Cox, M. (2000). Principles of biochemistry. New York: Worth Publishers.
Mishra, N. (1995). Molecular biology of nucleases. Boca Raton [u.a.]: CRC Press.


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If you have water on you, does it *actually* cool or down, or do you just *feel* cold?
I'm sure many people have noticed after getting out of a shower or out of a swimming pool that moving air makes them feel colder. It seems like one way to beat the summer heat is with water and also moving air. But, does having water on your body actually cool you off more with moving air, or is that simply what it feels like because water cools differently than air?

I'm voting to close this question as off-topic because it belongs to Physics.SE

@Remi.b It's really more about what people feel, the motivation is that people feel cold. You really think a bunch of physicists are biology experts who know the chemistry behind what would cause a different feeling? You can't determine the answer belongs in physics unless it already becomes answered and the answer is purely physics.

Could the question be rephrased Why do we not sense temperature but thermal energy transfer?? If yes, then I'd agree it belongs to Biology.SE

I don't think this is a physics question; it has everything to do with biology and how we perceive changes on our skin.

When your wet skin experiences air flow over it, water will evaporate. Evaporation causes cooling, as energy is transferred from the remaining water molecules to the ones that evaporate - energy in water molecules is being experienced as heat. Less energy -> less heat -> sensation of cooling.
This is why you feel cold, as opposed to when you stay submerged in the pool, or your skin is dry and it is just air movement - no evaporation is taking place.

For extra points do you have any references that can support that?

@DaneJoe This is rather basic chemistry, covered by any introductory chemistry text. Although we like references at biology.SE, usually we don't bother for basic textbook knowledge (it gets a bit too pedantic).

@BryanKrause Wrong. We don't know that enough water is evaporating at a high enough rate to account for this phenomena. I've studied chemistry, we definitely didn't study temperature change due to water evaporation induced by moving air.

It doesn't matter if the air is moving or not, except to speed the rate of evaporation. Surely in chemistry you learned about the heat of vaporization, which is quite high for water because of hydrogen bonds.


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Could homoplasy occur within a clade?
Consider the below phylogeny. taxon1 and 2 are sister taxa but:
- share a brown color coat
- differ from their closest common ancestor (light color coat)
Is this a case of homoplasy (Analogous trait)?

The definition of a homoplasy is a common characteristic to 2 or more branches, not shared by their common ancestors, so I'd say yeah, this qualifies as a homoplasy.

@MoBo If you feel like one of the two answers answered your question, you can click on the check mark next to your favourite answer.

According to Furtado and Pessoa (2014):
Homology: A similarity due to common ancestry.
Homoplasy: A similarity not due to common ancestry.
And, according to Futuyma (2006):
Homology: Possession by two or more species of a character state derived, with or without modification, from their common ancestor.
Homoplasy: Possession by two or more species of similar or identical character state that has not been derived by both species from their common ancestor
Therefore, the answer is quite clear: the trait here is an homoplasy, since it's not present in the common ancestor of A and B.
PS: Homoplasy and analogy are not, technically speaking, synonyms. Analogy is a special case of homoplasy.
PPS: A clade is just a monophyletic group. For instance, the hominids form a clade, Mammalia is also a clade, Vertebrata is a clade, even Animalia is a clade. Therefore, a clade can be very exclusive or very inclusive. Because of that, I'm skipping the title of the question ("Could homoplasy occur within a clade?"), whose answer is obviously yes1, and focusing only on your second question: "Is this [image] a case of homoplasy?"
PPPS: Furtado is me, and that quote was translated from the original.
Sources:

Furtado, G. and Pessoa, F. (2014). Liçoes sobre sete conceitos fundamentais da biologia evolutiva. Brasília: Editora UnB. (translation: On seven fundamental concepts of evolutionary biology)
Futuyma, D. (2006). Evolutionary biology. New York: W.H. Freeman.

1For instance, my metamery and the metamery of an earthworm is an example of homoplasy. Both myself and the earthworm belong to a clade called Animalia. Therefore, there is homoplasy within a clade

Thank you Gerardo for your ample response and clarification.

I added my own answer just because I wanted to emphasize a little bit on the concept of lineage and on the importance of not seeing a clade as something too atomic but your answer is good +1

What exactly is the difference between a homoplasy and an analogy?

Could homoplasy occur within a clade?

Note that the all of life is a clade! A clade is any mono-phyletic tree. So any homoplasy observed on earth is necessarily within a clade!
Let's replace the term clade by species to further the discussion

Could homoplasy occur within a species?

Wether you consider two lineages as being part of the same species or not changes nothing to the question of whether their shared trait was already present in the common ancestor or not. You can have homoplasy within a species and even within a population. Of course, the lower level you go, the less likely it is to observe a clear case of homoplasy.
It is important not to view a clade (incl. species and subspecies) as something too atomic. As a whole and single clearly defined entity but rather a whole complex tree (or network) of lineages. Any lineage may have evolved a trait that has already evolved independently in another lineage whether the two lineages are very closely related (within the same subspecies) or very distantly related. In this regard, you might want to have a look at this post.
So, yes you can observe homoplasy when comparing lineages within a clade.


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can we say that pumps are carriers that need ATP?
I know that pumps always use ATP , but i don't know what is the relationship between carriers and pumps .
are pumps a subdivision of carriers ?

see WP membrane transport protein

Yes, you can consider pumps are carriers used for active transportation (needing ATP).
A carrier is a specific type of transport proteins. They differ from channels or pores in the fact that during a certain instant, carriers only have one side of the protein open1. While pores are continuously open, and channels are either open or closed2.
Carriers can be involved in active transport3 or facilitated diffusion (passive)4. But as you mentioned, pumps always are used for active transport. Pumps, as Bryan pointed out in the comments, are just a name given to some transport proteins that use active transport, but not all active transport proteins are labeled as pumps.
I hope this clarified things for you.

Not all pumps use ATP. Some things named pumps use ion gradients. It's not very precise terminology.

Would a more precise terminology be to remove "that use ATP to function" and replace it with active transport? As ion pumps using gradients would be using secondary active transportation.

Yeah. I think the optimal answer would also address that "pumps" aren't a special protein category, just a naming convention for some proteins involved in active transport. Other proteins with nearly identical function are known by other names, like "transporters", without an obvious defining characteristic (that I am aware of). That is, all pumps use active transport, but not all active transporters are given the name "pump". Those that use ATP directly, like Na/K pump, are also known as "Na/K ATPase" etc.

thank you for your answers ;
but i have another question ; 1- can we say that all pumps do a kind of active transport but don't need ATP , 2- can you give me an example of one transporter that do active transport but isn't a kind of pump ? – user35622 47 secs ago   edit

1- All pumps do active transport, but not all use ATP to power (secondary active transport). 2- An example of a whole family of active transporters the don't use "pump" are the ABC Transporters (Wiki - ABC Transporter)


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How does adjuvant enhance the immunogenicity of antigen?
My question is, How does adjuvant enhance immunogenicity of antigen?
I just want to know deeply about it , Any suggestions will be helpful!

A couple of points as this is your first post. A title is independent of a question, so even if your title is your question you should repeat it in the body of the question. If I am reading this on a phone I might not be able to see the title. And if your title is deemed poor, it might be edited. The second is that this is a quite broad and basic area. I find it difficult to understand why you couldn't find anything on the internet as a search for "adjuvant and immunogenicity mechanism" brought up several promising articles.

Well, it was a miscommunication between myself and the actual person who had this question and for the title concern, I'll fix it!

It depends on the adjuvant. I think this is too broad.

This is a quick answer to a very broad question since the mechanisms of adjuvants are very different. I'll try to summarize just a few. For a deeper understanding please start reading this paper and its references.
1) Aluminum salts (aluminum phosphate or hydroxide)

Studies suggest alum salts work by causing the formation of an antigen
  depot at the inoculation site from where the antigen is released slowly.
  The trapping of soluble antigen in the alum gel may also increase the
  duration of antigen interaction with the immune system. Other
  mechanisms of action involve complement, eosinophil, and macrophage,
  activation and increased efficiency of antigen uptake by antigen
  presenting cells seen with particulate matter with a size under 10
  micron.

2) Calcium salts
They work pretty much like aluminum salts but they are much better tolerated by the organism.
3) Bacteria-derived (peptidoglycan or lipopolysaccharide)
They are naturally recognized by the immune system and for this reason, they are used to simply boost the immune response.
4) Emulsions
They form a depot at the injection site, enabling the slow release of antigen. The immune system has more time to recognize the antigen and react.
5) Liposomes
They help to extend the half-life of antigens in the blood leading to a higher antigen exposure to antigen presenting cells after vaccination. A Very similar effect is achieved using microbeads made of artificial polymers.

Unfortunately the reference cited is relatively old (2004; a decade is a long time in this rapidly-moving field) and so the answer is dated as well.  The depot effect has never been shown to be real. Aluminum salts and liposomes have both been linked to NLRP3 inflammasome and uric acid modes of immune activation; and so on. More recent references include here and here, but there are literally hundreds of recent papers on the subject.

@iayork thanks for the extra references. My answer is far from complete, it's a very basic overview. The reader should consult further the literature, of course.

I voted to close the question as it's far too broad to answer properly in this format and shows no evidence of basic research.

@alec_djinn's  Sorry I didn't knew much about immunology or vaccination, I just had the basic knowledge and have just started studying the the subject, I appreciate your efforts and will from now do my research beforehand.

@iayork your link to the nature article is broken.


text:
Biological meaning of read length
I have some FASTQ files in two datasets which are sequences from 16Srna region. The first dataset is amplicons form V4 region and the second is V3-V4 region.
However all the reads are 250 nucleotides long, whereas one region is strictly included in the other. So what is the biological meaning of the length?
I'm expecting reads to have the same length as the sequenced/amplified region. I don't know the size of the regions but one is obviously longer than the other.
Thank you
(I thought it was better to ask here rather than on bioinformatics.stackexchange.com)

This is absolutely on topic here, I just wanted to let you know that it would also be on topic on [bioinformatics.se] as decided in this meta thread. Which of the two sites you choose is completely up to you.

Could [edit] your question and clarify what seems strange to you? What length of reads were you expecting? What you describe is standard but something seems to be confusing you. What is that?

I edited my question after @terdon comment.

The read length has absolutely nothing to do with what you are sequencing. It is a characteristic of the sequencing technology you use. NGS sequencing techniques typically produce this sort of short read you're seeing. The read length does not change because you are sequencing a longer molecule. You would still get ~250nt reads even if you were sequencing an entire genome. Your reads are something like this (image source):

So the vast majority of your 250nt are overlapping and cover slightly different parts of your target sequence. This is one of the reasons why NGS analysis is not trivial. The first step in any NGS analysis is to assemble your reads into a bam file that covers your target region. If you need help on doing that, come on over to http://bioinformatics.stackexchange.com.

Thanks you for you answer. But there is something I don't understand: with this technique of "cutting the molecule" that has to be sequencing, where do you put your barcodes? (when there are multiple samples from different sources)

@MrSnake on the end of the read but that really should be a separate question.

My understanding is that if the reads come straight from the sequencing machine, they will all be the same length. That corresponds to the number of sequencing cycles that the machine was set to perform. This has no biological meaning.
I don't know what the machine will read once it reads more than the length of the fragment subjected to sequencing.
If the fragments are shorter than what the sequencer reads, there will be some library preparation adapters to remove from the sequences in order to recover the actual fragments. Then you should be able to see the real fragment lengths.
If the fragments are longer than what the sequencer reads, see @terdon's answer.


text:
What type of spider is this? VA, USA
Spider found in Richmond, VA. Can anyone identify?

Sure, I can identify this for you!
That is an Argiope Aurantia, most commonly known as a "Yellow Garden Spider". They're quite well known for the design of the webs they spin, and because of this, they also go by "Sewing Spider" and "Writing Spider". They may try to bite if startled (which can be easy to do), but their venom is harmless to humans, so no worries.


text:
How our body produce different T-cells?
I've heard in many documents said that :

There are 25 million to a billion different T-cells in your body. Each
  cell has a unique T-cell receptor that can fit with only one kind of
  antigen - quoted from askabiologist.

But I haven't found the mechanism of this. How our body produce too many different T-cells? Does our genome need to have 25 million to billion genes to encode for 25 million to billion unique receptor for those T-cells? Does each T-cell have a different gene region on their genome or they have a different turned-on/turned-off genes ?

You want to look for receptor re-arrangement and editing.

https://en.m.wikipedia.org/wiki/V(D)J_recombination


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Special visceral efferent
Why are special visceral efferent nerves are named as such?

They are supplying motor impulses to muscles of pharyngeal arch, which are both skeletal(facial) and visceral(laryngeal) 1, so why only visceral in name?
Why the name special?

I tried wikipedia but didn't find any information.

What nerves are you referring to specifically as special visceral efferent? The link you include only has the text "special visceral efferent" once that I can find, in the table at the top.

@kmm 5, 7 ,9 , 10 and 11c most probably.

I find this https://www.ncbi.nlm.nih.gov/pubmed/8109195 suggesting to change the terminology.

Why they are special?

They are also called Branchial efferent.
They are special because they supply striated muscles derived from Branchial arches.
https://en.m.wikipedia.org/wiki/Special_visceral_efferent
Like Mandibular nerve, nerve of 1st arch supply muscles of mastication and motor nuclei of facial nerve, 2nd arch, supply facial muscles and Stylohyoid.

Special Visceral Efferent (SVE)
  These fibres innervate certain striated muscles with a special embryological origin.
  They are referred to as the branchiomeric muscles.
  Structures that develop into gill arches in fish develop instead into various structures near or in the head and neck (muscles of the face, larynx and pharynx).
  Although these muscles are identical to normal striated muscle, neurons for branchiomeric muscles have a distinctive location in the brainstem.

..

Why only visceral?

This term is quite ambiguous. That's why some scientists prefer term Branchial efferents. https://en.m.wikipedia.org/wiki/Special_visceral_efferent
The nerves supply striated muscles(also called skeletal, though most facial muscles have no skeletal support).
These do not supply any smooth muscle of viscera (laryngeal muscles are striated too).
But, still they are called visceral.
Well, that is because the muscles supplied are actually mostly to various viscera.
Larynx is a viscera. Pharynx and palate are viscera too. All these are supplied by 5 , 9 and 10th nerve.(Nuclei - motor nuclei of 5th, Nucleus ambiguus for 9 and 10th)
 Nerve to stapedius is muscle of middle ear, again a sensory organ.
So, the word viscera was added.
Facial muscles and sternocleidomastoid and trapezius are of course not supplying organs(viscera). That is why some say branchial efferent to remove ambiguity.
Branchial efferent represents muscles derived from branchial/pharyngeal arches. That's what is important about these nuclei.

I'm having a difficult time finding meaning in your explanation of why "special" is used..according to your answer, you say, "*They are special because they supply striated muscles derived from Branchial arches". My question is, why does that then require  the usage of "special"? Or, what aspect of that is described by using the term "special"? Im not seeing the logical connection. Thanks.

@Charles I dont know of text for sure. But,  that is what are proffessors at college told us.

I see.. well, in the case, I believe that special has a very specific meaning, of which is being used to classify organs and nerves based on if an organ has to interact with another organ to perform a task, and by extension, whether or not the nerves of those organs run directly to the spinal cord or not.

1.They are supplying motor impulses to muscles of pharyngeal arch, which are both skeletal(facial) and visceral(laryngeal), so why only visceral in name?

Visceral is a derivative of the word viscus, which simply means "an internal organ of the body". I believe visceral is being used with this, more general, connotation.

2.Why the name special?

The word special is used because SVE nerves are involved with what are considered to be special senses, which is to say, senses that have "specialized" organs (and subsequently, "special" nerves) devoted to them. The special senses are: vision, hearing (and balance), smell, and taste.
To quote Wiki:

The distinction between special and general senses is used to classify nerve fibers running to and from the central nervous system – information from special senses is carried in special somatic afferents and special visceral afferents. In contrast, the other sense, touch, is a somatic sense which does not have a specialized organ but comes from all over the body, most noticeably the skin but also the internal organs (viscera). Touch includes mechanoreception (pressure, vibration and proprioception), pain (nociception) and heat (thermoception), and such information is carried in general somatic afferents and general visceral afferents.

Although this passage mentions  afferents, (I'm fairly certain that) the usage of "special" regarding efferents carries the same meaning.

Special was used for special senses is absolutely correct. But, only for afferent. These are special senses , meaning sensory. These prove nothing for efferent. Else, there would be no GSE. These muscle supply special organ eye, dont they?

GVE are aiding special senses as well.

@AnubhavGoel If special only applies to afferent nerves then how can the OP  be asking about SVE? Special Visceral Efferents


text:
Is there a hypernym for enzymes that "cut" other molecules?
I have searched on Google for a hypernym/umbrella term that encompasses all enzymes whose function is to cut other molecules, but I have yet to find such a term. The term I am looking for would encompass enzymes groups such as proteases, nucleases, and lipases.
Is there such a term in molecular biology?

Aren't all enzymes named with the suffix "-ase"?

Oh yeah d'oh. Don't know why I forgot that. Ignore me!

Hydrolases can "cut" other molecules using hydrolysis (see proteases), and Lyases can catalyze "cutting" with other reactions (see aldolases). These are umbrella terms for families of enzymes classified by function.
I think this is a fair open-access review of enzyme classification.

Please provide links to the EC classification or the like to support your assertion. You may be right, but how is anyone to know?

The term you want is "scission enzyme".  Scission is from Latin scissio, the same root as for scissors.  This is a broad umbrella term which does not speak to mechanism of cutting.

Never heard this used. Please support your suggestion by citations and links, otherwise they are likely to be flagged as low quality.

Also never heard this. Strongly doubt it is a common term.

I appreciate you 2 asking for clarification rather than just down voting.  Here is a google search with 632 uses of the term. It is such a broad category that the term is not that useful, which may be why you two are unfamiliar with it.


text:
What are these Cocoons/Seeds?
I have found these thingies in my institute at Tiruchchirapalli in India. I have no idea what they are:

Can someone tell me what they are, exactly?

Sorry if the picture isn't clear, the thingy must have been eroded a bit.

It's difficult to get an idea of how large/small this is, given the provided images.

@Charles It's about 1 cm across. I took a closeup shot for more accuracy.

They look like seeds from palm trees. It reminds me of seeds from Phoenix canariensis which I once planted. However, since this particular species is not native to India, they could be seeds from another Phoenix palm species. Do you have Phoenix palm species in your area in India?

We have lots of palm trees around here, since it's the tropics

Thanks for your answer, but can you validate it with pictures? I tried googling, but wasn't satisfied.

I can't tell exactly, sorry. You probably know more about palm trees than I do (I live in the Netherlands where no native palm trees grow). But it did remind me of Phoenix canariensis seeds. So I hoped you would know which relative palm species would be at your institute. Maybe you should plant them and see what comes out of it?


text:
What is exactly a phosphoester bond?
I've spent some hours trying to understand what exactly is a phosphoester bond, but I'm still confused and at this point I just want to throw myself out of the window. I've already read that post which treats the question but it doesn't really help me since, according to the link given by WYSIWYG♦:

A phosphoester bond is a bond between the phosphorous atom of a phosphate group and an oxygen atom.

But considering the answer of electronpusher:

Each nucleotide contains one phosphoester bond (between a phosphate O and sugar 5'-C).

It doesn't really make sense to me, since such a bond (in a nucleotide) is not exactly a bond between the phosphorous atom of the phosphate group and an oxygen atom (that is, it's a O-C bond, not a P-O bond).
So, what is exactly a phosphoester bond? Is it a O-glycosidic bond between the sugar (ribose or 2'-deoxyribose, in a nucleotide) and the phosphate group? Or is it the bond that there is between the phosphorous atom of a phosphate group and an oxygen atom of the same phosphate group?
I'm really confused and desperate by all this, so any help would be greatly appreciated. Thanks in advance!

You can find a diagram of the structure of a phospho diester bond in any biochemistry text eg. Lodish et al. and the definition: "A covalent bond in which two hydroxyl groups form ester linkages to the same phosphate group; joins adjacent nucleotides in DNA and RNA". So the question is do you know what an ester linkage is and do you know what a phosphate group is? If not you should try WIkipedia or a basic chemistry book. I shall vote to move to SE Chemistry but you should be able to answer this yourself.

A phosphoester bond is in fact a bond between the phosphorus atom of a phosphate group and an oxygen atom. Your confusion comes from the fact that electronpusher's statement is inaccurate.
Instead, electronpusher should have said:

Each nucleotide contains one phosphodiester bond (between a phosphate O & a 5'-C on one sugar belonging to one nucleotide, and then another bond between a phosphate O & a 3'-C on another sugar belonging to another nucleotide).

More elegantly put, "a phosphodiester bond occurs when two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds" (source).
The resulting bond is between O-C because the hydroxyl groups react with each other and transesterification occurs. The OH from the phosphate interacts with the OH (attached to the carbon) from the sugar, transesterification occurs, thus leaving only 1 oxygen, of which is the oxygen in the P-O-C bond sequence, exhibited in the following image.

The next image is a simplification of the reaction mechanism. Dehydration does not actually occur (transesterification does, as mentioned), but instead, this image is provided as to more easily identify which entities are involved in the reaction, as to more directly address the concerns expressed by the OP. The true reaction mechanism can be found here.

Thanks a lot for your answer! However, I still don't see why the bonds we are talking about are phosphoester (or phosphodiester) bonds, since they are both O-C bonds and not O-P bonds... :/

@AlissaDeschamps The resulting bond is between O-C because the hydroxyl groups react with each other (as can be read in the provided definition) and dehydration occurs (water is produced). The OH from the phosphate interacts with the OH from the sugar carbon, which produces H2O, leaving only 1 oxygen, of which is the oxygen in the P-O-C bond sequence, exhibited in the provided image.

Ok, thanks a lot for the clarification. Does that mean that the phosphoester bonds that everyone is talking about when they think of nucleotides are actually the bonds between the phosphorous atom and the oxygen one? And the O-C bonds would be glycosidic bonds?

Thanks a lot for the edit and the help, you're awesome! :)

You're quite welcome! Study smart, not hard ;)

Good answer, I would just say that  the condensation reaction shown is thermodynamically unfavourable. In realty, nucleotides are joined together by transesterfication. See this question and answers: https://biology.stackexchange.com/questions/61319/is-water-released-when-a-phosphodiester-bond-is-made-between-two-nucleotides-dur/61352#61352

@canadianer Thanks for that. I've updated my answer to include and reference this.

Thanks for your comments and edits ; do you know if transesterification occurs only for the linkage of the phosphate group with the 3'C of the sugar or if it occurs as well with the 5'C? (I'm asking this because my book, "Molecular biology of the gene" by Watson and al., says that dehydration occurs without saying there could be a difference between the 3'C and 5'C...)

@Charles - Nice job, and great attitude. I never heard of a phosphoester bond (only diester) until just now.


text:
PCR products with no band in gel
I am a PhD student and stuck with the no band in the gel  results.
I am using the following

1 microliter  Primer R (20mM)
1 microliter  Primer f (20mM)
1 microliter  dNTP  (10mM)
1 microliter  DNA Template ( 448 ng)
1 microliter TAQ polymerase
5 microliter Buffer (10x)  added MgCl2  by 1:1
30 microliter PCR grade water

Program:

95 for 4 minute
95 for 45 sec
55-65 for 1.20 minute
72 for 1 minute
Gradient 35 cycle
72  for 4 minutes

Gel:
110 volt, 200 mPA for 30 - 45 minute
I get PCR products as in the images. There are no bands  while there are intense bands at the bottom and some of the wells.
My question is,  is that at the bottom products??
what can be done to make them real? If not then why there are differences between the two lane of wells. Each 12 well are representing a one type of DNA template (I used three different organisms DNA).

First: Your PCR is working in principle, the bands at the bottom are beautiful primer dimer bands which indicate this. Then: What is the source of your DNA and has it ever been user successfully for PCR? How is it prepared?

Hi Chris, thanks for your reply.  The DNA are from LLactobacillus and Lactococcus  bacteria.  The primer has been designed as degenerated based on both of them.  Up to now I couldnt get the PCR work .

Ladder looks good...

Can you post the sequence you intend to amplify and the sequences of the primers you are using? Also, do you have any positive control for the Taq?

Do you use genomic DNA? Then you can try to enhance the outcome by using either less template or add additional MgCl2. You can also try different PCR methods (i.e. spiked PCR or Touchdown).

Use control primers targeting something which for sure gives a product. If you have none, ask your colleagues or take some out of literature. Make sure your product is small enough to be amplified in the time given and check for the correct band with a restriction enzyme.

I'm not sure about the scale of your ladder but regardless the DNA causing the banding is very small. They are most likely primer dimers. I would check the primer sequences to make sure there isn't a lot of complementarity. You can also try manipulating reaction conditions like concentration of magnesium chloride or the primers themselves etc. I would run an optimization set of PCRs with variable reaction conditions.

My first guess would be that you're using too much template DNA for these conditions. Your wells light up quite a bit, 448 ng is also on the high side.
Try lower concentrations of template DNA (1-100 ng), perhaps only with a 55 °C  annealing step. At the moment you don't have any product at all, so I wouldn't worry about non-specificity yet (and 10 °C is also quite a small range to fix that).
Other things that stand out:

I assume it's 20 uM primer, not mM
You're adding too much buffer
It looks like you're making each reaction individually (looking at the template amounts in the first 12), I suggest making a master mix and aliquot that out.
You have quite some space to run your gel longer, that might be very useful if you do get some product.

You should have a bit more information as well. What's the size of the products that you expect? Do you use high GC organisms? Did these primers work
before for other people? Did the genomic DNA work before for other people?
NEB has a lot of useful information about PCR and other DNA work on their website, check it out: https://www.neb.com/tools-and-resources/usage-guidelines/guidelines-for-pcr-optimization-with-taq-dna-polymerase

What you can try is different buffer (10 x) solutions, also with or without MgCl2. In the lab where I used to work with PCR, we had a panel of different PCR buffers in the freezer. We tested some of them, to see which one fitted best (hence which one gave the right size band). Just like your temperature gradient, to see which one performs best.

You can try a touchdown PCR. It is often helpful when no band is present.


text:
Effect of mutation on phenotype
Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?

Yes. It is actually the case of most mutations that affect the phenotype!
Only 1.5% of the human genome codes for proteins. About 5-10% of the human genome are regulatory sequences which do not produce any protein but greatly impact the phenotype by regulating the expression of coding sequences. A mutation in a regulatory sequence does not directly impact the protein sequence but can have drastic impact on the phenotype (and fitness).
There are a lot of such mutations that have been identified. Here are a few quick examples

Variation in Vertebrate Cis-Regulatory Elements in Evolution and Disease
A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens
A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig
Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element [..]

Do you have a reference for the statement that most phenotypic changes are caused by mutations in regulatory sequences? And what is the definition of 'regulatory sequence' in the context of the 5-10% number?

@Remi - Nice answer.

@AlanBoyd: Read the cired papers. For silky feathers, "The causative mutation is located 103 base pairs upstream of the coding sequence of prenyl (decaprenyl) diphosphate synthase, subunit 2" which is a regulatory protein.

@anongoodnurse I wasn't really asking about specific examples - obviously these exist - I was asking for a supporting reference for the 'most mutations' statement.

@AlanBoyd - Ah, sorry.


text:
DNA Dead skin cells
If the stratum corneum is anucleated, dead cells - how is it that we are able to get DNA from buccal cheek swabs? Are we grabbing more than just the stratum corneum with the swab (eg. the underlying cells that are nucleated)?

I'm curious: does the inside of your cheek feel anything like the palm of your hand?

Thanks! I just read that the inner cheek is one of the places in the mouth with nonkeratinized squamous epithelium. So the cells we collect with buccal swabs are not of the dry cornified type and retain their nuclei. And the stratum corneum and granulosum are absent from this lining mucosa.

Because our buccal cavity is not covered by skin but by oral mucosa (nucleated epithelial cells).

Why the down votes?


text:
Why do mountain gorilla eat just 1.7% fruit, while lowland gorillas eat 25%?

Eastern lowland gorillas have more diverse diets, which vary
seasonally. Leaves and pith are commonly eaten, but fruits can make up
as much as 25% of their diets. https://en.wikipedia.org/wiki/Gorilla#Food_and_foraging

The mountain gorilla is primarily a herbivore; the majority of its
diet is composed of the leaves, shoots and stems (85.8%) of 142 plant
species. It also feeds on bark (6.9%), roots (3.3%), flowers (2.3%),
and fruit (1.7%) https://en.wikipedia.org/wiki/Mountain_gorilla#Habitat_and_ecology

Have you checked what is the availability of fruits in the two environments? My first guess is that in the mountain environment you find fewer fruits due to altitude and climate.

Mountain plants have to be hardy, especially if they grow above the frost line. They are more likely to be tough vegetation (leaves, shoots, and stems) as mentioned in the mountain gorilla diet.
The lowlands have much more plant diversity (and generally better food). Sweet fruits have better calories for the effort required to forage and digest them, so you would expect the lowland gorillas to prefer fruit.


text:
Why do food items expire?
Why do food items and medicines expire after sometime?

Medicine doesn't expire so quickly, actually. Just recently, a large amount of pharma drugs were found, ones that dated back to the 1950s, and they tested their efficacy, and found that 10 of the 14 active compounds in the drugs still met FDA standards. Drugs "expiring" is a kind of lie that big pharma has in place to make more $$. I'll see if I can find some literature on this, and make a more formal response. http://www.npr.org/sections/health-shots/2017/07/18/537257884/that-drug-expiration-date-may-be-more-myth-than-fact

https://en.wikipedia.org/wiki/Shelf_life#Background If you read that section, it'll most of your questions.

Because the FDA requires it.

Expiring food items is obvious: for fresh food, it's almost always due to bacterial or fungal decay (spoilage).
Oxidization and sunlight doesn't really ruin food; it might alter the taste or decrease its appeal, although it remains edible even by first-world standards. However, it might destroy vitamins and other nutrients.
Medicines are a different matter. Some chemical compounds are slightly unstable, with half-lives measured in years. Instability can cause the compounds to randomly break into subcompounds that are ineffective for treating the intended condition at best and poisonous at worst. Unlike food, it's imperative to keep medicines away from sunlight (and oxidation in some cases) as both of these can further promote instability and breakage into subcompounds.
On the comment that Charles posted about medicine shelf life being much longer than advertised: The reason why they underestimate the shelf life is that it's better to have people throwing out potentially OK medicine than to have it sitting on a shelf for 20 years, going bad and sickening people, and prompting numerous lawsuits against the manufacturer. This type of deliberate underestimation in the name of safety is common in engineering - usually with weight limits advertised below the real weight limit. For example, an elevator able to haul 6000 pounds might be advertised as only 2000 because the manufacturer knows there's always going to be a few idiots who disregard the posted limit.

"Most of what is known about drug expiration dates comes from a study conducted by the Food and Drug Administration at the request of the military.  ...  What they found from the study is 90% of more than 100 drugs, both prescription and over-the-counter, were perfectly good to use even 15 years after the expiration date ... So the expiration date doesn't really indicate a point at which the medication is no longer effective or has become unsafe to use." -- Harvard Medical School https://www.health.harvard.edu/staying-healthy/drug-expiration-dates-do-they-mean-anything

With regards to your answer, it would be nice if you could provide some hard examples to support your statements.

Thanks @Charles for the link, it is helpful. I would not down vote personally. user1258361 does not make any opposing claim but mainly explain why there is a need for expiration date on medicine and what could happen to medicines.

I downvoted because I feel that @user1258361 doesn't answer the question fully, and only provides extremely basic information, that of which isn't supported by any external sources, for which I feel there is a lot out there. "Some chemical compounds are slightly unstable, with half-lives measured in years." IMO, that doesn't explain why, and is overly general. And regarding the food, sources for those claims would be nice. Also, the reason for which safety standards of elevators was implemented is not the same as why expiration dates for medicine was introduced.

https://en.wikipedia.org/wiki/Shelf_life#Background

"90% of more than 100 drugs, both prescription and over-the-counter, were perfectly good to use even 15 years after the expiration date" So 10% weren't perfectly good. In this age of excessive litigation, industry prefers to err on the side of extreme caution to avoid being sued in case they end up in that 10%.

There are a number of reasons

bacterial infection
fungi infection

Most fungi are not toxic in themselves but they release mycotoxins in the food, which are definitely toxic

Maggot infection
Other infections
Growth

E.g. a potato will slowly attempt to develop into a plant, slowly consuming the tuber (the tuber being the potato you would like to eat).

Oxidation
Unstable chemicals

Mainly for medicines. Note however that (from health.harward.edu; thank you @Charles for pointing that out):

Most of what is known about drug expiration dates comes from a study conducted by the Food and Drug Administration at the request of the military. ... What they found from the study is 90% of more than 100 drugs, both prescription and over-the-counter, were perfectly good to use even 15 years after the expiration date ... So the expiration date doesn't really indicate a point at which the medication is no longer effective or has become unsafe to use.

The main reasons are probably the first two (bacterial and fungi infection). Note that the list is incomplete.

Degradation of substances and chemicals don't happen only thru oxydation but also many other factors like light, microorganisms and othwr stuff. The chemical substance will also suffer a degradation without any external factors, and some are more likely to go thru such processes than others.

Food expires because its growing. Constantly. Every ingredient you put into making specific foods has a Date when its time has ended. Just like our bodies as we age. We are one year closer to expireing. We Grow old and Our skin starts to Wrinkle. Its just a way of life. If nothing ever expired we would over populate everything. Not to mention, if our foods didnt expire they wouldnt break down in our Bodies making it hard to gain nutrients from. Ending in a result of Death. We need the foods to break down in order to survive.

Umm... What? When food is thoroughly cooked, it isn't "alive" anymore and ceases to grow. The main cause of food expiration is due to decomposers (mostly fungi and bacteria) eating the food and converting parts of it into waste products ranging from "tastes bad" to "dangerous poison" depending on the decomposer. Oxidation and radiation exposure can slightly change the chemical composition of certain foods, although food generally remains edible after oxidation and irradiation.


text:
How did the largest/longest dinosaurs hold their head and necks up?
After seeing the images in the articles shown below, I am having a tough time understanding the mechanics of how these incredibly long and heavy necks can be supported outstretched like this. A rigid beam or tube would remain fairly straight through compression on the bottom and tension on the top, and since there is muscle, tendon, ligament and bone, I know the necessary mechanical functions are there somehow.
Is there one "neck muscle" along the top that holds the neck "up", or many short muscles between vertebra? Where is the origin of the tension, the shoulders or the pelvis, or is it all the tension distributed along the whole spine from neck to tail?
How does this work??

above: Titanosauria of Chubut from here.

above: A reconstructed Patagotitan mayorum, a 70-ton dinosaur discovered in Argentina. (Courtesy of José Luis Carballido) from The Washington Post article Which dinosaur is the biggest? There’s a new contender — and it’s alarmingly large.

above: A reconstruction of the newly named titanosaur Patagotitan mayorum. from The National Geographic article New Dinosaur Species Was Largest Animal Ever to Walk the Earth.

There are lots of papers on this. A good summary article is Why sauropods had long necks; and why giraffes have short necks, by Taylor and Wedel.  They list a number of anatomical features that allowed sauropods to support such long necks:

Several anatomical features enabled this extreme elongation, including: absolutely large body size and quadrupedal stance providing a stable platform for a long neck; a small, light head that did not orally process food; cervical vertebrae that were both numerous and individually elongate; an efficient air-sac-based respiratory system; and distinctive cervical architecture. Relevant features of sauropod cervical vertebrae include: pneumatic chambers that enabled the bone to be positioned in a mechanically efficient way within the envelope; and muscular attachments of varying importance to the neural spines, epipophyses and cervical ribs.

Let's take these one by one.

A stable platform for a long neck. Large, heavy quadrupedal bodies, so the long neck didn't unbalance the animal when it stretched out.
"A small, light head." Sauropods didn't chew their food, so didn't need large muscles or heavy bones in their head, so they didn't have a heavy weight at the far end of the long neck.
Numerous small, elongate cervical verterbrae. Sauropods had 12-19 vertebrae in their necks. By contrast, giraffes have seven, each of which needs to be large and heavy, limiting how long the neck can be.
Efficient respiratory system. Sauropods, like modern dinosaurs (birds) have a more efficient respiratory system than mammals, so they could tolerate the inefficiency of a long trachea.
Pneumaticity of cervical vertebrae Sauropod vertebrae had air sacs (i.e. hollow pockets of air) in them, making them much lighter than mammalian vertebrae of the same size and strength.

Edit to add Figure 4 from Taylor & Wedel, illustrating how relatively light sauropod necks must have been for their size:

Figure 4: Extent of soft tissue on ostrich and sauropod necks.
  1, Ostrich neck in cross section from Wedel (2003, figure 2). Bone is white, air-spaces are black, and soft tissue is grey. 2, Hypothetical sauropod neck with similarly proportioned soft-tissue. (Diplodocus vertebra silhouette modified from Paul, 1997, figure 4A). The extent of soft tissue depicted greatly exceeds that shown in any published life restoration of a sauropod, and is unrealistic. 3, More realistic sauropod neck. It is not that the soft-tissue is reduced but that the vertebra within is enlarged, and mass is reduced by extensive pneumaticity in both the bone and the soft-tissue.

Muscular attachments.  This is the aspect that most directly answers the original question, but it's first important to understand that other sauropod features as noted above allowed them to get away with less neck strength than you'd otherwise expect.  In fact sauropod necks were much less (relatively) muscled than, say, ostriches. They got away with this by improving mechanical advantage:

In effect, sauropods inflated their vertebrae within the muscular envelope of the neck, moving the bone, muscle and ligament away from the centre so that they acted with greater mechanical advantage: higher epaxial tension members, lower hypaxial compression members, and more laterally positioned paraxials.

Taylor and Wedel go into this in much more detail, with many helpful diagrams, and the paper is open-access, so I won't repeat all their points here. They talk about neural spines, epipophyses, cervical ribs, and muscle attachments in various combinations.
The cervical ribs are easily visible on the Patagotitan skeleton image in the question:

There's a long description of cervical rib anatomy and possible functions here:

My favorite hypothesis is that long tendons allow an animal to shift the bulk of the muscle–and therefore the center of gravity–toward the base of the neck, but that long unossified tendons can be distorted through stretching, which wastes muscular energy. Ossifying those long tendons is like putting bony wheelbarrow handles on each vertebra, allowing the muscles to move the vertebra from a distance without so much wasted energy, and probably with finer positional control.

That's just one aspect of the way sauropod necks were structured.
TL;DR: Sauropod necks could afford to be relatively light, because of the small head; their neck bones tended to be relatively hollow and light for their size; their scale and shapes meant that muscles had good mechanical advantage; and different species had other adaptations including ligaments and stiffening bones that also helped.

You know you've stepped up to the big leagues when your paper has to talk about "giraffes hav[ing] short necks"

"modern dinosaurs (birds)" :O Did I miss something? What do dinosaurs have to do with birds?

So, if they compensated the length/weight relation with hollow bone structure... Doesn't it mean that the neck, already a vulnerable part, becomes weaker? I mean, a strong enough bite or ram from the predator, and a spinal cord gets severed, thus rendering the dino immobile.

@Clonkex https://xkcd.com/1211/

@Clonkex Birds are dinosaurs. (and " Birds are descendants of extinct dinosaurs with feathers, making them the only surviving dinosaurs according to cladistics."

@BruceWayne (or should I call you... Batman...?) Oh duh, of course. I totally forgot that was a thing. Sorry, I'm not an evolutionist, I sometimes forget these things that most other people take for granted.

@oleksandr-firsov Since this is how their necks were structured, obviously natural selection determined that the benefits outweighed the costs. We don't know enough about predator/sauropod interactions to know why in detail. The neck was still very strong (look at the meshwork of cervical rib bones supporting it). Maybe most predators couldn't reach the necks (T rex was about 20 feet tall, just up to a full-grown titanosaur's shoulder). Maybe a thicker neck wouldn't have made any difference against a bite. But again, this is how they were, so that tells us a little about predators at the time.

Air sacs mentioned this week in NYTimes' New Clues to How the Biggest Dinosaurs Got So Big

The first sauropod in space!

new dinosaur question: Would anything limit an “invasive species” T. rex introduction now besides running out of food or intervention by humans?


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Why are childhood cancers less frequent than infant or adult?
According to data provided by Cancer Research UK, the lowest rate of cancer incidence by age occurs between 5 and 15 years.  Infants have a higher rate, and the odds of an adult developing cancer increase over time, especially during old age; until the odds plateau around age 85.
I understand that an accumulation of DNA damage over time increases likelihood of cancer with age.  But what explains the almost flatline rate of cancer amongst those aged 5-15?  Surely it makes more sense for the rate of cancer to increase uniformly every year from infancy?

"Surely it makes more sense..." doesn't correspond to reality, and isn't an argument. It made more sense for thousands of years that the earth was flat and that spontaneous generation of life existed (after all, people saw it with their own eyes.) Please take into account not only damage of DNA as a cause of cancer (in that case, there would be no childhood cancers) but genetic predispositions and other causes. "Childhood cancers" is easy to google.

@anongoodnurse I know I'm just supposing based on a general understanding, which is limited and incorrect; which is why I ask. :)

It's a good question (+1). The site asks that you make an attempt at answering your own question before asking. See the help section, or look at the close reasons. Googling childhood cancers and editing your question will likely get you a better answer. Thanks.

I think one of the conclusions you can draw from your chart is that older adults are more frequently diagnosed with cancer as a disease. Cancer is an accumulation of genetic abnormalities due to genetic instability, and so for children this occurs during embryogenesis (there are caveats), and we can see that these cancers seem to occur in cells that are quite active during development. We can actually see that adult cancers seem to occur in established tissues at an older age (probably due to inflammation, check out SITC's new book on immunotherapy and cancer).
So you can do this with cancerresearchuk's website: the stat for childhood cancers is that brain tumors and leukemia occur significantly more frequently, which actually differs in overall distribution from the world significantly (ref).

Figure 1. Cancer incidence in children 0-15 by type.
If you stratify by age by those particular cancers, it's much less of a flat line in the 0-15 age bracket. Explaining why is probably a different question all together. The distribution of types of cancer is different for children than for older adults. Thus, the comparison is made difficult because this isn't a straightforward comparison. The best answer is that certain cancers are actually more frequent in children than in older adults and vice versa.
You can start here. Some of the things you will find interesting:

Figure 2. Hodgkin Lymphoma, incidence by age bracket. Interesting to note that non-Hodgkin lymphoma does not occur with any appreciable frequency in children or young adults!

Figure 3. Leukemia, incidence by age bracket.

Figure 4. ALL, a type of leukemia, incidence by age bracket. Based on the data in the OP, you would expect incidence to be highest for 60-74yr olds, but this is not the case.

Figure 5. Brain/CNS tumors, incidence by age bracket.

Figure 6. Bone Sarcoma, incidence by age bracket.

There are 2 main causes of cancer: "born defective" (heritable or genetic problems producing a large predisposition to cancer) and "accumulated damage" (random mutations accumulated over life).
Due to how the UK health system rations treatment (and the recent stories about Charlie Gard being prevented from traveling to the U.S. or Vatican for treatment), it's likely that the government there often "deprioritizes" (complete guess, no idea if they actually do that) infants with severe heritable/genetic problems causing near-immediate cancer. Obviously this means that those cases never live to the 05-09 age bracket.
Cancer deaths peak at 65 rather than 90 or 100 on similar statistical grounds, although late-in-life cancers are almost always due to accumulated mutations  rather than being born defective. Cancer deaths drop off after age 79 because of the relatively large die-offs in the previous few age brackets, in addition to deaths from old age and related conditions.
If there was infinite funding for health treatment and enough hospitals to match, the graph might instead match your expectations as the public would do everything to maximize survival. This means that some of the 00-04 bracket would survive to later age brackets, with the largest cause of death in those cancers being failed treatment.

More to the point, I think, is the age at which the genetic insult that leads to cancer occurs.  It implies that there are two causes, the steady increase of genetic damage over time (standard environmental insults) and the introduction of a specific agent of cancer induction which emerged only recently.  Here's an explanation of one of many theories: https://vimeo.com/497792887
The specific mechanisms of action would be homologous recombination and insertional mutagenesis, which correlate with changes in the formulations of the agents.  This would explain gender differences in the pediatric population (XX vs XY).


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Can 12 mitotic divisions produce 6000 nuclei?
The following quote is from "Principles of Development" by Tickle & Wolpert:

"After fertilization and fusion of the sperm and egg nuclei, the zygote nucleus undergoes a series of rapid mitotic divisions [...] The result after 12 nuclear divisions is a syncytium in which around 6000 nuclei are present in a common cytoplasm"

12 divisions (starting from 1 zygote nucleus) should produce no more than 212=4096 nuclei, not 6000. Is this just a simple error in the textbook? Alternatively, is there a biological explanation that makes the 212 estimation invalid?

Good point, maybe Tickle & Wolpert weren't that good in mathematics, or the 6000 nuclei were really observed, but the 12 nuclear divisions are an estimate?

There are indeed some mistakes in that excerpt from Wolpert & Tickle. First of all, the blastoderm is not a syncytium, it is a cenocyte instead (have a look at my answer here). By the way, that's a wrong nomenclature used by all books on developmental biology I'm aware of... therefore, being so well established, that wrong nomenclature probably won't change anytime soon. We have to get used to it.
Back to the numbers:
The second mistake in that excerpt (also reproduced by most books on developmental biology) is the number of divisions: it's not 12, but 13. And that would give us 213, or 8192 nuclei. As you can see, that's more than the ubiquitous "6000" we see everywhere in the literature.
Now the question becomes inverted: what's the reason for the blastoderm having a smaller amount of nuclei compared to the expected number?
According to Miles et al. (2010), the number of nuclei depends on the size of the egg:

The number of nuclei at the cellular blastoderm stage also changed in response to selection, with large-egg selected lines having more than 1000 additional nuclei relative to small-egg lines. This increase in nuclear number in larger eggs does not scale with egg size, however, as nuclear density is inversely correlated with egg length. (emphasis mine)

And the most important part of that paper, which addresses your (now inverted) question:

After 13 mitotic divisions the maximum possible number of nuclei at the blastoderm stage is 213 or 8192 nuclei, considerably more than the classic value of ~6000 given in the literature (Zalokar and Erk 1976; Turner and Mahowald 1983). We found that cell number is not anywhere near constant at 6000 nuclei in the cycle 14 embryo, but rather is positively correlated with egg size. On average, our large-egg selected treatment had more than 1000 additional nuclei than the small-egg selected treatment, a difference that arose as a correlated response to selection for egg size. Yet, in comparing cell numbers in other (nonselected) lines and species, we conclude that cell number must not be entirely a consequence of egg size, but rather must itself be a genetically variable trait. For example, D. sechellia (mean cell number = 7448.7, some embryos approaching the 213 limit) and the Ind strain of D. melanogaster (mean cell number = 6569.1) have nearly non-overlapping distributions of cell number despite having almost identical egg length. (emphases mine)

Conclusion
213 (or 8192) is the upper limit when considering 13 divisions. The real number of nuclei is less than that and varies from blastoderm to blastoderm. The mechanical explanation for that smaller number is, probably, that some nuclei fail to divide.
Also, it's worth mentioning that, from the 14th cycle on, the divisions become asynchronous, that is, the nuclei do not divide at the same time: some of them divide faster and some of them divide slower, and the exponential 2n (where n is the number of divisions) for the total number of nuclei doesn't apply anymore (because, at a given moment, you have several different values for n).

Source:

Miles, C., Lott, S., Luengo Hendriks, C., Ludwig, M., Manu, Williams, C. and Kreitman, M. (2010). ARTIFICIAL SELECTION ON EGG SIZE PERTURBS EARLY PATTERN FORMATION IN DROSOPHILA MELANOGASTER. Evolution, 65(1), pp.33-42.


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Is my RNA-seq experimental design correct to use it for SNP calling?
I am a newbie here and would highly appreciate your advice about one particular experimental design.
We have data from RNAseq experiment which was originally designed to assess differential expression. The details of experiment are as follows:
2 modalities of the phenotype
Each phenotype is represented by 4 samples. 1 sample = 60 individuals pooled together at the stage of RNA isolation.
Molecule – polyadenylated mRNA
Sequencing chemistry – Illumina paired-end, read length - 2*100 bp
My question is whether it is correct to use this RNAseq data to call for SNPs? I made previous search and found that most of people calling SNP from RNAseq use 40-1000 samples (= individuals). But they initially designed RNAseq experiment for further GWAS. I see that this analysis cannot be applied to my data (at least because in my case individual flies were pooled without barcoding – 60 flies per a sample). However, can I still call for SNPs and upload the list to database as a list of potential targets for GWAS with, for example, estimation of functional impact upon protein structure? Will they be “true” SNPs, or our experimental design makes even this step invalid?
I found this paper https://www.ncbi.nlm.nih.gov/pubmed/27458203 where people used 2 phenotypes each represented by 2 samples what is almost like our experiment, but still have doubts.

Using RNAseq for SNP analysis is not the best tool available for several reasons. First, you will only find SNP in genes that are expressed (you need more than 120 reads per SNP in your experiment). Second, you will only find SNP in coding regions of the genes. For your particular experiment, where you have a pool of 60 individuals per sample, it's another drawback because you'll have 120 alleles in your sample (without knowing the allele combinations of the individuals).
Of course you can still try to find SNPs that are present in your phenotypes, but real GWAS kind of analysis is in my opinion not possible.


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Decomposition of human body after death
What causes decomposition of human body after death? Here it says autolysis, while Here it says that bacteria decompose the body. If bacteria decompose the body, why don't they do while we are living?

Bacteria don't decompose the body while your alive (or even when your at the office)
Because your immune system keeps the population safe, by eating them.
Both autolysis and bacteria cause decomposition.
But there are 2 types of decomposition. The kind that keeps you from being able to be rescusitated happens within 5 minutes at room temp after death.
This is oncosis.
The kind where you smell like French cheese happens later, as the cells pop and disintegrate, and then get eaten by bacteria, which release stinky chemicals.


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Does overfishing in one ocean hurt fishstock in another?
If there's overfishing in the Atlantic or North Sea - will this affect fish stocks in the Indian ocean? Are there papers on this?
The question I'm trying to answer is whether overfishing by developed countries has an impact on developing countries fishstocks?
I could see two different scenarios:
-fishstocks are connected globally and if you overfish in one ocean biomass from other oceans will 'flow in'
- the oceans ecosystems are more or less 'disconnected' and somewhat independent of each other
I would appreciate citations if there are any.


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Fisher's Method to melt p-values for CpG sites annotated to the same gene?
I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. Linked here is the Wikipedia page for Fisher's Method. I understand that an assumption of the method used is that each individual p-value being combined must be independent. I'm relatively new to biostatistics, so I'm curious if using CpGs from the same gene would violate this assumption.

Yes, it would very likely to violate the assumption for any two pvalues computed on data coming from the same chromosome. You might want to read this section of the wiki article to understand how violation of these assumptions may affect your results. However, one would need to know how you computed your pvalues in the first place to be definitive. How did you compute your pvalues?

p-values were computed using a paired t-test before and after treatment

You have to explain a bit more in order to understand whether these pvalues may be independent. What is the response and explanatory variable (or the two groups in your t-test if you prefer) and what is your treatment. But you probably have a good intuition of the biology and of the treatment performed yourself without having to explain of whether your data from one site to the next are independent or not.

This question may be better received in Bioinformatics.SE. Yes? No?

Ok I will elaborate as much as possible without divulging too much for the sake of confidentiality. The explanatory variable is a drug treatment given to patients. There are many potential response variables, but the one I am interested is an M-value, which is a log2 ratio of methylated to unmethylated probes detecting a single CpG site. Does that make sense?


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Why does the rain increase our chances of catching a cold?
Why do I catch cold after getting drenched in the rain? I don't catch cold after taking shower.
What special quality does rain water have which increases the chance of getting a cold?

Because the rain is colder than your shower. Plus the wind cool you down even more. Have a look at Why do we get runny noses in the cold? for more information.

@Remi.b Many people take cold showers.

I suspect you don't take a shower with your clothes on, then walk around in the wet clothes for a while.

Why do I catch cold after getting drenched in the rain? I don't catch cold after taking shower.
What special quality does rain water have which increases the chance of getting a cold?

To answer this, let's let's first compare (describe) the two situations:
Getting caught in the rain..

Perhaps you were going for a run, or were walking to class, but either way you're outside, and you got caught in the rain. It's (typically) a little colder outside when raining (and windy), and because you weren't prepared, you got fairly wet all throughout your body, and will remain wet (cooler) for possibly a considerable amount of time (15+ minutes).

Getting out of the shower..

You're in a bathroom that's (indoors and hopefully at least somewhat) clean, and you yourself are using soaps and shampoos. Perhaps the shower water is hot (and thus the bathroom is at a higher temp by the time you get out), or even just mildly temperatured (a cold shower is fine too). When you get out of the shower, you're (maybe) shivering and cold, but you quickly (within a minute or so) get a towel and dry yourself off, thus removing the cold water. Your body starts getting warmer, and then you get dressed (which further increases body temp).

The reason why people may catch cold after being rained on and not so much after taking (colder than not) showers is because the common cold (rhinovirus) thrives better in slightly cooler tempatures. Rain lowers environmental temperatures, and, when you get rained on, that'll further contribute to a lower body temp. Also, due to the fact that you're outside and not inside, there are (probably) more environmental risks, i.e., a higher prevalency of the rhinovirus. Lastly, if you get caught in the rain then your body is (likely) going to remain colder (wet) for a longer amount of time than if you were just getting out of the shower.
To support these claims of the common cold preferring cooler tempatures, I reference a study that was published in 2014, led by Yale researcher Ellen Foxman, in which they examined the performance of temperature-dependent (immune) defenses and their ability to fight off the common cold at various temperatures. From the study:

Most isolates of human rhinovirus, the common cold virus, replicate more robustly at the cool temperatures found in the nasal cavity (33–35 °C) than at core body temperature (37 °C). To gain insight into the mechanism of temperature-dependent growth, we compared the transcriptional response of primary mouse airway epithelial cells infected with rhinovirus at 33 °C vs. 37 °C.

..

These findings demonstrate that in mouse airway cells, rhinovirus replicates preferentially at nasal cavity temperature due, in part, to a less efficient antiviral defense response of infected cells at cool temperature.

So, ultimately, it's because some of our bodies' defenses against the common cold are temperature-dependent, with those defenses performing more efficiently at higher temps, and less efficient at lower temps.


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What are the most efficient heat exchange sites on the human body?
Where on the body would be the best place to achieve the greatest cooling effect with a "cooling undergarment"?  Concentrated over the kidneys, groin, inside the wrists, back of the neck?

@Charles yes, the suit's internal conditions would be the same; however, the external mechanics of radiating heat into space vs. into an atmosphere would not.  And no, I'm not asking "the best way to maintain a cool internal suit environment"; rather, I'm asking what points on the body are the best for heat exchange.

Gentlemen, the space suit, the environment, and the actor/astronaut is irrelevant.  The relevant question is "what points on the body are the best for heat exchange".

@Charles OK well it sure looks to me like the question asks what are the places on the body that would be the most effective to keep it cool inside a poorly-ventilated suit worn by an actor. The OP lists some locations, and wonders if these are the right ones or not. To me the question is simple and clear. It could be that mentioning space suits is a little distracting. It was brought up as background (how the OP got to this question) but it may not be helping the question about cooling an actor in a costume.

@Charles William'Scott'Baker is the OP.

@William'Scott'Baker asking questions in a new SE with lower rep has "special challenges". There's always someone who thinks they see an "easy mark". I liked your original question :) Anyway you might add back that it's for maintaining a healthy temperature in a suit for an actor with poor ventilation (rather than a patient undergoing Deep hypothermic circulatory arrest for example)

@Charles I have already deleted some of them.

@uhoh "I have already deleted some of them." Why not all of them? Future comments will get lost in the comment thread from where a previous, no longer relavent, series of comments still exists.

@William'Scott'Baker Though this doesn't directly answer your question, I'd recommend reading the following post:
https://outdoors.stackexchange.com/a/722

@William'Scott'Baker Also, I can't help but keep thinking of which parts of the body are also most important to cool, instead of just those regions that can transfer heat the best. For example, perhaps it's easiest to cool your fingers, however, it's more important to cool your head. Also, when you mention cooling "effect", it could be that perceived coolness is also important enough to consider. For example, regions that have higher sensativities to temperature may also be experienced more strongly by the person, than regions with lower temp sensativities. Definitely a good question.

the one i know, is our skin via sweat-evaporation.

@TanzeelAshraf are you literally saying that the answer to "where on a body" is "the skin"?  Aye cheers mate, my guess was injecting ice water in the liver.  :-)

Based on hte thermal maps from this paper it appears the most consistent place would be the along the spine on the back, with a small "V" like split near the neck. since this is where the most heat is radiation it is the place the most heat can removed. Oddly the neck appears to vary quite a bit in its cooling capacity, this may be a result of different muscle mass.
This does make sense physiologically since it is both the core of the body and he closest you can get to the largest blood vessels for the entire body, the abdominal aorta. It should also be consistent for males and females for this reason, even in the obese those portions of the body stay relatively uninsulated.
although according to trails for and with cooling vests and hyperthermia, no one part of the body can cool the entire body very quickly or consistently (the bodies own responses fight you on this) although it certainly helps with comfort.

From personal experience, the best places to put a cooler (at maximum metabolic load) are across the back and over the neck and head.
Good candidate areas for a heat sink or exchanger:
Any region where large volume per unit time of blood travels close to the skin. Some dinosaurs are thought to have cycled blood through spiny fins on their back to cool down (obviously this works for non-dinosaurs too, and even better if the blood vessels in the fin are pressurized (see Are there any known examples of animals with air-conditioner type cooling? ).
Regions where a lot of metabolic activity takes place, including muscles in active use and "brown fat" (see https://www.webmd.com/diet/features/the-truth-about-fat)