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What is the benefit of fever during infections?
When people get sick, they often develop a fever. What is the effect of an increased body temperature on viruses and bacteria in the body? Is it beneficial to the infected body? Importantly, often fever-reducing agents like aspirin are prescribed when people are sick. Doesn't this counteract any benefits of fever?

Fever is a trait observed in warm and cold-blooded vertebrates that has been conserved for hundreds of millions of years (Evans, 2015).
Elevated body temperature stimulates the body's immune response against infectious viruses and bacteria. It also makes the body less favorable as a host for replicating viruses and bacteria, which are temperature sensitive (Source: Sci Am).
The innate system is stimulated by increasing the recruitment, activation and bacteriolytic activity of neutrophils. Likewise, natural killer cells' cytotoxic activity is enhanced and their recruitment is increased, including that to tumors. Macrophages and dendritic cells increase their activity in clearing up the mess associated with infection.
Also the adaptive immune response is enhanced by elevated temperatures. For example, the circulation of T cells to the lymph nodes is increased and their proliferation is stimulated.
In fact, taking pain killers that reduce fever have been shown to lead to poorer clearance of pathogens from the body (Evans, 2015). In adults, when body temperature reaches 104 oF (40 oC) it can become dangerous and fever reducing agents like aspirin are recommended (source: eMedicine)
Reference
- Evans, Nat Rev Immunol (2015); 15(6): 335–49

why doe not Ebola gets cured by elevating temp of body of person artificially

Now, the missing bit is "why are the viruses/bacteria not benefitted by the additional thermal energy"...

@AnoE There are a lot of examples in nature where larger creatures can ensure more extreme environments than the smaller ones.  As an example, many bacteria use simplistic tools to maintain hydrostatic equilibrium with its environment which can fail if the salinity goes up (aka gargling with salt water).  Our cells use a more complicated mechanism which can adapt to that salinity.

That's a good point about fever reducing.  In fact, most of the things we think of as "disease symptoms" are actually immune response symptoms, and many methods of treating them end up suppressing the immune response and making the overall experience worse (and longer) rather than better.

Does this also play a role in health effects due to exercise? I run every day for an hour, my body temperature is then significantly elevated one hour a day, while people who are not active or only moderately active won't have such an elevated body temperature for such a  significant time per day.

@CountIblis exercise is good always. It boosts cognitive functions and immune response alike

Interesting fact about immune system... does that mean that it's better not to treat the symptoms as long as you can tolerate them (and doesn't endanger themselves too, certainly) and let the immune system does its work? Or is it more complicated than that?

Most sources attribute elevated temperature as a mechanism to minimize pathogen replication, however, I somewhat am not satisfied with this explanation. Many mesophilic bacteria grow fine even at 45°C. Higher organisms are more susceptible to elevated body temperatures because of their complex organs. I think that elevated temperature is more of a consequence of inflammation than a potentiator.

@WYSIWYG - Yes, now many bacteria can grow fine at 45 degrees, but that they always did. Bacteria has been evolving right along with us, so responses that killed most diseases in the past may not do anything to other diseases of the present. Think about HIV. Most diseases are killed by our white blood cells, under the direction of our T-cells (high school biology version), but HIV kills T-cells and completely circumvents the process, which makes it much more dangerous than other illnesses. That doesn't mean our immune system is bunk, it just means that illnesses are getting 'smarter'.

@EvSunWoodard, illnesses have been getting "smarter" for millions of years.  The body's immune system is pretty darn good.  Imagine how good you would be with millions of years of experience at biological warfare.  Obligatory xkcd.

@EvSunWoodard Not necessarily. Pathogen certainly evolve but non-pathogenic bacteria and naive WT strains also can easily survive at elevated temperatures. Bacteria are much more resistant to heat (or other adverse conditions) than humans. Our core organs are quite sensitive to heat shock. Fever may help but not directly by affecting bacterial proteins and stalling their metabolism.

@WYSIWYG - What I'm saying is that it's easy to point to something that exists now that isn't affected by our immune system response and say, "well this response is useless", but we have no idea how many diseases existed thousands of years ago which were eliminated due to the fever response. It may be none, but more likely, the fever killed off at least some strains of illness, meaning that it makes total sense for fever to be a immune response to try and kill bacteria/viruses, even if there are some bacteria today that can survive 45 degrees C.

@AliceD I think you might be confusing correlations with causation here. sinankzlyr answer hits on the reason behind the increased efficiency of the immune response, and that is signaling through cytokines. I don't think that he was wrong in saying that it was the hypothalamus response to circulating cytokines that drive the fever, and not the other way around, i.e. Temperature increased immune activity and release of circulating cytokines. I am not sure how the endocrine system effects the immune system, though it would not surprise me that there are circulating hormones that play a role.

Fever normally under hypothalamic heat center's control which stays at limbic system of brain . Hypothalamus sets its own set point 36.4-37.2 in healthy peoples by some molecules named exogenous and endogenous pyrogens, especially PGE2 ,TNF and IL1.
The most important mechanism for fever is directing blood flow from skin to deep vascular pools and preventing heat loss from skin. Thats also cause to cold distal parts of our extremities.
When pathogen microorganisms and their toxins invade our blood, our immune response is being activated. Inflammation process starts which have four components: "Tumor ,Rubor ,Calor ,Dolor".  So we experience swelling, redness, fever and pain in other words. Our white blood cells emits prostaglandin and leukotrienes that activating inflammation and those cells to migrate there.
After interact between our defence and microbes, these pyrogens activates hypothalamus heat center. Then temperature set point rises. That activates vasomotor and cortical response. With vasomotor activation, blood flow is directed to deep blood pools and the other side smooth muscles spontaneously contracting generate extra heat. With activation cortical pathways patient feels needing to increase heat or prevent heat loss by e.g wearing more clothes, getting in bed, changing posture to decrease heat losing total area...
So what are all these mechanisms for? Our body resistance increases. Also metabolism speed rises to fight with pathogen. Microorganisms and many toxins have protein components , heat helps denaturation of those proteins and being inactivated. But also our basis contains proteins. So too high temperature is dangerous for our body. When we take analgesics which also decrease fever, thats the purpose to control fever in acceptable intervals.
   (source:Pubmed)
for more read

Welcome sinankzlyr to Biology Stack Exchange. Thanks for your contribution to the site. Please can u provide references to support your claims.

@Mesentery These are all i know, should i still reference for them? Thanks for help. I added one reference.

Most bacterial proteins are stable even at 50°C; human proteins are more susceptible to heat shock. Whatever may be the beneficial actions of fever but pathogen protein denaturation is surely not one of them.

@WYSIWYG while proteins may not denature at 40°C, that can be enough to effect protein protein interactions that pathogens rely upon to sustain infections, buying us just enough time for the adaptive immune response to take over. I have to say that I think the first four paragraphs of sinankzlyr's answer do a better job of explaining the how behind temperature elevation, at least in mammals.

@AMR I agree but I don't think there are extensive studies on this. One should compare the HSR of pathogen and host and its effect on the corresponding cells. Whereas I have seen the claim of elevated temperature directly inhibiting pathogen growth so many times without adequate reference.


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Attraction and hormones levels
Why do we ignore all imperfections in people we fall in love with for a couple of months, but after a certain period we start noticing imperfections?
Can hormones - or any chemical - be used to influence someone to fall in love with you?

Related question: http://biology.stackexchange.com/questions/17250/biology-in-romantic-love  @murmansk

@Mesentery I would like to say that dopamine won't cause "romantic" attachment. It would only cause sexual attachment.

@kirill2485 I don't understand why u commented this :)

well thats what the question asks for. the other answer you linked said that dopamine is a love hormone, when it is a reward hormone, and I would like to make sure that flo knows that dopamine is not gonna cause "love" or "bonding"

Yes. The chemical/hormone that causes attraction is called serotonin. That's what causes attraction between two people. Theoretically, chemicals can be used to make people fall in love with you, such as MDMA, which increases serotonin levels. If the "animal" (such as a cat or a monkey), was in the same room as you and you gave the cat MDMA and you were the only one in the room, the cat would bind with you and seratonin would be released.
This is why MDMA and methamphetamine are known to cause homosexuality and fetishism, for the drug tricks the human into thinking that serotonin is formed with a guy who he is hanging out with or what he is doing at the very moment.
Another hormone that is a "love" hormone is called oxytocin, but this chemical will only cause bonding once the love is formed.
In short, serotonin makes someone fall in love with you, while oxytocin will keep someone in love with you.

References? This sounds like a tremendous oversimplification and exaggeration.

I didn't get this from any sources, just personal experience from participating in numerous clinical trials + knowing the science behind it. But if you want a source:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183515/ . "This was because oxytocin is not unlike the drug ecstasy, which triggers the release of serotonin, dopamine and oxytocin in the brain and heightens users’ feelings of trust and intimacy, even among complete strangers. "

@CharlesE.Grant Alright, I found an article that shows that MDMA is used as a date-rape drug by making the victim fall in love with the offender: https://www.ncbi.nlm.nih.gov/pubmed/16681170

No, the paper doesn't say that at all! It says that prosecutors, police  officers, and toxicologists have made that argument in date rape cases, but that it isn't really supported by the known psychology of the effects of MDMA. From the paper: "MDMA and amphetamines are not usually able to rob a conscious person of their free will. It is for this reason that producing unconsciousness is a likely aim of the person intending to perpetrate a drug-facilitated sexual assault, as distinct from those intending to engage in seduction, in which suggestion may play a significant role."

@CharlesE.Grant "sexual desire linked with methamphetamine use, remove a person's ability to give a reasoned consent, turning the person into "a helpless slave" to their own sexual desires and those of the alleged perpetrator. "

That's a selective quotation. The full quote is: "However, some law enforcement agents and others have recently obtained convictions by arguing that the empathy· generating and sensual effects of MDMA. and an occasional increase in disinhibition and sexual desire linked with methamphetamine use, remove a person's ability to give a reasoned consent. turning the person into "a helpless slave". That is, it is an assertion by law enforcement, not a demonstrated fact, and certainly not one demonstrated by that paper. (emphasis mine).

I've once overdosed on MDMA and all it was was serotonin syndrome and thats it..

If you actually read the paper rather than just the abstract you'd see that that's part of their point. Alcohol and GBH are used as date rape drugs because they render the victim comatose, and completely unable to resist. MDMA doesn't render the victim unconscious, so it's less likely to be useful as a date rape drug. It may disinhibit people, and that may lead some people into activities which they later regret, but that's a pretty far cry from turning them into sex slaves.

@CharlesE.Grant There's also this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023138/
but it doesn't say much.

Let us continue this discussion in chat.

For anyone reading comments, we ended the discussion with this link: https://www.hindawi.com/journals/pd/2012/603631/

source: Stack Exchange

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

sort: votes


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Can fever cure Ebola disease?
Why is ebola disease does not cured on elevating body temperature by body defense system?
Can we cure it either by elevating or reducing body temperature (in ice bath) and creating hostile environment for virus?

I'm not an expert on Ebola in particular but as far as I know its eclipse period is independent on the body temperature (well, of course, if the entire metabolism of the body slows due to hypothermia I guess its replication would also slow as a consequence), so it just don't make any sense trying to "kill" it by that. I would advice you to read up more on the Ebola replication cycle and our attempt at devising a vaccine for it. This will be more helpful finding a way to "kill" it, then replying on ice baths.

Fever, in and of itself, doesn't really cure any disease.  It does help, though.

Short Answer: Fever cannot cure Ebola simply because the virus is not temperature-sensitive.
Background: Fever is a defense mechanism of the body which is specific to temperature-sensitive virus and bacteria. It is so because high temperature induces stronger immune response and makes the body hostile for the pathogen1. Ebola virus, on the other hand, is not affected by this mechanism because it can survive over a much broader range of temperature. Ebola virus is moderately temperature-sensitive, and can survive in temperatures as low as 4°C2 and as high as 60°C3 (at least for half an hour). So, in practical sense, it is not possible to cure ebola disease by heating or cooling the body, either naturally or artificially. But, if we ignore practicality, then Yes, you can cure ebola disease if you take an ice bath or a steam bath for hours so that your core body temperature drops to 4°C (in former case) or 60°C (in latter case). However, it wouldn't be a very nice idea as your body would become hostile for yourself before becoming hostile for the virus.

Having cleared the point about making body hostile for the virus, we are now left with another option: inducing stronger immune response. However, this will not work either because of a peculiar, but dangerous, property of such viruses: they use our defense system against us. Ebola virus, coming under the category of Filoviridae4, attacks host's immune cells, specifically monocytes and macrophages, to replicate inside them. This serves dual purpose; first, the virus has its work done, and second, it kills the host's immune cells. Although how ebola enters into immune cells is not understood, but it has been shown that the virus is helped by the host's antibodies in entering into immune cells5 (quite ironic). Ebola virus can also accomplish this through a process known as macropinocytosis6 (a form of endocytosis). You can refer to this page for its life cycle as well as the diagram of the ebola virion which I've used above, or just have a look at the diagram below from here:

References:

What is the benefit of fever during infections? - Biology Stack Exchange
Okware SI, Omaswa FG, Zaramba S, Opio A, Lutwama JJ, Kamugisha J, et al. An outbreak of Ebola in Uganda. Trop Med Int Health. 2002;7:1068–75. doi: 10.1046/j.1365-3156.2002.00944.x
Mitchell SW, McCormick JB. Physicochemical inactivation of Lassa, Ebola, and Marburg viruses and effect on clinical laboratory analyses. J Clin Microbiol. 1984;20:486–9
Wikipedia contributors. "Filoviridae." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 24 Sep. 2016. Web. 5 Apr. 2017.
Takada, A. & Kawaoka, Y. Antibody-dependent enhancement of viral infection: molecular mechanisms and in vivo implications. Rev. Med. Virol. 13, 387–398 (2003).
Hunt, C. L., Kolokoltsov, A. A., Davey, R. A. & Maury, W. The Tyro3 receptor kinase Axl enhances macropinocytosis of Zaire ebolavirus. J. Virol. 85, 334–347 (2011).

Fair enough +1.

I really like a nice answer like this being posted in a controlled, well communicated,  and top notch style like this.

I want to upvote your answer but I am not currently (will do later) , as it may lead the script of Biology SE to detect this serial voting (I already have voted 3 of your answer in last 15min, all are very nice), and I don't want you to lose that reputation that you deserve.

@jaideepkhare I don't know how to tell you this...but those upvotes didn't add to my reputation :( I had already reacjed my daily repo limit, so your upvotes would only add to the displayed score. Anyways, even that would help, thanks for appreciation :')

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


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Use of pipe character in VCF info field
While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance):
CLNSIG=2|2|2|2|2|2|2

This is actually reported in this example, so I think the usage of the pipe is quite common for genomic annotations of this kind.
Which is the use of the pipe (|) character? I looked for it in the VCF file format specification; however, only the meaning of the comma (,) is specified (i.e., presence of multiple alternate value for that field). I am wondering, instead, what the pipe represents.
Thank you.

There's some documentation on the GO annotation (GAF) format which goes on to define the pipe to mean 'OR'. I think this is somewhat supported by the NCBI gene annotation format for gene names e.g. BRCAI | BRCC1 | BROVCA1 | FANCS | IRIS | PNCA4 | PPP1R53 | PSCP | RNF53. But it may still be specific for VCF, so I will dig a little more but if nothing else this is my understanding.

This was my suspect, actually. I think that, e.g., an annotation string such as GENEINFO=BRCA1|BRCC1,BRCA1|FANCS could mean that the GENEINFO annotation can take two possible values, each one suggested by a different annotation source: 1) BRCA1|BRCC1: the first annotation source suggests that the variant is located either on BRCA1 or on BRCC1; 2) BRCA1|FANCS: the second annotation source suggests that the variant is located either on BRCA1 or on FANCS. I cannot find any documentation, though, so I am not sure this is the right interpretation.

Yet another question that could have fit in a bioinformatics stackexchange...

@bli I completely agree with you. Unfortunately, Biology Stackexchange mixes biology and bioinformatics, and there is not a way of separating the two aspects. However, I agree that bioinformatics should have its own identity.

@bli https://www.biostars.org/ is so established at this point it diminishes the need for a bioinformatics SE other than having that integration with the other communities here (which would be nice, honestly).


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Scientific name of a certain plant from Philippines

Can someone tell me what is the possible scientific name of this plant? The seller told me it was sun rise plant but I can't seem to find it in the internet.
Location: Santa Rosa Laguna, Philippines

Please add a location to help us know where in the world you got it

Santa Rosa Laguna, Philippines


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What is the difference between Totipotent cells and Pluripotent cells?
I read the Wikipedia article about Cell Potency
(Article on Cell Potency)

Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism.

while pluripotency means

a stem cell that has the potential to differentiate into any of the three germ layers: endoderm, mesoderm, or ectoderm.

I don't quite understand the difference, then, between a totipotent and a pluripotent cell.

You might be interested in this.


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How to find sequencing data of a specific drosophila strain
I'm trying to correct low coverage parts of an assembly of these PacBio reads with Illumina data. According to PacBio they "have sequenced adult males from a subline of the ISO1 (y; cn, bw, sp) strain of D. melanogaster.  This is the same stock used in the official BDGP reference assemblies since the first genome sequence release in 2000."
Unfortunately the Illumina data sequenced by the same guys (also  ISO1 (y; cn, bw, sp) but 2057) "revealed significant differences" to the official reference strain. Something I found out as well.
Now I'm trying to find Illumina data for the reference strain at NCBI, but I'm pretty lost. There seem to be dozens of different strains and I can't figure out which one is the reference strain, mostly because I'm completely unfamiliar with the biological nomenclature like ISO1, (y; cn, bw, sp) and 2057 or D8, D20-C2, mbn2 and so on.
So I guess my question is: What strain exactly is the drosophila melanogaster reference strain used in BDGP and how do I find SRA data of this strain on NCBI?

As described in File S1 of Gutzwiller et al (2015) the relationship between the sub-strain of the ISO1 reference strain used by BDGP for the original Drosophila genome proejct, and the sub-strain in the Bloomington Drosophila Stock Center is complicated:

"We investigated the cause of the discrepancy of Wolbachia sequences in the Berkeley Drosophila Genome Project (BDGP) and Bloomington Drosophila Stock Center (BDSC) ISO1 genomic data by first establishing the provenance of these lineages. As documented in the BDSC database, the BDSC ISO1 sub-strain was donated directly to the stock center by Jim Kenni- son in 1994. The ISO1 sub-strain used by the BDGP was obtained from Gerry Rubin’s lab in the late 1990’s (Roger Hoskins, personal communication). The Rubin lab ISO1 sub-strain was obtained in the mid-1990s from Jim Kennison via at least one intermediate lab (Todd Laverty, personal communication). Thus, in contrast to naive assumptions, the ISO1 sub-strain at the Bloomington Drosophila Stock Center is neither a direct descendant nor progenitor of the ISO1 sub-strain used in the D. melanogaster genome project, and these two sub-strains have had independent trajectories since at least 1994."

The PacBio dataset you refer to was generated using the BDGP sub-strain. The Illumina data you refer to was generated using the BDSC sub-strain and is available here: https://www.ncbi.nlm.nih.gov/sra/ERX645969[accn]

Yes, but I'm looking for Illumina data for the BDGP sub-strain. It is exactly the problem that one of the data sets is BDGP and the other BDSC. Otherwise great background information!

As far as I know, there is no public Illumina DNA-seq data from the BDGP sub-strain of ISO1.


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What will CD spectroscopy show when L- and D- forms of proteins are mixed?
What will happen if equimolar concentration of L- and D- forms of proteins are mixed and we take the circular dichroism reading? Will the positive and negative ellipticity cancel each other out or will there be positive and negative ellipticity of identical magnitude?

I’d be interested to know how you would obtain the D-form of a protein. I presume this is a hypothetical theoretical question. You might consider this clear in the question. As it has no biological significance it doesn't really belong here. It might be better on SE Chemistry, where you are more likely to get an answer.

Interesting that my answer was blocked. It gave the shortest and most precise answer possible to the question. (L and D forms are mirror images and the signal from each cancel out.) That is literally what happens! And the question contain the explanation already!


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Am I entitled to the latlong coordinates of all specimens used in a species revision paper?
If someone publishes a species revision with distribution maps but without publishing all the data used in the paper itself - or in an attached or linked-to  file - are the authors nevertheless required to make all the data necessary to the paper publicly available on request?
I'm assuming they are as this makes sense from an accountability & replicability perspective (and nonsense of the idea of "publication" otherwise?) - but it's not clear to me from searching online.
Thank you!

Unfortunately, there are no general rules for this cases. It depends on the journals rules...

No - you're not entitled to anything. Authors may refuse to share because they want to control future publications arising from their data, either simply to inflate their own publication record or to prevent certain types of anlaysis of their data (see the 'data parasites' fiasco last year for an example of attitudes towards data sharing in some parts of the medical community - this, this, and others).
Alternatively they may simply no longer have the data. Nowadays this is less common, but if you contact an author about a publication from the 1960s it's pretty unlikely that any unpublished data is still in usable form.
Finally, certain aspects of data may not even have been recorded. Before GPS was widely used, accurate lat-longs of collection sites are unlikely to have been measured. As @Kara notes in the comments, it is not uncommon for the collection sites of older samples to be recorded at the country level.
This is why journals are increasingly adopting data-sharing policies (see BES, for example)
However, many authors are happy to share their data, and you lose nothing by asking. Good luck!

Just also wanted to add/re-iterate that in some cases, if the author was referring to old museum material during the revision, accurate lat-long information may be completely unavailable. Some older (1800s) specimens I've worked with in museums have only been labeled "India".

@Kara good point - I'll add it in.


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Why did S. serrata die?
We are interested to farm Scylla serrata which is a type of crab. We introduced the crab weighing 800 g into a environment with 22 ppt salinity with a pH of 8.2. The crab was feeding on around 12 g of chicken meat daily. However at the end of the 4th day, after flipping the crab to its back, it died shortly after. Previously it was able to flip itself back successfully. Note that salinity and pH did not vary much.
What are the possible root causes for death?

A complete species name would be better


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Why is uracil, rather than thymine, used in RNA?
This question was posed on SE Biology some time ago, but all the answers, including the accepted one, answered a different question instead: “Why is thymine, rather than uracil, used in DNA?”. I therefore changed the title to match the answers, giving notice that, if the change were approved, I’d post the original separately question myself (and answer it, if necessary). Here it is:

It is believed that thymine replaced uracil (the RNA base) in DNA because of the deleterious effects of slow spontaneous deamination of cytosine to uracil: by employing thymine instead of uracil, any uracil in DNA would clearly be aberrant, allowing a specific mechanism of repair (involving uracil DNA glycosylase) to evolve with impunity. As this was clearly advantageous, why didn’t RNA also evolve to use thymine instead of uracil?

N.B. By “why?” I mean “how can one rationalize the fact that?”. Obviously, the answer to this type of question is not, and probably cannot be, known with certainty.

I have now accepted my own answer to this question. However comments and criticism are still welcome as the answer should not be regarded as necessarily final.

Regardless of the question† of which came first*, RNA or DNA, it is possible to rationalize the absence of thymine in RNA by a cost–benefit analysis. There is a cost to using thymine, so there must be sufficient benefits to make this worth while.
Cost of using thymine rather than uracil
The most obvious cost of using thymine is the energy requirement for its synthesis (in terms of reducing power — NADPH).

An analogous conversion of rUMP to rTMP (if it existed) would incur similar costs. (There may be additional costs, but they may be contentious and this is indisputable, so it will suffice.)
Benefit of using thymine rather than uracil
For DNA the benefit is clear and stated in the question. By not using uracil as the complement to adenine, uracil produced by spontaneous deamination of cytosine can be recognized as abberant and removed by the DNA proof-reading repair systems. This presumably gives the organism an advantage (benefit) by reducing harmful mutations to DNA — the genetic material.
RNA is not the genetic material of contemporary autonomous organisms. Hence unrepaired C to U deaminations will not affect that aspect of the viability of an organism. How serious will they be for the cell, though? The largest and most long-lived RNAs are the structural ribosomal RNAs. Such mutations in the cells rRNA might have no effect on ribosome function as much of the RNA is thought to be structural. However, even if they did, the inactivation of a small percentage of the ribosomes of a cell would have little impact on protein synthesis. Likewise for the small tRNA molecules.
Messenger RNA poses a different problem as we can conclude that abberant proteins made from mutant mRNA are dangerous to the cell from the fact that a proof-reading mechanism exists to correct errors in the charging (aminoacylation) of tRNAs. I would argue that the relatively short half-life of mRNA compared with the frequency of deamination of cytosine means that the latter process is not responsible for a significant amount of mutant mRNA.
Conclusion
The benefits of using thymine — together with a repair system — in RNA would be marginal, and hence not worth the energetic cost this would entail.
†Footnote: We don’t need to argue about which nucleic acid came first
The current metabolic pathways for formation of dTTP from dUTP and the reduction of ribose to deoxyribose are strongly suggestive to me that RNA preceeded DNA in evolution. (They suggest nothing about whether RNA preceeded protein.) However, the rationalization presented here does not require this assumption. If DNA came first and RNA initially had T instead of U, the rationale could be used to argue why RNA changed bases from T to U. Indeed, the rationale can be employed by those who do not even believe in evolution — they could argue (and probably do) that some deity created things that way because it was more efficient in terms of cost–benefit.

In the absence of answers I consider satisfactory, I have answered my own question, as I 'promised'. Comments are welcome, and may be included in the answer if I think fit.

Answering this question accurately is difficult as it touches on the origin of life hypothesis. In the RNA World Hypothesis, RNA is the original "life" that is able to catalyze its own self-replication. There are various evidences of support for this hypothesis. Uracil's structure is relatively easy to synthesize in reactions that plausibly could take place on early Earth conditions. It could be that RNA used Uracil simply because of Uracil's abundance in nature. This seems to be the case for the use of Adenine in ATP. Guanine can also be used in an energy carrying molecule GTP, but those instances are vastly outnumbered by ATP.
However, there's no set in stone theory as to why either RNA uses Uracil instead of Thymine, or DNA uses Thymine instead of Uracil. Only a lot of circumstantial evidence. The inverse argument for DNA's use of Thymine could also support RNA's use of Uracil. In a competitive environment, a higher mutation rate afforded by the deamination of Cytosine to Uracil may have been an advantage to quickly promote change.


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Misincorporation of dUTP into DNA?
Uracil, the RNA base, has been replaced in DNA by thymine, (which has the same base-pairing with guanine). However the synthesis of dTTP (more usually written TTP) requires dUTP:

To what extent is dUTP (mis)incorporated into DNA?

This question is an attempt to complete a set of questions on the base and sugar differences between DNA and RNA. I will answer it myself if no other answers are forthcoming.

I have provided and accepted my own answer to this question as it was posted as an attempt to complete a set of questions on the base and sugar differences between DNA and RNA. This should not stop anyone commenting on or criticising of the answer — I shall be happy to make improvements.

There follows an attempt to answer my own question, which I think is important to consider in the general context of postings on SE Biology concerning uracil and thymine in DNA and RNA synthesis.

There seems to be little misincorporation because of the low concentrations of dUTP in cells.

Any small amount of misincorporation can be handled by the DNA repair system that exists in cells.

I base statement 1 on the work of Grogan et al., published in Biochemistry 50, 618–627 (2011). They showed that in both mouse and human cell lines that the normal concentration of dUTP (and dUMP) was low. I assume that this must reflect cellular activities of dUTPase and thymidylate synthase being sufficiently high to remove dUTP and dUMP, respectively as they are formed. When thymidylate synthase activity was inhibited by anticancer drugs, these nucleotides built up, as expected.
In support of Statement 2 I refer to a separate earlier study in fission yeast by Seiple et al. in Nucleic Acids Research 34, 140–151 (2006). They used the drug, 5-fluorouracil, to inhibit thymidylate synthase and found that it caused misincorporation of uracil into DNA with concommitant cell damage. The role of the DNA repair system in mitigating this damage was shown using a mutant in the Ung1 gene, which encodes DNA glycosylase — here the cell toxicity was much higher.
Although there are some inconsistancies between the different systems used, and difficulties of interpretation.  I think that they provide general support for the two postulates. It would be useful if it were possible to locate kinetic data on the relevant enzymes to test my assumptions regarding the reason for the low dUTP concentration.


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Is there such thing as a bird with infrared vision?
I am writing a story and I specifically need a bird with infrared vision. Worst case scenario I just invent one but that would break the pattern in my story.
The closest thing I have seen from researching myself was this statement, "tawny owl's retina has about 56,000 light-sensitive rods per square millimetre (36 million per square inch); although earlier claims that it could see in the infrared part of the spectrum have been dismissed."
So apparently it was proven that the Tawny Owl (Strix aluco) does not have infrared vision. I couldn't find a better forum to ask this on (I don't know, is there a zoology forum?) so my last resort would be a biologist.

I read somewhere it was suggested some falcons may have infrared vision, but I have no source. Also, if I remember well some nectar-feeding hummingbirds can see near IR, but no full blown IR vision.

I posted a recent answer that might give you some background here. A quick tl;dr is that true infrared vision (like in snakes) doesn't happen except for specialized organs that aren't really vision anymore. However, in other cases, infrared really just means "marginally red shifted vs. human vision" which is a lot more likely but also a lot less impressive.

I looked on Google Scholar for "avian infrared vision" and "bird infrared vision" and found nothing, so it seems fairly unlikely unless there is something very obscure. Frankly, I think it is unlikely that the physiology of enough bird retinas or behaviors have been studied to conclusively say there are no birds with red-shifted visual capabilities.

@BryanKrause I agree, it may be possible that such a bird exists but hasn't been properly studied... well thanks for the help I guess I'll work with what I've got

Just fort the record, @Alexlok: you confuse near IR with near UV. Opposite end of the spectrum. :)


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Does one need to perform two Chi-square tests?
A question from my University's Question paper 2016:

A newly identified fruitfly mutant, cyclope eye –large and single in the middle of the head is hypothesised to be autosomal dominant. The experiment started with homozygous wild type females and heterozygous cyclopes males. The data from the F2 generation was 44 wild type males males, 60 wild type females, 110 cyclops males and 150 cyclops females. Does this support or reject the hypothesis$^1$? Use chi square to prove.

I think the following should be a proper approach at solving it:
H0= The proportion of cyclope eyed male and female is not that same,i.e. the gene responsible is not autosomal. $or$ There is an association between the sex of fruitfly and the phenotype.$^2$
H1= The proportion of cyclope eyed male and female is the same, the gene is present on autosome $or$ There is no association between the sex and the phenotype.$^2$
Chi square contingency test with Male and Female (in the columns) and Wildtype and Mutant phenotype (in rows).
Once the H0 is proved wrong (if it is proved wrong), we consider a next Chi-square test, goodness-of fit, where :
H0= The proportion of mutant phenotype is the same as the wildtype i.e. 1:1 ratio is followed
H1=The proportion and the mutant phenotype is greater i.e. the allele responsible is dominant.
When the final H1 is accepted the $^1$hypothesis is correct or else wrong.
$^2$ I'm not sure which one is better / proper.
Is it alright?

The wording of the cited question is strange. Hypothesis testing does not "support" anything, and definitely does not "prove" anything. All you can do is reject the null hypothesis. This means the alternative hypothesis is consistent with the data, but does not prove it. Hypothesis testing is asymmetrical in this sense, and that is very important to grasp.

You should just have 1 chi-square test to test the hypothesis.
Note that the problem is asking about F2 generation, not F1.
H0 in a chi-square test is your prediction based on a model; H1 is that the real outcome differs from what is expected, so you have that a little backwards. H0 should be the expected counts knowing the initial proportions and expecting autosomal dominant inheritance.
Start with your prediction:
F1 generation will be half heterozygous males/females, half WT males/females, so F2 generation has 3 types of mating events:
Cc x Cc occurs 25% of the time, and 75% of offspring are affected
Cc x cc occurs 50% of the time, and 50% of offspring are affected
cc x cc occurs 25% of the time, and 0% of offspring are affected
Multiply these probabilities and you should have 43.75% expressing the phenotype; your prediction for the chi-square test is that you will see this same percentage regardless of sex.
From there, doing a chi-square test is simple and there are many many resources online for this (here is just one).

Is it a two-tailed test? Because the observed data can be significantly more or less than the expected 43.75% i.e 7/16?

@SanjuktaGhosh Chi-square is always one-tailed. It isn't a two-sided distribution like the normal, values that are off to the left are basically just "unexpectedly great fits" like if you flipped a coin 1000 times and got exactly 500. If you look at the math in the calculations they are based on squared differences, so 7/16 and 9/16 are treated exactly the same: if you predicted 8/16 in one case you have 1^2 in the other case you have (-1)^2.


text:
Are there animal species that sense infrared light with their eyes?
I asked a question earlier today about birds with infrared vision but this time I am asking about animals in general. I know that many snakes have receptors between their eyes and their snout that allows them to sense infrared radiation but I am looking for an animal that actually uses its eyes.
Googling and searching around found me this statement:

It's worth noting that, though there are numerous animals that sense
  infrared light, relatively few of them sense it with their eyes

The article didn't list any specific animal that used its eyes to sense infrared light, it just says 'very few'. However, I haven't been able to find any species that can sense infrared light with their eyes.

It is possible that the "relatively few" refers to invertebrates.

@BryanKrause Ah yes, that escaped me. I'll edit my thread accordingly.

It may be worth noting that, if an eye is defined as an organ that detects light, then the definition answers the question: if an organ detects IR light, it is a type of eye, therefore all animals that detect IR light do so with their eyes. This definition of 'eye' is currently used in, e.g., the wikipedia for 'eye':
"Pit vipers have developed pits that function as eyes by sensing thermal infra-red radiation, in addition to their optical wavelength eyes like those of other vertebrates".
https://en.wikipedia.org/wiki/Eye

@bshane then eyeballs (?)

@bshane If you look up scientific literature on pit vipers, however, their sense is (mostly?) never referred to as vision: sometimes 'vision' in quotes like that. I think, although a broad definition of eyes can be used for certain organisms, for vertebrates, arthropods, and mollusks, each of their eyes share a genetic and developmental origin, so when you talk about "eyes" those are the organs you refer to.

@BryanKrause In that case, a very good answer would say why IR pit eyes aren't 'true' eyes, whereas similar non-IR organs are called eyes.
AliceD's answer distinguishes between 'organs that detect IR' and 'organs that detect IR and other wavelengths', using 'and other wavelengths' as a stand-in for 'eye'. This answers the question the OP meant to ask (I think - and so have +1'd), but sidesteps the problematic definition of 'eye'.

Short answer
As far as I can see, there are no animalia with high-sensitivity infrared photoreceptors in their retinae. Instead, infrared is detected at low thresholds with a dedicated sensory system in some species - the pit organ. This organ is separate from the retinae and its output does not merge with the retinal image. However, red cones, and even green cones for that matter, have low sensitivity to infrared light and when intense enough, infrared stimuli may be detected by the eye, as was shown in a small study in ferrets.
Background
Infrared (IR) light is classified as light at wavelengths of 700 nm and up. In Fig.1 is depicted the light sensitivity of man under scotopic (dark-adapted) and photopic (light-adapted) conditions. It is readily apparent why we cannot perceive IR.
Species that can detect IR use it in general to detect heat. Notable examples are the blood sucking species, including mosquitoes, bed bugs and vampire bats as well as nocturnal predators including species of snake (source: National Geographic). Although this heat detection can be classified as IR vision, IR is not detected by their eyes. Instead, all of these species use specialized IR-sensing organs called pit organs to detect IR. Basically, these are heat detectors (source: NSF). While snakes are able to construct heat-maps, the IR image and visual images as detected by the retinae are not combined into a single image. As far as I understand, the visual image and IR images co-exist in snakes and are not fused (or 'overlaid') (Campbell, 2002).
So the most notable of IR detecting species have IR vision, but these heat maps are sensed by dedicated pit organs separate from the retinae and as far as I can see the images are not combined.
However, last but not least - IR cameras are often used to study nocturnal critters as it is assumed they cannot detect the IR. Interestingly, a study on a small population of 5 ferrets showed that 3 of them responded at above-chance level to light stimuli well into the IR (870 nm) (Newbold, 2007). It should be noted that sensing of stimuli is all about thresholds. The Fig. 1 shows a nearly zero-response in humans at 700 nm, but when we would make the stimuli strong enough, we may elicit a small response nonetheless. Fig. 2 shows the absorption spectra of red and green cones. As becomes apparent here, red cones and even green cones have spectral sensitivity in the IR domain. Then it might become a question not whether we can sense IR, but at what level we can detect it. Under normal everyday lighting conditions, we obviously can't, but that does not exclude the possibility we may perceive it at extreme light intensities.

Fig. 1. Human spectral sensitivity. source: Webvision

Fig. 2. Spectral sensitivities of red and green cones. source: Dowling, 1987)
References
- Newbold, Master's thesis. University of Waikato, NZ
- Kalloniates & Luu. In: Kolb et al (eds). Webvision. The Organization of the Retina and Visual System
- Schnapf et al, Nature (1987); 325: 439-41

Yes, Mantis shrimp have 12 photo-receptors and can detect the low-end of IR.
In H. trispinosa one of the photoreceptors, R3P, detects right at the edge of 'deep red' light and would detect infrared (700+ nm). Although this study didn't explicitly measure infrared detection, by the shape of the curve it's not a huge leap that they detect infrared at significant levels. Below is the link and a link to human photo-sensitivity curves for contrast.
Keep in mind 'infrared' is not a universal biological property, it's simply defined by the fact that our species doesn't see it.

Mantis Shrimp photoreceptor sensitivities
Link without paywall. Figure 1A
Human photoreceptor sensitivities for contrast
Electromagnetic emission from the sun

Enright, et. al. (2015) found that several vertebrate species -- including zebrafish and bullfrogs -- under certain environmental conditions red-shift the rods and/or cones in their photoreceptors by something on the order of 30 or 60 nm ("beyond the range of human vision", per article summary). The mechanism for this is production of Cyp27c1, which serves to convert vitamin A1 to A2 in the photoreceptor. Bullfrogs are found to have the A2 vitamin solely in the dorsal (top) retina, Likely enabling them to look downwards into murky water while at the surface (Figure 1, note G).
Enright, Jennifer M., et al. "Cyp27c1 red-shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2." Current Biology 25.23 (2015): 3048-3057. Link.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Trying To Identify this Fish

My 4 year old fell in love with this fish at the aquarium.
I'm trying to find out what species it is so we can learn more about it.

Welcome to Bio.SE. Please can u add the location and size of the fish. A clearer image would be appreciated.

You can also go to the aquarium's website (if it was commercial) and look up their fish.

It looks like a unicornfish (genus Naso), maybe Naso vlamingii, the Bignose Unicornfish. They're Acanthurids, related to surgeonfishes and tangs.
These are mainly found in Indo-Pacific ocean around the depth of 50 mts from surface. Coral reefs are their main habitat and destruction of coral reefs is their current biggest threat alongside trading by fisheries. A good source of information for this species is available here.
A copy of this fish.

Picture credits: UM Rosenstiel School

Yes, this is the right fish! There were other unicorn fish in the tank that actually had the "horn." I didn't realize there were other variations. Thank you so much!


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At what point, when connected, do DNA strands become a helix?
When synthesizing DNA strands and beginning to "connect" them, how quickly does it become a helix?
In this answer, canadianer says

The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously.

This then makes me think of the following scenario: say one is constructing two strands of DNA out of deoxyribonucleotides. Then, one begins connecting them with hydrogen bonds. Before the hydrogen bonds are added, my understanding is the two strands would be straight and not helical (if this is wrong, please correct me on this) so at some point as the two strands are connected, it would "spontaneously" become helical.
The question, then, is at which point. After one "connection"? Two? All of the connections necessary to complete the piece of DNA?

Yes, in general that's correct.

I will do soon, glad it helped.

@canadianer has answered your question, but you should be aware that it is of little interest to scientists because of its hypothetical nature and experimental untestability, and the fact that it does not address a problem in biological or physical sciences. DNA is polymerized by enzymes, and we understand something about what occurs in these reactions. We also know there is not the sort of folding problem that exists for proteins. We cannot add deoxynucleotides to a pre-existing helix (which involves making phosphodiester bonds) in the way you suggest without enzymes, template and primer.

In general, a single stranded nucleic acid is helical in the absence of other secondary structure. The base stacking that drives helix formation does occur  between adjacent bases in the same strand. Note, however, that such structures are dynamic and dependent on properties such as temperature and salt concentration. You can see an example of a single-stranded RNA helix in the following crystal structure (1MHK):

Note the blue helix at the bottom of the image is actually a duplex in the crystal.


text:
ID a marine creature found on a beach on the US east Coast
While walking on a marshy beach, I found this creature. It has no eyes, no feet, no fin, no gills. The only thing I know is that the skin lightly contracts. I found at least three of these. It is basically carried around by water.

Found this on a Maryland beach, roughly 150 miles east of Washington D.C.

Where was this found?

edited description to add this information.

nice and clear photos

It's positively a sea anemone. It retracts the tentacles when disturbed and become quite rigid. It's hard to identify it in this condition, leave it for a whlie in a jar with sea water and you'll see.

Based on your description, it could be a sponge (but I don't think sponges have a contractile skin), a tunicate or a sea cucumber.
I would favour the last option.

The following questions might help further identification: How many holes can you spot?
If there are 2, where are they placed with respect to one another?

I hope someone can propose something more precise.
Edit:
As noted in the comments, it could also be a sea anemone. In my experience, these have a quite soft body. In that case, it should have only one opening, and the opening should let tentacles out when the animal is left quiet in the proper environment.

Paranthus rapiformis has a similar form.


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Are VCF headers supposed to change over time?
VCF headers describing the content of the INFO field are supposed to give additional information about a variant.
Example. A VCF file can be annotated against genomic variant databases such as dbSNP or ClinVar. The annotations such databases add to the file are described in the headers.
For instance, the CLNSIG field (taken from ClinVar) describes the clinical significance of a variant. Such field description is contained in the following header:
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility, 255 - other">

As reported in the field definition, the set of values it can take changes over time:

Other non-standard terms are also used to meet submitter needs. ClinVar plans to add standard terms for other scenarios (e.g. somatic, pharmacogenomic, and mitochondrial variants) when they are available.

Do you know if this is a standard condition? Are headers supposed to change a lot over time? Is this condition valid only for clinical annotations (such as the ones provided by ClinVar), or something that is supposed to be considered for every annotation?
Thank you for your help.

As always with annotations, the annotation of a .vcf-file reflects the current knowledge. If that knowledge changes, the header of a file can be updated. Usually, this is not something you do by yourself but the providers of the file release new versions. However, I have no experience with clinical data and my statement is purely based on personal experience and common sense.


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Which are the most important carcinogens in tobacco smoke?
I am researching the neoplastic effects of tobacco smoke and would like to measure a set of key molecules in the saliva of several study subjects after they have smoked.
Which are the most relevant carcinogens originating from tobacco smoke that are detectable in saliva? I don't think there will be time or room to measure metabolites, as the saliva samples will only reflect short-term (<60 minutes) exposure to tobacco smoking.

So you're after compounds present directly after smoking? Some metabolites may also be present (?) so I'm just trying to get this question clear. +1

#AliceD The saliva will reflect only short-term (<60 minutes) exposure, so I don't think there will be metabolites

This is not an easy question - as tobacco smoke contains something like 5000 different chemical components, from which 70-100 are carcinogen. The list includes: Oolycyclic aromatic hydrocarbons (PAHs), N-nitrosamines, aromatic amines, aldehydes, volatile organic hydrocarbons and metals. I haven't found articles which specifically concentrate on the carcinogens in saliva, but my guess would be that you find them all because of the "application route" of the cigarettes.
Most of these carcinogens first need to be processed from the livers cytochrome P450 system to reach their carcinogenic potential. The enzyme complex converts these substances into forms which can then covalently bind to DNA.
A list of several different of the carcinogens can also be found in the Wikipedia. For further information see the references.
References:

Hazardous Compounds in Tobacco Smoke
How Tobacco Smoke Causes Disease: The Biology and Behavioral Basis
for Smoking-Attributable Disease: A Report of the Surgeon General.
Tobacco Smoke Carcinogens and Lung Cancer


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Why are ammonium ions reabsorbed in the thick ascending limb during acid secretion?
In order to produce HCO3- from glutamine and to subsequently reabsorb it,
H+ ions need to be secreted. The kidney does this by via ammonium ions
in the PCT. But why are the ammonium ions then reabsorbed in the TAL before
being put back into the collecting duct? Wouldn't it be more efficient if
they were just left in the tubule fluid where they would reach the
collecting duct eventually? The first method seems to be a longer way of
achieving the same result.

Isn't it all to do with the reabsorption of water, i.e. everything gets flushed out in the Bowman's capsule and then some stuff is reabsorbed to lower the water potential of blood, so water is reabsorbed as well.
I guess I figured it was easier to have a leakier sieve at the Bowman's capsule than try to only release the waste products via facilitated diffusion.

but ammonium ions are secreted in proximal tubule before being reabsorbed in the thick ascending limb. From here they're pumped into the collecting duct to be excreted. But if they were just left in the tubule fluid (without being taken up in the TAL), they would've also reached the collecting duct.

I don't know the specifics of this pathway, it does seem convoluted, but it could be something along the lines of ammonium ions are reabsorbed during non-selective cation reabsorption, then selectively secreted. Again it's easier to take everything up then get rid of what you want to than try and take up just the things you want to. Edit, try looking at the transporters (ion channels/pumps etc.) involved.

Why reabsorb $NH_4^+$ in the thick ascending limb if you're just going secrete it in the collecting duct

This is an excellent question. When you find an odd, seemingly inefficient aspect of physiology, it's an opportunity to learn something new.
This alternating secretion, reabsorption, and secretion starts to make sense when you look at the anatomy of the nephron.

There is no appreciable ammonia in the filtrate at Bowman's capsule (free ammonia is efficiently converted to urea in the liver by the urea cycle, so it's in very low concentrations in the blood).  As you say, it is produced in the proximal convoluted tubule. The amount that is produced is regulated by the acid load (more acid, more ammonia production). The proximal tubule is in the cortex (top of the photo).
$NH_4^+$ is in equilibrium with $NH_3$ in the tubule, and renal tubular cells and junctions are relatively permeable to $NH_3$ here, so the more $NH_4^+$ is produced and actively pumped into the lumen, the more $NH_3$ backflow leaves the tubule and enters the ECF. Because of this, the primary work of the PCT in acid base homeostasis by the kidney is not secretion (though $NH_4^+$ is actively secreted here), but rather in the production of new $NH_4^+$ and new $HCO_3^-$.
The bulk of the work of secretion happens in the collecting duct. There are a number of passive and active transport mechanisms for the secretion of $NH_4^+$ here, especially in the medullary collecting duct. These mechanisms are aided by a high concentration of $NH_4^+$ and $NH_3$ in the medulla (at the bottom of the picture).
So where does this high concentration of ammonia come from? It's from the reabsorption of $NH_4^+$ in the thick ascending limb. This is reabsorption (the tubular cells take $NH_4^+$ from the lumen and send it to the ECF), but you can think of it more as taking it from the cortex and putting it in the medulla. The filtrate flows along the lumen of the tubule, toward the collecting duct. Much of it is in equilibrium between the lumen and the ECF before it gets to the thick ascending limb. At the thick ascending limb, the permeability of the tight junctions and the tubular cell membrane changes. Solutes (the one we're interested in right now is $NH_4^+$) are taken out of the lumen and left behind in the ECF. Because the filtrate flows but not the ECF, and because the tubular cells are permeable before the thick ascending limb, and impermeable after, this substantially concentrates these solutes in the medulla, and dilutes the solutes in the cortex.
This is a process known as the countercurrent multiplier. The same principle is used to create a hyperosmotic ECF (and consequently, allow for a hyperosmotic urine if you've been wandering in the desert for hours).
Here's a diagram of the nephron from a decent review article that illustrates each of these processes for ammonia handling:


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How can grass-fed livestock generate fat?
How can herbivorous cattle get fat? These animals eat only grassy substances, think of cattle, buffalo, goats etc. For example, wheat grass contains 0% fat, and its nutritional value is limited to carbohydrates and fibers. Still, livestock can have substantial (10%) fat content and give milk with lots of fat on top of it.
Where does that fat come from?

Apologies for re-editing this question, but just to illustrate that grass basically contains no fat at all and to prevent discussions on nuts, seeds etc.

Perhaps I'm unduly picking nits, and I'm certainly not disagreeing with @AliceD's nice answer, but most grass does have some fat.  Here for instance are numbers for various types of hay: http://www.atascaderohayandfeed.com/hay.html (The first hit Google returned - so I'm lazy :-))

Short answer
Plants typically store energy in the form of starch. Animals, including livestock and humans for that matter, can digest starch, metabolize it into acetyl-CoA and turn it into fat.
Background
Plants contain sugars, formed by photosynthesis. Plants generally do not store energy in the form of fats, but in the form of starch, a glucose polysaccharide*. Animals digest this starch through hydrolysis catalyzed by the enzyme amylase back into glucose (Fig. 1). Cellulose is another polysaccharide. In grass-fed cattle, it is mainly cellulose that forms their source of energy. Cellulose cannot be digested by ruminants (cattle, goats, sheep) as they are unable to synthesise the enzymes needed to digest cellulose and other plant compounds. Cellulose can be hydrolyzed by cellulase enzymes in e.g. Ruminococcus species present in the ruminant tract in the guts of these animals. The cellulase enzyme endoglycosidase cleaves the disaccharide cellobiose from cellulose, and another type of enzyme, β-glucosidase hydrolyzes cellobiose into glucose monomers (sources: Microbe Wiki, University of Waikato).
Glucose is then degraded to pyruvate by aerobic glycolysis in the cytoplasm of the cell. Pyruvate is then transported into the mitochondria, where pyruvate dehydrogenase oxidatively decarboxylates pyruvate, forming acetyl-CoA and other products (Fig. 2).
Acetyl CoA can then serve as a substrate for citrate synthesis. Citrate, in turn, can be transported out of the mitochondria to the cytoplasm. There it can be split to generate cytoplasmic acetyl-CoA for fatty acid synthesis under the influence of anabolic factors like insulin in times of plenty (Fig. 3), referred to as lipogenesis.

Fig. 1. Starch is hydrolyzed by amylase. source: Biotek

Fig. 2. Acetyl-CoA formation. source: University of Utah

Fig. 3. Lipogenesis. source: Sharing in Health
*: Although plants usually store their energy reserves in the form of starch, there are important exceptions to this. Most notably certain seed pods, like peanuts and walnuts, contain substantial amounts of fat. Further, cell membranes and other components will add traces of fatty substances even in grassy plants. With credits to Marzipanherz.

Does this mean I can get fat even if i do not eat any fat?

@murmansk Getting overweight is not a problem of eating to much fat per se, but of taking up too much nutrients. Fats are more "dangerous" here, since they harbour more energy (calories) per gram than carbohydrates. But still, if you eat too much sugar and avoid fat completely, you can get overweight.

@murmansk The "Atkins diet" was a fad a few years ago based precisely on this concept: weight gain is a function of a disparity in calories in versus calories out. The source of calories is less important. More recent fad diets that take a similar approach are the "ketogenic diet" and "paleo" movement. All of them emphasize a reduction in sugars, rather than fats, for health and weight loss. (note: I'm not necessarily supporting any of these diets, just pointing out that they are somewhat popular and are based on exactly the science we are discussing here)

Same way animals can turn sugars to fats, chain reactions involving multiple enzymes. Some plants, e.g. potatoes, rice etc. will store very little fat. Most plants will only store a bit of fat in the seeds, but some - I guess nuts and olives are the main ones - will convert significant amounts of glucose (produced by photosynthesis) to fats, which we can eat, or extract oil from.
Edit: Looks like there's some good info here, but a bit dense :lipid biosynthesis


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Can a pyruvate reaction to acetyl coA be called as acetylation in any way?
Can the oxidation of pyruvate to acetyl coa be called as acetylation in some ways?
Please include credible sources in the answer.

Acetylation means addition of an acetyl (CH₃CO-) group, not formation of acetate. Pyruvate to Ac-CoA is quite a complex reaction. Please try to do some prior research before asking. The objective of your question is unclear.

Acetylation is defined as1:

Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into a chemical compound.

So, any reaction in which an acetyl (CH3CO-) group adds to another compound is an acetylation reaction. A common example is Friedel-Crafts acetylation reaction:

If the reaction is catalyzed by pyruvate dehydrogenase: In this case, first of all the reaction that you refer to is termed as pyruvate decarboxylation (rather than oxidation, although it won't hurt either). As @WYSIWYG has said in comments, it is not a simple reaction, it involves three steps (+ 2 steps for regeneration of complex), each catalyzed by different enzymes. The name given for the whole complex is pyruvate dehydrogenase complex (PDC)2. The steps involved are3:

The keto carbon of pyruvate reacts with the carbanion of TPP on E1 to yield an addition compound. The electron-pulling positively charged nitrogen of the thiazole ring promotes loss of CO2. What remains is hydroxyethyl-TPP.
The hydroxyethyl carbanion on TPP of E1 reacts with the disulfide of lipoamide on E2. What was the keto carbon of pyruvate is oxidized to a carboxylic acid, as the disulfide of lipoamide is reduced to a dithiol. The acetate formed by oxidation of the hydroxyethyl moiety is linked to one of the thiols of the reduced lipoamide as a thioester.
The acetate is transferred from the thiol of lipoamide to the thiol of coenzyme A, yielding acetyl CoA.

Now, pyruvic acid has the formula: $CH_3-CO-COOH$. So, if you look at the step C of reaction, then since CH3CO- has been added to coenzyme A, hence, in a way, it would be considered an acetylation reaction. Pay attention that the complete reaction will not be considered acetylation, only a part of it would be. This is also the reason why calling the complete reaction as oxidation won't hurt, because even decarboxylation is just a part of complete reaction.
If the reaction is not catalyzed by pyruvate dehydrogenase Taking the question out from pyruvate dehydrogenase (as you don't talk specifically about that), there is an enzyme Acetyl-coA synthetase whose job is catalyzing acetylation of coenzyme-A(!)4. The reaction looks like this:
$ATP + acetate + co-A \rightarrow AMP + pyrophosphate + acetyl-coA$
The enzyme is of two types: AMP forming and ADP forming5:

So, as long as the conversion is not one specifically catalyzed by pyruvate dehydrogenase, we can say that Yes, conversion of coenzyme-A to Acetyl-coA is an acetylation reaction.
References:

Acetylation - Wikipedia
Pyruvate Dehydrogenase - Wikipedia
Pyruvate Dehydrogenase and Krebs Cycle - Joyce J. Diwan; Rensselaer Polytechnic Institute
Acetyl-coA synthetase - Wikipedia
Hentchel KL, Escalante-Semerena JC. 15 July 2015. Acylation of biomolecules in prokaryotes: a widespread strategy for the control of biological function and metabolic stress. Microbiol Mol Biol Rev doi:10.1128/MMBR.00020-15

I would only regard the CoA-SH to A-CoA being the acetylation step. Otherwise the full glycolysis pathway could be called an acetylation reaction - hardly true isn't it?

I (accidentally) wrote the word acetylation while explaining about that reaction in my exam. It's only a part of a part of aquestion but if my instructor marks some of the points off, can I say that "it has acetylation in the process so its technically correct"? Both acetylation and decarboxylation are not stated in my textbook. Can I also say that acetylation IS oxidation? Sorry if it was too personal. I thought it was worthy enough to discuss the aspects here

@denniskim There is difference between acetylation and oxidation. Also, (assuming you're in high school where this is a single step conversion), you can say that its technically correct. You can discuss general concepts here, but personal exam questions are off-topic here.

@DennisKim I think the right way to think about it is this: most reactions operate on more than one molecule. In the case of pyruvate dehydrogenase, the reaction is decarboxylation of pyruvate and concomitant acetylation of CoA. (The decarboxylation steps is oxidative, so you could also call that part oxidation). Most people focus on what happens to the pyruvate, but as explained by many answers above, you can't have one without the other.


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What is this part of blastula called and how is endoderm formed?

Could you tell me what the yellow mass within the blastocoel is called ?
I know that blastocoel is a fluid filled cavity, so are the yellow coloured cells the inner part of blastoderm or are they some other cells ?
If they are the part of blastoderm itself, why is it not in the same colour of light-orange as the blastoderm, or is it the mesoderm, or the inner cell mass  ?
And is it the blastoderm that forms ectoderm , and endoderm pinches  off the ectoderm during gastrula phase? And could you also explain how the orange mesoderm formed ?

@Kaneri the diagram in your question is wrong. See this : http://wikivisually.com/wiki/Gastrulation

The blastocoel, as you say yourself, is a fluid-filled cavity (wikipedia) so it has no cells. Fig. 1 shows cellular and non-cellular regions of the blastocyst.
Your questions on the formation of the three germ layers during germination are nicely shown in the illustration in Fig. 2, right two panels.

Fig. 1. Blastocyst. source: wikipedia

Fig. 2. Formation of the germ layers. source: Class Connection

could you also answer whether the yellow cells within the blastula are cells of blastoderm itself or are they some other type of cells? And also whether purple cells shown within the archenteron are cells of endoderm itself ?

Just wanted to add, OP's image of blastula lacks inner mass so (without any citation) it is likely  referring to Amphioxus blastula.


text:
DNA Topology of two circular chromosomes
I'm reading DNA Topology: Fundamentals from where I quote :

Topological aspects of DNA structure arise primarily from the fact that the two DNA strands are repeatedly intertwined. Untangling these two strands, which occurs in all major genetic processes may prove rather difficult. In the simplest case of a linear DNA in solution, untangling is possible due to the free rotation of the ends of the DNA. However, for all natural DNAs, free end rotation is either restricted or forbidden altogether. Consequently, untangling the two DNA strands becomes topologically impossible.

And from Wikipedia:

However, a circular chromosome can provide other challenges for cells. After replication, the two progeny circular chromosomes can sometimes remain interlinked or tangled, and they must be resolved so that each cell inherits one complete copy of the chromosome during cell division.

Is there any evidence that proves the idea represented in the figure?

Yes, there is an abundance of evidence. I think the following electron micrograph is pretty convincing.

This image is from a review:
Gil-Ramirez G, Leigh DA, Stephens AJ. 2015. Catenanes: Fifty Years of Molecular Links. Angew Chem Int Ed 54:6110-6150.
It was adapted from the first paper to observe naturally occurring catenated DNA molecules, which were isolated from HeLa mitochondria:
Hudson B, Vinograd J. 1967. Catenated Circular DNA Molecules in HeLa Cell Mitochondria. Nature 216:647-652.
You can see this answer for an explanation of why catenanes form during replication:
How do catenanes form when DNA replicates?


text:
Epistasis: Why should a recessive allele be a hypostatic gene?
Let us take the example of Recessive epistatsis, an epistasis in which a double recessive gene mask the phenotypic expression of alleles  of another locus.
(adapted from: An Introduction to Genetic Analysis)
An example from the same book:

In  plant blue-eyed Mary (Collinsia parviflora), the biochemical pathway is as follows:

The w and m genes are not linked. If homozygous white and magenta plants are crossed, the F1 and F2 are as follows:

Complemention results in a wild-type F1. However, in the F2, a 9:3:4 phenotypic ratio is produced.
This kind of interaction is called epistasis, which literally means “standing on”; in other words, an allele of one gene masks the expression of the alleles of another gene. In this example, the w allele is epistatic on m+ and m$^1$. Conversely, m+ and m can be expressed only in the presence of w+.

Interpretation & Question:
The gene product of m$^+$ is needed to form blue pigment from magenta. On the other hand, in the absence of w$^+$ allele (i.e. w w genotype), no magenta (precursor of blue) is formed so the phenotypic expression of m$^+$ allele(s) is masked. Now, what has m got to do here? $^1$ It is not encoding anything.
Note:
On referring other books I found they do not suggest a hypostatic gene to be recessive (as $m$ has been considered here).
My idea of recessive allele is that one that due to loss-of-function mutation either produces a non-functional variant of the protein or the same protein at a lower quantity.
Has recessive allele been considered an hypostatic allele here considering that it might be able to code normal functional protein at a lower rate?

Scope of answer:
Which concept should be followed? Why (ideally with citation)?

I'm confused, what exactly is your question?

@canadianer Edited. If there are still issues, please point out the concerned paragraph.

It's called recessive epistasis because the recessive allele w masks the phenotypic expression of m+ and m. I don't understand this part: Now, what has m got to do here? It is not encoding anything.

If you see the flow chart m+ is responsible for the conversion of magenta into blue and not the product of m (something consistent with other books explaining epistatsis, in this case recessive epistatsis), so is my question.@canadianer

Does this help? I'm still not really following you. 1) The phenotypic expression of the m locus is dependent on the w locus. This is why the w locus is epistatic over the m locus. It is called recessive epistasis because the homozygous recessive genotype w/w prevents the phenotypic expression of the m locus. A w/w organism will be white regardless of the alleles at the m locus. 2) The m allele is considered recessive to the m+ allele because two m alleles are required to show a phenotypic effect. When a w+ allele is present, the organism will be blue unless there are two m alleles

'In this example, the w allele is epistatic on m+ and m' -m according to the dig. and as you said has no contribution to blue pigment then why its phenotypic expression has to be masked? (I can't put it in any better way)

Let us continue this discussion in chat.

In this example, the $w$ locus is epistatic on the $m$ locus or, in other words, the phenotypic expression of the $m$ locus is dependent on the $w$ locus. It is called recessive epistasis because the homozygous recessive genotype $w/w$ prevents the phenotypic expression of the $m$ locus. A $w/w$ organism will be white regardless of the alleles at the $m$ locus.
Now, to get to your question, consider the situation where the organism is $w^+;m^+$:
$$\ce{white \stackrel{w+}{\rightarrow} magenta \stackrel{m+}{\rightarrow} blue}$$
You can see that the phenotypic expression of the $m^+$ allele is a blue colour. Next consider a $w^+;m/m$ organism:
$$\ce{white \stackrel{w+}{\rightarrow} magenta \stackrel{m/m}{\nrightarrow} blue}$$
You're right that, at a molecular level, $m$ likely codes for some defective enzyme. But, in the case of epistasis, it is important to consider its expression at the level of phenotype. The phenotypic expression of $m/m$ is a magenta colour.  Finally, look at a $w/w;m/m$ organism:
$$\ce{white \stackrel{w/w}{\nrightarrow} magenta \stackrel{m/m}{\nrightarrow} blue}$$
Despite having the $m/m$ genotype, which should give a magenta colour, the organism will be white because of epistasis. In other words, the expression of the $m/m$ phenotype is dependent on the $w$ locus.
I hope that answers your question. Let me know if I still misunderstand or something needs to be explained better.

In the context of this textbook, m is simply an allele that codes for a non-functional protein product. The protein product of m is incapable of converting magenta pigment into blue pigment.


text:
Physical interpretation of a stoichiometry matrix all zero entries
Consider the following set of biological reactions:

I've assumed that the state space of the system wrt to concentrations could be depicted by vector $s$ as below:
$\dot{s} = \begin{bmatrix}\dot{a}\\\dot{x}\\\dot{c}\\\dot{b}\end{bmatrix}$.
So the stoichiometry and reaction matrices could be acquired as the following:
$\dot{s} = \begin{bmatrix}\dot{a}\\\dot{x}\\\dot{c}\\\dot{b}\end{bmatrix} = \begin{bmatrix}-1&1&0\\2&-2&-1\\0&0&1\\0&0&-1\end{bmatrix}\begin{bmatrix}axk_{1}\\x^{2}k_{-1}\\bxk_{2}\end{bmatrix}$.
Now let's assume that the concentrations of $A$ and $B$ (i.e. $a$ and $b$) are constant, thereby $\dot{a} = \dot{b}=0$.
Therefore the stoichiometry matrix will be reduced to
$\begin{bmatrix}0&0&0\\0&0&0\\0&0&0\\0&0&0\end{bmatrix}$.
It's a little bit weird and to me, it sounds like a system which has no evolving dynamics, as a totally static system of reactions, by which nothing is consumed or produced. Furthermore, the system always remains at $a=b=c=x=0$ as a global equilibrium point.
Is it a valid conclusion?...
In a general perspective, what is the meaning zero-coefficients matrix in biology?

I'm sorry, maybe I am missing something: you are talking about a system in which you have set all the concentrations to zero? I mean, sure, that's valid, but not particularly interesting - why do you care about such a system? I'm less familiar with the specific conventions you are using (linear algebra was a long time ago, and though I use applications of it all the time everything is numerical simulations rather than mathematical logic). And why do you think the meaning of a particular matrix would be different in biology vs. anywhere else?

I think this question from another SE site will help you understand a bit - maybe check in there and come back if you are still confused?

@BryanKrause: Answer1: I'm just setting two of the concentrations to zero, $a$ and $b$ not all of them! Furthermore. Answer 2: Because such zero matrix is not a dynamic representation in general theory of dynamic systems. Since I'm not a biologist, I'm just wondering whether there is something necessary to be considered in the scope of biology to interpret such situation.

Can you stick to a convention? Are we using A and B or a and b? or are you using them to represent something different? It seems to me that if B is zero, the second equation is useless. And for either, if you set A and B to zero and expect them to stay that way, well, then all the rates k must be zero too because otherwise A will not stay zero.

@BryanKrause: I'm using capital letters as the species and small letters as their concentration. then all the rates k must be zero: exactly! So, to me, I think if one sets the concentrations $a$ and $b$ to zero, then NO REACTION WILL OCCUR ANYMORE AND ALL SPECIES REMAIN STATIC. Don't you think?

Are you setting them to zero as an initial condition or decreeing that they stay zero forever? I would say yes, if a or b are products/reactants of a reaction and you order them to stay zero for ever, no reaction will occur. That is silly, and trivial - why even use the equations? If a=0 and b=0 to start, equation 2 won't happen because it is a one way reaction, B + X => C; if you have no B then you are missing a reactant, so nothing can happen. In equation 1, however, some 2X will become A and X, so even if a(0)==0, a(t)>0 where t is some time in the future.

(also none of this has anything to do with biology, you would say the same thing in chemistry, and in any other system described by such equations)

Also, shouldn't the second row of your matrix be [1 -1 -1]? Otherwise you are describing A <-> 2X rather than A + X <-> 2X

Wouldn't this be a better fit on Math?

@AliceD: I don't think so. Because my problem is fully context-dependent!

@BryanKrause: Thanks, mate. You're seemingly right about those entries.

I disagree that the problem here is context-dependent for biology, you are really just asking about implications of certain constraints on matrix algebra (i.e., if you say a=0 and da/dt=0), unless there is some other misunderstanding between us. But I don't think the question should be migrated to math, it needs some work and self-thought before it would be appropriate there.

Given the comments it seems the math behind it may need to be sorted out first before the biological interpretation can begin.

Stoichiometry matrix denotes by what numner different molecules change if a given reaction happens. It is static and does not change with time. What changes is the reaction rate. Your net accumulation rate (for all species dx/dt) would be S*r. Please try to read about this topic more carefully.

Stoichiometry matrix denotes by what number different molecules change if a given reaction happens. It is static and does not change with time. What changes is the reaction rate. Your net accumulation rate (for all species) would be
$$\frac{dx}{dt} = S\times r$$
Stoichiometry matrix cannot have all zero entries. It is meaningless (or it means that the reactions do not affect the molecules at all; which is meaningless)


text:
Why are antibacterial body soaps uncommon?
If body odor is caused by bacteria, and antibacterial soap kills bacteria, why aren't antibacterial body soaps hailed as the holy grail of getting rid of body odor? I can only find hand soap that is antibacterial.

Please don't use antibacterial soaps.. Unless you're a nurse or a doctor. This isn't a highly scientific link or anything, but I appreciate ASAP Science's work that they do in scientific literacy.

I recommend watching the video in the link I posted. And please, there is very little scenarios where you should be using antibacterials or hand sanitizer

Oh, but one occasion you should always use hand sanitizer - when entering a hospital/clinic/doctors office

@Bob: I had the impression hand sanitizer is pretty different from "antibacterial" soaps.

@Bob okay, I won't do it, but still my question stands. Shouldn't antibacterial soap be able to get rid of body odor altogether?

@sumelic It is! Usually hand sanitizer consists of 60-70% ethanol. Which isn't really harmful, and doesn't contribute to bacterial resistance. However, I do not see how killing your microbiota is beneficial. Hand sanitizer seems unnecessary, unless it's use is a job-requirement.

@vrwim I don't think so. I would even argue that it would make body odor worse since you'd be killing all of the microbes on your body - even the microbes that act to inhibit the growth of body-odor-causing bacteria

I think there are some misconceptions here. One, the bacteria on your skin are part of you normal flora and contribute to your body odor. If you kill everything, you leave yourself at risk for opportunistic infection and even worse body odor as the composition of your flora changes. Two, alcohol hand sanitizer will not kill all the bacteria on your hand in the 5 seconds you rub it to evaporation. Alcohol is a denaturing agent and requires 30-60s wetted contact time actually kill anything substantial. Three, triclosan isn't effective anymore: people have been using it improperly for decades.


text:
At what point is a picked flower considered dead?
Let a flower be picked from the ground such that its stem is cut and the flower is separated from the root system (as in figure).

Questions:
1a. At what point is it considered dead?

Does the flower and attached bit of stem continue to live for some time before dying?

Is this like asking when an limb that has been chopped off an animal dies - should we considered not the flower, but the root system?

1b. How does one define death for an organism without a nervous system?

In medicine, people have problems defining at what point a human is considered dead. Here we do not have consciousness (that we would know off), so I guess the flower is considered dead as soon as it is cut. It lost its ability to regenerate. The plant from which the flower was cut in most cases is still alive.

Thank you for your interest. The flower can still "live" for some time if placed in water/nutrients, correct? If the root system had a single flower before the plucking, could the root system still regenerate the flower?

Regenerate the same flower? No. Grow a new one if it is not an annual plant or it is at least early in the season, yes. The cells of the flower would still be alive for a while, but how you would decide that for the flower is more of a philosophical question.

i don't know about the flower in your picture, but a lot of plants will not die at all, but grow roots and become a new individual plant if you put a piece of it in water. about the bigger question, wikipedia has a list of things characterising "life" of all forms: https://en.wikipedia.org/wiki/Life#Definitions (but as with humans, i guess it's not always that easy to tell)

I've voted to close this since it seems to be both unfocused (there are at least two separate questions — one about the definition of death and another about how that applies to a cut flower) and unclear (how are you defining alive? — the answer you accepted makes it clear that this is somewhat arbitrary). Since you are taking the time to edit, please consider fixing these problems. Thanks!

This is very much analogous to your "limb" suggestion, or, since the flower is a reproductive organ, one can ask,

At exactly what point is the uterus considered dead after a hysterectomy?

or,

At exactly what point are the testicles considered dead after a male dog is castrated?

The organism (woman and dog respectively) does not die. Tissue dies. Tissue dies all the time. Red Blood cells die after about 120 days, give or take. Skin cells die faster than that.
It depends on the definition of death. If one of the requirements for "life" is the ability to reproduce, are both the woman and the dog now dead? Of course not. They had the potential, or perhaps they already reproduced.
If one of the requirements for "life" is the ability to grow, well, the uterus and the testicles are dead immediately upon removal. But we stop "growing", and we don't die.
If one of the requirements for "life" is the ability to respond to its environment, the uterus and the testicles are not dead. They are "alive" for a time, though the environment is toxic to them if thrown away. If placed in nutritious media, they will "live" a bit longer.
Common sense, which often isn't reliable in science, would dictate that the flower dies when it can no longer maintain cell turgor, i.e. can no longer absorb fluids. But the argument can be made that it is only "dying" at that point.
Basically your question depends entirely on the definition of life. And that has not been agreed upon.

Consider also that at some point the flower will be "dead" even if it is not removed from its plant.  The petals will wither and drop off, and if fertilized the ovary will develop into a seed capsule, which will in turn wither and die after  releasing seeds.  Then the stem which it was attached to may in turn wither and die back.  In extreme cases, such as bulbs, the entire above-ground part of the plant and much of the root system will also die, only to re-grow next year.

For a time, a cut flower with a stem, when placed in water can still absorb water. If other nutrients are placed in the water (such as sugar) the flower can continue to absorb those nutrients. If the stem is cut just below the node, and the water is changed, some cut flowers can stay alive for a few weeks.  They are alive in that they continue to absorb nutrients through the stem (including water) and some types of cut flowers will visibly grow for a time. However, at a certain point, growth will stop and the flower will begin to wither. The process is more gradual than in an animal, so the moment of 'death' would not be observable.
That said there are some flowers that will grow new roots from the stem, such as geranium. In that case, the cutting can be considered part of a process of regeneration or reproduction.

Welcome to Biology.SE! This could be a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— Thank you for taking the [tour], but please also consult the [help] pages for additional advice on [Answer] effectively on this site. In particular, the question should be ignored as it is off-topic (unclear & unfocused). Thank you!

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
How does methamphetamine (meth) damage neurons?
Meth is considered to be neurotoxic by forming reactive oxygen species and oxidizing the neurons. But unlike dopamine, which, by the way, is neurotoxic due to ROS induced dopaminergic stress, meth does not have any oxygen atom, and thus cannot be the direct cause of ROS.
So, how exactly does meth exert its neurotoxic effects?

There are many possibilities, asking "how exactly" in biology is usually not possible to answer. It also isn't strictly true that the neurotoxicity of methamphetamine is via ROS. One possible mechanism is through methamphetamine's direct effects on dopamine, which is then metabolized including to ROS, another is through glutamate-based excitotoxicity, and there are other possible contributing mechanisms via effects on mitochondrial function.

Nice question! I will directly begin with the process through which methamphetamine causes damage to neurons, putting in as much details as are known, and adding appropriate citations wherever required.
Methamphetamine (METH) is known to act by increasing concentration of dopamine in brain1. When excess of dopamine is produced, it causes oxidative damage to axon terminals2. This is because direct oxidation of dopamine leading to quinone formation3, iron-catalyzed dopamine metabolism via Fenton reaction4, and metabolism of dopamine by monoamine oxidase-A5 contribute to production of superoxide and hydrogen peroxide.
Methamphetamine is known to increase concentration of glutamate. This (supposedly) happens as: high concentration of methamphetamine D1-mediated striatonigral GABAergic transmission, which in turn activates GABA-A receptors in substantia nigra pars reticulata (SNr), leading to increase in GABAergic nigro-thalamic activity which increases corticostriatal glutamate release6 (since I can't explain all those terms in a single answer). Now, excessive glutamate activates the glutamate-activated NMDA and AMPA receptors which, in turn, increases activity of nitric oxide synthase7. Activation of nitric oxide synthase generates reactive nitrogen species which create an oxidative stress8.
Oxidative stress is further increased because of depletion of antioxidant enzymes due to methamphetamine itself9. Now, the oxidative stress has to be manifested somehow. This is done by lipid peroxidation and protein carbonyl formation10, and also by specific nitration and nitrosylation of proteins important for monoamine synthesis and release, including VMAT-2 and tyrosine & tryptophan hydroxylase7,11,12. Oxidative modification of these proteins restricts their activity and contributes to their degradation, thus playing a major role in neurotoxicity. Researches substantiate the significant contribution of oxidative stress to the neurotoxicity of substituted amphetamines antioxidant treatments have also been shown to be neuroprotective against the damage produced by methamphetamine or methylenedioxymethamphetamine13,14,15.
P.S.: oxidative damage is not the only way through which methamphetamine causes neurotoxicity. Other possible ways include altered metabolism16, damage to mitochondria17, peripheral organ damage18 due to oxidative modification of hepatocellular mitochondrial proteins19, activation of microglia in striatum, cortex and hippocampus20, etc. Also, cannabinoids are known to suppress inflammatory processes and damage during methamphetamine exposure21. But since this is out-of-scope for this question, I won't go into their details.
References:
 1. Cadet JL, Brannock C, Jayanthi S, Krasnova IN (2015). "Transcriptional and epigenetic substrates of methamphetamine addiction and withdrawal: evidence from a long-access self-administration model in the rat". Mol. Neurobiol. 51 (2): 696–717. doi:10.1007/s12035-014-8776-8. PMC 4359351Freely accessible. PMID 24939695.
 2. Schmidt CJ, Ritter JK, Sonsalla PK, Hanson GR, Gibb JW. Role of dopamine in the neurotoxic effects of methamphetamine. The Journal of pharmacology and experimental therapeutics. 1985;233:539–544
 3. Graham DG. Oxidative pathways for catecholamines in the genesis of neuromelanin and cytotoxic quinones. Molecular pharmacology. 1978;14:633–643
 4. Yamamoto BK, Zhu W. The effects of methamphetamine on the production of free radicals and oxidative stress. J Pharmacol Exp Ther. 1998;287:107–114
 5. LaVoie MJ, Hastings TG. Dopamine quinone formation and protein modification associated with the striatal neurotoxicity of methamphetamine: evidence against a role for extracellular dopamine. J Neurosci. 1999;19:1484–1491
 6. Mark K. A., Soghomonian J.-J., Yamamoto B. K., High-dose methamphetamine acutely activates the striatonigral pathway to increase striatal glutamate and mediate long-term dopamine toxicity. J. Neurosci. 24, 11449–11456 (2004)
 7. Eyerman DJ, Yamamoto BK. A rapid oxidation and persistent decrease in the vesicular monoamine transporter 2 after methamphetamine. J Neurochem. 2007;103:1219–1227
 8. Imam SZ, Islam F, Itzhak Y, Slikker W, Jr, Ali SF. Prevention of dopaminergic neurotoxicity by targeting nitric oxide and peroxynitrite: implications for the prevention of methamphetamine-induced neurotoxic damage. Annals of the New York Academy of Sciences. 2000;914:157–171
 9. Jayanthi S, Ladenheim B, Cadet JL. Methamphetamine-induced changes in antioxidant enzymes and lipid peroxidation in copper/zinc-superoxide dismutase transgenic mice. Annals of the New York Academy of Sciences. 1998;844:92–102
 10. Gluck MR, Moy LY, Jayatilleke E, Hogan KA, Manzino L, Sonsalla PK. Parallel increases in lipid and protein oxidative markers in several mouse brain regions after methamphetamine treatment. J Neurochem. 2001;79:152–160
 11. Kuhn DM, Aretha CW, Geddes TJ. Peroxynitrite inactivation of tyrosine hydroxylase: mediation by sulfhydryl oxidation, not tyrosine nitration. The Journal of neuroscience : the official journal of the Society for Neuroscience. 1999;19:10289–10294
 12. Kuhn DM, Geddes TJ. Peroxynitrite inactivates tryptophan hydroxylase via sulfhydryl oxidation. Coincident nitration of enzyme tyrosyl residues has minimal impact on catalytic activity. The Journal of biological chemistry. 1999;274:29726–29732
 13. Gudelsky GA. Effect of ascorbate and cysteine on the 3,4-methylenedioxymethamphetamine-induced depletion of brain serotonin. J Neural Transm. 1996;103:1397–1404
 14. Sanchez V, Camarero J, O’Shea E, Green AR, Colado MI. Differential effect of dietary selenium on the long-term neurotoxicity induced by MDMA in mice and rats. Neuropharmacology. 2003;44:449–461
 15. Fukami G, Hashimoto K, Koike K, Okamura N, Shimizu E, Iyo M. Effect of antioxidant N-acetyl-L-cysteine on behavioral changes and neurotoxicity in rats after administration of methamphetamine. Brain research. 2004;1016:90–95
 16. Pontieri FE, Crane AM, Seiden LS, Kleven MS, Porrino LJ. Metabolic mapping of the effects of intravenous methamphetamine administration in freely moving rats. Psychopharmacology. 1990;102:175–182
 17. Burrows KB, Gudelsky G, Yamamoto BK. Rapid and transient inhibition of mitochondrial function following methamphetamine or 3,4-methylenedioxymethamphetamine administration. European journal of pharmacology. 2000;398:11–18
 18. Smith DE, Fischer CM. An analysis of 310 cases of acute high-dose methamphetamine toxicity in Haight-Ashbury. Clin Toxicol. 1970;3:117–124
 19. Moon KH, Upreti VV, Yu LR, Lee IJ, Ye X, Eddington ND, Veenstra TD, Song BJ. Mechanism of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy)-mediated mitochondrial dysfunction in rat liver. Proteomics. 2008;8:3906–3918
 20. Pubill D, Canudas AM, Pallas M, Camins A, Camarasa J, Escubedo E. Different glial response to methamphetamine- and methylenedioxymethamphetamine-induced neurotoxicity. Naunyn-Schmiedeberg’s archives of pharmacology. 2003;367:490–499
 21. Yiangou Y, Facer P, Durrenberger P, Chessell IP, Naylor A, Bountra C, Banati RR, Anand P. COX-2, CB2 and P2X7-immunoreactivities are increased in activated microglial cells/macrophages of multiple sclerosis and amyotrophic lateral sclerosis spinal cord. BMC neurology. 2006;6:12

The king of referencing. +1

Mitochondrial damage turned out to be due to dopamine: https://www.ncbi.nlm.nih.gov/pubmed/12460681

@kirill2485 it is actually increased by dopamine. Dopamine activates NO synthase, same as what meth does. I didn't go into that point since it was out of scope here...

so meth + weed is saver than

@J.Chang (taking that as humor) I dont know much about weed, so I'd just say...two negatives dont really make a positive out of paper :P