text:
What does it mean to perform in vitro experiments with mutant bacteria?
I came across the following sentence while reading the paper:
Nanchen, Annik, et al. "Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli." Journal of bacteriology 190.7 (2008): 2323-2330.

These in vivo flux data are qualitatively corroborated by in vitro
  enzyme activities in the Crp and Cya mutants, which exhibited
  significantly reduced activity of the key glyoxylate shunt key enzyme isocitrate lyase ...

My understanding of in vitro experiments is: those performed in artificial set up , possibly only with part of the cell, where the complete cell is not potentially alive. For, example we can test the inhibition activity of a particular enzyme by a metabolite.
In the paper cited, experiments from which flux are derived (chemostat) are considered in vivo. What would it mean to say the enzyme activity was tested in vitro on the mutant? When we say the response of the a single gene knock out mutant, the cell should be intact except for lacing one gene, which would mean that the response is in vivo.
Please help me if I am misunderstanding some thing.

Answer clarified based on comment by @DurgaDatta

What would it mean to say the enzyme activity was tested in vitro on the mutant? When we say the response of the a single gene knock out mutant, the cell should be intact except for lacing one gene, which would mean that the response is in vivo.

The knockouts were performed inside the E. coli cells and, as you noted, the flux measurements were in vivo (in the cell) inside of the chemostat culture. They identified two mutants, Crp and Cya, that yielded much higher biomass. On page 2326, the authors write,

In the Cya (encoding adenylate cyclase) and Crp mutants that lack the cAMP-CRP complex, in vivo glyoxylate shunt activity was essentially abolished....

I am not familiar with these genes but the implication is that the wild type regulators have the cAMP-CRP complex. Because this complex is missing from the mutants, the enzymes no longer function the same. However, it would be possible that some type of interaction of the mutants with other enzymes caused the observed result in vivo. They therefore verified the result by extracting the Crp and Cya mutant enzymes from the cells and assaying their enzyme activity in isolation from the other enzymes (in vitro). The technique is explained in the answer by @dgg32.
In your comment to that answer, you ask.

what difference does it make whether the enzyme was taken from wild-type or the mutant one, since it is the same enzyme?

It is the same enzyme in name but not in function. The mutant enzyme lacks the cAMP-CRP complex so it cannot perform the same function as the wild type. In vitro, they first showed that mutant enzyme activity was altered relative to the wild type.  They then added the wild type enzyme to the in vitro test and restored normal wild type activities:

To verify that the observed changes were not due to polar effects of the still present marker gene or secondary-site mutations, we complemented the Crp mutant with the plasmid-based Crp gene and cultivated the complemented mutant under the same chemostat conditions. In vitro enzyme activities demonstrated that both the isocitrate lyase and isocitrate dehydrogenase activities were restored to the wild-type level

Yes, this was performed inside the chemostat cultures but only with the enzymes, not the living E. coli cells.

But the flux measurement were also performed in chemostat, which are considered in vivo here.

@DurgaDatta I fixed my answer in response to your comment.

It is possible to conduct an in vitro experiment with cell extracts. Meaning that you break up the cells and put their pieces into a reaction glass and do your experiment. It is assumed that the cell molecules (enzyme, sugar or cofactors) will still carry out their functions even though the cell is no more.
In other words, you used the mutant to produce the enzymes you need (minus the knock-outed one) to set up the desired reaction requirements. Once the products are there, you don't need the producers alive or intact any more.
Check the method part in your paper and see whether it is so.

If we would like to do test the activity of an enzyme (not encoded by the knocked out gene), what difference does it make whether the enzyme was taken from wild-type or the mutant one, since it is the same enzyme?

But based on your article excerpt, the authors seemed to knock-out a gene and see how the metabolism flux is affected, just like a police shuts down a street block to see how the traffic is diverted. Their approach gives them a more systematic view of the pathway rather than a single enzyme's activity. In that case, you need the cell extract.


text:
Neuroscience of confusion
How does (neuro)science characterize "confusion" that occur to "healthy" persons when engaged on a particular mentally-intensive task?
I would exclude the case where we are rationally and with clear arguments deciding one out of many choices (but remain undecided due to lack of sufficient resource/information). My thinking is more towards the case where, for example, we are trying to understand a mathematical problem and its solution, or an abstract reasoning, but in the process get lost: even have no clear idea of what part is 'not understood', or where to start learning (the parts involved) so that we can understand the original problem.
I am aware that I am unable to make my question very clear, I am actually confused how to formulate my thoughts.

Here's an article I found that seems to attempt to address this question, using a kind of machine-learning approach involving "Long Short-Term Memory" (LSTM)-Recurrent Neural Networks (RNN), to classify EEG from participants who were watching either "easy" or "difficult" online lectures - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620019/ .
It's not a complete account of their process, but the manuscript suggests that gamma-1 frequency bands in the frontal lobe (using a single EEG electrode) were the most valuable feature for distinguishing between trials in which participants were thrown into the middle of a challenging lecture, vs. trials in which participants were viewing the introductory background material at the beginning of the lecture. I'm interested in the same question as the one you proposed, so I hope to see more responses to your post!

source: Stack Exchange

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

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

sort: votes


text:
How much gas is exchanged in one human breath?
When we breathe, our lungs absorb a portion of the oxygen in the air, and replace it with some amount of carbon dioxide and water vapor.  Typically, how much $O_2$ (in grams, milliliters, or moles for instance) is absorbed and how much $CO_2$ and $H_2O$ are released in one breath of a healthy adult?
Of course, the exact amounts will vary from person to person and based on how deeply the person is breathing, lung health, etc.  I'm just looking for a ballpark figure.

Just as a side note, it's a common error to believe that you're just breathing out CO2 and H2O. You're also breathing out a fair amount of oxygen as well.

@Jeremy  Indeed.  This is why CPR includes breathing for the recipient.  If it was just CO2 and H20, you wouldn't be doing much good!

According to Wikipedia

"In a healthy, young adult, tidal volume is approximately 500 ml per inspiration..."

(tidal volume is the volume inspired/expired)
Using this figure, together with values for gas composition also taken from Wikipedia, I estimate that in each breath we take in 18 mg O2 (1.1 mmol) and we release 36 mg of CO2 (1.2 mmol) plus 20 mg H2O (1.1 mmol). These are, as you say, ballpark figures.
Sample calculation:
O2 inspired = 21% by volume; O2 expired = 16% by volume
O2 change = 5% by volume = 5*500/100 = 25 mL
1 mole gas = 22.4 L; 1 mmol gas = 22.4 mL
O2 change = 25/22.4 mmol = 1.1 mmol
MW O2 = 16
O2 change = 17.6 mg
The relative values are reassuringly close to what you might predict from the textbook equation for oxidation of carbohydrate: C6H12O6 + 6O2 -> 6CO2 + 6H2O

Thanks!  I guess all the figures I needed were on Wikipedia, but thanks for putting 'em together for me.  Fun fact: you lose about 1.5 pounds of weight per day just to breathing (since the CO2 and H2O are heavier than the O2; assuming 20K breaths/day).

@NathanReed, interesting point, but you have your numbers wrong. H2O is not heavier than O2. H2O is a single molecule of Oxygen with a couple of extra protons (H+). It will be lighter than O2.

@terdon I meant that the CO2 and H2O combined are heavier than the O2.

The textbook equation for respiration doesn't always hold. The molar ratios really depend on what is being metabolized by the organism, and that can depend on a number of factors including health and activity. For a more precise ratio you need to consider the respiratory quotient - see http://en.wikipedia.org/wiki/Respiratory_quotient

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


text:
Are there inherent problems in simulating marine environments, as compared to terrestrial systems?
We cultivate a number of terrestrial organisms in greenhouses and stables where they live in completely artificial environments. This seems to extend far less to marine organisms, such as fish. Aquariums (especially the salt water variety) seem to be quite unstable and require a lot of maintenance, and commercial scale installations, like salmon farms, are set up in the ocean, rather than in a separate tank.
Are there inherent difficulties in cultivating marine organisms, or is it just that mankind has not tried as hard as with land species?

It probably depends on the type of marine organism you're referring to, some will be much more hardy than others and some will not be able to adapt to change at all. Due to the vast scale of the environment that marine fish come from it's likely that in their natural habitat the conditions they live in are not subject to drastic changes in water chemistry or temperature [1][2]. So recreating those exact conditions for them in man-made habitats, let alone maintaining them is going to be extrememly difficult.  Also, if you think about the conditions that most (there will be some exceptions) terrestrial animals and plants have to deal with on a day-to-day basis they have to be able to cope with some fluctuations in humidity, temperature, weather, light etc and therefore are highly adaptable by necessity.
Other issues can be supplying the correct feed. In artificial settings food may have to be a non-natural substitute and this will likely cause problems for species who require a highly specialised diet. The terrestrial animals we tend to cultivate extensively are omnivorous/herbivorous which are not difficult needs to meet. On the other hand a fish from the sea that requires a particular other kind of fish only found in a particular area and that needs very specific conditions to thrive is going to be problematic.
Check out this article http://www.vliz.be/imisdocs/publications/301.pdf , it might be for a specific fish but it highlights some of the general issues i think you are referring to.
[1] http://www.bestfish.com/saltg.html
[2] http://www.aquaticcommunity.com/marineaquarium/
(both general articles on keeping marine fish)
hope this helps!

Large numbers of marine animals are actually cultivated in large aquaria. They're just generally not as conspicuous as farms and farm animals and are often located in difficult to access areas around estuaries or close to ports. There are also a number of specialised journals that focus on aquaculture such as the journal aquaculture. In addition to being cultivated in aquaria, large numbers of animals are also cultivated in more natural settings such as the salmon you mentioned or shrimp in shrimp ponds, which are widespread in countries such as Indonesia. A major problem in aquaculture is disease, although this can also be a problem with terrestrial livestock raised in high densities. If you're interested in marine aquaculture, I suggest you browse the various aquaculture journals to get an idea of what's going on.


text:
Insect species identification

I think it's a moth and need further identification like scientific name, order and family.
The picture was taken on May 30/2016 in my university laboratory window in South Korea. At that time there were so many moths on this building. The temperature was also high and it was also daytime around lunch time. What I want to ask related to flying time is do moths fly at daytime? as far as I know moths are nocturnal. Please clarify this too if this insect species is moth.

Hi, maybe you'll find these hints helpful in improving your question: http://biology.stackexchange.com/help/how-to-ask. Temperature was high... high for where? Also do moths fly in the daytime is a seperate question, as is are all moths nocturnal.

@ Troyseph what is wrong with my question,Sir?

It was poorly formatted such that the picture wasn't visible and you had a block of text with random '[' characters in it. You ask multiple questions. You show no attempt at your own research into its type. You gave details which are completely useless to us, i.e. the temperature was high... did your building have the heating on? Do you live in Florida or Iceland? is high 24 degrees C or 34 degrees c? Please put some effort into your question so that someone might put effort into an answer for you =]

@ Troyseph I think it's better to focus on answering the question rather than editing the grammar since there is n o misunderstanding. lol If it's useless and do not know the answer just stop criticizing period

I wasn't criticising your grammar, spelling or punctuation. Please read the guidelines and take my advice, then your question will be clearer and easier to answer.

@Meti please [edit] your question and post where exactly the picture was taken. in my university laboratory window is not helpful at all. I would also strongly suggest you take the [tour] and read carefully through the [help] to learn more about the site. Editing of questions (and answers) is encouraged, subject to some guidelines. You should also read this Meta.SE question, especially the section Editing and Formatting.

Am very sorry @ Troyseph I didn't know that. @MattDMo I will take all your suggestions and advice into consideration.

It is a moth and all moths and butterflies belong to the order of Lepidoptera. Based on the shape of the forewing and the orange color of the hindwings I think this moth belongs to the genus Catocala https://en.m.wikipedia.org/wiki/Catocala, see also here for some pictures.
EDIT:
theforestecologist did a excellent suggestion that this might be Catocala streckeri based on the wing pattern. This species does occur in Korea, see this website for a distribution map. So it may indeed be Catocala streckeri. However, Asia is very rich in Catacola species, and I know that this family often has species looking very alike, so I can't say with 100% certainty.
Most, but not all, moths are nocturnal. Some Catocala species are known to fly on sunny afternoons (Waring&Townsend 2006).

thank you for your response. The picture was taken in South Korea.

Catocala streckeri seems like a pretty good guess given the wing pattern. I'd add it as my own answer, but obviously cannot because the question is closed.

@theforestecologist: excellent find. I'll add it to my answer.


text:
Can someone identify this creature?
I discovered a few of these while cleaning an outdoor fish pond north of Sacramemto California. What is this?

Check the species ID tag info for some ways you can improve your species ID question to help get a good answer.

mayfly nymph of ephemoptera species

Wonderful! Now I will go intimidate my friends with this knowledge. Thank you!

This is a Burrowing Mayfly nymph (order Ephemeroptera), more than likely of the family Ephemeridae.  The Bugguide site has very few photos of nymphs, but you'll find a near miss here (the species shown is not Californian, but the related Ephemera simulans Walker, 1853 is; see here for other possibilities [you'll want to look for nymph photos of the species listed from "USA: SW"]).

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


text:
Differences between Heracleum mantegazzianum and H. sphondylium
I have heard about the hazards associated with Giant Hogweed and the trouble is when trying to identify it, it is very similar by the looks to normal hogweed.
When fully grown, there is a big difference in height with Giant Hogweed (hence the name Giant Hogweed, but when it is small, how can you tell the difference?
Giant hogweed (Heracleum mantegazzianum)

Image from WikiMedia
Hogweed (Heracleum sphondylium)

Image from WikiMedia

Yes, the species can be identified by the shape of the leaves. The leaves of H. sphondylium are more or less flat (in one plane); the leaves of H. manteggazianum are more crisped and much more pointed.
Here are two pictures from the Dutch wikipedia (h. sphondylium last):


text:
Help me identifiy this moth?
I found this moth in Bengaluru/India. Its body length was nearly 2cm. Brown colored with three yellow rings.

This looks to be a handmaiden moth (Syntomoides imaon) which has been observed in this part of India.

Source: India Biodiversity Portal


text:
Identify this bug
So we found this bug and it wasn't in our software for a change. Any help identifying it is appreciated. The bug was found in Cambridge, Massachusetts.
Three of the pictures are over 2MB, (and 2 of them are useful, I think), so I can't post them here, but I can give a link to the album: https://photos.app.goo.gl/DK7NBqZtfCaXi8BS8

I'll try to fix the links.

Well, it's a fly. Possibly a Robber fly (Asilidae) or Thick-headed fly (Conopidae)

How do you know it's a fly?

Agreeing with @RHA that you have a fly here (the fourth photo shows a haltere [AKA balancer] just above the hind leg/just below the wing, which is what Diptera have instead of hind wings); I believe that it's a Soldier Fly (Family Stratiomyidae), but would like other photos (if possible) before comitting myself to that level of precision.

@theresawalrus bugs should have their front wings hardened to wing-cases callers elytra. They are covering the remaining hind wings. Your specimen doesn't show that.

@ArthurJFrost there are more pictures on the google drive album if you need more.

@theresawalrus ... sorry about the tardy reply: one of the album photos was a great almost: the one with the specimen against a solid background might have helped if it hadn't lost resolution when zooming in.  If you still have the specimen and can get an in-focus extreme closeup of one wing, that would help immensely in confirming or denying my guess.

@ArthurJFrost Sorry, we put it out of its misery because it couldn't fly well anymore. It would try, but could no longer generate enough lift so would just glide down.


text:
How is the cell membrane protective?
Generally in biology books, it is written that the cell membrane is selectively permeable and that it has a protective function, as in here
It says that the cell membrane protects the cell from its surroundings. However the selective permeability is only for the hydrophilic substances, and not for any foreign antigen which may be dangerous for a cell.
So how does this count as protective?
Also for hydrophilic substances, carrier proteins are present, ready to take the ionic substances inside the cell.
Hence my only question here is how is the cell membrane protective?

Not sure but by selectively allowing the non polar molecules, it helps maintaining the electrical charges and/or acid-base neutrality and thus aiding in protection of the cell?

carrier proteins don't let just anything in, that is why viruses need to have mechanisms to penetrate the membrane without a membrane the dna/rna could just float in and start changing things

You are right that the membrane doesn't stop everything.  Its main purpose is to separate the inside of the cell from the outside so that you can accumulate resources in it.  Your potassium ions, proteins, sugars, RNA (and DNA, behind another membrane) have to stay inside the cell because they can't dissolve through it.  There are indeed channels and transporters from some hydrophilic substances as you say, but they are usually very specific about what chemicals they will transport.*
The membrane is actually very delicate but it is reinforced by a cytoskeleton, and proteins are embedded in it to transmit force to features outside the membrane (such as desmosomes and hemidesmosomes connecting to other cells or extracellular matrix) so that the membrane itself is never put under strain.  Think of it like a thin plastic bag that can hold water because you put it inside a much stronger container - even though the stronger container is not waterproof.
Many harmful chemicals would not be harmful if they could not get into your cells, so you should not be surprised if they are often hydrophobic and dissolve freely through the membrane.  Some cells have other defense mechanisms (pumps to try to expel the toxins or enzymes to try to break them down), but ultimately any true toxin is defined as the one for which nothing works well enough.
Many pathogens have evolved methods of crossing the cell membrane.  Bacteriophages famously break a hole in the membrane with a special injection apparatus, while many human viruses fuse a cell membrane section they carry around themselves with the victim cell membrane, using proteins that have evolved the right hydrophobic features.  It is hard to defend against such things because our cellular membranes need to be able to fuse with themselves for purposes such as releasing vesicles of neurotransmitter.  The same "no true pathogen..." argument applies - we only get sick from the pathogens that can infect us.  If we lacked these protections, we would be even more vulnerable than we are.

Exceptions, perforins and granzymes, prove the rule:  they are meant to kill the cell affected.

A nice answer, but exceptions only prove a rule when there is no other evidence than the granting of the exception that the rule exists. Check this out on the Internet. So, they are just exceptions with explanations. Nothing to do with rules.

However this does not answer op's question that how cell membrane protects the cell? From your answer it seems that cell membrane is not protective.


text:
Why are some parts of an rRNA structure diagram not labelled?
I've been looking at this structure diagram of the 16S rRNA and have been wondering why some parts of the diagrams have labelled base pairs while other parts are just lines and dots. I'm new to this field of science and am an undergraduate biologist just getting into reading this sort of scientific literature out of pure curiosity.

The diagram is a composite of all 16S RNA structures.
It has a summary with it that explains all.
"16S rRNA secondary structure, showing conserved parts for Prokaryotes (IUPAC letters) and amongst Archea/Bacteria (asterisks) all others as dots. Adapted (in SVG!) from Woese Bacterial evolution 1987"
The base pairs that are marked with A,U,C,G are present in all Prokaryotes studied so far.
The lines are base pair links (A-U and C-G)
There are a couple of lines that are pointers from the reference numbers e.g at 700 and 750


text:
What makes white phosphorus toxic?
What makes white phosphorous toxic?
I mean it causes liver and kidney damage, and altered blood coagulation, but it is hard to find anything about what biochemical mechanism this poison uses to kill liver and kidney cells and why the liver is not capable to neutralize it even in a 50mg/kg dose (LD50 in rats). It would take just a simple oxidation to convert it to phosphate, which is commonly used by living cells.
conclusion:
I think the main cause that white phosphorous is so toxic that it is not something common in the environment, so there was no evolutional pressure to adapt to it. The human body can deal with it relative fast, but it damages cellular organelles and causes possibly fatal liver and kidney damage in hours. Some of the metabolites are even more toxic and they can cause arrhythmia and disturb the CNS. Because the molecular mechanism of toxicity is still mostly unknown and there is only a short time to treat people before liver and kidney damage, currently I think there is no way to save somebody exposured to a high dose of white phosphorus.

There seems to be some difference on the development of symptoms depending on the route of uptake, but eventually poisoning with white phosphorus leads to kidney and liver damage.
Oral uptake leads to gastro-intestinal problems like abdominal cramps, nausea and vomitting, if you take up low doses chronically, this may lead to phosphorus laden stool (also called "smoking stool syndrome").
Since white phosphorus will ignite when it comes in contact with air, skin contact often leads to severe chemical burns. White phosphorus is also highly soluble in lipids and is therefore suspected to cross through our skin rather fast, leading to absorption in the body and subsequent poisoning by liver and kidney damage.
See reference 1 for a short overview and reference 2 for extensive information.
Regarding the exact molecular mechanisms is surprisingly little known and published. It is clear that poisoning with white phosphorus causes Triglycerides to accumulate in the liver, causing the fatty liver syndrome. Depending on the source it is also speculated that carbohydrate and/or protein synthesis in the liver is also affected (see for example here or here). Mostly this is explained by the high reduction potential of the phosphorus, which disturbs the fine balanced metabolic pathways. Finally this seems to leads to liver failure (see also reference 3).
According to the toxicology profile (reference 2) the damaged protein synthesis in the liver leads to fatty liver very fast.

Liver damage in animals exposed to white phosphorus progresses
  rapidly. Four hours after receiving a single oral dose of white
  phosphorus, minimal fatty changes in hepatocytes were observed; by 12
  hours fatty changes were extensive (Ghoshal et al. 1969). Exposure to
  white phosphorus has been shown to damage the rough endoplasmic
  reticulum and cause a disaggregation of polyribosomes (Ganote and Otis
  1969; Pam et al. 1972). This damage results in impairment of protein
  synthesis, in particular, a decrease in the synthesis of the
  apolipoprotein portion of very low density lipoproteins (VLDL), which
  are required for the transport of triglycerides. A significant
  decrease in protein synthesis has been detected as early as 3 hours
  after oral exposure (Barker et al. 1963). The smooth endoplasmic
  reticulum is also involved in the formation of the VLDLs, and damage
  to the smooth endoplasmic reticulum also impairs the formation of
  VLDLs. The net result of these ultrastructural changes is an
  accumulation of triglycerides in the liver (Ghoshal et al. 1969). This
  results in steatosis and fibrosis, which is one of the mechanisms
  involved in the hepatotoxicity of white phosphorus. The mechanism
  behind the damage to the endoplasmic reticulum is not known; also, it
  is not known whether white phosphorus itself or a metabolite of white
  phosphorus is the damaging agent. In addition to these damages, white
  phosphorus or a metabolite causes damage to the mitochondria and
  nuclei in the livers of animals orally exposed to white phosphorus
  (Ghoshal et al. 1969). The damage to the mitochondria may impair the
  cell’s ability to produce ATP, thus resulting in necrosis of the cell.

Another possible (and additional) toxic effect may be traced to the (possibly enzymatic) generation of phosphines from phosphorus and water which are highly toxic to the central nervous system (here my source is only german, you can find it here). According to reference 4 phosphines are interfering with the COS gasotransmitter signaling. They can cause cardiac problems by this mechanism. Phosphines smell garlic like, this is an observation often made, when victims of white phosphorus poisonings are authopsied.
References

White Phosphorus Exposure
TOXICOLOGICAL PROFILE FOR WHITE PHOSPHORUS
Biochemical changes associated with acute phosphorus poisoning (in
humans)
Sulfurous Gases As Biological Messengers and Toxins: Comparative Genetics of Their Metabolism in Model Organisms

While this is all true, the question is about how it causes liver damage. Probably I should rephrase my question if this was not obvious.

@inf3rno Yes, that would be good. It wasn't clear to me. I will have a look into this, too and edit the answer. But this will take a day or two.

Hard to find anything in the topic, but this might be interesting: https://books.google.hu/books?id=xZf-CAAAQBAJ&pg=PA195&lpg=PA195&dq=white+phosphorus+hepatotoxicity&source=bl&ots=yoiD7rlE8e&sig=--hsfvTfuc-Zth98NnR2qJPywEI&hl=en&sa=X&ved=0ahUKEwiK-oLrvPHZAhUzyaYKHZr7CzkQ6AEIUzAF#v=onepage&q=white%20phosphorus%20hepatotoxicity&f=false

It references this article: https://www.sciencedirect.com/science/article/abs/pii/0014480072900354

@inf3rno Interesting link. Since this paper is quite old, I will see who cites it, maybe some other useful papers will come out there. But this is nothing I can do from home, here I need the journal access in the institute.

Okay. I have already checked, there are a few relevant articles on the list after 2000, but I have read only the abstracts. Maybe the fulltext contains more about the mechanism.

@inf3rno I have now updated the answer, after I went through the articles. Still, there is little hard data on this, most likely due to ethical reasons (who wants to poison experimental animals simply for finding out why this is poisonous) and also due to handling hazards. Additionally to the toxicity, white phosphorus is also pyrogen, I wouldn't want to work with it.

Phosphines might interfere with the COS gasotransmitter. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216388/ Probably that's why they are so toxic.

@Chris Added some extra info to your answer.

@inf3rno Thanks. I would have looked at the paper tomorrow.


text:
How can heart disease cause excessive sweating?
According to google:

What can cause sudden sweating?
Excessive Sweating. A person with
  excessive sweating has a condition called hyperhidrosis. ... In
  adults, the most common cause of hyperhidrosis is emotional stress.
  However, excessive sweating is also caused by heart disease, lung
  disease, diabetes, and shock.

Sweating is seemingly unrelated to the heart conditions. By what mechanism can a heart disease cause excessive sweating?

I'm voting to close this question as off-topic because this is a medical not a biological question in terms of SE Biology.

@David I wonder why we have a pathophysiology tag then. Maybe you misunderstood what a "medical question" means here.

Tags do not define what is on topic, anyone can create them. The Tour and Help explicitly do so. Please read them.

I disagree that this is off-topic.

@David No thanks. I left these sites mostly because of self important admins who decide to close a question after 3 years and such things. I found that eventually every stack exchange sites turn this way. I rather go to forums, those are somewhat better.

The answer lies in compensation. Take myocardial infarction, for starters. MI, if large enough, severely weakens the heart, and hence, at the same level of stimulation, it can no longer pump blood effectively, causing what is called Heart Failure (inability to pump enough blood). This causes an excess stimulation of the sympathetic nervous system (or more technically, neurohumoral mechanisms) in an attempt to compensate, which by its effects on heart contractility and rate increases the amount of pumped blood to match the need. This sympathetic outflow also causes increased sweating, nervousness, dry mouth etc. Sweating, nervousness are cardinal signs of acute MI.
Additional point: This compensation can only work in certain cases, say for example where the heart failure is due to blood loss with a healthy heart. But in cases like MI, this compensation is not an optimal response, rather it worsens the case, since increasing the workload on an ischaemic heart (ischaemic levels of atherosclerosis being the commonest cause of MI), further damages the wall leading to chronic heart failure and disease. This is the Broken Compensation Model for chronic heart failure. This is why we use Beta Blockers to abrogate the sympathetic system's (or more technically, the neurohumoral mechanisms') unwanted compensatory efforts, and the observed efficacy and increased longevity substantiates the validity of the model.
References:
I added them in a bit of a haste. They might not be the best references available, but they are considerably credible. Pathophysiology of heart failure, ventricular remodelling and the involved neurohumoral mechanisms are well-studied, and you shall get several papers on it on pubmed or google scholar.

Books

Robbins and Cotran: Pathological Basis of Disease 9th Edition
Hutchison's clinical methods 23rd edition

Papers and links -Heart Failure pathogenesis

Kemp CD, Conte JV. The pathophysiology of heart failure. Cardiovascular Pathology. 2012 Oct 31;21(5):365-71. (General overview of the pathogenetic mechanisms underlying)
CVphysiology.com(A relatively less technical review)
Kırali K, Özer T, Özgür MM. Pathophysiology in Heart Failure. InCardiomyopathies-Types and Treatments 2017. InTech.
http://bestpractice.bmj.com/best-practice/monograph/61/basics/pathophysiology.html

Papers and links -Sweating as a symptom of MI

National Heart Lung and Blood Institute
Bruyninckx R, Aertgeerts B, Bruyninckx P, Buntinx F. Signs and symptoms in diagnosing acute myocardial infarction and acute coronary syndrome: a diagnostic meta-analysis. Br J Gen Pract. 2008 Feb 1;58(547):e1-8.
Gokhroo RK, Ranwa BL, Kishor K, Priti K, Ananthraj A, Gupta S, Bisht D. Sweating: A Specific Predictor of ST‐Segment Elevation Myocardial Infarction Among the Symptoms of Acute Coronary Syndrome: Sweating In Myocardial Infarction (SWIMI) Study Group. Clinical cardiology. 2015 Dec 1.
https://www.sciencedaily.com/releases/2005/11/051122183817.htm
http://www.webmd.com/heart-disease/news/20051115/sweating-prompts-heart-attack-care#1

Interesting answer. My educated guess would have been that blood transfers heat and this heat transfer is regulated with the speed of blood flow. So if the heart is not strong enough, then the heat transfer is not sufficient and the body overheats which results in excess sweating.

@inf3rno Sweating in this case is not because of temperature regulation. It is more of a side effect. The sympathetic effects on heart in MI is very well studied. Look up remodelling of the cardiac muscles.

Can you add some references about this to your answer?

@inf3rno Added.


text:
Does the cellular response to every receptor work the same way?
I heard somewhere that activating any receptor results in the same intracellular response (signaling) which involves NF-κB. If that is true, I hardly understand how the cells distinguish between different types of stimulis coming from different types of receptors. I guess I am missing the point... :S

Figure 1 - signal transduction - source

If you check this picture about signal transduction. What you can see that there are about 10 arrows pointing to the inside of the nucleus, and there are about 10 receptor categories involved. Afaik. there are much more genes in the nucleus, so how is it possible to regulate the expression of so many genes with only a few signaling pathways?

I don't have an answer other than to say that signal transduction is an immensely complex interaction of many different proteins. The schematic you posted represents idealized pathways and omits a lot. Also, how a cell responds to a signal (ie which genes become activated) is largely dependent on the state the cell is already in.

Short answer: No, it's not like this. First, there is a broad variety of different receptors and then there is a wide variety of different receptors within one class. GPCR are not all the same for example, their G$\alpha$-parts are not the same. The same is true for RTKs, which are grouped on homology, but have different ligands for example. I can write a more comprehensive answer later, as this is a complicated topic.

In concur with @Chris: no

It's a complicated answer. More than 200 cell types, each type of cell inherits a unique expression of receptors, internal and external. Diffusion of signals through the plasma membrane and/or nuclear compartment may act directly as cofactors, activators, etc. The specific sequestration, and pattern of expression of external receptors also influence what signals become bound and relayed. The cell will also have a motif of internal/cytoplasmic/nuclear proteins expressed that complex or become directly activated by interaction with any of the above, etc. So the currently expressed set of internal, and external proteins determine not only how the cell interprets the signal, but also how they respond.
As for the actual genetic material, you'll find inherited motifs like DNA methylation, histone acetylation patterns etc. influence what parts of the DNA can actually be accessed. Per the above schema of signaling pathways, the signals received by each individual cell differ based on the actual cell type. In any case there are patterns of activators/repressors, enhancers/silencers that are switched on or off by these signals. Some journals are also introducing evidence insoluble receptors like EGFR+ligand can actually internalize and translocate to the nucleus and act as transcription regulators.
The final note, is that due to alternative splicing and transcription of proteins that promote or repress splicing sites, in a combination with the above concepts a cell can regulate for thousands of genes. This is a very general answer, however. The concept to take home, though, is that differentiated cells have their own specific motifs they express that make "reading" different signals possible, and also makes differing responses to what could be the same signal possible. These motifs also allow for the accurate expression of the relevant portions of the genome (not all genes are expressed at all times in all cells).

I heard somewhere that activating any receptor results in the same intracellular response (signaling) which involves NF-κB.

I don't think all receptors activate NF-κB (Pro-growth signals activate it, mostly).

how the cells distinguish between different types of stimulis coming from different types of receptors.

The cell need not, sometimes, know where and how the signal came from, unless it has to interact back to the origin of signal (as in case of neural synapses). Some pathways such as growth and inflammation can be triggered by many kinds of signals; the responses generally converge to a common pathway (If all that cell has to do is to boost up inflammation, then it would be costly for the cell to keep a unique pathway for each kind of trigger.)

there are much more genes in the nucleus, so how is it possible to regulate the expression of so many genes with only a few signaling pathways?

Some genes are co-regulated because they fall in the same pathway. They collectively comprise what is known as a regulon.
Also, it is possible that multiple signaling pathways have a different response in combination compared either of them individually. Such mechanisms exist in differentiation pathways during development (Can't think of an exact example; will provide one in a while).


text:
Does crude oil or kerogen contain ancient DNA?
According to wikipedia by the formation of oil there are a lot of organic materials present including DNA. Is it possible that this DNA is conserved somehow for millions of years?

I don't see DNA mentioned at all in either the petroleum or kerogen articles...

I'm sure if you look hard enough you could probably find some nucleotides or other components of DNA/RNA. Finding intact nucleic acids would be very hard, even under ideal conditions, DNA doesn't last forever, and this oil has been under high heat and pressure for a long time.

@MattDMo Organic material = DNA along with other biomolecules.

@user137 What about the kerogen? It was not under high heat...

According to some of the DNA decay kinetic studies, it is not possible to extract older DNA than 6 million years. But ofc. that is just a model, we have to wait another 6 million years to prove it. :D Interesting topic btw.

@inf3rno Your odds may be better there, but I don't know how long DNA lasts in an anaerobic sludge. Depends on pH, temperature, residual nuclease activity, etc. And the DNA decay would probably begin by nicking and cutting the long DNA into shorter and shorter strands. Eventually, even if you could pull DNA out of the sludge, it would be too short to do much with. That being said, some work has been done to sequence well preserved DNA from Neanderthals and other ancient organisms, though these samples were much more recent than oil and kept under better conditions.

@user137 Yepp, I reached the same conclusion.

@user137 Feel free to add an answer with references.

@inf3rno That's the problem, I don't have references.

@user137 http://scholar.google.com/scholar?as_ylo=2011&q=million+years+old+dna

@inf3rno the wording of your question implies that Wikipedia states that there is a lot of DNA present along with other organic materials. It would be better to [edit] your question to clarify this.

@MattDMo edited.

According to Live Science, the temperatures are in the 120 to 300 degree-Fahrenheit range (48-148 degree-Celcius) when crude oil is forming. DNA in "dry" conditions completely degrades at temperatures above 190 degree-Celcius. Which means that there could be DNA in the oil itself if there are some surviving cells, however, outside the cells there are DNases which will chew up DNA.
So the DNA they are talking about is like the DNA studied by Gong et. al, where they're looking at the live bacteria in the crude oil, which would be descendants of the bacteria that was around when the oil first began its degradation from organic material.
On both NCBI and PLOS ONE there appear to be a number of papers studying the bacterial growth in crude oil. Which would be why you may have seen articles about DNA in the oil.

This does not answer the question with a yes or a no.

The thing is there is no REAL answer to what DNA is actually being looked at. It is possible that there is DNA in the oil itself is being looked at but most likely they are looking at the DNA of bacteria that's growing in the oil @MarchHo.


text:
Can light pollution cause cancer?
Impaired circadian rhythm is associated with cancer. Light pollution affects the circadian rhythm and the circadian rhythm affects the metabolism. But what is the (molecular) connection between impaired circadian rhythm altered metabolism and cancer?

Do you have a link to the full text of the linked paper? It is not open access. Additionally, just from reading the abstract, the authors are proposing a hypothesis, and haven't actually tested anything. Correlation is not causation. Using Google Scholar, I couldn't find any actual research studies that cited this article testing this hypothesis.

@MattDMo It is not that hard: http://kepfeltoltes.hu/150529/795452382N_vtelen_www.kepfeltoltes.hu_.png I don't have full text either by most of the articles. Only libraries and universities use to buy access only, it is too expensive. So if you are member of a library then you can probably read the full text at least by some of the online journals.

@MattDMo Another relevant articles I have found: http://link.springer.com/article/10.1007/s13277-012-0611-0  http://www.sciencedirect.com/science/article/pii/S030438351300709X http://informahealthcare.com/doi/abs/10.3109/07420528.2013.782315 http://www.sciencedirect.com/science/article/pii/S0016648013001731 http://www.ncbi.nlm.nih.gov/pubmed/24729125 http://www.pnas.org/content/108/46/18790.full


text:
Branch taking over a tree trunk
I stumbled upon a birch growing in sandy soil in a coniferous forest in central Russia.
It looks like over time the tree trunk got bent towards the trail and one of the branches became the new trunk as it now grows straight up, whereas the old trunk is pointing sideways.1
The tree isn't dead, I visited that place during summer time and it was covered with green foliage.
I'm wondering what's the name of such phenomena, how common it is and what usually causes the tree "to change it's mind"?

1. I apologize in advance if the terminology I'm using is inaccurate, so feel free to edit my question.

This phenomena has elements of what,  in the UK, are termed Phoenix Trees, however this term, and the term Phoenix Regeneration, is more often used when describing characteristics of ancient and veteran trees.
The principles that underlie what the photo shows is that new growth on trees will always grow strongest where there is the most light available, and so in this case as the trunk has become bent towards the canopies, and the shade, of neighbouring trees this branch has become the part of the tree to encounter the most available light.
It is possible to find many trees in a woodland that may show elements of this phenomena; your photo is of a tree that is on the more extreme end of the spectrum for a tree that is still standing. It has developed a different 'dominant' stem to the one it 'started' with.
It is probably not now possible to discover what has happened in the past to cause this tree to bend over in this way; it could have been perhaps a heavy build up of snow or ice at a particularly vulnerable point in its growth, or more likely one or more other trees, or a part of another tree perhaps falling in such a way to knock into it and stay in that position long enough for this tree to adopt this shape in its trunk. If this was the case it may be that the tree/s that fell into it has since been cleared, or decayed away if it was a dead tree or branch.
Often trees that are completely blown over can remain alive because enough roots remain in the soil for it to survive. When this happens the branches on the trunk start to grow upwards into the new space and light that has been created by the tree itself falling. Over time the result is a tree where the main trunk is lying on the ground but the canopy is now a series of branches at right angles heading straight up.
The name for a tree that continues to live and grow after it has fallen over is a "Phoenix tree", named after the mythical bird that regenerates itself after catching on fire; it rises from the ashes.
This term is often applied to old trees, but it could, and does, also be used to describe any tree that has fallen over but continued to grow.
References can be found in Natural England's excellent publication on Veteran and Ancient Tree management
http://publications.naturalengland.org.uk/publication/75035
For example in Chapter 2 "What are Veteran Trees and why are they important?" Section 2.3.4.6 (page 21) of Veteran Trees: A guide to good management
Old trees may fall over completely and then re-grow or collapse and layer well away
from the original base. This is characteristic of lime, willow, alder, black poplar, medlar
and bird cherry but can occur in any species. A particularly notable example is the
Tortworth Chestnut.

The term phoenix regeneration has been applied to trees that have fallen over, or
split apart, and successfully continued growing.

Nice name for these kind of trees, was new to me (+1). Could you add a reference for it? that would make it awesome.

@RHA Thanks, I have added a reference for the term Phoenix regeneration and have also added that the term is commonly used in the UK. I didn't know that there is a date tree that is commonly known as a Phoenix tree, so that could be confusing.


text:
Fluffy creature
Can anyone help identify this little creature?  It was found in Gulf Shores, Al., USA. Approx. size 2-3 inches (5-7,5 cm)

What is its size?

Maybe 2-3 inches long, looked like it had guinea pig fur


text:
Can anyone identify this creature that looks like a stick?

This thing was on me. I thought was a stick until it moved. It had a black worm like thing come out one end and stood up and thats how it moved. It would stick to fabric also. In Louisiana

Looks like a terrestrial Caddisfly, the order of Trichoptera. Please add the location (country) were you found it, we might be able to answer your question.

It may be a Caddisfly (Trichoptera). Though my guess is a moth (Lepidoptera). Specifically one of the Psychidae family, also known as "bagworm moths." They are common pests in most parts of the world and while they're typically seen fixed in place they spend much of their life mobile. Both of these groups spin a case from silk and attach detritus to the outside so without a better look at the resident insect it is basically impossible to distinguish them from a photograph. However, as a general rule (with some exceptions), Caddisfly larva tend to be aquatic.
Here are a couple of links to descriptions of the groups (with pictures!) as they appear on BugGuide:
Psychidae
Trichoptera

Hi David, and welcome to Biology.SE. Answers in general should include supporting reference(s). Species identification answers in particular are best with a representative picture of the species for comparison as well. For a good example of how to answer a species-identification question, see these answers by @theforestecologist

Knowing the location, I think you are right this is a bagworm. In North America there is only one terrestrial Trichoptera and that species looks different.

@David. Welcome to Bio.SE! As De Novo mentioned, please add some support (preferably from a reputable source!) to strengthen your answer. I agree that this is likely a bagworm (see previous posts on the subject here and here). It's very unlikely to be a trichopteran larvae outside of an aquatic setting.

This is a clothing moth.  Casebearing clothing moth. The larvae wraps itself in a fabric or cotton like cocoon and feeds on soiled clothing or anything made from animals. The worm like larvae will emerge from the cocoon

Welcome user70847. This answer could be improved by the addition of one or two references, even a picture showing the clothing moth - as answers here are expected to explain why they are correct and be supported by references where possible. Please take our [tour] and refer to the [help] for our guidelines. Enjoy the site.


text:
what's the species identification of that camponotus queen
City: Antalya, Turkey
Date: July 27 night
Specific location: I found it in the middle of the city

In what kind of environment / ecosystem did you find them?

antalya, turkey ... summer +40 celcius, winter 10 celsius on avarege. seaside , and haliday city. There mediterranean coast. if you write antalya on google picturen you may see . :)

I meant "micro-environment" (I should have been clearer). In the middle of the forest in the shade of large trees, right up on the beach, in the middle of the city, in houses as pest, etc...

sory :) . I found it in the middle of the city. when I dronk a cup coffee she drop my table on the July 27 night .


text:
ID of this flower/plant and origin if possible
Hello again all you helpers out there!
So this plant or flower is found in Virginia (USA) rural area mainly woodland and grassplains, when it comes up, it rarely last for very long, so with a photo of the plant in its glory, i hope some of you could tell me, what kind of plant/flower it is and where it came from, thank you very much and have a great weekend!
/Beo

I assume you mean Virginia, USA, so I've edited that. Feel free to change if you mean Vancouver or whatever.

Look like a Spider lily (Lycoris radiata):

Source: NC State University

Yea it does look like that one, thank you for your answer, ill try and read up on this one.


text:
What moth is this and how do we get rid of them?

This bugs are everywhere in my house and we've tried so many home remedies, but they won't leave. Can anyone help us!?

Welcome to Biology.SE! I suggest you to take the tour to learn about the site and earn your first badge. Also, it is useful to include your geographical location when looking for a species identification.

Also check any cat or dog dry food if you have any.

That is an Indian meal moth Plodia interpunctella. Family Pyralidae. They are very common household pests. https://www.doyourownpestcontrol.com/indian_meal_moth.htm
They breed in grains or cereals. You need to look through your pantry, and find out what they have been breeding in. Seal up your grains and cereals in plastic, or put them all in the fridge.

They are also known in some areas as pantry moths, due to their association with that location, i.e. infestation. Note that plastic bags will not keep them out as both the adult moths and the grubs can chew though thin plastic. Infested plastic bags will have a multitude of silk threads, small uneaten food particles, and grub cases in it. The plastic containers need to have thick solid walls with an airtight lid.

Yes, you need to go through the items in your pantry, probably you will find some infested bags/boxes. Discarding them will help in getting rid of them.

This is probably a common flour moth or a similar pyralid species. It has probably laid eggs in some cereal-derived products (pasta, cous cous, but also rice, oatmeal and the like) of your kitchen. First of all, check carefully your pantry for infested food and throw it away. Then (from the above Wikipedia link):

None of the stages of the organism (eggs, larvae, adults) are very temperature tolerant and all can be killed by a week of freezing or by brief heating in a microwave or conventional oven when such treatment is practical. Scrubbing infested areas with a mixture of soap and water or vinegar is also effective. [...] Nontoxic traps are also available to monitor outbreaks. One type of trap is a triangular box with a pheromone lure and sticky walls inside. These traps are generally known as pheromone traps. In this case, male moths are attracted inside by the female pheromone (the lure) and then get stuck against the sticky walls inside the box.

From personal experience, it can be sufficient to check the pantry and seal all the cereal-derived food into plastic bags.

It's possible you had a different species to the one I encountered. Mine were capable of chewing through plastic bags and infesting them. See my comment on Karl Kjer's answer.

I know this question is old but for the possible sake of later readers, with respect to mentioning plastic bags - at least some, if not all of the moth species commonly known to infest households do have a reputation for being able to bite through thin plastic bags, both the larvae and the adult moths.
Where that's the case, or can be suspected anyway, recommendations I have found are to use hard plastic containers with a tightly (and forcefully) closing lid for endangered food etc.
Quick sourcing (I did have sufficient original reputable sources when I wrote this answer passing by, the memory of them just eluded me):
This internet article states, though rather informally,

the larvae ... can bite through plastic and cardboard, [or] work their way through a screw lid jar if it’s not tightly closed.

This official page of this U.S. National Pest Information center* states explicitly (first paragraph there as of time viewed)

Larvae can chew through plastic bags and thin cardboard, so even unopened packages may become infested.

NPIC is, from the page footer here and on other pages, a cooperative agreement between Oregon State University and the U.S. Environmental Protection Agency.
NOTE: Sourcing to continue as required...

Sources for this are pretty common across the web so no special citations here in this case (unless it gets requested and I find the time)

Please always provide citations when posting answers on this site. Otherwise, your post is likely to be downvoted or removed. Thanks!

oops - got called out within 2 minutes for not adding explicit sources and citations. Received a downvote along with a message with that. Well, received. But please, @theforestecologist and everybody, just give me some time for that, will you?

BTW, for the hygiene of the knowledgebase - which I accept - I might temporarily retract my answer but I'm uncertain about whether that would remove it irrecoverably. Would that be a way to go, @theforestecologist? Thanks again for the heads-up. - Background information: I am really right now doing my due prior research for another question that I believe is not in the system at all but exactly to make sure it really is distinct I am reading all the QAs that the system thinks they might be. That's how I came across this question in the first place.

This post was written with no other intention than to be helpful. Please.

As for the "screw lid" part, I haven't consciously read that anywhere else but here the critical factor seems to be "if it's not tightly closed". Big deal.

@theforestecologist does this qualify for this answer to be reset to +- 0 votes?

Welcome to Biology.SE! Thank you for taking the [tour], but please also consult the help pages for additional advice on [Answer] effectively on this site. Unfortunately, I think you've answered a question different from that originally posed. I would vote this up if the question was something like "Can pantry moths really chew through plastic bags?". As it stands you've made a detailed comment on a side issue rather than an answer to the OPs question. Since you've put in so much work maybe you can find a question that this does answer? Thanks!

thanks @tyersome, will try. As stated in my other comments, I was just dropping by doing adjacent research and thought I'd add a missing bit to be helpful to any latecoming readers because of other comments and I could not do that simply in a comment bc rep, however much I would have loved to. I very much appreciate your analysis and suggestion (and your not adding another downvote :-)), just if I could be allowed a little time for that?

On moving this answer: Have now checked using the site search for "Can pantry moths really chew through plastic bags?", some variations of that, and "moth chew plastic" (all yield zero), then "moth eat plastic" yielded exactly this. Now I guess this would really be an edge case as the accepted and high-rep only answer does briefly mention the essence of this answer, giving the same reputable source and link on the point. Now to look what part of the help pages would cover what to do here?

To me that question still doesn't really fit your answer. I think you might want to post a question about how to use your answer on [meta] — the moderators will often answer questions there. One possibility is for you to post a question and then answer it yourself, but I'm not completely sure how well that would be received ... ———— As for downvotes, to the extent possible it is best not to take them personally. Some users downvote ⋯ enthusiastically ⋯ without giving useful feedback, but many new users ignore feedback or respond angrily to comments. Stick around and you'll also see upvotes!

Thanks again tylersome (can't 'at' two users) - I'll take your advice to ask about that on Biology Meta, even more so as the intersecting answer I mentioned was @theforestecologist's and they are a mod. I might first complete my research on the other question I'm preparing though as it might help with explaining what I was doing in the first place (was doing my due prior research on that question by which I came across this question and noticed that it might help late readers if I added a missing bit, which could have been a comment if ...)

Thanks again @tylersome - I'll take your advice and ask on Biology Meta. Please note another comment I just added above this one (to ping theforestecologist for the reason given there, system is telling me I can't 'at' two users in one comment)

@somebody_other thanks for updating with some citations and support. I've removed the post notice. We get many unsupported posts here, so quickly responding with post notices is paramount for trying to get users to take that aspect of our site's expectations seriously. (see our help page and take our [tour]). This is an especially big problem with a topic like species ID, which is typically rampant with inaccuracies across the internet. Nothing personal. Just nipping the problem in the bud to cut down dealing with it later. Thanks Shahin for the update

Regarding rep limitations: these are in place partially to force you to get involved in our site so that you learn the ins and outs. You can only earn rep through asking, answering, or editing. Each of these are "graded" by the community here through voting. In other words, you only earn rep if the community approves. You earn more priveleges the more rep ("trust") you earn. Just a few upvotes or a handful of edits enables you to comment. So please stick around, get to know how things work a bit more, edit some posts, answer more questions, and you'll be on your way in no time!

@tyersome, apologies for consistently mistyping your username unawares so I guess you didnt get my ping. In case you're interested, see above. Thanks a lot for your helpful comments.

@theforestecologist might I get your opinion as a mod and the author of this: I 'd un-offtopic my answer as tyersome suggested by making it a separate question (that I could link to, too). I worry whether the second-last line of your above answer would make a "sort of" duplicate of it, though. AFAIS there's no "real" duplicate yet. tyersome suggested I should ask about this on Biology Meta (a bit high?) - now as it concerns your answer and you are a mod yourself, what do you say I should do? And thanks a lot for the explaining & encouraging!


text:
Are proteins a different shape in space?
Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth?
If the structure and shape is in fact affected, then would it be enough of a change to cause a change in protein function?
I've found studies from NASA saying that when protein crystals are grown in space, they are larger and form more perfect crystals than on Earth but I want to know about the effect of gravity on proteins that have already been formed.
Thanks!

Can you provide a link to the NASA article please ?

https://www.nasa.gov/mission_pages/station/research/experiments/1320.html

Please note: Life depends on enzymes and other proteins. People have lived in space for long periods of time. If protein structure (3-D) were affected by being in space, do you think life would be possible there?

Yes of course I've considered that before asking the question but I thought there could be minute changes that wouldn't cause serious illness. Also, space flight definitely takes a toll on health and the weightlessness does mean muscle mass is lost. I thought perhaps as opposed to this simply being because of the lack of use of muscles, it may be because of changes in the shape of proteins that govern their structure and the production of muscles. So, I just wanted to know if gravity would have an effect on protein structure.

You can also do a rough estimate about the energy involved - the amount of energy a protein would gain from moving a distance of its radius (protein mass)(acceleration of gravity)(protein radius) is about a billionth of the typical scale of thermal energy in the cell (kT = 4 piconewton nm).

However, once you get around the range of hundreds of microns in length scale, there can be some gravitational effects in the cell: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789854/ - this is why protein crystals (at a large length scale) can be distorted by gravity, even though proteins aren't.

Proteins are not made to be one way up or the other as they flow around and surround cells, so sea-level to space gravity gradient will not be the major cause of change to proteins at different altitudes.
Pressure is more of a factor on proteins, and it has been studies very much, both for protein shape and protein interaction with elements and other molecules.
http://www.annualreviews.org/doi/abs/10.1146/annurev.pc.44.100193.000513?journalCode=physchem
People have awesome health when they are born and raised at altitudes of 4000 meters, there are even people living at 4800 meters OK. the pressure gradient there is halfway in between sea level and space. 100m depth also stresses nitrogen toxicity and other severe effects more than proteins, but deep sea fish do have specially adapted proteins because depths at 10000 meters require different proteins than the surface.

Note: the sea-level to space gravity gradient is much lower than sea-level to even geostationary orbit gradient.


text:
Heart failure and pleural effusion
Why does pleural effusion usually occurs in the right hemithorax in acute heart failure? Could someone explain the mechanism? Thank you.

where did you see/read that pulmonary edema usually occurs in the right hemithorax? as far as I typically see it's generally in both lung fields on a chest x-ray when it's present

Sorry i just realized i wrote it wrong. It should be pleural effusion, not pulmonary edema. I cannot say any reference textbook. Because it is written on a book for medical exams.

thanks for clarifying... I still have the same question... where have you seen that pleural effusions occur on the right instead of the left? can you cite that in your question?

@VanceLAlbaugh I am curious about this question though I don't know the answer. Searching for the source of this information I think OP might have it slightly wrong; bilateral pleural effusion is by far most common, but unilateral pleural effusion is typically in the right. This seems to be commonly reported, here's one example, here is another.

completely agree @BryanKrause


text:
can a point mutation cause a frameshift?
During translation initiation, a tRNA loaded with Methonine binds to the small ribosomal subunit. Subsequently, a mRNA molecule, recognized by the 5 cap, binds to the small subunit, and the tRNA scans the mRNA molecule for the presence of AUG which is the start codon. A point mutation could result in the the sequence AUG to be present after the ribosome binding site, but upstream of the "true" start codon.
Question 1:Will translation start at the mutated site?
Question 2: Could the mutation result in a frameshift, with a truncated protein as a consequence?
I have not found much information about this. I did find one homepage, with lecture notes from a genetics course at University of New Mexico referring to this type of mutation as a start-gain mutation.
http://www.discoveryandinnovation.com/BIOL202/notes/lecture14.html
"Start gain. A start-gain mutation is a point mutation creating a new ATG start codon upstream of the original start translation site. If the new ATG is close enough to the original one (so that it is within the processed transcript and downstream of a ribosome-binding site) and in frame, it will be used to initiate translation, adding amino acids to the amino terminus of the original protein. It is also possible for a start-gain mutation to be out of frame, which will not affect translation of the original protein. In general, start-gain mutations have a low impact on gene function."
I have not come across the term start-gain mutation before, but it sounds like what I am describing.
Question 3: If the start-gain mutation is out of frame, why will it not affect translation of the original protein?
Question 4: It is my understanding that the start codon sets the reading frame, and not the bases prior to the start codon. If the bases prior to the start codon are also "read" in triples, which position in the mRNA transcript sets the reading frame?
Thanks

where have you looked for this answer?

Welcome to Biology.SE. Homework questions are off-topic here unless you have shown your attempt at an answer. For more information see our homework policy.

I saw the OP edited it's question quite a lot.. This answer answers the questions before the edit, I will not delete this because it will maybe help other people
I'm not sure if you fully understand the terms you used so I will start with clarifying these.
Missense mutation

a point mutation in which a single nucleotide change results in a
  codon that codes for a different amino acid (wiki)

Example
    DNA: 5' - AAC AGC CTG CGT ACG GCT CTC - 3'
         3' - TTG TCG GAC GCA TGC CGA GAG - 5'
   mRNA: 5' - AAC AGC CUG CGU ACG GCU CUC - 3'
Protein:      Asn Ser Leu Arg Thr Ala Leu

-------------------------↓↓↓↓↓↓↓--------------------------
    DNA: 5' - AAC AGC CTG CTT ACG GCT CTC - 3'
         3' - TTG TCG GAC GAA TGC CGA GAG - 5'
   mRNA: 5' - AAC AGC CUG CUU ACG GCU CUC - 3'
Protein:      Asn Ser Leu Leu Thr Ala Leu

The 4th codon which was CGT (and GCA on the other strand) is changed because of a subtitution of the G for a T. Because of this change the codon will not code for Arg anymore but instead it will code for Leu. So a missense mutation causes the sequence to be in the same frame as before however a codon is changed and subsequently an other amino acid is added to the polypeptide chain during translation (this is not always the case see wobble)

Frameshift mutation

A frameshift mutation (also called a framing error or a reading frame
  shift) is a genetic mutation caused by indels (insertions or
  deletions) of a number of nucleotides in a DNA sequence that is not
  divisible by three. (wiki)
  Example

    DNA: 5' - AAC AGC CTG CGT ACG GCT CTC - 3'
         3' - TTG TCG GAC GCA TGC CGA GAG - 5'
   mRNA: 5' - AAC AGC CUG CGU ACG GCU CUC - 3'
Protein:      Asn Ser Leu Arg Thr Ala Leu

-------------------------↓↓↓↓↓↓↓--------------------------
    DNA: 5' - AAC AGC CTG CTT ACG CT C    TC - 3'
         3' - TTG TCG GAC GAA TGC GA G    AG - 5'
   mRNA: 5' - AAC AGC CUG CUU ACG CU C    UC - 3'
Protein:      Asn Ser Leu Leu Thr Leu ..........

In this case the nucleotide T is removed and thus causing a framehift because we need tree bases to form a codon. by removing a nucleotide we just read further till we find a third base and this will be our "new" codon. This new codon does not code for Ala anymore but will code for Leu. (I added the dots because of the fact that the stop codon will/can be shifted and the transcript can be either shorter or longer (the previous stop codon will no longer exist).

Could a missense mutation cause a frameshift

In the case of a missense mutation the DNA sequence will be in the same frame (no nucleotide is added or removed) and in the case of a frameshift a nucleotide needs to be added or removed and therefore a missense can't cause a frameshift.

such that a mutation results in the sequence AUG?

Both a missense and a frameshift could result in a start codon.
Example (frameshift)
mRNA 5'     AAC AUU GAC 3'
Protein:    Asp Ile Asp
    -------------------------↓↓↓↓↓↓↓--------------------------
mRNA 5'     AAC AU G  AC.... 3'
Protein:    Asp Met   ........

Example (missense)
mRNA 5'     AAC AUU GAC 3'
Protein:    Asp Ile Asp
    -------------------------↓↓↓↓↓↓↓--------------------------
mRNA 5'     AAC AUG  GAC 3'
Protein:    Asp Met  Asp

So both a frameshift mutation and a missense mutation can introduce a Met --> a start codon.

a mutation results in the sequence AUG to be present in the transcript
  but upstream the start codon?

A gene is only transcribed if this gene is preceeded by the appropriate sequences:

The start codon will be present in the first exon so the only way to put a start codon before the "old" start codon while remaining all other sequences(UTR,promtor, enhancers etc.) in tact is to "create" one just behind the 5' UTR and before the "old"  start codon in the first exon. This can be done by just inserting AUG in there, HOWEVER we are talking about point mutations:

A point mutation, or single base modification, is a type of mutation
  that causes a single nucleotide base substitution, insertion, or
  deletion of the genetic material, DNA or RNA

The start codon we are talking about is positioned AFTER the 5' UTR (as said above):

By inspecting the "general" 5'UTR sequence we can see that there are already "start codons" (not really start codons because they are not translated") present before the start codon. We could probably add one using a frameshift or a missense mutation as described above and in your edited question:

If the new ATG is close enough to the original one (so that it is
  within the processed transcript and downstream of a ribosome-binding
  site) and in frame, it will be used to initiate translation, adding
  amino acids to the amino terminus of the original protein

As far as I can reason is the only way to create a start codon BEFORE the old one is to change the UTR. As stated in your queation this can only "work" if the UTR parts which have an important function are not affected. Further to get this working the 5'UTR should contain a (not "important" )sequence which can be mutated tot form an AUG (see my explanation above)


text:
Translation of RNA into proteins
What's the least number of tRNA molecules needed to form a polypeptide chain that contain 50 amino acids of 15 types?

I know that each type of amino acid has at least one unique type of tRNA that recognizes it and transport it, so according to my understanding the 15 types of amino acids need at least 15 tRNA molecules of different types unless there was a reason that prevents one tRNA molecule from transporting two identical amino acids (two alanine) to the same polypeptide chain

•In other words:
Can one tRNA molecule carry two identical amino acids (ex: two alanine) to the same polypeptide chain that's being synthesized or not?

No, there is no way the same species of tRNA can carry two different amino acids no matter how similar they are. Each tRNA carries only one particular species of amino acid and there is no way it can just "switch to" any other one.

@YordanYordanov although physiologically I agree, and it answers the question, I just am wondering: there must undoubtedly be chemically modified amino acids variants that will be inserted into the growing peptide as well right?

I have to check this out but aren't the amino acids modified after they become inserted into the growing chain, not before. I will make a quick search online now. Here is one paper I managed to find with a very "quick" online search-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130931/ . As far as I can see all modifications are done after translation, not before. But there might be exceptions yet. I guess I would have to go deeper for this question.

@YordanYordanov — "Use comments to ask for more information or suggest improvements Avoid answering questions in comments." You see these instructions when you click in a comment box. Please follow them or you are breaking the SE model.

Please clarify what you mean by "of the same type".

@David amino acid having the same code ex: two amino acid molecules with (GCG) code.

@David - it often happens that users do not feel confident writing up a full answer and comment. In my opinion, that is not breaking the model but making helpful comments to the user that won't do as a full blown answer. See e.g. meta

Jasmin, each codon (not code) specifies only one amino acid (in a given organism and subcellular compartment). GCG is the codon for alanine. If you think a codon can specify more than one amino acid (except in the special cases of selenocysteine) then you should study an elementary text on the genetic code.

@AliceD — I didn't make the rules, but I subscribed to them when I signed on. I also understand them. They are clearly explained on http://biology.stackexchange.com/tour. When the people who have set this site up feel so strongly about this rule that they put a reminder in the comment box, there is really no justification for flouting it. If one person does it others think it is permissible and one ends up with the sort of discussion forum and chit-chat that StackExchange expressly is not. If people are uncomfortable with the rules they should go somewhere else.

The only thing that comes to mind would be an error in tRNA charging.

@David  Can't there be two amino acids of the same codon be found in one polypeptide chain of protein, as alanine to be present more than one time in the chain?!

Jasmin — Of course. But it was not obvious to me that this is what your question was about. Assuming that this is not a homework question  (is it?) you need to explain very clearly what your question is. 1. When you say "particular tRNA molecule" do you mean the same identical one molecule in the cell or molecules of the same class, i.e. with the same anticodon. 2. When you say "two similar amino acids" you need to make it clear that you are refering to two alanines or two glycines (I would use identical, rather than similar). Your question is still unclear, which is why it has close votes.

@David I hope that my question is clearer now. (Sorry for the inconvenience, but English is not my first language)

Jasmin — OK, but a strange question. And there are 20 different amino acids encoded in the standard genetic code, so I don't know why you picked 15, although a 50 amino acid protein could conceivably be lacking five amino acids. I suppose I have to answer your question now though.

Yes we can imagine that a tRNA can be recycled to incorporate the same amino acid into the same peptide chain multiple times so 16 tRNA could form a 50 amino acid chain but that will never happen thermodynamically. You need large concentrations of tRNA of all kinds for this reaction to take place, if you mix a single ribosome, mRNA and 15 tRNA with abundant free amino acids the reaction chemistry won't function.

@David - I know the rules and you are right. The thing is that it is a gray area. Personally, I indeed never give answers-disguised-as-comments, only when I expect the question to be closed and close-voting myself. Anyway, point taken.

In the basic model of protein synthesis the events involving tRNA and amino acids are as follows (see any standard text, e.g. Lodish et al. section 4.4):

An amino acid is attached to the appropriate tRNA (the one with the anticodon that recognizes a codon for that amino acid) by one of twenty specific amino acyltRNA synthase enzymes in a reaction requiring ATP. This is called charging or aminoacylation of tRNA.
The tRNA corresponding to the mRNA codon is brought to the ribosome by an elongation factor (EF1) and the peptidyl transferase activity of the large ribosomal subunit catalyses the formation of a peptide bond between the growing polypeptide chain* and the amino acid of the tRNA, releasing deacylated tRNA.

I am unclear why you are concerned with this problem, but if there were two alanine codons in the mRNA, in theory after a particular discrete tRNA molecule had inserted the first alanine it could be recharged by the aminoacyl tRNA synthetase and then be used to insert the second alanine. However the concentration of tRNA molecules in the cell needed to support protein synthesis is such that the actual probability of this same discrete molecule being used, rather than another tRNA carrying alanine, is remote.
*A real-life complication is that a polypeptide chain has to be initiated by an initiator methionine-tRNA that is distinct from the methionine-tRNA that inserts internal methionines (see Lewin et al. section 4.5).


text:
The parameter for setting the number of mismatches in standalone blast
In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to set score.
-q => Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3
-r => Reward for a nucleotide match (blastn only) [Integer] default = 1
What do I do if I only require hits with a maximum allowed mismatch or gap of 2 per alignment.

There is no direct option like that but you can set percentage identity filter with -perc_identity
However, this is only for reporting. BLAST will still perform all the alignments. That is why I suggested you to use bowtie.
EDIT-1 (getting long for comment)
If you want a word type of search then use the -n option. But it always starts from the 5'end which is quite justified in case of miRNA because the seed region is in the 5'.
Setting -n to 0 means no mismatch in seed region. -l option defines the seed length; I would advise that you use something like 10. -e refers to maximum mismatches in the non seed region but it is not the number of mismatches; it means maximum tolerated sum of phred score of mismatches (fasta files are assigned a default phred score of 40 at all residues. So, for 2 mismatches you have to mention -e 80).
EDIT-2
Yes. Increasing mismatch and gap penalties would make the search more stringent if you have already specified a cutoff on score.

got it.. gonna go for bowtie.. I guess it would be -v 2 for the maximum number of mismatches set to 2, and -e 0.01 for the quality score, --norc for the plus strand and which parameter would be the equivalent of the word match limit.

and one last question for future reference, do you think increasing the mismatch penalty from -3 (default value) to maybe -5 or -6 would serve this purpose?


text:
Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?
Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an area around the match area for structure prediction.
In one paper, I found that ~70 flanking nt of match area was taken as pre-miRNA for structural analysis while in this paper ~100 flanking nt of the match area was taken for pre-miRNA structure prediction. Any idea why so?

There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides.
The maximum length of a human miRNA hairpin is 180nt for mir-3648 (90nt per half hairpin). In such cases you may take more flanking residues. But these cases are rare.


text:
Steps to confirm if predicted miRNA is good or bad
I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in this paper). I have also isolated the pre-miRNAs (+100 nucleotides from either end of the match area). What would you suggest as ideal ab-initio methods to confirm that these miRNAs do exist in that particular genome? Some papers I found use mFOLD like this.
What would you suggest as best steps to confirm if a predicted miRNA/pre-miRNA is really present in the genome.

you can look at my answer in your previous post.. BTW, How did you obtain the miRNA sequences?

@WYSIWYG I downloaded all the available mature sequences in miRBase. Removing duplicates is an issue. What would you suggest is a good tool to remove duplicate miRNAs among 30,000 sequences.

There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you can use fastx_collapser to collapse redundant sequences. However you will lose the name of the miRNA. You can use awk also for this and it will keep the sequence header from the first organism in the list.
awk '/>/{$0=h} !(/>/){if($0 in a){next} else{a[$0];print h"\n"$0}}' organism1.fa organism2.fa ... organismN.fa

Make sure that there are no extra newlines, otherwise you might need a small modification
To know if something is an expressed miRNA you would need to do a small RNA sequencing. There are some tools like mirdeep and mirSVR which you can use to discover miRNA sequences.

Do I really need to use mirDeep now that I am trying to match the already existing list of all available miRNA to the genome rather than find new novel sequences. I thought that was what miRdeep was for.

It does not just find novel miRNAs but it also checks for the features such as hairpin formation and assigns scores. mirSVR uses a machine learning algorithm to find miRNAs (I have never used it though)


text:
What is indirect vs direction selection of genes?
As the title suggests, what is the direct and indirect selection of genes. Couldn't find a straightforward answer. Is it the same as direct and indirect fitness?

Direct selection is when the fitness is directly associated with a certain gene. The beneficial alleles of this gene get selected.
When an allele gets selected not because of its direct effect on fitness but because of other reasons for e.g. strong linkage with other genes which in turn are being selected, then it is said to be undergoing indirect selection.
From Kirkpatrick and Barton (1997)

Female preferences have caused the evolution of extreme male mating
  displays throughout the animal kingdom (1–3). One mechanism that might
  establish these preferences is indirect selection, which occurs when
  preference genes are associated (that is, in linkage disequilibrium)
  with other genes that are spreading under selection. Indirect
  selection is invoked by two types of theories (2). The first are “good
  genes” theories, which interpret male mating displays as indicators of
  high viability. In this view, the expression of the male display is
  correlated with the presence of alleles that increase viability.
  Because associations naturally develop between preference genes and
  male trait genes, as the high viability alleles spread by natural
  selection, preference alleles for extreme displays also spread. The
  second class of theories that postulates indirect selection involves a
  “runaway process.” Here alleles that exaggerate a male mating display
  decrease survival but nevertheless spread because they enhance male
  mating success. Genes for extreme preferences can then be established
  as the result of their associations with these spreading male trait
  genes.


text:
What are ways to compare the "costs" and "gains" of food production systems?
I'm looking for methodologies to compare the costs a food production requires with the gains it delivers (not in economic terms).
I'm aware of energy returned on investment. Are there other methods used in literature (also including qualitative approaches)?
To be a bit more precise (or rather unprecise?): Costs may include the input of fuel, feed, energy in general or - for me most interesting - the environmental burden to our environment (for example the carbon footprint) while gains should refer to the nutritional output of the product (energy, protein content, other (rare) nutrients).
The purpose is to link (or discuss) the burden of food production chains to their benefits but to find a unit that is quantitative comparable (except the pure energy content) doesn't seem so trivial - so I'm very happy with suggestions how to approach that - in the best case with a link to studies that employed the method.

This is called "Life cycle analysis"

@David Thank you. I'm fully aware of that :) I'm rather looking for factors that have a comparable unit when they enter and leave a food production system. Sure, there is for example the output of CO2 linked to the consumption of fossil fuels but I wonder if there are some that are more obviously linked, also speaking in terms of being easier to understand.

Calories and dollars are the most obvious and straightforward, but including additional variables complicates the accounting. . A great paper that used energy has been updated in a more recent publication. Emergy is an interesting alternative.
Current work includes the Natural Captial project that "aims to integrate the values of nature into all major decisions affecting the environment and human well-being". Of course, this approach exchanges a simple currency for a more comprehensive one.
Climate regulating value is also a relatively straightforward and relevant currency that can be used to compare the value of food production systems.


text:
Regeneration capabilities in humans?
To what extent can humans, (mammals in general), theoretically regenerate, and is their a way to speed up and/or exceed this original extent.

What do you mean by "theoretically"? Regenerate what? Toe nails, for example, are easily regenerated. Livers, less so. As it stands, this question is too broad for this site.

Regeneration - or actions perceived as regeneration by popular culture - depend highly on age and specific type of cells (epithelial tissue cells are a fine example). But you can't regenerate a leg-bone once removed.
But to get a more specific answer you to make a more specific question and define the terms you're using.


text:
Can I heat Trizol?
I wonder if I can heat Trizol reagent for 30 min 65C. The goal is to disrupt protein-RNA complex while inhibiting nucleases. (I can't use RNasin cause it's inactivated in 65C, and can't use RVC cause reaction contains EDTA).
I realize that heating Trizol is not safe and its vapors are hazardous, but i can perform it in the hood.

As far as I know, Trizol disrupts protein-RNA complexes on its own - check the protocol. Also, phenol, a major component, is flammable. I don't know what the flash point of Trizol is, but I would be extremely careful. This protocol claims you can heat it. Does your experiment not work at RT?

Heating wont be a nice idea. But if your cells are too resistant to lysis then you can keep the tubes in a warm water bath. However, bring it back to RT before adding chloroform.
BTW what sample is this?

If you are worried about safety, contact your university's Environmental Health and Safety office (or the equivalent). They can (should, and will) advise you on safety issues.

What kind of cells or complexes do you have? I have worked a lot with Phenol based reagents but never found problems to work with it at room temperature. Besides that Phenol is volatile, especially at higher temperatures. You will have to do that in a good fume hood, otherwise this is a serious health issue. And definitely cool down before adding Chloroform.

Working with hot phenolic solutions is rarely been done due to the dangers of this. Phenol needs to be handled in the fume hood anyway, at higher temperatures it gets even more volatile. So if you plan to do this, do it with extra care to avoid injury.
There is one paper that describes this method for bacteria, but this should work for other samples as well: "Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation". However, there is another method, which was developed for extracting RNA from plant material infected by bacteria which is also worth a try (although it might need some adaptation), which works without hot phenol: "An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7".

So what happens if you don't keep your phenol:chloroform in the fume hood? Because I haven't. Am I going to die? I also occasionally touch a gel that contains ethidium. Should I be writing my will?

You should be very careful with Phenol as this causes nasty and long lasting chemical burns. It basically desintegrates the cells, thats why we use it for setting the nucleic acids free. Inhaling is a bad idea. EtBr on the other hand should be handled with care, but most guides about the dangers are overrated. It is mutagen (can cause mutations) and teratogen (can cause damages to the developing embryo) but I haven't seen any proof yet, that it is cancerogen (except when causing mutations). This is different for benzene for example, which is directly cancerogen.

Also: EtBr has a very good water solubility (which means it doesn't cross the skin barrier very easy, especially not as a charged molecule) and it is light sensitive. So use it with care, but don'T overreact.


text:
Are all mutagens carcinogens?
Not all carcinogens are mutagens. Alcohol and estrogen, for example, does not damage DNA.
It's one of the assumptions of the Ames test that mutagenicity implies carcinogenicity, but is this always the case? I assumed that it was, but then I saw one of the comments here. I did some more research but the internet seems to be reluctant to be definitive on the subject. This guy claims 'no', but I'd prefer sources or at least a response that handles counterexamples like HPV. This paper claims 'yes', but doesn't list any specific examples. Some mutagens might be more specific to genes involved in cell cycle regulation, so I could see how a weak mutagen is a powerful carcinogen.
My question is, can you go the other way? Are there mutagens that just do not cause cancer? If they do not exist or are not known to exist, are they even possible?

Short answer
All mutagens are potential carcinogens unless the mutagen is highly specific to a site. As noted in the question, carcinogens need not be mutagenic.

HPV causes oncogenic transformation of a cell because of certain proteins that it expresses. HPV is considered a carcinogen by the IARC. Some retroviruses are oncogenic: they might carry an oncogene or insert randomly near an endogenous proto-oncogene and cause oncogenic transformation; this phenomenon is called insertional mutagenesis (Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses). They can also integrate within a gene and knock it out. Many of these viruses are considered carcinogens by IARC.
Hepatitis viruses (B & C) can also induce carcinogenesis but insertional mutagenesis is not the sole mechanism (Cougot et al., 2005; Fung et al., 2009; Lemon & McGivern, 2012). Hepatitis viruses are considered carcinogens by IARC.
Ethanol in alcoholic beverages is considered carcinogenic by IARC. There are many substances listed as carcinogens by IARC but they are not mutagenic. The general mechanism of carcinogenesis by these substances may be prolonged inflammation or ROS generation.
Loss of function of the tumour suppressor gene p53 leads to cancerous progression (Chiche et al., 2016; Venkatachalam et al. ISBN:978-1-59259-100-8). So an siRNA that targets p53 should be called a carcinogen. It would however not cause any mutations and is hence not a mutagen.
If you consider the tools developed for genome editing, such as ZFN, CRISPR-Cas and TALEN as mutagens then they are not carcinogenic. However the term mutagen is not used for these molecules. Mutagen almost always refers to a molecule that causes random mutagenesis thereby making it a potential carcinogen.

I'm no expert on the matter, but just quoting from Wikipedia:

Mutagens are not necessarily carcinogens, and vice versa. Sodium Azide for example may be mutagenic (and highly toxic), but it has not been shown to be carcinogenic.

It cites Toxicology And Carcinogenesis Studies Of Sodium Azide.
So it would appear the answer is no. Not all mutagens are carcinogens.

Sodium azide is only mutagenic part of the time(half of the strains tested), and there's http://www.ncbi.nlm.nih.gov/pubmed/2671718 this paper that shows that sodium azide isn't a mutagen in mammals. It's still poisonous (cerebral necrosis!) but neither a mutagen nor a carcinogen in mammals.

It seems like there should be a counter-example (a mutagen with zero or negligible carcinogenicity) but I can't find one.


text:
Ferredoxin synthesis pathways
I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of the pathway in databases (ecocyc,kegg). Does any of you know if the biochemical pathway and the genes involved in synthesis are known?
Thanks,Martin

Wikipedia:"ferredoxin". Ferredoxins are proteins containing FeS centres.

Yes, that is the definition of them. But in which biochemical pathway are they produced...

They are proteins: encoded by genes, synthesised by ribosomes.

I do understand that! But I am interested with which genes are they encoded!

http://www.plantphysiol.org/content/134/1/255.full is a link to the full text of a paper about the ferredoxins of Arabidopsis. That should get you started: if you are interested in ferredoxins from some other species you could obtain the sequences of the A. thaliana proteins and use those to search in other genomes.

http://www.ncbi.nlm.nih.gov/gene/?term=ferredoxin

Ferredoxins and variants such as fladidoxins and rubredoxins are simply electron carrying protein that need to be regenerated, like the more energetic NADPH.
The key thing to remember is that redox balance is key. You cannot have electron pair accumulate so there has to be a terminal acceptor. In the case of aerobic resipration it is oxygen, in the case of iron or sulfur dissimilation it is iron(III) or sulfate, in the case of fermentation it is a small highly oxidised carbon (e.g. methanol, ethanol, butanediol, formate, acetate, propionate, lactate, succinate, fumarate). Carbon fixation requires electron pairs, which come from somewhere. The mechanism of how the carbon dioxide is assimilated can be via the Calvin cycle (plants and cyanobacteria), the Wood-Ljungdahl pathway or from the 3-hydroxypropionic cycle Prof. Fuchs described in Chloroflexi and Sulfolobus. In all three electrons come from somewhere (generally water, carbon monoxide and sulfur respectively).
The reason why there are both ferredoxins and NADPH is a tad harder to explain, but has to do with redox control and the fact that not always ferredoxin is regenerated by a NADPH reductase (also: NADH = catabolic, NADPH anabolic), but could be a fumarate reductase or similar.

Thanks for your answer - Could you add resources and references?