text:
Why does RNA synthesis in E.coli begin with a Purine?
From Berg's Biochemistry:

Most newly synthesized RNA chains carry a highly distinctive tag on the 5′ end: the first base at that end is either pppG or pppA.

Is there a reason why the synthesis initiates with a purine?

From this paper, which is the 2nd result of a Google search for rna synthesis begin with purine, the abstract ends with this sentence: "Our results suggest that the purine-rich sequences at the 5' ends of the nascent transcripts of many genes act to stabilize the early ternary complex." You can read the papers citing this one to learn more if you wish.

I didn't find any suitable result with the keywords I was using. Anyways thank you. @MattDMo

Purine-rich sequences at the 5' ends of the nascent transcripts of many genes act to stabilize the early ternary(elongation) complex.

P.S.Source: MattDMo's comment.


text:
Is inbreeding really efficient at producing homozygosity?

Inbreeding results in homozygosity.

I've come across this concept many times  and there's a question that comes to my mind every time I read it.
Let us suppose the character we are trying to establish is dominant trait controlled by a biallelic gene and the two individuals (animals) we have selected to inbreed  both have the genotypes Aa.
Aa x Aa = AA/ Aa/ aa in the ratio 1:2:1
So the possibility of having a homozygous dominant is 25% while that of heterozygous is 50%.
As the breeder has no access to technologies and find out the genotype of the F1 individuals there's a possibility that he would choose two F1 individuals with Aa genotype once again (which has the highest possibility of occurrence). And the same is repeated , production of F2 offsprings with 50% possibility of heterozygous individuals.
Edit:
So getting a homozygous dominant individual is very less likely to happen.
My question, is inbreeding really efficient at producing homozygosity?

Depends on the allele variants and their frequencies in the population. You can calculate the efficiency if you know these parameters. It also depends on the effects of the genotype on fitness.

I think this "problem" is somewhat contrived, as the modern breeder will have access to genetic technology, but even in "the old days", they would be selecting for a certain trait, whatever that may be. They then just take the offspring that exhibit that trait, backcross them, and so on and so on for as many generations as is needed (10 pops to mind for mouse knockouts/transgenics).

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text:
Are there any photosynthetic catalysts in use other than chlorophyll?
When I search for catalysts other than chlorophyll on Google, I only get references to artificial photosynthesis. When I look up photosynthesis, I see accessory pigments mentioned, but it appears that the chlorophyll family is crucial.
These chlorophyll variants all have the chlorin (not to be confused with chlorine) ring in common.
Are there any photosynthetic organisms that do not use a chlorin derivative? Why is chlorin so predominant?

There are photosynthetic organisms that use retinal-rhodopsin complex. However, the mechanism of photosynthesis is different in these organisms than those that employ chlorophyll dependent photosystems. In these organisms, the light causes the rhodopsin-like membrane proteins to pump proton out of the cell and create a proton gradient which in turn is used by the ATP synthase to make ATP.
See this post too Why are there no known photosynthetic archaea?
This mechanism of "photosynthesis" is not as efficient as the chlorophyll dependent one (page 22, Baltscheffsky, 1997†). Moreover, it does not produce NADPH.

† Baltscheffsky, Herrick. Origin and evolution of biological energy conversion. New York etc: VCH, 1996. Print. ISBN: 978-0-471-18581-9

What is the efficiency of that process, compared to chlorophyll photosynthesis?

I think you would do better to ask that as a separate question, rather than commenting on a four-year old answer.

I would say even photolyase counts since it uses light to change chemical bonds in DNA repair.

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text:
BLAST with minimum E-value cutoff
It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?

the only manner (of my knowledge) is to use a script (R, python, java) to do this

There is no such option. You can perform the alignment and filter the hits later. However, I wonder why you really need that. Lower E-value indicates lower chance of an alignment randomly picked from a database, to have a given score.

I'm looking for records that are moderately similar, not highly similar, to my query.

@PhilipHeller As I said, there is no option for that. You have to filter the results. If you have to look for similarity then you should look at percentage similarity/score instead of e-value.

I second WYSIWYG comment, I think it would be the easiest way. Extracting the results and filtering them using scripts could help you out a lot but would need a bit of time if you don't know any scripting langage.

Setting a minimum E-value threshold will result in literally every single entry in the database with E-values above that value, as they will have very large E-values. You will expect a million hits with 1000000 E-value, and as a result you will not get any useful information from the search.
Can you explain why you want to set a minimum E-value?

I'm looking for records that are moderately similar to my query. Normally those records would be at the bottom of the hit list, but there are hundreds of thousands of records that are highly similar to my query and I'm not interested in them.

If you want moderately similar hits can you not just use discontiguous BLAST or blastn with a custom matrix?

A suggestion to get less hits is to take another database, for proteins you could use the PDB database and get orders of magnitude less hits.
Thinking a little bit more about your question: Blasting is probably not the right approach for whatever you want to do. Even if you manage to set a minimum e-value, you'll probably still get huge clusters of similar proteins around that value, and I guess that's what you're trying to avoid.
Blasting is really good to find similar proteins, if you want to get a cross-section of whatever-ases, you need to dig into bioinformatics a lot more.


text:
Is it safe to feed an adult fire salamander with slime maggots?
As a reminder, maggots feed of a flesh, while fire salamander consumes his prey alive, without killing it.
Can it happen that the maggot will start eating the salamander from the inside?

I'm voting to close this question because it is off-topic for Biology, and instead should be posted at [pets.se].

Maggots typically eat dead/rotting flesh, not live. Maggot therapy is used in clinical settings in the US and around the world for debridement of necrotic wounds.

@MATTDMo reluctantly I can see your point. I feel it could be edited into a more general question about ingesting live larvae that would be on-topic for Biology though - OP, would you have any objection to that?

@arboviral no objections, since i've got my answer.

Although I am afraid I don't know much about fire salamanders specifically, it is certainly possible for ingested fly larvae (or larvae hatching from ingested eggs) to survive ingestion and subsequently cause intestinal damage. Parasitic infestation by fly larvae that grow inside the host while feeding on its tissue is called myiasis. Enteric myiasis (also called gastric, rectal, or intestinal myiasis to indicate the affected part of the digestive system) occurs occasionally in humans following the ingestion of cheese infested with cheese fly maggots. Casu marzu, a traditionally produced Sardinian cheese, is supposed to have live cheese fly maggots in it, and cases of bloody diarrhoea following its consumption are known. If they're dead the cheese is considered unsafe to eat (although personally I'd correct that to 'more unsafe').


text:
Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?
Agar is a relatively cheap substance from red algae.  And it contains a saccharide agarose as well as a small amount of pectin.
Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed.  What happens when a gel is run in agar?  i.e. why remove the pectin?
If you can guess, how is the pectin removed?  I know there are enzymes that might do it, but not sure what's really used.

@dd3 has put down a great answer - esp with the figures in the answer!  Would love to see an answer to what the industrial process is like.

The answer to the first part of your question can be found on Wikipedia:

Agar is a heterogeneous mixture of two classes of polysaccharide:
  agaropectin and agarose. Although both polysaccharide classes
  share the same galactose-based backbone, agaropectin is heavily
  modified with acidic side-groups, such as sulfate and pyruvate. The
  neutral charge and lower degree of chemical complexity of agarose make
  it less likely to interact with biomolecules, and, therefore, agarose
  has become the preferred matrix for work with proteins and nucleic
  acids.

This page compares the result of using agar gels to that of using agarose:

The second part of your question: here's a patent, although I have no idea whether this method of agarose purification is widespread.  Propylene glycol purification of agarose does seem to pop up a lot.  I think people who  purify their own agarose use that method, but I am not sure if biotech companies have other methods.
EDIT: it's propylene glycol, followed by ethylene glycol, that is commonly used, but PEG has been used at least once.

thanks for doing this answer!  I looked at similar patents after looking at the one you are pointing to and as late as 1987 they are precipitating agarose with glycols or PEGs... looks good!

You're welcome. It was a good question, and I enjoyed finding an answer.

Using DMSO (dimethyl sulfoxide), agarose can be separated. After heating and stirring around 2 hrs you will get a yellow stiff gel of agarose by filtering.

this is cool! have a recipe?  I'd like to try this!

@shigeta: here is a paper


text:
Do schooling fish make sounds that predators could detect?
Do schooling fish make sounds, voluntarily or involuntarily? A general internet search for "schooling fish sounds" doesn't provide many answers, but I found a paper from 1960 describing sounds from some fish in Bermuda. The description of the sound wasn't clear to me.
I'm wondering if there has been recent evidence that predators might clue into the presence of schooling fish as prey by the sounds that they make? And might ocean noise interfere with these interactions?

Yes, fish make sounds that predators can use:

Like us, fish produce sound both unintentionally and intentionally. Unintentional sounds from fish come all the time, resulting from hydrodynamic patterns during swimming and feeding. These sounds can provide information to other fishes. In fact, the fishing industry has recognized predatory fishes’ ability to take advantage of unintentional sounds to find prey and have designed fishing lures that emit low frequency sounds that mimic those produced by injured prey fish.

The opposite is also true:

Many fish take advantage of the noises other species make. We know that some sharks use sound to help them locate prey, while some smaller fish can detect the sounds larger predators make in their hunting. Furthermore, it is believed that a few fish species, including herrings and American shads, can detect the ultrasonic echolocation sound produced by hunting dolphins from a distance of up to 200m.

Interesting tidbit:

The oyster toadfish doesn’t need good looks to attract a mate – just a nice voice. To generate the foghorn sound, the toadfish contracts its sonic muscle against its swim bladder thousands of times a minute. At nearly three times the average wing beat of a hummingbird, toadfish have the fastest known muscle of any vertebrate.

Marine Seismic Part VII: Fish Are Big Talkers

This is a really thoughtful answer! Have you considered joining at the Bioacoustics SE beta?
https://area51.stackexchange.com/proposals/126698/bioacoustics?referrer=NmU1NDBjYzAxYjYyYTFkNjAxNjVhYTI4MjliM2MzYjliMjVmNzUwYWZlYmE3ZTNmMTU5ZmE2MWRlYzI0YmY1MYeOtoZRE6WnbORfi0NHJsJJl-XVap8qWmQEw-3uUKCT0

@etgriffiths - Thank you for the compliment, but I know very, very little about bioacoustics!

Piranha's bark as a warning to each other for frenzies.
Most fish have a lateral line, which detects water pressure, so it acts like an ear.
Predators use it to orient themselves towards prey, and to follow the vortices generated by fleeing prey.
Prey use sound to detect water displacement from incoming predators and for schooling, territorial defence and mating.
The lateral line system and the inner ear of fish are often grouped together as the octavolateralis system (OLS). The former hears bass and the latter hears high frequencies.

Seasonally, many adult fishes produce sound to synchronise gamete release in spawning aggregations or in courtship interactions for mate selection, with many of these calls forming sustained choruses lasting from weeks to months (Amorim et al., 2015).
Teleosts have the capacity for complex acoustic interactions (Mensinger, 2014).
When a threat or possibility of a threat exists, fishes produces sounds as spontaneous outbursts. They also use sound to control shoal grouping.
Fishes may also generate sounds in stressful situations including when they are attacked by predators or handled by fishermen.
About 20% of fish are thought to produce sound.
About 2/3rds of fish sense electricity, teleost species.
https://onlinelibrary.wiley.com/doi/10.1111/jfb.13867
https://en.wikipedia.org/wiki/Lateral_line
https://blog.nature.org/science/2018/04/18/what-does-the-fish-say/
Keywords: Bioacoustics, hydrophone

Schooling fish do produce sounds voluntarily and there is a cool library of recordings from various species available via Discovery of Sound in the Sea: https://dosits.org/galleries/audio-gallery/fishes/ Each species page includes information regarding the role of the sounds produced and their properties alongside recordings that you can listen to!
Regarding schooling fish specifically, an example includes herring that produces series of click-like sounds (here [enter link description here][1] is a paper describing these pulses).
Underwater noise can impact the way fish (and other animals) use sound in various ways: it can limit the acoustic space of individuals trying to communicate via sound, which means that finding mates can be harder (particularly for individual animals rather than schooling fish) and predators might not be able to hear vocalising animals until they are relatively close to them.
Predators can also listen to the ambient sound to find fish and sperm whales, killer whales and other marine mammals have even learned to associate the sounds from fishing gear and salmon farming acoustic deterrents with an easy source of food.
I hope this helps and I am happy to share more references to academic papers if this topic is of interest to you. :)
Reference:
Wilson Ben, Batty Robert S. and Dill Lawrence M. 2004. Pacific and Atlantic herring produce burst pulse sounds. Proc. R. Soc. Lond. B. 271S95–S97.
[1]: https://doi.org/10.1098/rsbl.2003.0107

There is also a website at https://fishsounds.net that has a searchable collection of recordings and information about the behaviours with which they were associated. (Disclaimer: I was involved in the making of the website. But it is good and helpful.)

It is a good idea to list the name of websites, and provide a proper citation for papers as links can change and die. Other then that, great answer!

Understood, thank you @etgriffiths! :) I added the reference to the paper I mentioned. @Sarah Vela are you aware of the Bioacoustics Stack Exchange proposal? (I hope it is okay to mention this here) https://area51.stackexchange.com/proposals/126698/bioacoustics?referrer=ZjMwMTczNDIwZTFiNmUxNzhjMTBiZDkwYzA2YmRkODNmNDg1ODk0NzBkMzM5NmQ3YWYzZmRlZDViODMzYTE1ZSAFiHme-ipoTC99ChnDokzyCUcQmD_38gXTKUbXa1780

You might find this paper by Torres (2017) interesting.
It reviews the different type and scales of sensory cues used by cetaceans to sense their environment and find their preys, including acoustics:
The author lists a few studies that found evidence of passive listening from dolphins, locating their preys using the fish calls, beyond the echolocation detection range.
Similar mechanisms have been hypothesized in baleen whales, who could use the sound produced by schooling anchovies, herrings and krill as cues to locate food patches, but it remains theoretical.
From there, it is highly likely that increased noise pollution could have masking effect with repercussion on the ability of predators to rely on sound for foraging.

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Why does the 'Positive-inside Rule' exist?
Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a given transmembrane domain, typically a helix.
My question is what are the physicochemical, or biochemical explanations for this rule? Although the literature talks about it in depth and has many examples of the rule being employed, I can't seem to find anything about the "behind the scenes" explanation.

Isn't  the electrostatic polarity across membrane enough for the explanation to you?

@243 It would be if there was a negative-outside rule, which it turns out that there is! I found many examples of the negative-outside rule, but they were statistically masked by the rarity of negative residues.

There are not much explanations available, as far as I can see. The best explanation that I have found is that the positive charge allows the orientation of the protein in the membrane. The orientation for membrane proteins is important as a lot of them are transporters which have a dedicated transportation direction. The same is true for receptors, which transport a signal from the outside to the inside of the cell. Most of the positively charged arginine and lysine residues are found in loop regions which are located between transmembrane regions (often hydrophobic helices).
References:

Topogenic signals in integral membrane proteins.
Positive charge loading at protein termini is due to membrane protein
topology, not a translational ramp
The Positive Inside Rule Is Stronger When Followed by a Transmembrane
Helix
Membrane-protein topology

Proteins insert  according to the positive inside rule because positive charges tend to stay in the cytoplasm.  Cells tend to have an electrostatic polarity across the membrane boundary that will hold the positive area inside, and because  higher pK values make the positive areas harder to deprotonate, these interactions tend to make the protein stay that way.

Please add some references!


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Does pH affect Michaelis constant?
I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in the 21.5. According to this paper, Fig. 2C, the normalized specific activity of the enzyme is about 70% at pH 6.3 and about 47% at pH 7. If I divide 34 mM at pH 6.3 by 0.7 (which should get me the optimum Km at the optimum pH of 5.5) and then multiply by 0.48, then I get 23 mM. However, the paper says Km is between 30 - 38 mM, so if I divide 30 and 38 separately by 0.7 and multiply by 0.47, I get 20 and 25.6 mM respectively. Because my value falls within this range, this then must mean that I have the right enzyme and the same result as the paper.
So my questions are:

When the paper says Km is "34 +/- 4 mM", can I assume that means the Km can be anywhere between 30 - 38 mM? I'm surprised to see how wide the range is. I assumed Km is usually just one value with a deviation of at most 0.1.
Do pH change Km values? I understand that pH changes the shape(s) of the enzyme and/or substrate. Therefore that must affect how much it wants to bind to the substrate. If the enzyme's desire to bind to a substrate decreases due to increase in pH, for example, that would mean more substrates are needed to surround the enzyme, thus increasing Km.
If pH does change Km, is this how I determine the Km value of a different pH value if the Km value at another pH is already known? I know that specific activity and Michaelis constant are different, but how much product can be converted per minute depends on how much the enzyme likes to bind to a substrate, which is represented by the Michaelis constant. Did my reasoning and calculation arrive at the right conclusion? If not, how is the calculation done?

A very brief answer is yes, pH levels almost always effect enzyme efficiency. An example is lysosomal enzymes which are optimally active in the acidic environment of the lysosome, but are ineffective in the near neutral pH of the cytosol. This protects the cell should a lysosome rupture; the enzymes will not digest the cell itself. From the wikipedia article "The value of K_\mathrm{M} is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.". And try not to forget Maud Menten.

Thanks for your reply. But is there an equation or method to calculate the relationship between Km and pH? If there isn't, was my calculation valid? I want to verify that if pH = 6.3 and Km =34, then Km must equal twenty-something at pH 7.

@wswr No that assumption is not valid because the relationship between Km and pH can be non-linear and vary between different enzymes.

Actually now that I think about it: I was confusing Michaelis-Menten constant with specific activity. My calculation was invalid. At pH 6.3, the specific activity is high, and the Km value is 34. The Km I got at pH is 21.5, but according to the paper, at pH 7, the specific activity is lower, which mean the Km should be higher. Can it can be assumed that the higher the Km, the lower the specific activity, and vice versa?

This paper might help you: Current IUBMB recommendations on enzyme
nomenclature and kinetics

From the derivation of Michaelis-Menten kinetics you can see that:
$$K_m=\frac{k_f + k_{cat}}{k_r}$$
Where $k_f$ and $k_r$ are binding and unbinding rate constants (for Enzyme-Substrate binding), respectively, and $k_{cat}$ is the turnover number. This is for the Quasi-Steady-State approximation (QSSA). For the equilibrium approximation:
$$K_m=\frac{k_f}{k_r}$$ which is same as the association constant.
In both the cases pH can affect the rate of binding and unbinding by affecting the affinity between the enzyme and the substrate. For example lets assume that the substrate binding site is negatively charged. Low pH would increase the electrostatic potential of the substrate binding site towards zero by affecting the ionization of the functional groups.
pH can also have indirect effects on the substrate binding site because it can modify the overall structure of the protein.
Many enzyme catalysed reactions involve acid-base catalysis i.e. there is a transfer of proton. In reactions like these, pH can affect $k_{cat}$.

If pH does change Km, is this how I determine the Km value of a
  different pH value if the Km value at another pH is already known?

You can do that by making a Lineweaver-Burk plot for the changed pH.

I did make a Lineweaver-burk plot to get the Km of 21.5 at pH 7. But because the only Km value I can compare to verify the enzyme activity is at the different pH value of 6.3, I want to know if there is another way to see if my result is correct.

@wswr Make a LB plot for pH 6.3 and then compare. If your measurements are done accurately, your result should be correct. Result is what you observe; so there is no question of correct or incorrect. Unfortunately, there is no simple relationship between Km and pH. You can perform LB analysis at different pH and try to find a relationship by regression. But this would be applicable only for your enzyme.

In a pedantic tone, "unbinding" would idiomatically be described as dissociation.

I just noticed, isn't Km = (kr + kcat)/kf  = dissociation rate constants:association rate constant?

@wswr kr is dissociation rate constant. kcat is the turnover number or the rate constant of product formation. Both these reduce the concentration of the [ES] complex.


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Will two Type IIS restriction sites cut if they are directly back-to-back?
I want to put two BbsI (or BsaI) restriction sites right next to each other, facing out, like this:
       \/ |BbsI||BbsI|  \/
CTCAAATGCGGTCTTCGAAGACGTTTTAGAG
   /\                      /\

Should I expect this to cut, or are the two restriction enzymes going to block each other?


text:
Why do boys sweat more than girls during exercise?
I noticed that boys sweat more than girls in the PE class performing same physical activity. Is there any other specific reason except muscle mass?

I've often assumed something similar, but when you look at athletes, they sweat buckets irrespective of sex! I'm starting to think that boys are just more willing to throw themselves into a sport and will therefore appear to sweat more. The study cited by @rrirower has N=37 which is incredibly small after stratification and is essentially anecdotal evidence with statistics applied! Also note that muscle mass difference applies only to mature adults, not children.


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How to pipette accurate volumes from BSA solution without air bubbles?
I'm new to immunohistochemistry and there's one step I'm having problems with. Generally I can pipet volumes pretty accurately and avoid air bubbles, but:
1) The BSA solution that I made (with PBS and BSA crystals - then vortexing) had a lot of air bubbles that wouldn't settle over time
2) I couldn't avoid air bubbles in my pipet even though I placed the tip under the layer of bubbles
How should I improve my technique? (Also, will having slightly different concentrations of the blocking and primary antibody serums greatly affect the result?)
Thanks,
L

Never vortex the BSA solution. The best way to prepare a BSA solution is to put the BSA powder on the buffer solution (or water) instead of the other way round. Tap or rock the tube to dissolve the BSA. If there are some tiny clumps then pipette very gently (use 1ml tips; cut the tips if needed) but tapping/rocking should usually do the job.
From CSHL protocols:

For a 10% (100 mg/mL) stock solution of BSA, dissolve 1 g powdered
  Fraction V or molecular biology grade BSA in 10 mL of distilled H2O;
  to avoid clumping, dissolve by layering the powder on the surface of
  the liquid. Gently rock the capped tube until the BSA has dissolved
  completely. Do not stir. Store in aliquots at −20°C.


text:
Can an RNA anneal to its complementary (not reverse) sequence?
Say I have a target RNA strand:
5'--AAUGGCCCUUUAAA-->3'
I know that this strand will readily anneal to the sequence
3'<--UUACCGGGAAAUUU--5'
which is the reverse-complement. I'm wondering if this strand will also anneal to it's "forward" complement, namely:
5'--UUACCGGGAAAUUU-->3'
?
In other words, can RNA form parallel helix structure?

Possible duplicate of why is DNA antiparallel? Can it be parallel?

No. The 5' end has to anneal to the 3' end of the other strand. Here your 5' end is AAU and the 3' UUU, so you can see that U will not pair with U.

It is, of course, a matter of opinion, but my opinion is that if this question can be answered in two lines it is a poor question for which the poster shows no evidence of having done any research himself. (It may even be a homework question.) I would say that this comes under the category of questions that should be ignored and the poster encouraged to do some research of his own as this site requires.

@charlesdarwin why is that?

@mike-flynn, I don't really understand your comment. In a double-stranded DNA helix, if you move along the helix, one strand goes in the 5'-3' direction and the other strands goes in the 3'-5' direction. So, if you want to pair 5'--AAUGGCCCUUUAAA-->3' and 5'--UUACCGGGAAAUUU-->3' you have to flip one over, align them and check that all nucleotides are complementary. When you flip over 5'--UUACCGGGAAAUUU-->3'  you get 3'-UUU...5' and you can stop here because you see that the third U does not match the U in 5'--AAUGGCCCUUUAAA-->3'.

@charlesdarwin, I'm talking about paring without flipping them over. Taking two free floating RNA strands that are complementary only in parallel direction (5' to 3'), will they form a helix. Can helices form with 5' ends going together towards 3' ends - or why not? That is my question. I don't think you have to "flip" them over as you say, I don't think that's chemically necessary.

@mike-flynn I think they do need to be parallel to pair up.


text:
Why is the spirit bear/Kermode bear a subspecies of the American black bear Ursus americanus?
The Kermode bear Ursus americanus kermodei is only found in British Columbia,Canada. The Kermode bear has single nucleotide polymorphism at the melanocortin 1 receptor gene (mc1r) locus which cause the white color. 1 out of 10 indviduals are white and are refer as Kermode bear. However, is the black version of the Kermode bear still a Kermode bear Ursus americanus kermodei? If not, why?

It is because somebody wrote a paper that described it as such, and the paper was published. I don't mean to be flip. Its just that taxonomy is done through publication, not committees (although the peer reviewers could be considered a kind of committee). Subspecies are less stringently regulated than species, and this subspecies does have a particular unique set of gene frequencies that occasionally (as you mentioned) show up in the phenotype. The fact that it has been culturally recognized as special may also have something to do with its subspecies status. A subspecies need not be reproductively isolated from its parent species, and need not have any fixed characters.


text:
Is there any evidence of causation for breathing rate to affect blood pressure in a human?
I did some research and trials, and with 5 trials for a normal heart rate and 5 done 45 seconds into breath holding, the results came back showing that my heart rate of 116/65 mmHg increased to 138/90 mmHg. I was interested in the cause of this, but couldn’t seem to find any evidence online to explain why this happens, exepct for some simple studies that showed that their is a correlation.
So my question is: has there’s been any studies that hypothesize or found a reason for breath holding to affect blood pressure?

My first thoughts are this has to do with some kind of j-receptor pathway like the one mentioned in this abstract - https://www.ncbi.nlm.nih.gov/pubmed/4698499

Interesting question, it has been studied because sleep apnea is associated with hypertension in humans.
It's not my field of research, so I read a few sources to give you an answer.
There is a open-access review here (https://doi.org/10.1152/jappl.2001.90.4.1600) on the topic of episodic hypoxia, which is similar to the experiment you conducted. Two studies in dogs (https://doi.org/10.1152/jappl.1996.80.3.773 and https://www.jci.org/articles/view/119120) showed that neural reflexes, but also arousal, explain a part of the acute increase in blood pressure but here caution has to be used, as acutely holding breath may have different mechanisms on blood pressure elevation than the chronic hypoxia induced by sleep apnea.
Finally, a review (https://doi.org/10.1038/ajh.2009.43) in 2009 summarizes the evidence between sleep apnea and hypertension.
Overall, there seems to be multiple mechanisms. First, there is a sympathetic discharge during asphyxia, releasing catecholamines which can induce elevation in blood pressure by activating the baroreflex.  These are supported by studies of denervation in multiple organs. Secondly, there is activation of the renin-angiotensin-aldosterone system, a central player in blood pressure regulation. Thirdly, the animals studies show that arousal is an important factor in the acute blood pressure elevation ; in other words, being conscient of holding your breath itself induces blood pressure elevation. I cannot find the exact mechanism linking arousal to blood pressure elevation, though.

Good answer, thank you. In my research I hadn’t considered sleep apnea, that was a strong angle to use for this topic.


text:
How old is the action of sneezing?
Is there an estimate for when the ability of sneezing evolved? A little bit of research, and some critical review of my memories tell me that:

Many, if not maybe all mammals sneeze.
Some reptiles sneeze, like turtles and iguanas.
According to this answer, I see some consider also some fish and even sponges to be capable of sneezing. However, I'd be curious to know if this is the actual same concept of sneezing, and not a stretch of definition, given that fish and sponges don't have lungs!

If it's common among mammals, I infer that it is very likely that this ability exists since at least 200 million years. I'd in fact suspect to be very unlikely that all mammals developed it independently after branching out from common ancestors. I am confident the sneezing of turtles is really comparable to ours  and that although more explosive, also iguanas'. These reptiles (according to my superficial and inexperience Google research) are known to exist since more than 215 and 190 million years respectively.
However, I don't know how old a common ancestors of turtles, iguanas, and mammals can be dated. Or how likely it is that they independently developed this skill.
I'd be very curious to know if any expert ever dated this ability.

I went and read the article indicating sponges sneeze here https://www.cell.com/current-biology/fulltext/S0960-9822(07)02261-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982207022610%3Fshowall%3Dtrue . The authors appear to define sneezing as any method of expelling unwanted or potentially harmful material, which imo makes sense for fish as well. Sponges use a much more basic intracellular communication system to identify unwanted material and trigger its expulsion, but the concept is the same.

@Astrolamb thanks for the information. For what concerns my question however I'd say that's stretching the concept. I'm curious to know about our specific way of sneezing, which is still found in many other animals.
According to that large definition arguably also urinating, spitting, crying, and sweating could find a fit. Not sure how our sneezing can be defined in biology though.

@Astrolamb Throwing up and coughing also fits that definition.

@raggot Sneezing (and ejaculation!) is a kind of cramp. That rules out several of the behaviours on your list.


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How can seedless fruits not be GMO?
Biology is the closest I could find to botany on SE.  Grafting can not occur naturally and so if a fruit does not have seeds there is no way it could reproduce in nature.
That logic makes complete sense to me so I am wondering why seedless fruits claim to not be GMO?
Take for example, Satsuma oranges.
Were they somehow crossed like a mule?  See here.  And then grafted over and over again?
It appears they occur naturally and are then grafted.  See here.
So the deeper question is does grafting create a "clone" of the grafted organism?
And deeper yet, what defines genetically modified ( GMO ) from simple genetic variation?

The production of seedless fruits is quite well described on: https://en.m.wikipedia.org/wiki/Seedless_fruit

The difference between genetic variation and GMO is something better discussed on a religion site.

"GMO" is a tricky concept. The wheat we've been eating has was first genetically modified by humans 8000 years ago, and today you'd laugh at what was called 'corn' 10,000 years ago. When humans make new hybrids, we have genetically modified a species. Something that comes from a genetic mutation is still a genetic modification. I think we're just getting into more sophisticated ways to get what we want (and what we don't intend as well...)

Pick a question, but most of your issues can be answered by asking what is a GMO, because the answer is nobody can agree.

@jamesqf ????? Huh?? Not at all. And in fact, such a question best belongs here on Bio.SE

@anongoodnurse (and John)  It's not too tricky; but rather it's surrounded by a lot of misinformation. The term "GMO" is strictly applied to genetic modifications due to human-mediated transgenic manipulations. The genetic variation that arises from cross-breeding (even if it's "unnatural" in a cultivation setting) is simply a "natural" result of subsequent normal biological processes. Such crossbred crops do not have their genes modified directly by humans and are therefore considered to simply be "crossbred" and not genetically modified.

@theforestecologist - I believe you. That's what I would reserve it for as well. But conceptually... how different is animal husbandry selecting for a particular trait over decades vs. splicing in a few genes associated with that trait and getting it in a couple of years  It's ever more sophisticated manipulatioin of the gene pool. But you'll get no more serious argument from me. I get it. I just think of decline in Monarch butterflies, a totally unconsiderd side effect of GMO corn. (for fighting corn worm borer)

@anongoodnurse I think most scientists in the field would agree that it isn't all that conceptually different which is why any furor about GMO safety is a bit silly, the exception being the economic arguments, though there could also be an argument that the speed at which we are able to make changes makes it more likely that those changes will have unintended side effects.

GMO stands for Genetically Modified Organism.
Grafting a plant to a rootstock of another plant is a form of plant husbandry -- a farming technique -- but this isn't changing the DNA code of either of the plants. Sort of like you receiving a donated organ wouldn't be the same as Genetically Modifying you. When a desired trait arises in a plant this is a way to keep reproducing it without having to wait for cuttings or seeds to grow.
There are some plants such as seedless watermelon that are reliably made by crossing two seed species. You take two species of watermelon, Species 1 and Species 2. Both of these are normal -- they make seeds. When you cross them, you get seeds that grow into AB hybrids, seedless watermelons. These AB are infertile, so you have to cross A and B again each year to get more seeds to plant.
Species 2 has twice the number of chromosomes as 1. They are able to cross and make seeds that grow. But when the [1x2] plants grow and try to form seeds, those cells have an odd number of chromosomes. The process of making seeds and pollen -- meiosis -- has a step when half of the chromosomes go into one cell and half in another. Because there is an odd number, the process never finishes and you get no seeds.
to demonstrate how this doesn't work, lets look as a simple example.
Species 1 has two chromosomes [A and B]. It has two copies of each chromosome in all of its cells (one from each parent), and just one copy in its sex cells
Species 1 Normal Cells [AA BB] and sex cells [A B]
Now, Species 2 has a different set up. It has twice the chromosome number
Its normal cells are [aaaa bbbb] and its sex cells are [aa bb]
this means that when you cross pollen from one with seed from the other, you get
[aaA bbB] or [AAa BBb]
When these crosses try to make seeds, its impossible to halve the triplet chromosomes.
True GM technology is used to do things such as, in olives taking the genes that cause oil production to occur, and copying them many times. This gives you more oil production.
Or, in tomatoes -- when you pick a tomato the cells of the skin start expressing a gene that makes the skin soften and break apart. This facilitates seed dispersal. GM deletes that gene, making the fruit bruise less, reducing need for packaging and quadrupling the shelf life.

The system has flagged you as a new user to me and other list members who help monitor this site. I have noticed quite a few other answers from you which have also been flagged as requiring additional references, so can I point you to the Help on Answering Questions. The reason we ask for supporting references on SE is if you post an answer, how do I or anyone else know it is right? What if someone else disagrees? One may feel: "this is my area" or "I taught this to students for years", but one has to demonstrate one is correct to others.

This is a very good answer, but, as David stated, sources are usually required for this site. Having said this, it's nice to see such a good, detailed, and correct answer.

Starting with your last question: The USDA (United States Department of Agriculture) defines genetic modification as "heritable improvements [...] by genetic engineering or other more traditional methods". The EU defines GMOs as "an organism, in which the genetic material has been altered in a way that does not occur naturally" using DNA altering techniques.
These are rather legal than biological definitions. For example, the EU Court of Justice has recently ruled that organisms produced by mutagenesis are technically GMOs but do not fall under the GMO legislation.
So, let's look into how seedless fruits are produced:
This can be achieved by making a plant, that is able to grow fruits but fail to produce functional seeds due to unsuccessful meiosis. This is done for bananas and water melons by crossing a diploid with a tetraploid plant, which produces a triploid plant where chromosome pairing during meiosis is unlikely (more on this in the wiki article). For oranges this is done by growing genetic clones together. Since they cannot self-fertilize (and identical clones cannot fertilize each other), they don't develop seeds but still grow fruits.
These techniques don't require any genetic modification by targeted manipulation of the DNA. Crossing two plants with different characteristics is also done in conventional breeding, which is also not classified as GM. However, it would be possible to genetically alter plants to block seed production and produce seedless GMOs. It would probably be a legal dispute whether this change is "heritable" when there are no seeds, so classification might depend on country policies.
The problem with seedless fruits is that you need seeds in order to grow new plants. To produce new seedless water melons you always have to cross the parents again. Plants that are able to reproduce vegetatively (parts of the plant can grow new plants), can be propagated by replanting branches. For plants, where this doesn't work very well, grafting is a solution to improve the process (a well growing plant is used as a root). Vegetative propagation in any case produces genetic clones, as you have pointed out correctly. The propagation method is independent of the technique that first produced the seedless plant and does not decide the GMO or non-GMO classification.


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Are there any examples where 'magic bullet' drugs have worked in cancer treatment?
Magic bullets are drugs that can be administered on a micro local scale. In this context administration/binding would occur in or near the tumour by exploiting the different surface antigens that cancers expose. Basic lectures teach that a "magic bullt" drug could attach via an mAb (attached to the pro-drug) and then a conjugated enzyme cleaves or converts the pro drug to a drug. This would eliminate a lot of side effects from chemotherapy.
Use in clinical trials. Some mAbs have started to be used in clinical trials, almost 40 years after they were first proposed. My question is simply; have there been any cases of mAbs being used as a successful treatment for any disease? If not, what makes the R&D of this drug type so difficult?

Do you understand magic bullets only in the way of directly attaching to surface antigens or do you also see special made drugs for certain cancers under it?

I'm not necessarily interested in other “magic bullet” concepts. Paul Ehrlich’s magic bullet idea was first discussed in the early 1900's so I'm sure there are enough ideas out there to fill many textbooks by now! Hopefully my edit cleared it up - I only care about this mAb proto drug idea.

There are, indeed, several such mAb based treatments. From the Mayo Clinic:

The monoclonal antibody drug rituximab (Rituxan) attaches to a specific protein (CD20) found only on B cells, one type of white blood cell. Certain types of lymphomas arise from these same B cells. When rituximab attaches to this protein on the B cells, it makes the cells more visible to the immune system, which can then attack.

(...)

Cetuximab (Erbitux), a monoclonal antibody approved to treat colon cancer and head and neck cancers, attaches to receptors on cancer cells that accept a certain growth signal (epidermal growth factor). Blocking this signal from reaching its target on the cancer cells may slow or stop the cancer from growing.

(...)

The monoclonal antibody bevacizumab (Avastin) targets a growth signal called vascular endothelial growth factor (VEGF) that cancer cells send out to attract new blood vessels. Bevacizumab intercepts a tumor's VEGF signals and stops them from connecting with their targets.

(...)

Ibritumomab (Zevalin), approved for non-Hodgkin's lymphoma, combines a monoclonal antibody with radioactive particles. The ibritumomab monoclonal antibody attaches to receptors on cancerous blood cells and delivers the radiation.

(...)

Ado-trastuzumab emtansine (Kadcyla) is one such drug approved to treat HER2-positive breast cancer. Ado-trastuzumab emtansine contains an antibody that attaches to the HER2 receptors on the breast cancer cells. The cancer cells then ingest the antibody, which releases a few molecules of chemotherapy.

It does eliminate side effects, although the treatment is not side effect-free.
Personally, my suspicion with this approach is this: At its heart, cancer is a problem of uncontrolled cell division. Most cells in the body do not divide rapidly, and this slowing down of proliferation is integrated into differentiation into whatever tissue the cells are in. The most obvious cells that divide rapidly are stem cells (themselves carcinogenic!). Furthermore, it seems to be a common theme in cancer that the less differentiated (or more de-differentiated) you are, the more easily you divide, and hence the nastier the cancer you generate.
As such, the worst cancers out there are going to be very undifferentiated, and express few eligible surface markers. What's more, tumors evolve. If you start selecting against cells which express your marker, you will encourage the tumor to simply evolve and stop expressing that marker. Back to the benchside to look for a new marker - meanwhile your patient gets worse and worse.
This is why generalized chemotherapies (or radiotherapy) are so attractive. They attack the rapid division of cancer cells, and the cancer cells cannot evolve to lose this property, because if they did, they would not be cancer cells.


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Do all gene mutations in pathogens lead to more harmful consequences for humans?
It seems that the concern we always hear is that bacteria and viruses mutate to dodge our treatments either through random mutations or survival of the fittest. Do harmful living things ever mutate to become not harmful?

Mutations are random; the (pathogenic) bacteria (or any living being) will randomly acquire mutations that may be beneficial, deleterious or neutral to its fitness. Only beneficial and neutral mutations will survive the selection. Random mutations and survival of the fittest are not two independent mechanisms. The random mutations can alter the fitness as I mentioned and natural selection ensures the survival of the fittest.
Many pathogens have reduced genome (number of genes) compared to their free living relatives (Weinert and Welch, 2017). This is because they lack most of the genes required for synthesis of different metabolites required for survival. They rather obtain these metabolites from the host and hence they have the parasitic lifestyle. It is not possible for the pathogens to acquire that many genes to stop being pathogenic and become a free-living organism. It may be possible via lateral gene transfer wherein a bacteria may obtain an entire gene (or a set of genes) from another bacteria but the likelihood of that happening to convert a pathogenic bacteria to a non-pathogenic bacteria is negligible.
It is certainly possible that pathogens might lose the activity of some of the pathogenic genes (for example those required for toxin production) due to mutations. However, they may no longer be efficient pathogens and would be outgrown by the others who still retain those genes.

Its also worth mentioning pathogens often evolve to be LESS harmful, not killing your host is a good thing, most of the really deadly pathogens are are ones that jumped from a different host species, and have not had a chance to evolve to be less harmful.

@John that would perhaps not be that straightforward. It depends on several parameters so making a general statement on that would be risky. AFAIK, there is a post here that exactly addresses that topic.

@John it's often even more simple than jumping from different host species. A commensal microbe that finds itself in the wrong niche on the same host can all of a sudden become a big problem. A happy bug in your colon is an unhappy bug in your urethra, for example. Much of infectious disease comes from inconclusive negotiations for symbiosis.


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Michaelis-Menten equation type - how it is derived?
Can somebody explain how is the following differential equation found? It is about the blood alcohol content.
See this article (pages 3 and 4).
They say the concentration of blood alcohol satisfies (in the drinking phase): $$\dfrac{dC}{dt}=u-\dfrac{\alpha C}{C+\beta}\quad; \quad C(0)=0,$$ where $\alpha, \beta$ are the liver and the kidney parameters. For the Recovery Phase we have: $$\dfrac{dC}{dt}=-\dfrac{\alpha C}{C+\beta}\quad; \quad C=C_{max}.$$
I can't see how they came to these equations. The only thing they say about the origin of this model is that it comes from a continuity argument: the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body.
I wonder if there is a model which takes into account all parameters in the above article plus the amount of food in the stomach.

Are you asking about how the Michaelis-Menten equation is derived or why it was deemed appropriate to model blood alchohol levels? The former is off-topic to BioSE since the Michaelis-Menten equation is used in many fields of science, and its derivation belongs to mathematics (maybe suitable for MathSE).

@fileunderwater really? I always assumed the MM equation was closely related to biochemistry (enzyme-substrate interactions). I was unaware of any other application of the MM equation ?

Given that the two individuals it is named after were noted biochemists Michaelis-Menten, it is difficult to imagine any other SE that would be more relevant than Biology.

Based on the appearance of your source I would caution you about taking it too seriously. I does not seem to be published in a peer-reviewed journal and is just a manuscript (for example the first reference is to another unpublished URL and the second reference does not contain enough information to allow one to find it).

@RoverEye Same thing, different names: the Monod equation is used to model bacterial growth and the Holling disc equation is used to model the functional response of consumers/predators. There are other examples as well. I've seen the Michaelis-Menten equation being used/mentioned many times as a general modelling tool/functional shape.

Microbial growth, Prey-predator ecology, and enzyme-substrate kinetics in protein chemistry, yet you posit that it is off-topic for Biology SE? A better reason might be that there is no mention of any of these versions of the equation in the source our OP cites.

@RoverEye These kind of equations denote saturation kinetics and they are not just applicable for enzyme-substrate reactions but to other kinds of biochemical reactions too. Examples include transcription regulation, ligand-receptor interaction etc.

@mdperry I think that the question is unclear and/or off-topic, given what the OP is actually asking for ("... explain how is the following differential equation found?", "...how it is derived?"), but whether the Q should be closed is up to the community. No close votes have been cast so far, and it is up to the OP to clarify what he/she is actually asking for.

These kind of equations (the Michaelis-Menten [MM] like term) denote  saturation kinetics. The basic mechanistic assumption behind saturation kinetics is this:
A rate (of lets say product formation) is dependent on the concentration of a molecule such that the rate increases linearly with increase in the concentration of the molecule.

Example 1: Substrate in an enzyme catalysed reaction
Example 2: Transcription factor in a transcriptional activation

However at a certain point increasing the concentration of the molecule will have no effect on the rate of reaction. For the above examples this point will arrive when (respectively):

Active sites in all the enzyme molecules are bound and there is no more space to accommodate a new substrate molecule.
All the binding sites in the DNA are occupied by the existing TF molecules and no more can bind.

In other words, the reaction kinetics changes from first order to zeroth order.
We can provide mechanistic explanations for some cases but in many we do not know how exactly the saturation happens. In modelling we just use a function that will mimic this kind of behaviour.

Why functions of the form $\dfrac{X}{K+X}$ ?

In deterministic modelling using differential equations, it would be preferred to use a continuous function (instead of using a piecewise linear function) because:

Numerical integration is better in case of continuous functions
In biochemical systems, operations are always continuous. There is no digital logic.

The MM function can actually be derived using an equilibrium or a quasi-steady state approximation (See the wikipedia page for the explanation).
In the MM function, when $X \gg K$ then the function is almost 1. This multiplied by the maximum rate constant will give you the max catalytic rate. At $X=0$ the rate will also be equal to zero. Note that in this model the catalytic rate will not indefinitely increase with $X$.
There are several functions that have values between 0 and 1 for increasing concentration of the substrate. Hill function and logistic function are common examples. However MM is a simpler model. You can always revise your modelling approach when you have better information of the biological system.
Now back to your question:
In this model $C$ denotes alcohol concentration $\alpha$ denotes maximum clearance rate and $\beta$ denotes half saturation concentration (concentration of alcohol at which the rate of clearance is half the maximum rate). Intuitively you can think about the mechanism like this: rate of clearance of alcohol depends on the level of alcohol i.e. if you have a lot of alcohol the amount of it removed per unit time will be higher. Think of it as water that is pumped through a pipe; more water in the tank will result in higher flow rate. However when the kidney (or pipe) is overloaded or "clogged" with an already excess of alcohol then clearance rate would remain the same (the maximum that the kidneys can excrete).

the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body

That is called mass balance which can be summarized as follows:
Accumulation = Input + Production - (Output + Degradation)

Note that MM kinetics is outdated, currently the unified enzymatic activity modulation equation is the best approach. http://biology.stackexchange.com/a/23561/3703

@inf3rno No it is not outdated. No model is outdated unless it is proven universally incorrect. Your choice of model depends on what you are trying to ask. You can always plug in more parameters to make it precise but the question is what level of precision do you want.

These equations are working, not doubt, but they are the bad approach. Ofc. we can talk about what "outdated" means in your dictionary and in mine, but I think that would be off-topic here.

@inf3rno I have had a huge debate about this elsewhere. A bad approach is, IMO, one where one does not select the method that is suitable for an approach, rationally. Quantum mechanics answers questions that classical mechanics does not. Moreover quantum laws are applicable for macroscopic systems as well- that does not mean that you should study the mileage of your car using quantum mechanics.

I think you got the wrong analogy here. Both the unified and the MM model describe enzyme kinetics on the same level, while classical mechanics and quantum mechanics are very far from each other.

@inf3rno The post that you link to, seems unclear in this context. Also, I am not sure what you are trying to indicate here. Either the link is insufficient or the argument is not valid in this case. There are no inhibitors here. Why should you consider them?

Right my mistake, I only skimmed the text.


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Can roots have cuticle, especially aerial roots?
In my school biology book, it is written that cuticle covers the epidermal cells in aerial parts of plants and root epidermis doesn't have cuticle. My question is that whether aerial roots, in plants like kalanchoe, also not have cuticle?
Do all kinds of roots not have cuticle?

I don't believe that any class of root has cuticle tissue. The cuticle is special layer designed to work with the mechanical transport of leaves etc, which roots don't have. Different types of roots have different methods for absorbing and retaining water.

According to this article, Selaginella aerial roots have a thick root cap that possesses a cuticle. Roots that have breached the soil do not have cuticles.

Basically roots don't have cuticle while stem and leaves contain cuticle. As roots have to absorb water cuticle is not present in them


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Why is the resting potential of a neuron so close to the equilibrium potential of K⁺?
I know this has something to do with the K+ leak channel. I just don't understand how.
I know that 3 Na+ are pumped out for every 2 K+ pumped in. This makes the cell interior net negative.
I know that K+ is allowed to leak out slowly via K+ leak channels.
How does this place the resting potential of the cell so much closer to the equilibrium potential of K+ than Na+?

Lets just go with the basic Hodgkin-Huxley equation:
$$C_M \frac{\text{d}V}{\text{d}t}=-g_{Na}(V-E_{Na}) -g_K(V-E_K) -g_L(V-E_L)$$
At rest ${\large\frac{\text{d}V}{\text{d}t}}=0$ and therefore $V$ is dependent on the conductances ($g_X$) of different ions. Since $g_K \sim 30\times g_{Na}$, the resting potential is closer to $E_K$ (Nernst equilibrium potential of K+).
What it basically means is that since potassium has higher membrane conductance, it diffuses faster thereby attaining equilibrium faster than sodium (in isolated cases assuming only one ion at a time). When both ions are present the resting potential is because of both the ions but since K+ diffuses faster, it has a major contribution to the resting potential compared to Na+. Leak current that is described in the above equation is a general leak (non-specific). Other channels like rectifiers and voltage gated channels are important when talking about action potential and all these channels contribute to the conductance; however you can group all that into a single metric called membrane conductance. Voltage gated channels can be considered separately when studying the dynamics (in this case the conductances themselves become a function of voltage).

Well, thank you. However, could I ask for a slightly less technical answer? Basically the potassium ions are 30x more conductive, so they have greater determining power over what the resting potential is? So K+ leak channels don't really have anything to do with resting potential.


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What's a protein pulldown assay?
I'm reading a paper and the authors mention a "protein pulldown" assay.
I've never done this before, and googling doesn't bring up much. Could I get a rundown of the basic theory behind it?
Also does % coverage have anything to do with this assay?

Pull down mostly refers to immunoprecipitation, however pulling down can be done using other interactions such as streptavidin-biotin or His-tag-Nickel.
In a protein pull-down a protein is enriched along with the molecules bound to it. When the DNA that is bound to a protein is studied, the experiment is called ChIP (Chromatin ImmunoPrecipitation). When other proteins that are bound to a given protein are studied then the experiment is called Co-IP.
Similarly RNA bound to protein can also be studied.
It is also possible to pull-down an RNA or a DNA fragment using complementary oligonucleotide, streptavidin, antibodies etc and study their interacting partners.
In the linked paper, they have immunoprecipitated a HA (haemagglutinin) tagged protein using an anti-HA-tag antibody (Note that this is just a small tag of 9-10 amino acids and not the entire HA protein. Such tags are useful when you don't have the antibody for a given protein).
They have done both co-IP and ChIP:

HA-tagged, full-length PfSET10 protein and interacting proteins from
  3D7/PfSET10HA and control line 3D7 were purified using anti-HA beads

Chromatin Immunoprecipitation (ChIP) and Transcriptional Profiling
ChIP analysis was performed as described (Flueck et al., 2009).

Coverage is a term used in sequencing experiments which usually refers to average number of reads that map to any locus; this is also called depth. This is commonly used in RNA/DNA sequencing studies (See this post too). In this paper, as mentioned in the other answer, the term coverage is used for peptide reads (analyzed by mass spectrometry) and it is the horizontal coverage not a vertical coverage. Horizontal coverage refers to the fraction of actual molecule (DNA/RNA/protein) covered by the assembly of reads.
Coverage has got nothing to do with the pull-down assay; it is used in the context of the downstream experiment.

From Life Technologies

The pull-down assay is an in vitro method used to determine a physical interaction between two or more proteins. Pull-down assays are useful for both confirming the existence of a protein-protein interaction predicted by other research techniques (e.g., co-immunoprecipitation) and as an initial screening assay for identifying previously unknown protein-protein interactions.

It is essentially the same as an immunoprecipitation experiment but using proteins instead of antibodies.
Coverage comes into play for identifying the pulled-down proteins as they used an LC-MS/MS analysis. You essentially have to map back the short peptide reads you get from the MS to the actual pulled-down proteins which gives you a coverage score, i.e. how much of the full protein sequence you covered with short peptides.


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Which was the first DNA-based genome to be sequenced?
The Wikipedia article on phi X 174 states that:

The phi X 174 (or φX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA-based genome to be sequenced.

But, the article in Wikipedia on Whole Genome Sequencing states:

The first whole genome to be sequenced was of the bacterium Haemophilus Influenzae

So as bacterial genomes are DNA-based, I am confused as to which organism was the first DNA-based one to be sequenced.

Did you follow up the references for the two claims? Which is the oldest? And are you sure there was no qualification to the second claim.  You can surely answer this question yourself. In any case, you should remember Wikipedia articles are written by anyone. There is no central organization and the only checking is that done by people who are interested. There are other sources of information on the internet.

Another thing to consider is that some scientists (and lay people) do not consider viruses to be true "organisms" as they are incapable of reproduction on their own and therefore not truly alive.

@David yes, but my point was about which was the first organism sequenced - some people may have left previous phage work off the list because they didn't consider them to be organisms or have proper genomes, especially if it's ssDNA. I don't know, I'm just speculating.

I shouldn't have, but it was simpler to give you the answer with links to my sources.

@David, Thank you so much for the answer and I am extremely sorry for so much inconvenience that I caused you . I will try my best to learn from my mistake. Again, thanks a lot for the help.

Expanding the question to the history of the sequencing of genes and genomes in general, I present a timeline taken from a review by Giani et al., entitled “Long walk to genomics: History and current approaches to genome sequencing and assembly”.

The graphic shows how the size of sequenced genes and genomes has increased since 1965, which reflects developments in sequencing technology that are discussed in this and other articles which may be more accessible. It should be noted that the more modern methodologies are not intrinsically more accurate than earlier ones, but can be employed more rapidly.
I see no value in the “Guinness Book of Records” approach to biology, but to satisfy the poster, the genome of bacteriophage φX174 was the first DNA genome to be sequenced (1977), and that of H.influenzae the first bacterial genome to be sequenced (1995). But the RNA genome of my old friend bacteriophage MS2, was the first genome to be sequenced (1976).
And the first human chromosome to be completely sequenced is not on the graphic as it was only published in Nature a few weeks ago (July 2020) — chromosome X.

Postscript
For the record, the quotation from the whole genome sequencing article is actually a caption for a (gratuitous) image of the bacterium, is unqualified, and, thus, is incorrect. But when reading Wikipedia articles it should be born in mind that they are written by people like you and me. Anyone can edit them, and nobody need check them or correct them. Peer-reviewed papers can also have mistakes, but where they are of this type, the referees should pick them up. (But by the time you read this I will have edited the Wikipedia article.)

I understood the part of Wikipedia, thank you for suggestion and your answer helped me to clear all my related doubts within me. And I am truly sorry for so much inconvenience and I  got your point on representing question(Not to use Wikipedia as a reference). Though my question was a weird approach to biology because its not going to come anywhere, I felt satisfied that I am clear with my knowledge because of all help. Thank you so much. Your answer helped me a lot in various aspects. Thank you.


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Can encoding of miRNAs in introns not cause dysregulation of gene expression?
For example, consider a gene X which has an intron which encodes a miRNA that downregulates expression of another gene Y.
When the gene X is translated, this miRNA will appear as a byproduct of splicing, then expression of gene X will inhibit expression of gene Y, which could be deleterious.
How did the mechanisms of gene expression evolve to avoid possible unplanned interference in gene expression?

Deleterious effects on gene expression are selected against.

evolution does not think. The ones with any interference would have a disadvantage during selection.

Agree with the two above comments, selection will select against such a deleterious effects.

i understand that evolution is not planned, but how enconding of miRNAs in introns could be used as a regulatory mechanism? For example, are there patterns?  miRNA enconded in the intronic sequence of the gene regulating the expression of the same gene, or a related one? Because if miRNAs occured randomly in introns they would not be good regulators.

I think this might constitute part of the epistatic effects that are being discovered as simple variations turn out to be insufficient in explaining phenotypical differences. So, yes, there must be patterns. There are two recent papers showing that many more miRNAs exist and are expressed in tissue dependent manner. My guess is the patterns will be slowly established by looking into the new intronic miRNAs and their targets.


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How can E. coli proliferate so rapidly?
The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides per second.
By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so more than an hour). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved.
However, in optimal conditions, E. coli can actually duplicate in ~30 minutes.
How could that be possible?
OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.

http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.26.120192.002311 seems to suggest that there is only one origin of replication in E. coli.

Though Escherichia coli has only one origin of replication (oriC), replication proceeds in both directions from it. Thus, based on your calculations, DNA replication takes 40 minutes (which is still too long if the doubling time is 30 minutes). The solution is to start replication again before the previous round has completed, and here's some research which shows just that:

Yoshikawa H, O'Sulliven A, Sueoka N. 1964. Sequential replication of the Bacillus subtilis chromosome. Prod Nat Acad Sci 52:973-980

Obviously, dichotomous replication is advantageous for bacterial growth because the bacteria can replicate chromosomes faster than by having one replication point. With one replication point, the replication time, and consequently the cell generation time, would be limited by the maximal rate of DNA polymerase.

Cooper S, Helmstetter CE. 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Bio 31(3):519-540

…cells growing faster than 40 minutes per doubling must initiate new replication points prior to the completion of DNA synthesis at the previous points; in other words, there should be multiple forks.

Skarstad K, Boye E, Steen HB. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5(7):1711-1717

In rapidly growing cultures, with parallel replication of several chromosomes, cells will end up with 2n (n = 1, 2, 3) chromosomes if initiation occurs simultaneously at all origins. A culture with asynchronous initiation may in addition contain cells with irregular numbers (not equal to 2n) of chromosomes. The frequency of cells with irregular numbers of chromosomes is a measure of the degree of asynchrony of initiation.

Fossum S, Crooke E, Skarstad K. 2007. Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 26(21):4514-4522

…initiation occurs at two origins in the ‘mother' cell. It can even occur in the ‘grandmother' cell at four origins if the time it takes to replicate and segregate the chromosome exceeds two generations.

This last image is interesting because you actually see the multiple replication origins in single cells by fluorescence microscopy.

Cell division rates may exceed DNA replication rates, because DNA replication can occur in parallel, while cell division is always serial. In a circular chromosome like E. coli, replication starts at the origin of replication. Once the origin is replicated, another chromosome replication can be initiated there, while the former isn't even finished. This parallel replication hence allows for cell division rates exceeding chromosome duplication speeds.

Forked replication in E. coli. Source: Fossum et al. (2007)
 Reference
- Fossum et al., EMBO journal (2007); 26: 4514–22


text:
Why is beta- D fructofuranose two different structures when in free form and as part of sucrose?
This is the structure of fructose in free form:

The right moiety is the fructose as part of sucrose. The left one being glucose:

Both of the fructose are beta-D fructofuranose. But as it can be seen they both are clearly completely different structures. The anomeric hydroxyl group seems to be in an opposite position while the rest of the structure hasn't even changed shape.
Where am I getting this wrong. Thanks.

In sucrose, the two saccharides are linked by their anomeric carbons.

I'll try to explain this to you, but you should really look it up here: https://pubchem.ncbi.nlm.nih.gov/compound/beta-Levulose#section=3D-Conformer&fullscreen=true
This is the structure of beta-D-fructofuranose, as a 3D conformer. On paper, or as a 2D figure, we cannot visualize the -OH groups at positions 3 and 4.

They appear to be inside/outside the ring, but in reality, they're not really positioned that way. Both the -OH groups are oriented in an opposite manner, but in a plane perpendicular to that of the furan ring.
So when we flip it over to represent it in sucrose, the orientation of the -OH groups in the molecule flips too.
Think of it this way: if you have a piece of cardboard  (representing the ring) with a pin pierced into it (representing the -OH), and you flip the board over, the pointy side of the pin will face down too.
Moreover, if we represent it this way, the absolute configuration of the side chains at each of the carbons of fructose remain the same.
You could check that using their RS configurations.
For more on RS configurations, check out : https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Chirality/Absolute_Configuration%2C_R-S_Sequence_Rules


text:
Difference between cerebroside and globoside
I have a general idea about their difference that cerebrosides have a single sugar while globosides have more than one sugars.

This is the structure of a ceramide (syphingosine and a fatty acid linked through amide linkage).
It's not clear to me that do cerebrosides have a single monosaccharide on only one -OH group of the syphingosine, two monosaccharides on each of the two -OH groups, or one oligosaccharide on only one -OH group.
Likewise I am not sure if globosides have a single oligosaccharide on only one - OH group of syphingosine, or two monosaccharides on each of the two -OH groups, or two oligosaccharides on each of the two -OH group.
If you have any knowledge about this, please share. Thanks.

This is Encyclopedia about cerebroside

https://www.guidechem.com/dictionary_keys_cerebroside-p1.html
and this is about globoside

https://www.guidechem.com/dictionary_keys_globoside-p1.html
https://en.wikipedia.org/wiki/Globoside
I hope this can help you.

We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed.


text:
Is there a difference between polarity and hydrophobicity?
From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms?
For example what is the difference in these sentences:

Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.
Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.

Hydrophobicity means aversion to water which results because of increase in entropy of the system due to the water-"solute" interaction.
As already pointed out in by inf3rno, polarity of a molecule is because of its net dipole moment. It is true that polar molecules can dissolve in water (because they can interact with water via van der Waals' forces especially Keesom and Debye forces).
CO2 is apolar but dissolves in water (it actually reacts with water). Most apolar substances cannot interact with water via van der Waals forces.
To sum up, usually polar substances are not-hydrophobic (i.e they are hydrophilic), however some polar molecules such as nitriles, ketones and esters can be hydro-neutral (midway between hydrophobic and hydrophilic. See here). Even large polar molecules are insoluble in water such as 1,2 dichlorobenzene and nitrobenzenes (For something to be soluble the solute-solvent interactions should be stronger than solute-solute interactions. "Water insoluble" may not be equivalent to "hydrophobic").
Conversely, apolar substances are hydrophobic (unless they are reactive solutes such as Cl2 and CO2).

I fully agree. :-)

Hydrophilic means attracted to water, while polar means the molecule has electric pole(s).

A hydrophilic molecule or portion of a molecule is one that has a
  tendency to interact with or be dissolved by water and other polar
  substances.

wikipedia - hydrophile

A polar molecule has a net dipole as a result of the opposing charges
  (i.e. having partial positive and partial negative charges) from polar
  bonds arranged asymmetrically.
Bonds can fall between one of two extremes — being completely nonpolar
  or completely polar. A completely nonpolar bond occurs when the
  electronegativities are identical and therefore possess a difference
  of zero. A completely polar bond is more correctly called an ionic
  bond and occurs when the difference between electronegativities is
  large enough that one atom actually takes an electron from the other.
  The terms "polar" and "nonpolar" are usually applied to covalent
  bonds, that is, bonds where the polarity is not complete. To determine
  the polarity of a covalent bond using numerical means, the difference
  between the electronegativity of the atoms is taken. On the Pauling
  scale, if the result is less than 0.4, the bond is generally nonpolar
  covalent. If the result is between 0.4 and 1.7, the bond is generally
  polar covalent. If the result is greater than 1.7 the bond is
  generally considered ionic.

wikipedia - chemical polarity

Water is polar. because oxygen (3.5) is more electronegative than hydrogen (2.2) and the difference (1.3) is between 0.4÷1.7. So the oxygen has a slight negative charge, while the hydrogens have slight positive charges in water.
Polar molecules are hydrophile. e.g NH3, EtOH, etc... Apolar (or nonpolar) molecules are usually hydrophobe, but there can be exceptions e.g. Cl2 is apolar, but more water soluble than CO or CO2, because of a chemical reaction (Cl2 + H2O → HOCl + HCl). Alcohols contain the polar -OH group. Short chain alcohols are water soluble and so hydrophile, while long chain alcohols are less water soluble, they are hydrophob, because most of the molecule contains apolar bonds. Molecules with ionic bonds, like NaCl are hydrophilic, but not necessary water soluble (e.g. AgCl is poorly soluble in water). So I think hydrophilicity and polarity are not synonyms. However these are just the exceptions, most of the hydrophilic compounds are polar and most of the hydrophobic compounds are apolar.
Amino acid residues (and ofc. side chains) are no exceptions, so in the case of them these terms are synonyms (at least by the 20 common amino acid certainly).
The HP (hydrophobic-polar) protein folding model comes from the article of Dill. He talks mostly about solvophobic and solvophilic residues. In the context of water use the terms hydrophobic, polar and charged amino acid residues. This kind of amino acid classification might be older, but (I assume) it was not so important before the HP model.

solvent to a medium consisting of pure solvophobic residues. For the
  treatment of water-soluble proteins, -(q - 2)g thus describes the
  transfer of hydrophobic residues from water to a hydrophobic
  environment; for the treatment of membrane proteins,
  -(q - 2)g characterizes the transfer of polar or charged res idues from an apolar medium to a polar environment.

1985 - Theory for the folding and stability of globular proteins

According to Dill's article residues can be

charged (1 times)
polar (2 times)
hydrophilic (0 times)
solvophilic (8 times)
apolar (0 times)
non-polar (0 times)
water-insoluble (1 times)
hydrophobic (3 times)
solvophobic (23 times)

I checked the google either:

google "* amino acid residue" search

ionic 7
charged 104 000
polar 42 000
hydrophilic 917 000
apolar 101 000
nonpolar 326 000
non-polar 44 000
hydrophobic 111 000

google "* residue" protein search

ionic 2 110
charged 120 000
polar 53 000
hydrophilic 33 000
apolar 4 690
nonpolar 15 600
non-polar 284 000
hydrophobic 148 000

So all of the hydrophilic, hydrophobic, nonpolar, polar, charged words are used frequently. I checked some books and articles, some of them use the "hydrophobic-polar-charged +/-" classification (just like Dill) which seems to be elder than the "nonpolar - polar (neutral, acidic, alkaline)" classification in other articles.

wikipedia - amino acid
Basics of Protein Structure - The 20 Amino Acids and Their Role in Protein Structures
condmat - Amino acids
tutorvista - Amino Acids

Now the question still stands.

For example what is the difference in these sentences:

Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.
Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.

I don't think there is any difference between the meaning of these two sentences.
I think the more interesting question is which amino acids are in which groups. I checked some hydrophobicity scales.

Figure 1 - hydrophobicity scale summary

Amino Acid Hydrophobicity for the Kyte - Doolittle (kd), Wimley - White (ww), Hessa  - Heijne (hh)
Hydrophobicity Index for Common Amino Acids for the two indexes
tutorvista - Amino Acids for the pI values (pI can be used to filter the charged ones)

It seems to be far from obvious. As you already mentioned it is a continuous spectrum and hard to create groups. It was interesting that Trp (which is strongly apolar) had negative numbers on two scales (maybe the data was not reliable). What you can tell, which amino acids are certainly polar (hydrophilic) and which are certainly apolar (hydrophobic). Based on this information you can tell which residues will be in the apolar core (hydrophobic residues) and which will be on the polar exterior (hydrophobic residues) and which will create the backbone hydrogen bonds (polar residues) and probably salt bridges (polar, charged residues). Ofc. all of these can more or less depend on the pH...

There is ambiguity in the way we talk about hydrophobicity. For example; polarity is a spectrum between non-polar and polar. However hydrophocitiy is a spectrum between hydrophlic and hydrophobic. I also suppose I want to know about domain hydrophobicity and polarity rather than the entire protein. Will edit to clarify.

@GoodGravy I think the two sentences mean the same. I'll try to find evidence, but I think it will be hard.

@inf3rno I had an inkling they might be (for all intents and purposes!). I'll dig around more too and see if there is something we are missing.


text:
Why isn't a virus "alive"?
The recent news about a new supermassive virus being discovered got me thinking about how we define viruses as non-living organisms whilst they are bigger than bacteria, and much more complex than we first gave them credit for.
What biological differences between viruses and cellular organisms have made viruses be deemed non-living?

You might be interested by this [http://biology.stackexchange.com/questions/1842/how-did-viruses-come-to-be] post as well. It concerns the origin of viruses.

If this is a topic that really interests you, I'd suggest searching for papers/reviews/opinions written by Didier Raoult.  Raoult is one of the original discoverers of the massive Mimivirus and his work will lead you to some truly fascinating discussions that I couldn't hope to reproduce here.
The main argument for why viruses aren't living is basically what has been said already.  Viruses are obligate parasites, and while plenty of parasites are indeed living what sets viruses apart is that they always rely on the host for the machinery with which to replicate.  A parasitic worm may need the host to survive, using the host as a source for energy, but the worm produces and synthesizes its own proteins using its own ribosomes and associated complexes.
That's basically what it boils down to.  No ribosomes?  Not living.   One advantage of this definition, for example, is that it is a positive selection (everyone "alive" has got ribosomes) which eliminates things like mitochondria that are sort of near the boundary of other definitions.  There are examples on either side of something that breaks every other rule but not this one.  Another common rule is metabolism and while that suffices for most cases some living parasites have lost metabolic activity, relying on their host for energy.
However (and this is the really interesting part) even the ribosome definition is a bit shaky, especially as viruses have been found encoding things like their own tRNAs.  Here are a few points to think about:

We have ribosome encoding organisms (REOs), so why can't we define viruses as capsid encoding organisms (CEOs)?
Comparing viruses to a living organism such as a human is absurd, given the massive differences in complexity.  A virus, really, is just a vehicle or genetic material, and would be more rightly compared to a sperm cell.  Is a sperm cell alive, or is it a package for genetic material that is capable of life once it has infected/fertilized another cell?
The really large DNA viruses often create cytoplasmic features called virus factories.  These look an awful lot like a nucleus.  What is a nucleus anyway?  Maybe it's just a very successful DNA virus that never left.
Viruses can get viruses.

I'll wind down here, but suffice to say that while our current definition may have sufficed for a while, and still does, it is no longer quite solid.  In particular, there is a theory alluded to above that eukaryotic life itself actually formed because of viruses.  I can expand on this if you like, but here are some great sources:
Boyer, M., Yutin, N., Pagnier, I., et al.  2009.  Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.  PNAS.  106(51):21848-21853 (http://dx.doi.org/10.1073/pnas.0911354106)
Claverie, JM.  Viruses take center stage in cellular evolution.  2006.  Genome Biology.  7:110. (http://dx.doi.org/10.1186/gb-2006-7-6-110)
Ogata, H., Ray, J., Toyoda, K., et al.  2011.  Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.  The ISME Journal.  5:1143-1151 (http://dx.doi.org/10.1038/ismej.2010.210)
Raoult, D. and Forterre, P.  2008.  Redefining viruses: lessons from Mimivirus.  Nature Reviews Microbiology. 6:315-319. (http://dx.doi.org/10.1038/nrmicro1858)
Scola, B., Desnues, C., Pagnier, I., et al.  The virophage as a unique parasite of the giant mimivirus.  2008.  Nature.  455:100-104 (http://dx.doi.org/10.1038/nature07218)

One correction: by the suggested definition, mitochondria are alive since they have ribosomes. (See, e.g., Properties of human mitochondrial ribosomes).

The rRNA in mitochondria is encoded there, but the ribosomal proteins are all nuclear.

I came to reread this and was fascinated all over again! Great answer.

It is only a question of definition. You can set the boundaries between living things and not living things anywhere.
Some philosophers have argued that using a clear boundary between living and non-living things is not such a good solution. In nature, there would rather be a continuum from a stone to a bacteria.
It is true that in thinking of viruses such as Lausannevirus or Marseillevirus we might be willing to integrate them in the category of living things. These viruses are giant, and even can be parasitized by other viruses.
Viruses are made of proteins and contain nucleic acids (RNA or DNA). If you consider that they are alive, what would you say about viroids? A viroid is just a nucleic acid that is able to infect a host and cause the replication of itself. What about a prion? A prion is a protein that, roughly speaking, has the same consequences as that of a viroid.
I think (one should check the literature, I might be mistaken) that there is a species of parasitoid wasp that produces out of its own genomes, viruses that reduce the host immune system in order to make the caterpillar a suitable habitat for the egg. Is this virus alive? Isn't it just a toxin of the wasp?
I guess one reason for considering viruses as non-living is that we do not know how to branch them in the tree of life! Some might argue by the way that viruses would not at all form a monophyletic group.
There are several people tackling the question of "what is alive". Unfortunately, the best book I know on the subject comes from the French literature; it is Comment définir la vie? by Bersini and Reisse. In this field, the most popular authors are Varella and Maturana. Again, if I'm not mistaken, the definitions of life are quite different among philosophers, people having an interest in the origin of life, and people seeking a definition suitable for extra-terrestrial life.

There is a nice discussions along these lines also at the very beginning of the very nice essay by Jacques Monod "Le hasard et la nécessité", where he speaks about distinguishing "natural" (living) objects from human artefacts.

The indirect question is basically "what is 'life'?". In other words it is a question of the definition of 'life'. Now, sometimes there is a natural category that fits well our intuition and sometimes there is not. I would argue there is not for 'life' but this, I agree is a question open to debate (mainly in philosophy). However, it changes nothing to the fact that the question is about the definition of life. The term 'life' did not exist before humans and is here to be discovered. It is obviously a human choice to offer a sense to a term.

I agree with the answers already given, these are the reasons that viruses are not considered alive. I want to point out though that this isn't an area you find 100% agreement on; there is a decent subset of biologists who do consider viruses alive. I would say - completely on the basis of personal observation - that virologists themselves are the group most likely to claim that viruses are alive.
This paper and this article from the Scientific American have some coverage of the debate if you want to read more.

Do you know of any specific literature pushing towards the definition of a virus as a living being? I would be curious to read that.

@nico: I've updated my answer with a couple of links.

There are quite some different definitions of being "alive", but a common one includes the need to have responsiveness, growth, metabolism, energy transformation, and reproduction (found from the Encyclopedia Britannica). Viruses depend on host cells to do all this, so seen alone as a virus outside a host cell, they are not alive.
There's another short, but to the point blog entry about this.

A neat answer, but I'm not satisfied. There are lots of parasites (and symbiotes) that rely on the host for biological processes, so I'm not sure if this covers such a niche point of taxonomy. I also disagree with that blog post about "passive" chemical reactions. In that case we are all none living as all our cells just passively carry out reactions with one another.

But the parasites, symbionts and multicellular organisms do reproduce and act (not only re-act). As I said, there are different definitions of life. But most of them agree, that to be called alive an organism has to at least fit one of the criteria (some definitions also include more criteria to choose from, for example when I was at school, movement was in the books.). Viruses fit none, but parasites do, as far as I am aware. And as far as science is aware. "Life" is a critical point, it is hard to define both scientifically and philosophically.

@BrandonInvergo, that's not really true.  Many viruses encode proteins that regulate viral replication.  In fact that is a major part of the replication cycle for many viruses, determining the early/late or lytic/lysogenic activity during infection.  Many other viral proteins are enzymes that specifically cleave or modify both viral and host proteins.  Viruses often play a very active role in their own replication.

Despite great answers from Amory and Remi.b, I want to emphasize this: there is continual debate about the definition of life because "life" is not something that exists in the real world.
People seek a definition of life that satisfies an intuitive notion of what alive should mean.  They feel that, say, intracellular parasites should be considered alive, but (say) only if they have an enclosing membrane, like Rickettsia, and not if they are just a virus, or just an RNA molecule like a viroid.
While people have a built-in intuition that, for example, reliably categorizes a tiger as alive and a rock as not alive, that intuition can't be precisely bounded by a definition such that everyone is satisfied by the boundary.  There are arrangements of matter in the physical world that fall outside the clear region of the intuitive concept of life, and this leads to continual, unresolvable, argument on what a precise definition of life should be, and what it should include.

@AlwaysConfused, my point is that the definitional controversy about "life" is only a controversy about how to define a word, and not a controversy about the characteristics of the actual arrangements of physical entities and how they interact.  There is no controversy that both viruses and Rickettsia are "replicators" (that is, things that replicate themselves in suitable environments), nor that viruses do not have a lipid membrane but Rickettsia do.  The "life" controversy is just one of definition: "Include viruses."  "No, don't."  "Yes, do!"  "No, don't!" ...

@AlwaysConfused You might want to further your understanding of the question in play on Philosophy.SE as you seem to have issue in philosophy of logic and philosophy of knowledge.

In addition to the good answers given here, I would like to propose a more intuitive argument against viruses being alive.
Viruses are, at one point of their "life", simply a piece of DNA (or RNA). Would you consider a piece of DNA to be alive? If so, then are transposons alive? Are chromosomes alive? How about synthesizing a piece of DNA - is that creating life? The answer will probably be "no" for most people.

One could argue that that is true for any cell...

@nico sorry I didn't understand - how is a cell a piece of DNA/RNA?

at some point a cell was just a piece of DNA, before its mother cell split in two... Really the important point is that the virus is not able to replicate itself without the "help" of some other cell

@nico: I disagree: a cell is never simply a piece of DNA, it always has membranes, organelles, proteins, etc. The division of mother->daughter is not the creation of a novel cell de novo from DNA but rather a process of growth followed by division. Even DNA replication is semiconservative - both copies are one part original, one part newly synthesized so neither can really claim to be more original than the other.

@JackAidley: dsRNA viruses also have semiconservative replication so that doesn't really apply... I am just saying that your answer does not give an explication because you need to define what "life" is. You cannot just say "A virus is not alive because DNA is not alive", as that just begs the question "why is DNA not alive?".

@nico that is why I wrote "the answer will be no for most people", i.e. under most definitions of life. I do not know of any robust definition of life that considers a piece of DNA to be alive. Also I completely agree with Jack - a cell is never a piece of DNA, under any possible definition.

@nico: You said that a cell is a some point just DNA. This is false; it is never just DNA.

@JackAidley: and why would that be? It really depends on definitions, which are not given here. When the DNA replicates is the newly formed DNA already part of the new cell? Or it is part of the mother cell? Is the new cell "coming to life" only after division? You cannot just skip through those (and many other) points when defining whether a virus is alive. Otherwise you are just saying that a virus is not alive because it is not alive. Not very useful definition...

@nico a cell has a relatively clear definition and it must have its own membrane. A cell with double the DNA is not 2 cells, it is one cell with double the DNA. There is a point at which the cell divides and the membranes are separated - that is when it becomes a separate entity.

Perfect, then the point of the virus being a DNA at some point is just non existent. A virus without capside is not a virus. A virus starts existing as a separate entity the moment it assembles its DNA/RNA into a capside, before it is not a virus. And that does not give us any clue on whether it is alive or not.

@nico actually you are mistaken. It is not true that the virus exists only when it is assembled into a capsid. The correct name is virus at all stages (you can check the definition). When it is in a capsid it is called a virion.

@Bitwise: I know (I may have passed my virology class a while ago but I still remember this :P), but a virion is not a virus. It is a virion. And whatever the name you call it if you do not exactly define what life is you cannot state something is alive or not. Look at Amory's answer for a great deal of good refs