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Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur?
I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.
The only specific suggestions that I could find was because of the DNA replication process and the negative polarity of hydoxyl group on the phosphates. Moreover, after flipping one strand, the DNA nucleotides form enantiomers. Are these possible reasons, or are there others?

this question should cover it : https://biology.stackexchange.com/questions/27839/why-is-dna-antiparallel-can-it-be-parallel

I have not previously reviewed  that answer and many others but the questions stated above still remains. I would appreciate if someone could objectively answer them

Related: https://biology.stackexchange.com/questions/58156/are-there-functional-examples-of-parallel-dna-double-helices

@canadianer — I have changed the title again. Your revision ("Why isn't Watson-Crick base pairing used in parallel DNA helices?") had the falsse implication (I am sure unintended) that parallel DNA helices existed in the sense that they were reasonably widespread, or that those that had been engineered had complementary base-pairing, but of the non-WC type. My revision retains the emphasis on the lack of WC base pairing in parallel helices, but removes these implications, for the most part. Trust this is ok.

@David Yes, sounds good to me.

“The only specific suggestions that I could find was because of the DNA replication process and…”

No. The explanation can have nothing to do with DNA replication. If the structure does not exist, you can’t replicate it, if it does, Nature will evolve a mechanism. (The related SE question, mentioned by @Gilleain, asked whether it could still replicate if it were parallel, i.e. using the enzymes that have evolved for parallel DNA.)

I know that parallel DNA helices exist…

Let us clarify this first. Perhaps the most extensive parallel duplex DNA, the structure of which has been determined, is that described by Parvathy et al.. The two parallel strands of this are shown below:

The following points should be noted:

This parallel DNA (and the shorter examples that preceded it) is not a pure stretch of complementary base pairs.
It is stabilized by what the authors refer to as “CC+ clamps” at either end. One is left to conclude that without these the duplex would not form.
All the complementary base-pairs are of the type AT (actually reverse Watson–Crick base pairs). Presumably GC base-pairs would have destablized the structure.

(You can inspect this structure in three-dimensions here. Choose ‘Licorice’ style and colour ‘by chain’ and notice the non-planarity of the three base ‘pairs’ at each end.)
So although the question refers specifically to parallel DNA helices with Watson–Crick base pairs, it should be recognized that extended parallel DNA helices composed of any kind of complementary AT and GC base pairs are not found, and the question applies equally well to them.

“In the diagram if we were to flip one of the strands while keeping the other same, hydrogen bonding is still possible”

The diagram in the question is two-dimensional; DNA is three-dimensional. It is only by considering the three-dimensional structure of DNA can you approach this question.
So how would one do that? One must consider the free energy of alternative structures in the relevant millieu to determine which will occur (i.e. be more thermodynamically stable).

This will tell you whether single DNA strands with parallel sequences will form a double-stranded (ds) structure or not.
This will tell you whether ds-parallel DNA is more or less energetically stable than a ds-antiparallel DNA. Hence, even if both can form (which I doubt, without some special circumstances*) the lower thermodynamic free energy of the anti-parallel dsDNA would give organisms adopting it an evolutionary advantage.

And the answer to the question?
It seems unlikely that one single factor is responsible or it would have been pointed out in elementary text books such as Berg et al..
To answer would require a complete theoretical analysis of the structure or structures. First one would have to build a model of a proposed parallel structure that could accommodate Watson–Crick base pairs. This in itself is a problem because there are likely to be many alternative structures. Perhaps there are computer programs that can find the structure with the lowest energy. This would be calculated in the classic manner, calculating the positive contribution of hydrogen bonding (which depends on distance and angle), ionic interaction etc.*  against the negative contribution of charge and steric repulsions.
*Etc? The two-dimensional diagram fails to consider the contribution of base stacking (how could it?), which contributes to a considerable extent to the stability of nucleic acid helices, as the original cover design of Stryer’s Biochemistry is a constant reminder:

Could you please explain what you mean by 'CC+ clamps on either end”?
And what i meant was that the hydroxyl group,
Now represented by a negative Oxygen molecule in the diagram attached to the phosphorus on either end are negatively charged, which might cause them to repel and therefore to some degree constitute the formation of Antiparallel DNA

do you think the parallel dna model would continue to form hydrogen bonds or would this be disrupted,  moreover how would one calculate the free energy associated with the two dna models?

@AnamikaGhosh — 1. I have expanded my footnote to explain the CC+ clamp, which is in the paper I cited. 2. I have removed my reference to your remark about the phosphates as at is peripheral to the main argument and not worth getting bogged down in. 3. I will explain about calculating energies in a further footnote sometime this weekend. If you are impatient think about this section of Berg et al.

Thank you,  it makes a lot more sense to me now.

Glad it was of use. I learned something too. I have now added a link to a 3D view of the structure at the Protein Data Bank.


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The Water hyacinth and its ability to absorb pollutants from the water
What genes makes the water Hyacinth able to absorb pollutants from the water it lives in? (2) can this gene be successfully harvested? And how?

Genes don't necessarily work in isolation (most don't). An ability to absorb pollutants would likely be a combination of many genes.
Also, what constitutes a "water pollutant" is very broad - you could be talking about pesticides, heavy metals, fertiliser, organic waste... If water Hyacinth absorbs all of these, it could just be the result of absorbing more water than other plants (with pollutants accumulating in the plants). Who knows - you should state your source of information.
In terms of how to figure out what gene(s) are responsible, you could consider a radioactive tracer to tag the specific compound (or even element) that you consider Hyacinth to absorb better than other plants. This might give you some idea of how it's doing what it's doing. For example, if you think it's absorbing a compound, you can tag that compound with a radioactive tracer, see where it's being accumulated (even it's path), and from there figure out what's happening.
The fastest path to figuring out which gene(s) are responsible from there would be to build up a list of all the genes you think might be involved in this path and create an array of cloned plants with those genes removed. If you remove the correct gene(s) from the equation, the plant will have less or no proclivity for absorbing the type of pollutants in question.

Ronald Greeff thanks for your reply. I would like to start by informing you that I am not a biologist, so I may need a little more help.
(1) How would I build up a list of genes likely to be involved?
(2) And create an array of cloned plants with those genes removed?

@NnekaOnwuachi-Iheagwara (1) I would check the literature. Usually, you would knock a gene out then try to figure out its function by looking at the effect of the gene's loss. You could also search the BLAST database. (2) You should take a look at "gene targeting", specifically using Agrobacterium. I believe today most people would use CRISPR/Cas

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DNA synthesis in nucleus
I read somewhere that according to a research, I don't remember what the date was, that our cells stop synthesising DNA around noon and restart it around the sunset. The research told that it was actually a survival benefit for cells when ozone was not formed so that the DNA does not get damaged. Would somebody like to guess how our cells know when to do so and if it is a protection against present ozone depletion due to CFCs?

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How to choose right volume of DNA and SYBR Green
I'm testing fluorescence level of a sample having dsDNA, SYBR Green and milli q water but I'm facing difficulty in choosing right volume of dsDNA and cons level of SYBR Green.
Details of sample: dsDNA:1000 nano mole, SYBR Green:1X (1000 times diluted from original stock)
Sample_1: dsDNA (3ul) + SYBR Green (5ul) + milli q water (27ul)
Sample_2: dsDNA (3ul) + SYBR Green (5ul)
Result: In first sample I haven't got any signal but in second case I got( But I want 5 times higher then what I got).
Please tell me how it work and how these things depends on each other. I'm not a biologist if possible suggest me resource as well.

I had to look it up online, but I eventually found here an important information: the detection limits of SYBR Green.

dsDNA at 300nm transillumination: 60 pg
  Oligonucleotides at 300nm transillumination 1-2 ng

You should first check the size of your DNA of interest, and from its size figure out its approximate molecular weight (for example using this online calculator). Then, you should check that 1000 nmoles of your DNA corresponds to a mass greater than 60 pg. If not, you should increase the amount of DNA in your assay accordingly until the mass introduced in the assay exceeds the detection limit of SYBR Green.
Now, do you know the concentration of your DNA? In other words, how did you choose to use 3 uL of DNA? How do you know that these 3 uL contain enough material? (1000 nmoles as in your protocol, or better, that this is higher than the detection limit in terms of mass).
Also, did you use the 1000X stock solution of SYBR Green without intermediate dilution? If so, the final concentration of SYBR Green is much larger than the final 1X you want, in both of your samples:

sample 1: 5 uL of 1000X SYBR Green in a total volume of 3 + 5 + 27 = 35 uL means that the final concentration is 1000X * 5 / 35 = ~143X.
sample 2: 5 uL of 1000X SYBR Green in a total volume of 3 + 5 = 8 uL means that the final concentration is 1000X * 5 / 8 = 625X.

What you need is either use 1 uL of 1000X stock solution of SYBR Green + whatever amount of DNA that will be above the detection limit + buffer to adjust the volume to 1000 uL final (which will bring the SYBR Green to 1X final), or make an appropriate intermediate dilution of SYBR Green so that its final concentration is 1X by following the sample preparation as described in your question.
The sample preparation you describe here yields a composition that is way off the one suggested by your protocol, at least for the SYBR Green. Until you try again with proper final concentrations, do not conclude that it didn't work. :-)
Good luck with your project.


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Does the brain always enter alpha/beta waves upon brief awakenings during the night?
If you realize you are awake briefly before falling back asleep, have you necessarily exited REM sleep or another stage? That is, is the experience of waking briefly (tossing and turning, etc.) always tied to conscious beta wave patterns?


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What is the "stimulus" that initially triggers an action potential?
There are many steps detailing the depolarization and repolarization of axon nodes to describe how an action potential is transmitted from a neuron. But, after looking at many different sources, I still see one clear thing missing: what causes the action potential in the first place? Every source simply says something vague like "stimulus" or the ever redundant "depolarizing current." But, how is this stimulus generated, and what exactly does it do to which chemical to start the chain reaction of moving sodium ions to create the depolarization in the first place?

In addition to my answer, I would add that there is absolutely nothing redundant about the phrase "depolarizing current."

"how is this stimulus being generated" -- have you heard of neurotransmitters?

@BryanKrause Yes there is, simply explaining what triggers depolarization as a "depolarizing current" does not explain much.

I disagree somewhat, but please see my answer.

That answer requires wayyyyy more detailed than "depolarizing current."

I didn't say "depolarizing current" was sufficient as an answer, just that I disagree that it is a redundant term. Hyperpolarizing current can also trigger action potentials in some cases, for example, due to activation of intrinsic conductances and deinactivation of sodium channels.

But if a stimulus is sufficient, then by the definition of an action potential, the axon must undergo depolarization anyway.

There are several possible answers, which is partly why the sources you are reading are being vague: they are discussing the chain of events that happen after the initial depolarization, the source of which doesn't matter much for that chain of events.
Receptor potentials
Sensory receptors consist of some machinery that eventually lead to ion channels opening, often cation channels. This machinery can be direct, where a stimulus directly opens an ion channel, or it can me mediated through g-protein coupled receptors. There are many many examples, but one favorite toy example is the TRPV1 receptor, part of the "transient receptor potential" family.
TRPV1 channels open when exposed to high temperatures or chemical agonists like capsaicin (which gives chili peppers their 'heat').
There are mechanically gated channels in the inner ear that are stretched open as sound waves pass; there are G-protein coupled receptors in the retina that are activated in response to light - when they are activated, they close channels which reduces neurotransmitter release and therefore changes the amplitude of the post-synaptic polarization.
Ligand-gated ion channels
Synaptic transmission between neurons is often mediated by ion channels that are gated by neurotransmitters. A presynaptic cell releases a neurotransmitter, for example glutamate, and that neurotransmitter binds glutamate receptors on the post-synaptic cell, for example AMPA receptors. These receptors are non-specific cation channels, and when they open sodium comes in and depolarizes the cell. Other neurotransmitters, including inhibitory ones, work a similar way.
Gap junctions/eletrical synapses
Although they only occur between particular populations of neurons in mammalian nervous systems (for example, some inhibitory networks in the brain and between cardiac myocytes), some cells are coupled through channels that allow ions to pass between cells. Therefore, depolarization in one cell can be transmitted by ions flowing through that gap junction and begin to depolarize the adjacent cell.
Intrinsic conductances
It doesn't really apply in the context of a "stimulus" but in some types of cell there are intrinsic conductances that can bring a cell to threshold and trigger an action potential. One example would be in the pacemaker cells of the sinoatrial node that initiate cardiac contractions.

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Microbroth dilution
I have performed MIC test for fungi candida albicans, Cryptococcus neoformans and Aspergillus fumigatus in a 96 well plate by broth microdilution method by drugs Amphotericin B and fluconazole..followed was picking up colonies just after the result i.e. after MIC test.. the next well with growth to be plated onto SDA plates then after incubation and further growth..now I have been asked to transfer them to SDB (500ml) in flasks..I would like to know why is this done..thankyou.


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Variation of fixation probability over time in Wright-Fisher model
In Wright-Fisher model of population size N and initial mutation frequency of 1/N, how does the fixation probability vary over generations. So, mathematically, what is the function that maps the generation to its fixation probability?

Is your question "What is the probability P(t) that a neutral mutations at frequency 1/2N fixes after t generation given that it will reach fixation?"?

@Remi.b Yes. I know that fixation probability is 1/N eventually. In a sense that, if we let the population evolve for enough generations, fixation probability becomes 1/N. But how does it actually vary over generations? Thank you.

The answer is probably in Kimura and Ohta 1968. From there, the expected time to fixation of an allele at frequency $p$ is $\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0)$

But how can we describe the variation of fixation probability over time using that equation? Thank you.

Are you thinking of a case where a population where a population starts without any genetic diversity and hence there is little fixation at early generations and then the rate of fixation plateaus or are you looking for a variance in the number of fixation events from generation to generation in a equilibrium population?

The first one. I realize that fixation probability is low initially and suddenly explodes to reach 1/N and saturates. I am looking for an equation that describes that behavior. Thanks.

You might want to edit your question to clarify this point. By curiosity, can I ask what simulation platform you're using (or if you wrote your own code)?

You might want to edit your question to clarify this point. By curiosity, can I ask what simulation platform you're using (or if you wrote your own code)? (see Sequence evolution simulation tool).

The function probably look like $r(t) = A + B e^{-C t}$, where $r(t)$ is the rate of fixation at time $t$ (in generation). The reason for this exponential is that the probability that a mutation happens after $t$ generation is given by the exponential distribution.
As the rate of fixation at equilibrium must be at $2N\mu \frac{1}{2N} = \mu$, $A=\mu$, that is $r(t) = \mu + B e^{-C t}$
As at $t=0$, the rate must be 0. As $e^{0} = 1$, you should have $B=-\mu$. Hence,
$$r(t) = \mu - \mu e^{-C t}$$
$C$ here represents the steepness of the curve. I don't know how you could calculate it a priori but it must depends upon your population size $N$. As the expected time to fixation starting at frequency $p_0$ is (from Kimura and Ohta 1968)
$$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0)$$
For $p_0 = \frac{1}{2N}$
$$\bar t\left(\frac{1}{2N}\right)=-4N\left(2N-1\right)\ln\left(1-\frac{1}{2N}\right)$$
or
$$\bar t\left(\frac{1}{2N}\right)=\left(4N-8N^2\right)\ln\left(\frac{2N-1}{2N}\right)$$
if you prefer. Maybe $C = \bar t\left(\frac{1}{2N}\right)$ leading to
$$r(t) = \mu \left(1 - e^{-\left( \left(4N-8N^2\right)\ln\left(\frac{2N-1}{2N}\right) \right) t}\right)$$
Let me know if it matches (I'd pretty amazed)!


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Can bats echolocation discern what insects they are preying on?
Insectivorous bats feed on many different types of insects such as mosquitoes, moths, beetles, and bees.  According to the Bat Conservation Trust, bats can discern insects from other objects but I'm having trouble finding any research saying whether bats can discern between the insects they are chasing?

Why don't they just use their ears? I can tell a mosquito just from hearing it.

Yes, some bat species can distinguish the species of insects by echolocation. One of the better studied species is the greater horseshoe bat (Rhinolophus ferrumequinum).

Echolocating greater horseshoe bats (Rhinolophus ferrumequinum) detect insects by concentrating on the characteristic amplitude- and frequency modulation pattern fluttering insects impose on the returning echoes. This study shows that horseshoe bats can also further analyse insect echoes and thus recognize and categorize the kind of insect they are echolocating.
von der Emde, G. & Schnitzler, HU. J Comp Physiol A (1990) 167: 423. https://doi.org/10.1007/BF00192577

Further reading:

Hans-Ulrich Schnitzler, Elisabeth K. V. Kalko; Echolocation by Insect-Eating Bats: We define four distinct functional groups of bats and find differences in signal structure that correlate with the typical echolocation tasks faced by each group, BioScience, Volume 51, Issue 7, 1 July 2001, Pages 557–569, https://doi.org/10.1641/0006-3568(2001)051[0557:EBIEB]2.0.CO;2

Ulanovsky, N., & Moss, C. F. (2008). What the bat’s voice tells the bat’s brain. Proceedings of the National Academy of Sciences of the United States of America, 105(25), 8491–8498. http://doi.org/10.1073/pnas.0703550105

Roverud, R.C., Nitsche, V. & Neuweiler, G. J Comp Physiol A (1991) 168: 259. Discrimination of wingbeat motion by bats, correlated with echolocation sound pattern https://doi.org/10.1007/BF00218418

Hearing by Bats (edited by Richard R. Fay)


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How does BH2 reduction to BH4 need only one NADPH molecule?
Dihydrofolate reductase (DHFR) reduces dihydrobiopterin (BH2) to tetrahydrobiopterin (BH4). Someone told me that this reaction needs only one NADPH molecule (I am not sure if this is correct), namely, NADPH provides one hydride atom and becomes NADP+.
Could someone explain to me how is this possible? How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

Information, such as standard biochemical reactions is readily available on the web. Please check this before posting and provide a link for those who may not be familiar with the reaction (and /or post an image). This is a courtesy to the site and you will see that it is explicitly expected of posters if you read the help on asking questions.

@xusr, David is right, your comments belongs to an answer. Please rewrite them in an answer, I do not want that someone deletes them.

@xusr, I did not request to delete them, I just said that they would be more organized in an answer. There were valuable info in them, it would be great to rewrite them in an answer please. Additionally, I would be able to vote you up and accept the answer if it really answers me.

This is a very interesting question. It is impossible to ever prove a chemical mechanism, but there can be evidence gathered to support the mechanism. I found this article http://www.pnas.org/content/111/51/18225. So the hydride, being a nucleophile, will attack at the N5 atom (the one between the hydroxyls and nitrogen). This then pushes the electrons in the double bond onto an electrophilic nitrogen. These lone pairs, being a nucleophile can abstract the second hydrogen atom. The second hydrogen atom that shows up on the nitrogen could be from water or from a residue on the enzyme itself.

@86BCP2432T, you are absolutely right, I was searching yesterday and found the same what you explained. However, does the H.OH becomes only OH-?, or does it bind to the NADP+ and becomes NADPOH?

@xusr, may I ask you to repost you comments? they had very interesting information.

Oh sorry, chemist brain went to mechanism first. But what I was trying to get was that NADPH is a source of hydride (the anion of hydrogen), so it will behave as a nucleophile. The other hydrogen on the nitrogen should be an electrophile (or H+). This H+ could either be from water or from the enzyme DHFR. It shouldn't be from another NADPH because a hydride already has fulfilled its 2 electron shell and it would be extremely hard to put in more electrons. And water undergoes self ionization, so some exists as H30+ and OH-. The H-O-H that had it's H+ abstracted becomes OH-.

The short answer is that in reduction of BH2 to BH4 by dihydofolate reductase not only is a hydride ion (a proton plus an electron) transferred from NADPH to BH2, but the product also picks up a proton from the solvent: N5 of BH4 is protonated.
$$\ce{BH2 + 2e- + 2H+ <=> BH4\tag{1}}$$
Enzymically (see EC 1.5.1.34):
$$\ce{NADPH + BH2 + H+ <=> BH4 + NADP+\tag{2}}$$
Thus the reduction of BH2 to BH4 involves 2 electrons and 2 protons. NADPH donates 2 electrons and 1 proton (as a hydride), forming a new carbon-hydrogen bond. The solvent accounts for the other proton. The situation is very similar to the alcohol dehydrogenase reaction (discussed below).
The reduction of biopterin all the way to tetrahydrobiopterin by dihydrofolate reductase is a 4-electron reduction, and requires 2 NAD(P)H.
Background
There a couple of points about NADP-linked enzymic oxido-reduction, and about oxido-reduction in general, that possibly need clarification.

NAD(P)-linked enzymes, almost invariably (and perhaps always), catalyze the direct, stereospecific transfer of a  hydride ion (a proton plus two electrons) as a single entity between the nicotinamide cofactor and acceptor.

This statement probably needs some explaining.  The fact that NADP-linked oxidoreductase reactions are consistent with the transfer of a hydride ion is one of the great contributions of Westheimer to enzymology (see here). In many cases, this results in the formation of a carbon-hydrogen bond.
Secondly, hydride transfer is stereospecific. Amazingly, NADP-linked oxido-reductases distinguish between the two hydrogens at C4 of NAD(P)H.  This is an example of prochirality (the Ogston effect in the Krebs cycle is another).
For simplicity, the two hydrogens at C4 are called the HA and HB.  The work of Westheimer,  Vennesland and co-workers showed that NAD(P)-linked enzymes can be divided into two classes: those that transfer HA from cofactor to substrate (A-sterospecific dehydrogenases) and those that transfer HB (B-stereospecific dehydrogenases).
It is now known that sterespecificity of hydride transfer is one of the most evolutionary conserved traits of NAD(P)-linked oxido-reductases. Enzymes that may be shown to be descended from a common ancestor by amino acid sequence analysis invariably display the same stereospecificity of hydride transfer (Yeast and horse liver alcohol dehydrogenase is an example) 1†.
In addition hydride transfer displays apparent absolute stereochemistry fidelity: the 'wrong' hyride is never transferred.  Transfer of HB by lactate dehydrogenase, which is A-stereospecific, could not be detected experimentally, for example (see here).
A great review of this aspect of dehydrogenase biochemistry has been published by You (1985), available as a a pdf from here. (An earlier review may be found here)
Finally, a brief word on oxido-reduction in general. Oxidation is the loss of electrons, reduction is the gain of electrons.  An ionization is neither an oxidation or a reduction, and neither is hydration/dehydration. This, of course, is 'basic stuff', but seems to sometimes cause confusion.  When dealing with oxido-redution reactions we can add in as many protons as we like, or take out as many protons as we like, and this may be important stoichiometrically, but  ionization does not change the oxidation state of a molecule.
An Illustrative Example - Alcohol dehydrogenase
Alcohol dehydrogenase (EC 1.1.1.1) catalyzes the following reaction, the 2-electron reduction of acetaldehyde to ethanol with NADH as hydride donor:
$$\ce{Ethanol + NAD+ <=> Acetaldehyde + NADH + H+ \tag{3}}$$
This very nice diagram, taken from Cornforth's nobel lecture, Asymmetry and Enzyme Action, illustrates all the points made above.

The hydrogen labelled with the asterisk it HA. Stereospecific transfer of hydride to acetaldehyde results in the formation of a new carbon-hydrogen bond.  If the asterisk represents deuterium or tritium, the result is deuterated or radiolabelled ethanol.

If, instead, HB is deuterated or tritiated, the result is deuterated or tritiated NAD+, with no transfer of label to product.

Formation of the alcohol involves 'picking up a proton' (from the solvent).

Transfer of hydride acetaldehyde is also stereospecific. The hydride is stereospecifically transferred to one of the faces of the planar carbonyl group.  I am ignoring this aspect here (but see Cornforth's lecture) 2†.

To be very pedantic, HA is more correctly called the pro-4R hydrogen, and  HB is the pro-4S hydrogen.

(In Cornforth's original diagram the H+ was left out).
The Specific Question Posed by the OP

How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

As stated above, BH4 (tetrahydrobiopterin) contains one more pair of electrons than does BH2 (dihydobiopterin), but (like the alcohol dehydrogenase reaction) there are two protons involved. The fact that reduction involves hydride transfer accounts for one. The other is picked up from the solvent.
This is illustrated in the diagram below, where the key point is that the carbon atom at C6 now has a new carbon-hydrogen bond.  This bond accounts for 2 electrons plus 1 proton. But the nitrogen atom at C5 has also picked up a proton.
(We must be very careful when dealing with reduction of the pteridine ring because of the quininoid form (see here).  This is why I first picked  alcohol dehydrogenase as an illustrative example, and I am ignoring such complications here).

The OP chooses an interesting substrate for DHFR, an unconjugated  pteridine. The 'more usual' substrate, of course, is the conjugated pteridine, dihydrofolate (FH2). Although DHFR does catalyze the transformation of BH2 to BH4 , the enzyme usually associated with this transformation is dihydropteridine reductase (EC 1.5.1.34).
One final point.  Both chromosomal and plasmid dihydrofolate reductase, although unrelated from an evolutionary point of view, are both A-stereospecific with respect to hydride transfer from NAD(P)H.
(The above diagram was modified from one found on the internet. The original may be found here)
Four-Electron Oxidoreductases
Most NAD(P)-linked oxidoreductases catalyze a two-electron reduction that involves just one molecule of nicotinamide cofactor.
A few, such as dihydrofolate reductase can catalyze two sequential 2-electron reductions, where the  first 2-electron product is released into solution before it is reduced to the final product by a second encounter with enzyme. (In the case of DHFR,  the reduction of folate to dihydrofolate is a two-electron reduction, and the reduction of dihydrofolate to tetrahydrofolate is another 2-electron reduction).
Some oxido-reductases, however, catalyze a four-electron oxido-reduction where the intermediate product is not necessarily released into solution. Such enzymes are called four-electron oxido-reductases, and are very rare.  They have been reviewed by Feingold & Franzen, (1982).
One example is histidinol dehydrogenase (EC 1.1.1.23), that catalyzes the reduction of an alcohol to an acid (the aldehyde being the intermediate 2-electron reduction product).
$$\ce{L-histidinol + 2 NAD+ + H2O = L-histidine + 2 NADH + 3 H+ \tag{4}}$$
Another example is HMG-CoA reductase (EC 1.1.1.34), a key enzyme of cholesterol metabolism (that is inhibited by statins).  In this case, the enzme reduces a substrate formally at the oxidation level of a carboxylic acid (but 'activated' by thiol ester linkage to coenzyme A) all the way to the alcohol.
$$\ce{Mevalonate + CoA + 2 NADP+ = 3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ \tag{5}}$$
A third example is UDP-D-glucose 6-dehydrogenase (EC 1.1.1.22), which catalyzes the reduction of the C6 alcohol group of UDP-glucose all the way to the acid.
$$\ce{UDP-D-glucose + 2 NAD+ + H2O = UDP-D-glucuronate + 2 NADH + 2 H+}$$
So, a four electron NAD(P)-linked oxido-reduction is possible.  But such reactions are relatively rare. The key to the biochemistry of the NAD(P)-linked enzymes, IMO, is to realize that a hydride is transferred as a single entity (and that hydride transfer is stereospecific).
Footnotes

Alcohol dehydrogenase from Drosophila is unrelated to the yeast and horse liver enzymes from a evolutionary perspective, and is B-stereospecific.
The same Cornforth that reputedly said that if the β-lactam structure of penicillin was correct he would give up chemistry and grow mushrooms (see here).


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Is carbon dioxide dissolved in plasma same as carbonic acid?
Carbon dioxide is transported through blood via 3 methods :
1. Dissolved in plasma 2. As bicarbonate  ion 3.through RBCs. The carbondioxide when transported as bicarbonate ion i.e HCO3- and H+.  What i dont understand is that dissolved carbon dioxide in plasma should also yield H2CO3,  so is writing co2(aq)  the same thing as writing H2CO3? Further shouldnt this carbonic acid also dissociate and form bicarbonate ion and proton? Doesn't this make both the processes equivalent?
What i found out is that H2CO3 has a low   ionisation constant of the order 10-4, is this tbe reason why they are separate events? Implying that carbonic anhydrase  catalyses the formation of bicarbonate ion while some part of H2CO3 is not ionised and that is what refers to co2(aq)

Please put more effort into presenting your questions in a readable manner. You can do this by: 1. Using paragraphs to separate different ideas or different points. 2. By making sure that you capitalize the letters representing chemical elements (CO not co), 3. More difficult subscripting or superscripting chemical formulae. There are two ways of doing the latter. I use HTML markup e.g. numeral and +. This will work in questions and answers (not in comments) 4. Capitalize "I" in English.

Im sorry for being sloppy,  i typed it on my phone and didn't pay much attention to details, what do you think about the answer?

Well if you can find a computer and take the trouble to clean the question up as I suggested — and if nobody has answered in the meantime — tomorrow I might look out the lecture notes I used to use on carbon dioxide transport and bicarbonate buffers and provide a comprehensive answer. In SE the idea is not to provide a limited answer for one person, but to provide answers to biological questions that will be of use to many.


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Why is there a low rate of kidney disease related deaths in the Baltic countries?
A noticeable feature of the map of kidney disease related deaths is that the Baltic countries, Norway, Finland, Estonia, Latvia, Lithuania, etc have lower rates:

Why is this?

The poor separation between the color scale makes it really hard to tell what the rates are, except for the high countries. I'm not convinced that the Baltic countries have lower rates. Are there actual numeric data anywhere?

would be really useful to have a link to the source.

To me, the best correlate of cancer rate here looks like population. I wonder if this is a similar effect to Gelman's US kidney cancer example.

Affluent countries have higher rates of diabetes which is the major cause of renal disease.

Baltic countries include only Estonia, Latvia, and Lithuania. And if you meant baltic region, then what countries are included is a little bit up to everyone's defintion but you would definitely include Russia (which rate of Kidney disease is quite high). So what countries did you mean exactly?

Looking at this map I can't see any obvious difference with the baltic states (or states of the baltic region of whatever you meant). Mongolia, central Africa or central America does not seem to have a lower rate of kidney diseases.


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What is the weight of a single human sperm (spermatozoon) compared to a single human egg
While the difference in dimension is well covered, I have been unable to find the mass measurements of each.

Hey tohster! What attempts to answer this question have you already taken? We ask that all question posters here attempt to search for an answer to their own question and explicitly indicate what research they've already done, what they learned, and what is still confusing or unknown to them. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way :). Please take a moment to edit your post with this additional detail, and it will likely be received more positively by our community. Thanks!

OK. That is new. I'm a member of quite a few stackexchange sites and I've not seen a requirement to document what efforts the user has gone through to answer the question. I used reasonable efforts to search online for an answer but was unable to find one, which is why I made the effort to post the question here so that others do not have to go through the same process.


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Is biotin a hapten? If so, how does it work as a hapten in the human body?
https://en.wikipedia.org/wiki/Hapten
Hapten's aren't synonymous with allergens. It is defined as a foreign molecule that can bind to an antibody but does not evoke an immune response unless combined with a carrier protein.


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Find the length of DNA sequence?
Given $N=5\times10^3$ and mutation rate is $\mu=10^{-5}$ per site, find the length of a DNA sequence so that the probability of mutation occuring M, is greater or equal than 0.95.
Is there a method or a formula for this type of calculation?

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

Hint: Try to compute the probability that a mutation occurs at a single site (in a single generation). Then compute this same probability for 100 sites. And from there you should see what is going on.

is $n$ the population size? We typically use $N$ for the population size. Also, I would assume that $\mu$ is the per site (per base pair) mutation rate. Finally by probability of mutation, I would assume it is meant probability of 1 or more mutations, just like the formula is suggesting if $M$ means the number of mutations.

I just realized there are two ways to understand the question. By mutation do you mean mutant allele or do you mean mutational event (see here)?

I mean by an event , yes

So, you don't need any a priori about the sequence. The probability of a mutation to happen at a given site on a given haploid is $10^{-5}$. What is this probability for the whole population (don't forget individuals are probably assumed to be diploid)? You can then compute this probability for 100 sites and you'll understand the pattern. Does it make sense?

Ok, so for each site: $P(M>0) = 10^{-5} $ meaning that for $N=5000$,  we get $P(M>0) = 5000*10^{-5} = 0.05$ for one site?

I am really not sure how this method would allow us to find the length to ensure $P(M>0)\ge 0.95$. I know that $\theta = 2 N \mu $, which I think may be used so that $\theta=0.1$ per base. But i don't get how to answer this in terms of the actual question

Ok, good! 0.1 is correct. (0.05 would be correct if assuming haploidy). Now for 100 sites? And then just ask for how many sites is the probability 0.95

The mutation rate per haplotype per site is $\mu = 10^{-5}$. Assuming diploidy and a population size of $N=5000$, the population wide mutation rate per site is $10^{-5} * 5000 * 2 = 0.1$.
$0.1$ is hence the probability that a mutation occurs a at a given site (in the whole population). For 10 sites the probability that a mutation occurs at at least one site is $1 - (1-0.1)^{10} = 0.65$.
The probability we are aiming for is 0.95. So let's write the equation
$$1 - (1-0.1)^{x} = 0.95$$
, where $x$ is the number of sites we are looking for. You just have to solve for $x$ now and round up to the larger integer.

Ok, so this is in terms of the number of sites, so to calculate the length of the sequence in terms of base pairs, would we multiply by $10^3$ say? I am trying to read up on base pairs and this is what i gathered, but i may be mistaken. (Otherwise this answer is perfectly fine, i just see in many literature the lengths are usually given in bp?)

A site is a bp. The number of $x$ is the length of the sequence (in sites of in base pairs) that you were looking for. If you want to express the answer in kilo bp, then you can divide the result by $10^3$ but I would not recommend it. $x$, once rounded, is your answer

Ok! I am comparing this to mitochondrial dna which is generally 16,500 bp in length, so solving the above equation of 29 seems very unusual.. (ref: https://www.ncbi.nlm.nih.gov/m/pubmed/26798311/)

The answer depends upon the question. You typically don't attempt to answer everyday the question "what is the sequence length which probability to be hit by a mutation in a given generation is 0.95?". I don't think you should expect from yourself to have much intuition in the answer and therefore there is nothing unusual to be found. I don't understand why the length of the human mtDNA matters here.

Only because for instance the mutation rate (per site) of mtDNA is also generally $\mu  = 10^{-5}$ so i just wanted to compare

oh ok. Sure... so yes, a lot of mutations happen on mtDNA every generations (even more so if you consider 7 billions people).


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Are agave plants perennial?
If I were to harvest an agave plant for its nectar, would it kill the plant? I have watched videos of the process and it seems quite invasive.

When harvesting agave nectar, generally the whole plant is harvested at once to get to the core, where most of the sap is. There isn't exactly an easy way to continually get nectar from the agave plant since it is herbaceous, whereas something like maple trees can be tapped because the wood can support the spigot.

Agave is more closely related to asparagus and hyacinths than to cactus. They are perrenial, you can harvest the lowest half of the leaves to make it look like a little palm tree, it will die after flowering, it takes 10-15 years to flower.

Agave are pretty tough. The way I propagate them is to cut the head off, and lay it on the ground, and come back in a year or so. I live in a semi arid climate. They grow faster if I water them every few weeks or so in the dry season.


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What does the "Psi" in "Psi broth" stand for?
When making competent cells I've been using a medium called "Psi broth", which per liter consists of 20 g tryptone, 5 g yeast extract and 5 g MgSO4. Today I got curious about why it's called "psi". Is it an acronym like SOC and LB?

Psi is the Greek letter ψ.  Psi broth is sometimes referred to as ψ-broth.
Here's an example:

L-Broth or ψ-broth can be used instead of SOC medium, but efficiency may
  be reduced.

L-broth： 10 g Bacto tryptone, 5 g Bacto yeast extract, 5 g NaCl, pH to
  7.5 with 1 M NaOH, bring to a final volume of 1 L, and autoclave.
ψ b-broth： 5 g Bacto yeast extract, 20 g Bacto tryptone, 5 g
  MaSO4･7H2O, pH to 7.5 with 1M KOH, bring to a final
  volume of 1 L and autoclave.

This only partly answers the question. The key thing which is missing is where the "psi" came from. (e.g. why "psi" and not "zeta" or "epsilon" or even "gimel"?)


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How to attain a deep conceptual grasp of key atomic/molecular/genetic/ notions?
It's a total noob question, I know.
I'm a layperson trying to come to grips with basic scientific terminology. I always face a conceptual hurdle in trying to understand micro-talk. The way I'm using the expression 'micro-talk', I take it to refer to any kind of discourse that relies extensively on concepts that refer to unobservables like DNA, adenosine triphosphate, other molecules/compounds, chemical elements, atoms, etc. i.e. the kind of quasi-tangible entities that we can never perceive directly owing to our particular evolutionary history that prioritized engagement with mesoscopic objects.
Whenever I read anything in an introductory textbook, the talk of such entities is always presented as a given to me. It's not explained on how on earth we know about them (or even if such explanation is given, it's usually quite shallow and circular i.e. it makes references to the entities in question). I can recite, or rather parrot facts about them just fine. If you ask me why a second magnesium ion is important for ATP, I retort that that's because of its functional role in regulating kinase activity. I might be able to successfully make certain inferences between sentences that involve such concepts. So I might even successfully pass a scientist's Turing test, but that's all there is to it. I don't really have an understanding of what I'm talking about. I feel like I'm a robot or a medieval scribe.
How can I get over this conceptual chasm? Learning about a historical development of a particular discipline might help, but I need to find a way to systematize my study and I can't have a recourse to university right now (even if I did, I'll face the same conceptual hurdle). I have library loans and will to study, but I haven't internalized a good number of micro-talk related concepts and they feel so foreign to me.
This is quite maundering, but I couldn't put it any more succinctly. If there's anyone who experienced a similar frustrating feeling to the one I've described, I'd be very grateful if they could offer me some tips. Thanks a lot.

You should study chemistry, and the history of chemistry would also be good, like atomic models, Rutheford, Bohr, etc. Some software of visualization of molecules, like RasMol, could help as well.

here are chemistry animations, if you learn well with visuals. https://www.youtube.com/results?search_query=chemistry+animations&sp=EgIQAw%253D%253D

Although I think this question is off-topic here (is there an eduction of psychology SE?) I find your attitude interesting. It may reflect a general attitude of people who are put off by molecular sciences or your own particular research mind. The question is whether it would help you reading  texts that described the way the atomic theory and then molecular theory was developed and the evidence supporting them. Or would the uncertainty be still too great for you. How mistakes (e.g. phlogiston) persisted for years before being discarded. How simple theories had to be revised. You could try.

@David, I think that would definitely help. I couldn't find any historically oriented textbooks for either chemistry or biology. The closest example I can give comes from math - Kline's 'Mathematics for Nonmathematicians' (but being well versed in the topics covered in the book due to math background, my evaluation might be very skewed). I did come across history books on chemistry, however they were clearly aimed at experts and presupposed substantial knowledge on the reader's part

When I was at secondary school in the 50s (sic) the text books (physics, especially) adopted that approach, partly for contemporary pedagogic reasons, partly because less was known then. I'm not sure how you would get hold of a (more condensed) chemistry text with a similar approach today. Many/most major conceptual breakthroughs did not follow the "scientific method", but involved ideas of how matter might be, for which support was slowly obtained by the results of experiments, generally inconclusive in themselves. The logic of the ideas appealed to me, so I could accept the uncertainty.

Just to clarify, I'm not craving Cartesian certainty, divested of all doubts. I articulated it clumsily in the OP, all I want is for these concepts to 'click'. I can follow some inferential connections between them, trace the logic of their behaviour even. Yet I feel like I'm learning how to move chess pieces without grasping why the rules are set up the way they are (in the case of chess, it's a matter of convention, which is where the analogy breaks down). The concepts are free-floating and only connected to colourful idealized pictures in textbooks.

For me a lot of clicking happened thanks to structural biology. Actually seeing how each molecule of that enzyme looks physically, and how it interlinks with others, made everything much easier to imagine. Try adding "PDB" (or PDBe if you prefer the UX) to a search for a protein and usually you'll find something nice to look at. Also, this: https://www.youtube.com/watch?v=X_tYrnv_o6A

I'm assuming you have a reasonable high school education otherwise you probably wouldn't have posted your question.
Do a basic science course and/or read - maths, physics, chemistry, biology texts. 1st year university level should be good.
If there is anything you don't understand in these texts, go to more basic books - plus Wikipedia is good for the sciences (I wouldn´t like to read them on, say, the Arab-Israeli question), but I've never seen any egregious errors in the scientific area!
Then read Klug and Cummins "Concepts of Genetics" from cover to cover.
If there is anything you don't understand in Klug and Cummins, go back to basic texts.
I had a good background in the  sciences and then majored in Genetics with minors in Biochem, Microbiology and Immunology. I read that book from cover to cover taking notes in 3rd year (of a 4 year degree programme) and have done very well in the field.
The book covers the history of the discoveries in a very readable and approachable fashion. Obviously it is no substitute for doing a degree in the subject, but if you really wish to at least have a good understanding of the science, you could do worse than read that text!
You could also read popular science books aimed at the "interested and educated layperson" - Stephen Jay Gould, Richard Dawkins for example. Try National Geographic and even Scientific American or New Scientist. You, at least intially, will have to make a real effort, but it is very rewarding - there is nothing more fascinating than biology generally and molecular biology/genetics in particular! Best of luck on your journey!


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Peruvian insect identification
The above is an insect I found while visiting Peru. I’m no biology expert, and I was just curious to know what species of insect this was. I found it on a rock while exploring the ruins near Pisac, if that helps.

Looks like a Megaloptera juvenile.

Definitely not Megaloptera. Looks like a lampyrid (firefly) larval or female form. Note especially what look like single tarsal claws (on the end of the feet). This is diagnostic for Lampyridae (Coleoptera).


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Is this a bed bug or some other bug?
This white/yellowish bugs are crawling over my walls under cracks and below my wardrobe. I am not sure if they are bed bugs or some other bugs, there are very small in size thus I zoomed very much on the photograph, I hope someone would be able to assist me on identifying the bug.!

This isn't a bed bug (see this page for the genuine article); I'm sure it's a book louse, but can't go further than that without a better picture; you should probably add the "entomology" tag to your question as well.

@ArthurJFrost I agree. It is a psocopteran. I am guessing that the post is more about worrying if it is a bedbug than precise identification. You should post your answer. : )

definitely a psocopteran. Not a bed bug.


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Why are monotremes so rare?
There are currently only five species of monotremes remaining, and all of them are found in Australia. Additionally, I read a science article claiming that competition from marsupials essentially forced monotremes into the water, where marsupials couldn't follow without drowning their young.
Why are monotremes so rare? Are the traits that define a monotreme (such as egg-laying) inherently less competitive, or is their relative scarcity more of a quirk of fate?

Can you please link to the article you're referring to?

@Remi.b Sure, there you go.

When you stop to think about it there is one big reason live birth has an advantage. Lets assume with habe organism A and organism B, A and B both have offspring of exactly the same size and needing the exact same amount of resources (nutrients, etc.) A lays and egg and B gives live birth. A needs to have all of the nutrients its offspring  will need all together at once because once it forms hte egg it cant add anything while organism B does not need it all, they can keep eating and supplying the nutrients over an extended period of time, as they gain it, so they need less "on hand" as it were. A and B may be putting the same amount of resources into their offspring but A does it all at once but B can spread it out over a long period of time meaning it does not need to build up huge reserves before breeding. As an added benefit if times are bad B can dump the offspring and try again later, saving all that would be wasted material for itself, so it can survive famine and drought better.

Its hard to definitively say "why" some groups are more successful than others. Without replication, answers can simply be "Just-so stories". But there is some replication here. Monotremes have been eliminated everywhere they once existed, except for Australia, and New Guinea. There is a similar replicate of what happened to the marsupials in S. America when the Panama isthmus connected the eutherians of Central America to the marsupials in S. America; extinction of many of the marsupials in S. America. The same thing happened in Australia when eutherians were introduced, but on a lesser scale (so far). These are two examples of eutherians outcompeting marsupials. I know, not the same as monotremes. That monotremes found refuge in Australia may not be a coincidence in that they did not need to compete with eutherians. Marsupials not laying eggs may have been an advantage that allowed them to outcompete monotremes. But there is not similar replication to move beyond "Just so".


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Why does the funnel-mantle locking apparatus exist, and how / why does it work?
I was looking up argonauts, and found this article. As someone who builds things for a living, I was intrigued, but could find no information on how it actually functions in order to help the cephalopod.
Since locomotion is mentioned, I'm assuming that the creature cannot locomote efficiently (or at all) unless this locking apparatus in engaged?
Reference images of some kind (even if scribbled) would really help to explain geometry  / motion.

Argonauts and other octopuses have a muscular mantle which is the outside of much of the body other than the arms.  A cavity is formed by the mantle in which the gills are located.  Water is pulled into the cavity through valve-like flaps and expelled through the tubular funnel (also called siphon or hyponom).  Here is a video of the flaps and funnel as an octopus breathes.
A typical octopus most often moves slowly by crawling across the sea floor.  They have a faster mode of locomotion, though, which is to quickly contract their mantle to force water out the funnel at high velocity.  This jet of water forces the body of the animal in the opposite direction. Here's a drawing of an argonaut moving with this mechanism:

(Here's a video of an octopus using its jet.)
As this jet propulsion is often used for escape, it is important for efficient movement that jet be directed so that the rounded mantle leads the movement and the arms trail.  Since the funnel is flexible, there is a need for a way to keep the funnel aimed away from the mantle.  The funnel–mantle locking apparatus exists for this reason.  A protrusion on the mantle fits into a slot on the funnel and while the animal is propelling itself holds the funnel in place.


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File sizes in Proteomics Experiments
I was wondering what file sizes does a typical proteomics experiment outputs in each phase (identification and quantification).|
Also, how does the type of the quantification (relative, absolute) affect the size of the output files.

I’m voting to close this question because it is about file sizes rather than biology. It might be appropriate for [Bioinformatics.SE], but please check that sites guidelines before reposting.

This can vary a lot depending on the length of run, the sample itself, type of method, and maybe even the instrument manufacturer.
There are also various approaches to doing relative and absolute quantification, but I would not anticipate these factors to have the largest impact on file size. Certain method parameters like profile/centroid settings and run length are likely the biggest factors.
I have proteomics files for TMT-label quantified samples with a 2 hour duration that were collected in centroid mode for ms2 and ms3. These ones are 800-900MB. A smaller sample load with the same method has a file that is 600MB.
I also have files with the same setup, but collected entirely in profile mode that are 3-4GB.

Maybe you should define "typical proteomics experiment" a bit more. In general @Nathan is right with his comment about centroid / profile mode.
From my point of view, a typical experiment would be a data-dependent acquisition (DDA, aka "shotgun proteomics"), using a 90 min gradient on a common ThermoFisher Orbitrap instrument. This would typically lead to file sizes of about 400-500 MB.
Spiking peptide or protein standards to perform absolute quantification will not make the files considerably larger.

Welcome to SE Biology. Please finish reading the Tour. When asking posters for more information about questions you should check the date of the post. Unfortunately old posts sometimes come up again when someone does a spring cleaning job on a particular tag. An answer to an old question is ok. A request to the poster is likely to get no response.


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Does any one know which species of insect is this one?
I found this insect, in multiple zones of Imbabura - Ecuador. https://en.wikipedia.org/wiki/Imbabura_Province
Sorry for not having something to scale with, but it's about 15 cm long.

Another picture here:

In general, it helps identification if you add the location where on earth you found the animal.

I edited the question @Marzipanherz. It is very important!

That is a male dobsonfly. I know this is a male because it has long mandibles which are used in mating. Female dobsonflies have short mandibles. larval dobsonflies are called hellgramites,and it really hurts a lot when they bite you.Look here https://en.wikipedia.org/wiki/Dobsonfly or here entnemdept.ufl.edu/creatures/misc/eastern_dobsonfly.htm

Yes, Megaloptera, Corydalidae, Corydalus cornutus

Just in case, does anyone know its name in Spanish?

I edited the question @peter . So I should suppose that the second photograph is a female, right?

I found the Spanish name. A dobonsfly is a "Mosca de pescar oriental"

I didn't see the second picture. when I saw the first picture, I thought "I know what that is!" and just jumped at it. The second picture is a female, the long mandibles of the male are used in mating.

Not Corydalus cornutus. That species is only found in Eastern North America. There are several other Corydalus species found in that part of South America. It would require an expert in them to get a more specific ID. Note that the pictures are of two different insects as well. The one on top is a male, the bottom one a female (as the earlier answer noted, females have shorter, more robust and powerful mandibles, though males and females can each draw blood with a nip (personal experience)).


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This strange looking thing was on the leaf, can you identify what this is?
I found this today on one of the plant that I grow in the container at home. I cannot identify what kind of insect it is.

Where is the leaf located in the world?

That is a butterfly chrysalis. Since it is clear, and you can see the wings, it is about to emerge. A chrysalis is the naked pupal stage of a butterfly, as opposed to a "cocoon", which is covered in silk.


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Growing bacterial culture on gelatin
I'm very new to experimental biology and don't know much about it. So, i was looking to grow some bacteria in petri dishes and looked up how to do it. Unfortunately, I'm finding it difficult to get my hands on the 'agar-agar' required to make the culture medium. So, is it possible to use any other alternative which would give the same results? Like for example regular gelatin?
My school lab teachers have also shown little to no interest in helping me with my project, so I'm on my own here. Any tips would be greatly appreciated!

You can try using agar powder also known as falooda powder which can substitute gelatine.it is used in Indian homes to make jelly.

You can use Gelatin - actually this was used by microbiologists before agar came in use. That gelatin is more or less completely abandoned in this field tells quite a story, right?
Gelatin has the main disadvantage that it cannot be autoclaved together with the medium to sterilize it. Using it would need some experience and probably advanced techniques to which you have no access.
But there are some good news as well: Agar is also used as a geling agent when making food, and when you cannot find it in your local supermarket, Amazon can deliver it. You don't need much, around 15 gram/litre.

sadly Amazon doesn't ship products to my country :( (Bangladesh)

what other option would i have?

You can use gelatin. The problem you will find is that many more common organisms are able to break it down. Hence, it won't hold up very well. Depending what you put on it, it might work.

Can you add some references to your answer just to back it up a bit? Also, if there are any special preparation methods that should be followed or anything of that sort, please add that information and/or some reliable links to webpages with those instructions. PS... Welcome to Biology S.E., if you have any questions or concerns, please feel free to visit the Help Center, here https://biology.stackexchange.com/help :)


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Could Cannabidiol steady a hand?
Can Cannabidiol be used to steady shaky or nervous hand for precision work like surgery?
I have used it for shooting pool/billiards and I'm not sure if it is a placebo or it is helping? but I am more steady.
I have seen where Cannabidiol helps this man with Parkinson's stop shacking.
https://www.youtube.com/watch?v=rAdDdTZuNA8

I'm voting to close this question as off-topic because it is a question of applied medicine. The question would be on-topic on Health.SE.

I'm also voting to close this question as off-topic because it is a question of applied medicine. Please Migrate The question would be on-topic on Health(health.stackexchange.com).

surely you should migrate it rather than close it?

This question is self-help and in its current state it cannot be migrated to Health.

I think this is a fantastic question.
As far as the Parkinson's application, it's definitely within the realm of possible. Taken form a recent review:

Preclinical research in animal models of several movement disorders
  have shown variable evidence for symptomatic benefits but more
  consistently suggest potential neuroprotective effects in several
  animal models of Parkinson’s (PD) and Huntington’s disease (HD).
  Clinical observations and clinical trials of cannabinoid-based
  therapies suggests a possible benefit of cannabinoids for tics and
  probably no benefit for tremor in multiple sclerosis or dyskinesias or
  motor symptoms in PD.

Kluger et al. in Movement Disorder, 2015 (The Therapeutic Potential of Cannabinoids for Movement
Disorders)
As far as every-day hand steadiness, I haven't been able to find any good sources yet. I'll keep reading, and update this if I find anything interesting.


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Does Penicillium roqueforti produce penicyllin?
I have recently discovered that blue cheese is produced with Penicillium roqueforti. As I know that some Penicillinum sp. produce penicyllin I wonder whether it is produced by P. roqueforti too?
The Wikipedia article does not mention penicillin, it mentions "compounds that can be employed as antibiotics" instead.
However the article on P. glaucum also do not mention penicillin, while P. glaucum is mentioned in the article on the history of penicillin.


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What's the best way to measure biodiversity?
As I understand it there are various ways biodiversity is measured, with varying results. From what I have been told on these boards, part of the difficulty is because it's hard to define a species exactly, so it's hard to count them.
What I really want to know is whether genetically engineered organisms count towards increased biodiversity but my last attempt at asking that question foundered on the rocks of species definition.

Could you narrow your question? Biodiversity is not just the number of species, but also the phylogenetic range of diversity. For example, a Tuatara is the only representative of its kind. Does one Platypus species count the same as one Drosophila species? But if you want to know if genetically engineered organisms count as species; No, they don't. They are not different species, but simply have a gene inserted to provide some trait like herbicide resistance. If that is the question, then ask that.

Hi I'd like to narrow the question and agree that a gene inserted isn't a new species, and there are those definitional problems as people have pointed out to me. But I think that genetic engineering is going to soon be more than just tinkering with genes but designing whole new organisms. So I'm trying to look into the future a bit here.
So I could rephrase as "If in the future new species are engineered, will that count as an increase in biodiversity, and will it be a significant increase ?"

If genetic engineering actually does create new species, they would be counted in biodiversity studies. I am not an expert, but I do not think that these "new species" could ever be approved for release into the environment. There are pretty strict rules about this. They would also need to be formally described. I don't know where you are getting your information, but I am skeptical that there will be a significant flood of human-engineered new species.

Well, I'm speculating in a science-fictiony way somewhat, and looking at efforts like Craig Ventors to synthesize genomes, and other stuff like this
https://www.technologyreview.com/s/610180/why-redesigning-the-humble-yeast-could-kick-off-the-next-industrial-revolution/
"Instead of engineering or even editing the DNA of an organism, it could become easier to just print out a fresh copy. Imagine designer algae that make fuel; disease-proof organs; even extinct species resurrected."
So if that industrial revolution does take off, does that mean more biodiversity ?

OK, well that is not happening now, and if it ever did, it would need to be under tight regulatory control. Estimates are that there are at least 10 million species. A couple of engineered organisms, even if they were approved for release into the environment would do nothing to increase estimates of biodiversity. Could you modify your question? As written, it is not clear what you want to know.

I disagree with a couple of things there Karl. The environment in this case is a lab. It's not environment just because it isn't a forest or ocean. There's a history of new species arising in human made environs and these will be more. As to how many organisms there will be, I can imagine a lot, even just from what articles on MIT Review say. They're talking about a biotech revolution. Regulation is also only part of the story, lots of unregulated things happen, presumably they always will, though I think regulation is pretty important here.

That does not change the fact that your question does not ask what you want to know. It seems you already know the answer.

Sure it asks what I want to know. I'm only speculating, so I want to see if people more knowledgable than I can let me know if it's reasonable speculation ?

"If genetic engineering actually does create new species, they would be counted in biodiversity studies."
Karl, Ventor says he has created a new species. I know people debate what counts as a species. If that IS a new species, then has he increased Earth biodiversity by one bacterium ?
https://www.scientificamerican.com/article/scientists-synthesize-bacteria-with-smallest-genome-yet/
"the genome of the minimal cells is like nothing in nature. Venter says that the cell, which is described in a paper released on March 24in Science, constitutes a brand new, artificial species."

A very good way to measure biodiversity would be to do environmental barcoding with high-throughput sequencing methods, and then use an algorithm that estimates genetic distance to get both species count estimates, and then calculate higher-level diversity, such as genera and families. Then you would repeat this procedure over several collections to obtain a species accumulation curve, so you could then estimate the asymptote. The future possibility of biogenereed organisms would not be worth reporting among the thousands of species at a given location.

OK, but what about by methods used now, particularly the ones that are used to tell Joe Public like me what the state of the world is in a typical news outlet ?
Currently the news is that biodiversity is on the slide due to human activity. I've no doubt it is. But, counting all organisms including ones that may be man made, will this always be the case ?
It may or may not reflect a pleasant planet to live on, but will it be the case ?

No. You seem fixated on a hypothetical that somebody used to sell magazines. Not going to happen. And if it ever did, it would be such a tiny fraction of biodiversity, that it would not be significant in the counts.

Why won't it happen ? Why would it be a tiny fraction ? How much is significant ?


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Is summation linear in a passive membrane?
I am not too sure what it means for summation to be linear? I am running a simulation and as I decrease time for the second EPSP the amplitude decreases. Does summation being linear mean that there is a direct negative linear relationship between delay of onset and amplitude? I also noticed there is no change when I double or triple my conductance value.
I am just not too sure what the relationship is telling me.

For a membrane to satisfy the conditions for linear summation implies that when two EPSPs of amplitude $A$ and $B$ are summed at the integration zone, the resulting output signal will be of amplitude $A+B$. Since the signal dissipates due to time and length constants, increasing the delay between the two inputs means that the later input will be dissipated so $A+B$ will be smaller than it would have if the delay was shorter. Under this scenario, inputs $A$ and $B$ are still summed linearly. However, if the delay is shorter than the time constants or the inputs are delivered closer in space than the length constant, then you may get non-linear summation since the output signal at the integration zone will be larger than $A+B$.
Have a look here for more information (especially Figure 7):
Silver RA. Neuronal arithmetic. Nature reviews Neuroscience. 2010;11(7):474-489. doi:10.1038/nrn2864.


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Infection treatment without anti-biotic
When we have some bacterial infection, say throat infection (pharyngitis) we take antibiotics as treatment. I was wondering how throat infection was treated when there was no antibiotics at all, before 1940's I think.
Throat infection is just example, It can be post surgical operation, urinary track infection etc, basically anything where we use antibiotics currently. So in a way replacement of antibiotic tablet when antibiotic wasn't available.

https://health.howstuffworks.com/wellness/natural-medicine/chinese/how-to-treat-a-sore-throat-and-stress-with-traditional-chinese-medicine.htm

The use of antibiotics to treat pharyngitis is either useless or unnecessary in most cases. (See e.g. Wikipedia article ) Such use of antibiotics has contributed to the rise of multiple drug resistant bacteria. Did you do any research of your own before posting this question?

I'm voting to close this question as off-topic because, although answers might provide information to contemporary biologists about medical practice in advanced industrial societies in the early twentieth century, this is not within the remit of SE Biology.

@David: I researched and only found out that , during some infection people used to have several cuts on the body, which will lead to blood loss and might kill the bacteria. and thought this is not the answer that I expect. I mean slitting body for just throat infection??

Interestingly, treatment of mild pharyngitis before the advent of antibiotics wasn't too different from what it is today - it was (and still is) mostly symptomatic. First of all, viral pharyngitis, which is quite common (Hidreth et al., 2015), is not affected by antibiotics (no viral infection is), and they are not indicated in such situations. Second, mild and self-limiting bacterial infections, including pharyngitis, most often do not warrant prescription of antibiotics, as this leads to the growing problem of antibiotic resistance, which, according to the World Health Organization is "one of the biggest threats to global health." Many guidelines can be quoted, urging clinicians to prescribe antibiotics sparingly, but pharyngitis is so common (literally everyone has had it, multiple times) that one can simply turn to one's own experience - simply put, when you have a mild case of soar throat, your doctor doesn't give you antibiotics (if you even bother going to the doctor about it), most often you are advised to take only symptomatic medications (many of which are OTC). These most often include compounds with analgesic, antiseptic, and/or anti-inflammatory properties. Interestingly, such compounds were widely available long before the advent of antibiotics and even the pharmaceutical industry itself.
Menthol, for example, is a selective agonist of κ-opioid (Galeotti et al., 2002) and a modulator of GABBAa receptors (Watt et al., 2008), thereby eliciting analgesic and anaesthetic effects, respectively. Moreover, by disrupting bacterial cell membranes, menthol (and similar compounds, such as thymol, for example), elicit antibacterial activity, as well (Trombetta et al., 2005). Thus, wild mint, peppermint, and thyme are much more often indicated in cases of soar throat than antibiotics! Their use in the form of infusions and decoctions likely predates most, if not all, modern countries. Moreover, the analgesic and anti-inflammatory properties of willow bark, which are due to the salicylic acid contained therein, were known to Hippocrates (Norn et al., 2009), quite possibly dating back much earlier. Furthermore, it is known that caffeine potentiates the analgesic effects of many nonsteroidal anti-inflammatory drugs, including salicilic acid (Granados-Soto and Castañeda-Hernández, 1999). Unsurprisingly, this combination is often found in many modern drugs (many OTC), being marketed all over the world. Whether this effect was known before the advent of the pharma industry, however, is hard to say. Willow bark has been used as an analgesic and anti-inflammatory medication since ancient times, but coffee was brought to the West in the XVI century.
This is only a handful of traditional medications for pharyngitis, and I'm sure many more can be found, as well as many other treatments for many other conditions. The point is that treatments of mild pharyngitis were available before the advent of antibiotics, as a matter of fact, many of those treatments are still first-line therapy in most cases, even to this day.

"In those times". 1940s US and Western Europe? Have you actually done any research on the history of medicine?

Yes, I have, and the question referred to the entire period of human history before the 1940s, all over the world. What makes you think of the US and Western Europe specifically?

The question obviously relates to North America and Western Europe (and Australia etc) because that is where antibiotics were introduced. If you make statements about the properties of herbal medicines, please back them up with references in reputable peer-reviewed journals. You cite nothing in support of the statements you make.

No, it is not obvious that the question refers to a specific place because it simply doesn't, that's entirely your own (mis)interpretation. Nowhere does it refer to a specific place, it asks what people used before the introduction of antibiotics, i.e. it applies to any place people live. Asking for references is a fair comment, of course, and I will gladly provide references after a proper lit search, I'm just not going to do it around midnight.

I'd save your efforts. If this question is about the history of folk medicine it's off-topic here. In fact, if it's about the history of medicine, rather than science, it's off-topic. Answers about analgesics, anti-inflamitory drugs, innate or herd immunity etc. might be relevant if they related to mechanisms. But I don't see you going in that direction.

I was simply answering the question but you make a good point that I should make my answer more mechanism-oriented. I will try to find the time tomorrow  to improve and substantiate my answer, hopefully turning your downvote into an upvote.

@Stefan: Exactly!. my question is not location specific. Its for entire world.

@Stefan.. Thanks for the info but It was for  antibiotic in general. Updated my question.

http://www.eliava-institute.org/?rid=6
Bacteriophages. Institute in Georgia

Please do not post link only answers.


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Why Can't The Immune Systems of Uncontacted Tribes Handle Our Common Colds?
I'm sorry if this is a stupid question, I'm just starting my first year of a biomedicine degree and I'm curious - googling didn't find me any answers.
I know that the Aboriginal Australians and many other native peoples have been wiped out by diseases such as smallpox, influenza, the common cold, and malaria. A lack of immunity to our diseases is currently an ethical concern of contacting previously uncontacted tribes.
Seeing as we can't properly develop full immunity to the common cold - as it's always changing - but we manage to always fight it off, and (I think) our immune systems are all fundamentally the same, why can't their immune systems just quickly learn to handle something like the common cold? Can't they simply develop antibodies? Why does it become fatal when introduced to a new group?
Thanks!

I think your question stems from your assumption that different human populations share an immune system that is fundamentally the same. This is not the case. In fact, some of the greatest genetic variability in human populations can be found in the human leukocyte antigen (HLA) gene complex. The HLA genes codes for the major histocompatibility complex (MHC) proteins in humans. These cell-surface proteins are involved in regulating the immune system.
Different human populations have different levels of innate immunity to certain pathogens based on their historical exposure to different pathogens at different frequencies over evolutionary time.
I'm going to use the generic terms 'indigenous person/people' to refer to non-European indigenous people who encountered Europeans for the first time between the 15th-late 18th centuries. They can be Aboriginal Australians, Native Americans/First Nations, Amerindians, etc.
The primary reason that indigenous people were historically so vulnerable to European diseases is that the Europeans had been exposed to these pathogens for a long time, which led to them developing resistance to the pathogens. This is natural selection at work. The individuals most likely to survive were those with an immune system able to fight off those particular diseases.
Prior to European contact, indigenous people would never have encountered the pathogens that the Europeans brought with them, they lacked any immunity to them as a result. This allowed contagious disease like smallpox to spread quickly and kill a lot of people these groups.
You might ask why didn't Native Americans' diseases wipe out the Europeans when they came into contact with them?
One of the main reasons for that was domesticated animals. Europeans, by mainly the luck of the draw, had lived in close contact for centuries with a large variety of domestic animals, and thus, got exposed to a large number of species-hopping diseases, thus developing immunity. Native Americans had very few domestic animals, and got far less exposure.

References:
Riley E, Olerup O. HLA polymorphisms and evolution. Immunol Today. 1992
Sep;13(9):333-5. Review. PubMed PMID: 1361325.
Patterson KB, Runge T. Smallpox and the Native American. Am J Med Sci. 2002
Apr;323(4):216-22. Review. PubMed PMID: 12003378.
Markov PV, Pybus OG. Evolution and Diversity of the Human Leukocyte Antigen(HLA). Evolution, Medicine, and Public Health. 2015;2015(1):1. doi:10.1093/emph/eou033.
Guns, Germs, and Steel by Jared Diamond

To expand Its not that european population were not hit just as hard by these diseases, but they were hit that hard in the past, and one at a time. The europeans were getting hit one by one with these diseases as they evolved, while the native peoples are getting hit with several at once compounding the damage.

This is generally a good answer about an important aspect of the immune system that is variable and under selective pressure, but is not directly relevant to the question about the common cold. Most viruses associated with the common cold syndrome are poorly immunogenic, don't require antigen presentation for clearance, and so provide no selective pressure on HLA alleles.

Following on from @ValentinianMc's answer, Europeans may have been in contact with more people in total than native Americans and Australians. European populations would have had trade and contact with Asian and African populations. This could introduce more vectors for certain diseases (e.g. plague from Asia, via the Silk Road or Smallpox from Africa), which might have exposed Europeans to more pathogens than isolated communities. Exposure to diseases could possibly increase the Afro-Eurasian immunities to them. However, this also has the added effect of introducing epidemics such as the Black Death of the 1340s-50s, so it's not really a good thing to have more disease vectors.
However, this isn't to say that Native Americans were completely sparsely populated. In fact, the Aztec capital of Tenochtitlan was one of the most densely populated cities in the world (population ~250k in the 1510s). This might imply that the density of people is not the cause of the European immunity, but the total number of people in contact with one another.
You could also question whether differences (or the existence) of plumbing systems between Afro-Eurasian and other populations. If the Native Americans had a more advanced sewage system than European nations, they would be exposed to fewer water-borne diseases (and possibly not develop an immunity).
Lastly, the Colombian exchange was both ways and some evidence suggests that Europeans received (from Native Americans) an increased susceptibility to Rheumatoid Arthritis. This could demonstrate how all populations have diseases, and that the fact that Europeans fared better than Native Americans wasn't due to Europeans having any better overall immunity, it may have been the fact of which diseases were transmitted.


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Why does maintaining contraction of muscles require ATP?
So from my understanding, if I maintain the contraction of my muscle, the myosin head will be bonded to the actin. Why is ATP needed to maintain this bond?

Actually, it is not. ATP releases the myosin bonded to the actin, so when it is absent, the muscle remains contracted. This is, actually, precisely what happens during rigor mortis after death.
However, as long as you are alive, on a molecular level this is a dynamic process - actin release and bonding - and maintaining it requires energy. Moreover, muscle relaxation is not achieved by stopping the ATP flow, but incurrs additional ATP cost - it happens by actively removing calcium ions required to enable the actin to bind the myosin.


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Are resonances the reason receptors work?
From Visual phototransduction - Wikipedia:

When struck by a photon, 11-cis retinal undergoes photoisomerization to all-trans retinal which changes the conformation of the opsin GPCR leading to signal transduction cascades which causes closure of cyclic GMP-gated cation channel, and hyperpolarization of the photoreceptor cell.

From the physics point of view, does this mean the proteins in the eye are combinations of oscillators, each of them in charge for a specific wavelength, so that if one oscillator resonates with the photon, the signal is produced? In general, does all receptors work this way? Note that physical oscillators should have exponential or sinusoid functions. See this Photography question: How to capture a swinging pendulum?

Photoreceptors themselves dont act as oscilators, a single receptor is either 'on' or 'off' - it does not respond differently to different wavelenghts. Humans have Trichromatic vision, which means that we have 3 different kinds of photo-receptors that respond differently to light of a given wavelength at a given intensity. By combining multiple signals from these 3 different receptor types the brain can translate this to different colors (its actually kind of similar to how RGB color works).
Therefore I would say that even photo-receptors don't work like oscilators, only their specific ligands switch between the 11-cis & trans state, but this is more of a statistical and physico-chemical process (which does involve resonance between the energy of the photons and the electrons in the cis bond)

In general, how is a sensory receptor stimulated? I suppose that by the peak of intensity of the signal, right?

Receptors accept a huge variety of molecules as ligands.
In the example that you outline the receptors are called photoreceptors. The ligands for photoreceptors are generally contain alkene backbones which switch cis and trans forms on exposure to a certain wavelength. The oscillator analogy holds true to a certain extent.
However, not all receptors function similar to photoreceptors. Photoreceptors are designed in a way to sense a wide signal spectrum (the visual spectrum). On the other hand receptors which work on a much local scale e.g. delta receptor for the notch ligand are not similar to oscillators at all i.e. there is no factor of resonance with external stimuli.

Do you mean the ligands of photoreceptors switch cis and trans back and forth, which has two and only two configurations? That's not what I mean by oscillators. Physical oscillators should have exponential or sinusoid functions. See this Photography question: How to capture a swinging pendulum

The function will definitely be not exponential as the receptor will be recycled i.e. it will come back to ground state as negative regulation of receptors exists to maintain homeostasis. I think the process can be modeled sinusoidally. However, there will be lag periods between two peaks as the receptor has to be primed to be able to respond to the next stimulus.


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Is photosynthesis faster in aquatic plants rather than terrestrial plants?
For example : In which of these two plants photosynthesis is faster and why? water hyacinth or sedge?


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Is there a term for the group of individual organisms whose matrilineally descended female ancestors all share a common ancestor?
A group of individual organisms that are all descended from a common ancestor is a clade. Is there a term for a group of individuals whose matrilineally descended ancestors (mothers, maternal grandmothers, maternal grandmothers' mothers, etc.) are all descended from a common ancestor?

I'm not aware of any one-word term for this. The term "common mitochondrial ancestor" is often used to refer to a shared female ancestor of a genetically related group. If you want to specify female descendants only, perhaps you could say "females sharing a common mitochondrial ancestor". I think that's about the shortest way to say it.

Thanks for this. I'm not specifying only females at the end of the chains, but every link above every group member must be female until you get to a female who is a common ancestor. So "all individuals who share a mitochrondrial ancestor" does the job nicely.

I don't think there is a word for that.
However, you can refer to this specific DNA sequence as being exclusively maternally inherited (such as mtDNA for example; see also mtEve). For this sequence, the classical vocabulary from the field of phylogenetics and population genetics apply nicely.


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Can light destroy auxin?
In my biology textbook, it says that plants grow towards light because auxin is laterally transferred from the light side to the shaded side, so more auxin stimulates growth and hence the plant bends towards light. My textbook also specifically states that light doesn't destroy auxin. Yet, recently I searched online and find that light will actually destroy auxin by photo-oxidation. I am confused, can someone tell me which is the correct mechanism (or both)? Thanks!


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Understanding the genotype written in terms of two genes
I have some doubt in understanding the following genotypes: HCV-Tg/AID(+/+), HCV-Tg/AID(-/-) and HCV-Tg/AID(+/-), where HCV-Tg stands for "Hepatitis C Virus (HCV) core proteins" and AID for the gene "Activation-induced cytidine deaminase". So it is about two different genes. It is clear though what is meant by for example AID(+/+) in terms of ist alleles, but in the case I am talking about these are two different genes. In the case HCV-Tg/AID(+/-) it could for example mean that one allele is mutated at each of the two genes, but it could also mean that in the first gene (HCV-Tg) one allele is WT and in the second gene (AID) one allele is mutated. And lastly it could also mean that in the first gene both alleles are WT and in the second gene both alleles are mutated.
Can somebody help me understand what is exactly meant ?
Many thanks.


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Is it possible to cure dandruff?
If dandruff is caused due to oleic acid released by fungi malassezia then is it possible to control it by applying any base in our scalp ? Since base nullify the effect of oleic acid or base cause any further hairloss complication?

isn't just anything possible in the future? What are you after?

It might be a better fit for worldbuilding.SE but I am not sure

why did you totally change the question and post? Just leave this one closed as it was, and take your new question and post it as a new post.

we already transfer memories with books and movies, If are talking about direct transfer then the answer is no, because different brains already have different patterns of connections, so even if you could somehow for an exact copy of a single small pattern to form in someone's brain it will interact with the rest of the brain if very different ways.


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What happened to pertussis incidence in the US between 1955 and 1974 and why?
The Wall Street Journal ran a great collection of infographics in 2015 superimposing the dates on which vaccination was introduced for various childhood diseases on their incidence:
http://graphics.wsj.com/infectious-diseases-and-vaccines/
For the most part, it's a fantastically clear story and a useful resource when explaining how effective vaccines are to skeptics. However, what's going on with pertussis?

The note below the heatmap mentions that vaccination was introduced in 1914. A bit of digging online suggests one factor could be the introduction of the (more effective) combined diphtheria-pertussis-tetanus (DTP/DPT) vaccine in 1949 - is this the whole story? Did the original vaccine have any effect? Did anything like coverage, availability, pricing and/or legal requirements for vaccination improve significantly at the same time as the new vaccine was introduced?
And why did the CDC stop collecting data on pertussis cases from 1955-1974 during a period when you'd have expected them to be keen to track the effectiveness of the vaccination programme?
(I realise that the CDC data gathering question might seem like a separate issue, but (a) it's necessary to understand this figure, and (b) the point of lumping these together is because I have a strong suspicion that antivaxxers will point at that gap and come up with a conspiracy theory, and I'd like to be able to point to a full explanation of the data behind this figure in one place. So, to be useful for explaining this figure to sceptics, they need to be answered together.)


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What happens to the brain during meditation?
I've read several experiments on the internet according to which it is possible to reach a psychedelic state without taking any psychedelic drugs like DMT, LSD and other tryptamine derivatives.
It may sound stupid but I was thinking that the brain produces some minimal amounts of a psychedelic drug.
Maybe it is a tryptamine derivative (from the metabolism of the amino acid tryptophan, or from melatonin). I think that there is an undiscovered biological pathway for endogenous psychedelics (I can imagine DMT or 5-MeO-DMT).
What do you think about this? How can the brain go into a psychedelic state without taking any psychedelic drugs?


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Crispr-Cas9 method and nobel
Since i had my first cell class at university i have heard about Cripsr Cas9 method. But I am quite surprised about one fact.  Why actually wasnt rewarded by Nobel price? Is it something like Einsteins relativity (to early to reward it)?

I'm voting to close this question as off-topic because it is not about biology in the terms of SE Biology.

This question might be on topic on Academia.SE but not on Biology.SE.

i am so sorry but i thought there will be some kind of biological problem with this  method and not only rivarly with money thing.

My guess is that some people (likely Jennifer Doudna, Emmanuelle Charpentier and Feng Zhang) will eventually be awarded a Nobel Prize for the discovery of CRISPR and the development of its applications for genome editing, because it really is a major advance. But for now, the University of California Berkeley and the Broad Institute are still legally fighting over patent conflicts, and the patent situation worldwide is generally complicated. I think this is a possible reason why the Nobel committee decided to wait.


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Rapid polymerization inside cells
I am interested in (rapid) polymerization or (rapid) long mollecule synthesishappening in the intracellular space.
Clearly protein synthesis or DNA/RNA synthesis are examples of elongation of molecules, but these are relatively slow.
I wonder if someone can suggest examples of polymerization processes that happen at a much faster pace, for example one monomer added to the mollecule every millisecond, or every few milliseconds.
The underlying question is: what is the fastest example of long-molecule elongation inside the cell? At physiologically viable concentrations, what is the fastest monomer addition process that we could find?

I have now found examples of polymerases approaching 1000 nucleotides per second. Is this correct? Any other examples? Specific polymerases that can reach this incorporation speed or even higher? Other polymerization examples?


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What are these flower like cells in the photo attached?

I am a student of BSc. Zoology... I was doing a TC of RBC of my blood when I encountered these strange flower like cells. Are they lysed RBCs ? If so, why are they so geometric in shape ?


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Banana peel bruises after a hit
When a banana fall on the floor or get a certain impact, the impact location gets darker (it bruises) after a certain amount of time. The darkening affects the peel as well as the fruit itself. Why does this happen?

Related: https://biology.stackexchange.com/questions/16523/what-exactly-makes-bananas-go-brown

@LinuxBlanket Thx :) I saw that but, I was wondering what is happening when the banana fall and not only the normal ripening process. From what I have read online, it seems that when a certain pressure is exerted on the peel, the cells are damaged and they release an enzyme that will make the ripening faster. Nevertheless, I am waiting for a technically detailed answer describing the process.

Fruit is discolored in the first place because, when certain compounds are altered (oxidized), they turn brown.
In a banana (and most fruit) those compounds are phenolic compounds, and polyphenoloxidase is the thing that oxidizes them.
In an undamaged banana, the phenolic compounds and the polyphenoloxidase (that can turn them brown) are physically separated.
When the banana is crushed/dropped/etc, the structure of the banana is damaged so that the phenolic compounds and the polyphenoloxidase come into contact.  The polyphenoloxidase oxidizes the phenolic compounds, and you get that brownish color.
A nice summary (which links to a more detailed reference) can be found here: https://www.scientificamerican.com/article/why-does-bruised-fruit-tu/