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Is there a free software for manual sequence annotation?
I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence on top and tracks at the bottom that highlight which part is an alpha helix or a beta sheet.
My final annotated sequence would look like this:

Benchling is free for academics and makes sequence annotation really easy. Check out an example sequence I annotated here: https://benchling.com/s/1m8QllV2/edit It's all on the web, so you can sign up at https://benchling.com :)

You might find some success with using WebApollo or JBrowse
WebApollo allows you to perform many manual annotation functions for your genes, such as editing exon boundaries, fixing coding sequences, and merging or splitting gene predictions, which looks like what might have been done in the UCA-At2g42245. It can also be used for adding various attributes, GO terms, pubmed info, or generic attributes. WebApollo actually uses JBrowse, but JBrowse itself has very flexible options for displaying annotations. The part about highlighting the alpha helix/beta sheets is not built in, but JBrowse can be configured to do lots of different renderings, and I could provide more details if you are interested. Disclaimer: I'm a WebApollo developer/JBrowse contributor.


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Is it possible to express the cistrons from a polycistronic insertion fragment in a single plasmid?
I have a insertion fragment that I wish to express from pUC19 in Escherichia coli. The insertion fragment is a sub-section from a larger operon sequence and contains just the last two cistrons from this operon.
I plan to insert this fragment into pUC19 under the control of its single lac promoter. Therefore, there will be two cistrons under the control of a single promoter (which is of course, very similar to how it would be expressed in the WT operon).
In my mind, expressing both the cistrons under the control of the single pUC19 lac promoter should allow both genes to be translated; once the mRNA is transcribed, both cistrons have their respective Ribosome Binding Sites upstream of their ORFs, and should be translated.
My question is, has anyone ever had experience expressing poly-cistronic fragments from plasmids using just a single promoter for the entire fragment? I cannot see any glaring issues with this in theory, but I thought i'd ask before I went ahead. Ultimately, I'd rather express both cistrons from a single plasmid, rather than express each cistron on a separate plasmid.
Cheers!
Izaak

If I understand correctly, you are seeking option for polycistronic expression. Have you considered using T2A or P2A sequences? These come from virus and essentially break polypeptide into two parts, so-called self-cleaving peptide T2A. Real mechanism of its work is that ribosome stalls on the sequence and unable to create peptide bond, effectively re-starting translation with next after T2A amino acid.
Of course, you lose independent control over expression, both products will be expressed at same level (but degradation might be different).
So, you should consider creating construct that looks something like that:
lac:gene1-T2A-gene2-stop
Thing is that a) it might not work in E.coli and b) it might not be necessary, because primary purpose of T2A is equal expression level of two polypeptides. And, if your 2 genes are big, for bacteria it is easier to handle two separate plasmids, rather than one but much larger.

Ahh, intresting! I don't T2A is necessary though; the genes themselves have their natural transcription termination sequences, so the ribosome should be able to 'parse' the ending of each ORF separating the products. The genes are prokaryotic, so I think the natal RBS's of the operons should work. I just wanted to check it over on here to see if there is any big no no's.

The genes form a hetrodimer together so equal expression is what I'm after  ;) cheers for the help. I didn't know about T2A, but its a useful one to know!

your guess seems correct. I never bothered with several-genes expression, so idk. however, since there is a plasmid for what you describe, it should work: https://www.snapgene.com/resources/plasmid_files/pet_and_duet_vectors_%28novagen%29/pETDuet-1/

never bothered with expression several genes in bacteria

pETDuet is close, but its not exactly what I want to do. pETDuet requires me to split the PCR fragment (containing both genes) so each of the two genes will be expressed under one of the two promoters on the pETDuet plasmid. There are two promoters and two separate MCS in this plasmid. I want expression under just one promoter.

However, I think I may order pETDuet just in case single promoter expression from pUC19 expression doesn't work ;) Cheers for the help man!

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Recessive alleles at Hardy-Weinberg equilibrium
I've run into a question that I disagree with others on but I would like to receive the input of others. The question is:
If a population is at Hardy-Weinberg equilibrium, which of the following can be predicted for the recessive alleles in the population? 1) They will eventually disappear, 2) They will be selected against, 3) They will be maintained at the same frequency, 4) They will be expressed in the heterozygous condition, and 5) They will become dominant.
Some people said that the answer to this question was that the recessive alleles would be selected against, but I interpreted the question as having the answer that the allele frequency of the recessive alleles would not change and instead would be maintained at the same frequency.
My rationale for this was that Hardy-Weinberg equilibrium means there is random mating and basically no radical shifts in allele frequencies from outside sources, such as gene flow, natural selection, etc. I would think that the allele frequency would not change, but I may be incorrect.
Is my methodology correct?

In short: No, you're wrong. Hardy-Weinberg is nothing but a formula that link genotypes frequencies to allele frequencies (under random mating). Allele frequencies will change in response to selection so does the genotype frequencies. The only think that doesn't change is the relationship between allele frequency and genotype frequency. (the above assumes that selection occurs on survival, not on fecundity).

@Remi.b I think you're conflating Hardy-Weinberg frequencies with Hardy-Weinberg equilibrum. The former are exactly what you say, "nothing but a formula that link genotypes frequencies to allele frequencies (under random mating)". The latter imply stable maintenance of these frequencies via the term equilibrium.

Let's go through the possible answers. Which of the following could be predicted? Not (1), because we don't know whether selection favors or disfavors the recessive alleles. Not (2) for the same reason. Not (4) by definition. Not (5) because recessive alleles don't magically become dominant.
This leaves us with (3), which also seems correct: not only do we know that frequencies don't change under the Hardy-Weinberg assumptions, but also an equilibrium is by definition a state at which frequencies remain the same.
An aside: this question fairly clearly recalls G. Udny Yule's confusion about the fate of recessive alleles, which lead Punnett to enlist G. H. Hardy's help in deriving Hardy-Weinberg equilibrium. Yule expected recessive alleles to decline in frequency by virtue of their recessiveness; Hardy showed otherwise.

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Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?
During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other when mentioning UAF or UBF, so I want to know if they are actually the same thing.
Another source of confusion is that Wikipedia has article for both:
https://en.wikipedia.org/wiki/Upstream_activating_factor
https://en.wikipedia.org/wiki/UBTF
Thanks in advance.

Many sources: http://www.ncbi.nlm.nih.gov/pubmed/7982918, http://jcs.biologists.org/content/126/21/4815.long

Another source: http://biochemical-pathways.com/#/map/2
If you look at nucleolus part of chart, there's only UBF mentioned.


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Why does liver wrap around inferior vena cava?

As shown in the image, the liver wraps around inferior vena cava, which takes blood from liver via hepatic veins. Is there an advantage of having the inferior vena cava closer to the liver rather than abdominal aorta? I am guessing it has to do with lower blood pressure in the veins, but I want to check.
It could also be evolutionary thing that has no reason for such structure, but that wrapping around structure seems to have a purpose.

Nice image, where'd you get that from? ;) I don't know much about this, so my guess would be that hepatic portal vein joins in to vena cava after leaving the liver, so the liver forms such structure around inferior vena cava instead of abdominal aorta.

I got took a screenshot from this website: http://www.healthline.com/human-body-maps/hepatic-veins.
Also about your point, there are also arteries flowing to the liver from abdominal aorta, so I can imagine liver wrapping around the abdominal artery as well.

I get your point. I think it could be that keeping vena cava nearer would be better (maybe to easily transport blood from hepatic portal vein due to its low pressure or some other reason I can't think of) or keeping abdominal aorta at an inch distance wouldn't be any bad or probably it was just a matter of chance ;)

It is really only a matter of two vessels passing "through" an organ; where they are situated depends entirely on their function. The IVC delivers it's supply to the right side of the heart "through" a right sided organ; the aorta leaves the left side of the heart and so is situated to the left of the IVC. Just makes the most sense anatomically in this case.

Possibly related to the absence of valves in the hepatic veins


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Determining the percentage of the query of an alignment from a BLAST output
Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that tells me how to calculate this.

I have given it a go and valued it as 145/147, but I'm not too sure on this. Can anybody clarify whether or not this is correct? Any help is highly appreciated

Please don't post images of text. Instead, use the formatting tools and add the text directly into your question. That way, we can copy it and test our answers. Also, since this is essentially a scripting question, please clarify what operating system you are using so we know what type of answer to provide. I assume you realize that your output shows that residues 4 through 146 of a 146aa query are aligned, right?

qcovs and qcovshsp are reported.. In standalone BLAST you can specify the output format too

How can I do it without using BLAST? Just by looking at this output.


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How do prions transmit their conformation to other proteins?
I was reading about prions and many sources say something to this effect:
"Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the misfolded prion form. In this way, the prion acts as a template to guide the misfolding of more proteins into prion form." (Wikipedia)
How can/does a prion cause another protein to change its shape to match the prion's?

As the definition says, they act as a template - think "mold"

@Gerhard Yes but how exactly does a protein mold another? Does the prion bind to it forcing it to change its shape? If so, why does that happen? If not what does happen?

They don't misfold other proteins. They do that to other prionic protein molecules. An auto activation of sorts.

@WYSIWYG but if prions are misfolded proteins, that would mean that when they "misfold" other "prionic protein molecules", they're misfolding other proteins...in fact "The protein that prions are made of (PrP) is found throughout the body, even in healthy people and animals...The normal form of the protein is called $PrP^C$...[which is] a normal protein found on the membranes of cells."

Is there a confusion between "misfolded" and "denatured"? Although I'd agree that " misfolded" probably is not the best choice of word here.

@Gabriel PrPc is capable of switching but at a lower rate. This is accelerated in the presence of the alternative (beta-rich) state -- PrPsc (hence autocatalytic). I meant that the prion protein does not affect any random protein (which the statement in your question implies). The mechanism is mostly unknown. There are many other prion like proteins too, which are not pathogenic and such switches are involved in memory formation as well.

It is thought that infectious prions exist as clusters forming a crystalline structure. When a protein with the same primary structure is encountered but with a different tertiary structure, the normal protein undergoes a conformational change in order to integrate into the cluster. Presumably there are molecular forces involved that induce the conformational change.
http://www.rsc.org/chemistryworld/Issues/2005/October/prions.asp

Like other forms of amyloid, aggregated prions form a beta-sheet structure, where individual beta-strands are linked together by hydrogen bonds between their extended peoptide backbones, and hydrophobic interactions between the side chains on either side of the peptide backbone.  The beta-strand at each end of the beta-sheet has unpaired hydrogen bonds and hydrophobic side chains on the exposed end, which act as a template to link with an incoming prion.  Thus an incoming prion molecule can be unfolded as it joins with the exposed beta-strand, rather like a zip, and a new exposed edge is formed, waiting for the next prion to join.
This chain reaction is rather like normal crystalization, except that the process of aggregation also involves a conformational change from a folded globular molecule to an extended beta strand, which is catalyzed by the presence of existing beta-strands.  So the aggregation of prion effectively catalyzes more aggregation in a positive feedback loop: Once a seed has formed, the aggregation process will continue to unfold and recruit normal protein molecules.  Thus BSE/CJD was originally thought to be a virus as the aggregated conformation appears to be "infectious", passing its information about its aggregated state to a native folded prion molecule.
See for example:
http://www.annualreviews.org/doi/abs/10.1146/annurev.bioeng.4.092801.094202
http://www.annualreviews.org/doi/abs/10.1146/annurev.pathmechdis.3.121806.154326
http://www.nature.com/nrn/journal/v11/n3/abs/nrn2786.html
Or just google "prion aggregation mechanism review"


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Why is polysome loading affected by double stranded structure?
Why polysomes are not able to load properly onto a transcript if a transcript has a double-stranded structure in it?

You mean to say a single ribosome is loaded but multiple ribosomes are not loading? Do you have any data on this or you just heard it somewhere? Usually secondary structures are resolved by elongation factors (4A). In general secondary structures will impede ribosome movement. You should add more details in your question.

I was reading the following article "C. elegans and H. sapiens mRNAs with edited 3′ UTRs are present on polysomes". According to it, polysomes are not able to load properly on to the transcript if two inverted alu repeats make a double stranded structure within a transcript.


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Need clarification on Coalescent with Recombination
I've been reading about recombination with coalescent. The link to that file is as follows:
http://www.stats.ox.ac.uk/__data/assets/pdf_file/0008/4688/Reading_for_Recombination.pdf
I get the part where it says (page 142) that the rate of a coalescence event is k(k-1)/2 and the rate of recombination is kp/2. The image they have on the same page shows the intensity of coalescence and recombination. But I don't quite understand how those have been calculated. I mean the first event is a recombination event and not a coalescence event. I know they are using the rate formula I've mentioned above but I don't understand what sequences they are considering. If someone can give me a detailed answer I would really appreciate that.
I've attached the image as-well incase you don't want to read the pdf :)

Can you provide citation for the now-broken link?

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Need clarification on HKA test
I understand that HKA test tests for neutrality. And under neutrality we say that "ratio of segregating sites with species (S1) and fixed differences between locus (F1)" (S1/F2) at one locus is equal to S2/F2 of another locus.
But what will S1/F1 > S2/F2 signify? And what will S1/F1 < S2/F2 mean?


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largest bootstrap support
I was reading about bootstrap in phylogenetics and it got me wondering that amongst all of the methods (UPGMA, Maximum Likelihood, Parsimony, Neighbour joining method) which method generally provides the largest bootstrap support? Or does that vary from problem to problem?

For sequence data, UPGMA is not really accepted anymore. Maximum parsimony and Neighbour-joining are usually used because they are quite fast and they give you a relatively good idea about the phylogeny.
You should not decide based on which method gives you the highest bootstrap.
For publication, it is recommended to use either Bayesian consensus tree (MrBayes is popular program) or a maximum likelihood tree (RAxML or MEGA are popular for ML). For maximum likelihood bootstrap (BS) is used and the confidence is relatively high if at least reaches 80 (%). For Bayesian, instead of bootstrap Bayesian posterior probability (BPP) is used. For BPP it has to be at least 0.95 to be significant.

Any sources you could add?


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How does translation invariance in vision happen?
Convolutional neural networks are very popular these days in computer vision.  One of the things they do quite well is recognize objects with translation invariance.  The way they do this is by "tying together" the strengths of certain synapses, so that they all change in the same way during learning.  This is apparently not biologically plausible.
My question is this: what is known about how biological visual systems achieve translation invariance.  For example, how is it that if we learn to recognize a new object with our left eye, we are automatically also able to recognize it with our right eye.  What is the neuro-biological basis for this invariance?  My field is mathematics/machine learning, not biology, so I would appreciate responses that are not overly technical (although I understand that might not be possible).
Thanks!

Great question - unfortunately I think what you are asking is actually quite broad. I'm hopeful someone might come along with a reasonable answer, but in fact this is a very open field in biology right now. We know a bit about what areas of visual cortex show some translation invariance in their tuning, but my understanding is that's about it, beyond computational modeling that shows feasible approaches.

From the perspective of machine learning, consider that the visual cortex has many more layers than a typical artificial neural network, and the layers are interconnected in a much more complex and less strict hierarchy. This organization allows for incredibly complex computational abilities. Importantly, biological neural networks have simultaneous bottom-up and top-down processing, allowing brain areas with very abstract representations to make predictions about less abstract features. Additionally, attention and related processes allow for online reorganization of networks.

@BryanKrause you gave a very good general insight to seemingly broad question. I would like to know if you pulled this insight from a paper? I would like to read it. Especially about "simultaneous bottom-up and top-down processing".

@gfdsal I didn't have a single paper in mind, but Felleman, D. J., & Van Essen, D. C. (1991). Distributed hierarchical processing in the primate cerebral cortex. In Cereb cortex. is a good place to start. You could also look for recent reviews about "predictive coding", though this is only one of the schemes/frameworks used to think about hierarchical processing and it remains to be seen if it's the best description. I also think you'd find at least some discussion in an undergraduate neuroscience textbook like Purves or Kandel.

+1 for providing credible references and direction to take.


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What is the expected number of children that need to be born for every possible point mutation to occur once?
I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:

In the Paleolithic, with 100000 children per generation, it would have taken 8000 generations, or 160000 years, for each possible mutation to occur once.
Today, with more than a billion children per generation, every possible point mutation now appears about twenty times per generation, or almost yearly.

Using his probability, I get that you need 1 / (175 / (3 * 10^9)) (which is about 17 million children). But he writes that for the Paleolithic era, you need 10000 * 8000 = 80 million children! Can someone help me reason out how he got that number?
EDIT
My math was wrong :-) leaving up the og calculation. Here's the reference that he cites:
"Estimate of the Mutation Rate per Nucleotide in Humans" by Michael W. Nachman and Susan L. Crowell
In the abstract they write "The average mutation rate was estimated to be 2.5x10^-8 mutations per nucleotide
site or 175 mutations per diploid genome per generation."

Does he give a reference for this mutation probability? I remember smaller numbers.

This is assuming that mutation rates are constant across the genome, which is generally not the case (see e.g. Smith et al. 2002. Deterministic Mutation Rate Variation in the Human Genome). So I think the statement/calculation rests on unfounded assumptions, and therefore vote to close as "primarily opinion-based".

The authenticity of that text seems doubtful.

I added the reference that he cited.


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Can one use a hemocytometer on a compound upright microscope?
I'm posting this as a follow-up on What to look for when buying a light microscope?. The answerer states that you would need to use a an inverted microscope to count cell in the hemocytometer(counting chamber).
I've read, partly, a book on lab diagnostics tests and it was not written that there. Moreover, they mentioned things about microscopes featuring a compound upright microscope both in words and picture.

Yes, you should be able to! The reason I suggested the use of inverted microscope was because I put a number of other things in the same sentence such as dishes etc. Inverted microscope is used in those cases to reduce the distance between the objective and the sample when looking at the dish with cells. In most cell culture rooms that I have worked in, an inverted microscope is used! Inverted light microscopes also tend to have a phase contrast, which is helpful in viewing cells!

I have now made an adjustment to my response to reflect this point!

@Bez Sorry to bother, but what features would I want to have on my microscope(on a upright compound one) for lab work(urinalysis, blood work, cytologies, histologies, fecals and all other)?

I'm a molecular biologist (fluorescence and cell culture) so I do not know much about urine or blood work analysis microscopy. This is best posted as a new question but please show some degree of research into the question to prevent it from getting a close vote!

Yes it can. You will want to use a thin hemocytometer and the working distance of the objective (20x) needs to be long enough to focus both the cells under the cover glass and the grid under the hemocytometer. Because you are looking at it from the top it would be helpful probably to have some phase on the scope to increase your contrast so that you can more clearly see the grid.
Hemocytometers are most commonly used with inverted microscopes because inverted microscopes are the most convenient microscope for performing tissue culture, and 's a commonly used to count cells when passaging or setting up an experiment etc, as they allow you to view cells in a culture plate. Upright microscopes require that you make a slide.

You can use a hemocytometer(counting chamber) on whatever microscope for transmitted light, regular scope, inverted, whatever. It doesn't make any difference.
But you should keep in mind what a counting chamber is designed for: to count red or white blood cells, reticulocytes, yeast cells, whatever.
They're not designed with having the best possible image in mind. Their dimensions fall far outside the specifications microscope optics are calculated  for.
I measured a few (regular Thoma from the well known brand Assistent): thickness is 4 mm. The standardized coverslips to be used with those are 0.4 mm thick.
There's a very small chance, some minor distortion will be visible in the image ;-)...


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Hydrophobia Outside of Rabies?

RELATED:
Why does rabies cause hydrophobia?
Agony, Hydrophobia and viruses in the light of evolutionary principles

Has hydrophobia been found outside of rabies?
I have only seen it being mentioned as a symptom of rabies.

You are correct that hydrophobia is often considered pathognomonic of rabies. However, I offer for your consideration:
Hydrophobia as a rare presentation of Cotard's syndrome: a case report.1
Cotard's syndrome itself is a bizarre psychiatric condition that the authors of the above paper define well:

Cotard’s syndrome is a rare condition where the central symptom is a nihilistic delusion, which, in its complete form, leads the patient to deny his own existence and that of the external world.

The patient described in this case report harbored delusions that his internal organs were shrinking. He asserted that his abdomen would rupture if he internalized anything. The hydrophobia was secondary to this concern. When given a glass of water he showed a panic reaction and attempted to keep away. Orientation and memory remained intact.
The authors go to length to point out that this was not, in fact, a case of rabies (as thought that were in question at this point!). Also, the patient himself was not aware of symptoms of rabies, ruling out "rabies hysteria" (a hypochondriacal delusion that one has rabies).
Hydrophobia, then, is a rare manifestation of a rare psychiatric disease in addition to the more frequent and well-known association with rabies.

1. Nejad AG. Acta Psychiatr Scand. 2002 Aug;106(2):156-8; discussion 158.

Hydrophobia is mostly attributed to rabies, most of the sources refer rabies as hydrophobia. Technically Hydrophobia is the intense fear of water.

Hydrophobia is an intense, irrational fear of water that can be commonly diagnosed at childhood and should be treated as soon as possible. Certain types of hydrophobia may also appear in later stages of contracting rabies, which would require treatment on an immediate basis.

Also the Wikipedia link for Rabies states that

Signs and symptoms may soon expand to slight or partial paralysis, anxiety, insomnia, confusion, agitation, abnormal behavior, paranoia, terror, and hallucinations, progressing to delirium. The person may have hydrophobia.

So rabies and hydrophobia are distinct and hydrophobia is a symptom of rabies.

Hydrophobia may, however, more readly be confronted with hysteria, acute mania and tetanus.

Hydrophobia is incidental to other diseases, it can be observed, occassionally, in tetanus,hysteria,cynanche,tonsillaris,tracheitis and certain inflammations in stomach. Tetanus is strongly believed to cause intense hydrophobia conditions.How ever, there is always a belief of hydrophobia linked with rabies.

The pathology of Hydrophobia and Tetanus is found to have great similarities and there is a great similarity in the distribution of lesion in the central nervous system as well as a certain analogy in the kind of lesion. The special localization of symptoms of both disease, in the tongue,throat and neck was associated with the special prevalence of the lesions in the medulla oblongata and especially in the neighborhood of the nuclei in the fourth ventricle etc.
Reference :THE Medical Times and Gazette - J & A Churchill

So it is possible to cause hydrophobic conditions when Tetanus is affected and also hydrophobia can occur from mental disorders.


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Is heat released during work due to ATP breakdown or a increased blood flow?
Is heating up of a body during work or exercise an effect of increased speed of blood or is it because of the extra energy released while harvesting energy from the ATP

ATP breakdown is the major cause of it. The body can use 45-55% energy liberated by ATP hydrolysis, and the rest part dissipates as heat.

Additionally, increased blood flow occurs as a result of increased ATP hydrolysis.

@Forest umm I doubt it. Any reference for that?

@another'Homosapien' I'm not sure why the first suggested edit you made was automatically rejected, probably because I was editing my own post at the time. Could you please suggest that original edit again and I'll approve? Thanks!

@another'Homosapien' - I figure that increased blood flow is due to increased heart rate, which means burning more energy, which must involve ATP hydrolysis. I suppose I could have included those steps in my first comment...Does this make sense to you, though?

@Forest as you say "increased heart rate, which means burning more energy" the only thing I can conclude from this is that increased heart rate leads to more ATP hydrolysis. So ATP hydrolysis seems more like a result than a reason for increased heart rate.

Is heating of a body the result of increased blood flow or extra energy from ATP?
It is mainly because of the breakdown of ATP (Adenosine Triphosphate, a type of nucleic acid with an Adenosine base, a Ribose sugar, and 3 Phosphate groups), alternatively and more formally known as ATP Hydrolysis. During hydrolysis by water, ATP splits into Adenosine Diphosphate (ADP) and an inorganic Phosphate (Pi), releasing some energy. I'll explain more below how exactly this works.
How or why does ATP Hydrolysis release energy?
If you take a look at a diagram of an ATP molecule, you'll notice that it has 3 phosphate groups, each with a Hydroxyl group (-OH) that has a net negative charge due to Oxygen being highly electronegative and hogging electrons from the Hydrogen bonded to it. Consequently, you have 3 molecules with slightly negative charges attached to each other. If you've ever played with magnets, you'll know that like charges repel. So overall, the ATP is highly unstable because of these repulsive forces that are situated so close to each other. When the bond between the 2 inorganic phosphates is broken, a large amount of energy is released. Here's a diagram from Campbell's Biology 9th ed (note that the Hydrogens in the phosphates are not shown for simplicity):

When the last phosphate is broken off, you are left with one molecule of Adenosine Diphosphate (ADP) and an inorganic phosphate group (Pi). Energy has been released. However, this is not the entire story. Generally speaking, ATP Hydrolysis does not occur without another component: an endergonic process. An endergonic metabolic process is any which requires energy input in order to proceed. Think of it with the following analogy: imagine a ball trying to roll uphill by itself. At the bottom of the ramp, the ball is very stable and has low potential for performing work. But uphill, the ball would have a higher potential energy. It is impossible for the ball to roll uphill from a state of low energy to a state of high energy. Thus, we first need an input of energy--say the mechanical energy of our hand pushing the ball--in order for it to move up.
Our endergonic process (such as in protein synthesis by a ribosome or the phosphorylation of glucose in glycolysis, the first step of cellular respiration) requires some energy input from ATP in order to proceed in an exergonic manner--that is, in order to release energy without any help. With our analogy, this is like pushing the ball to the top of the ramp and then letting go, allowing the ball to roll back down from a state of very high potential energy (and therefore instability) to a state of low energy. The energy that we had to input from ATP is known as "activation energy", because it's literally energy that we need in order to unlock or "activate" an endergonic pathway.
Example of ATP Hydrolysis releasing heat:
When you have an infection in your body, your hypothalamus will raise the body's set temperature point to induce shivering. Shivering consists of many muscle contractions, all of which require hydrolysis of ATP. The result is a release of a large amount of heat that increases body temperature to a point at which pathogens cannot survive.
What about blood flow?
Blood flow does not actually produce heat by itself, but it can direct heat to the surface of the skin, such as when the body needs to cool down. The main source of heat in the body remains the ATP.
EDIT: much of the information here can be reviewed in this wonderful YouTube video by Andrew Douch

I'm afraid this is not very accurate. ATP is only one form of energy in metabolism, and ATP hydrolysis is thought to be only about 1/3 of heat loss in typical oxidative metabolism; respiration itself, ion gradient dissipation, and ATP synthesis make up the larger part. Note that this concerns heat, for free energy, ATP utilization is indeed the major portion. The details of ATP structure and activation energy are not really relevant here, this is a question of thermodynamics.

My apology if the post is not helpful to the OP. I was just trying to be thorough so that I wouldn't have to explain various things in multiple posts. I felt like ATP structure was relevant, since structure is related to function and the OP's question was related to ATP function in heat production. Also, I'm about 99% sure that ATP's role in metabolism and activation energy are fairly relevant to thermodynamics. I was just trying to explain "how" exactly the heat is produced, since I've had far too many teachers who just tell me "well, it just does".

Is heat released during work due to ATP breakdown or a increased blood flow?
Short answer: neither. Most of the heat generated is due to poor efficiency of metabolism.
It is a common misconception that ATP is the same thing as energy when it comes to metabolism. ATP is certainly a very important energy carrier, but human metabolism is far from efficient at capturing the energy in nutrients in the form of ATP. A large fraction of the energy stored in sugar, fat, or other substrates is lost as heat already in the process of making ATP, much in the same way a car engine runs warm because most of the energy in gasoline cannot be captured in a useful form.
It is thought that most of the heat produced during oxidative metabolism (as in muscle contraction) occurs during respiration and ATP synthesis in mitochondria. This is probably because the mitochondrial respiratory chain involves physical pumping of protons across membranes (chemiosmosis) which causes a lot of "friction" (rougly speaking). This review estimates that only about 1/3 of the heat generated comes from ATP utilization and downstream processes, like actin-myosin contractions. It is difficult to quantify heat loss in metabolism, so I think all estimates should be taken with a grain of salt, but I think this general picture is correct.


text:
What happens to the cell during post-hypothermia?
A friend of mine said that the cell membrane somehow changes after rewarming from hypothermia and that the body does not recognize it's own cells, thus leads the immune system to attack it self. Is this true? And do anyone know how/why the cell changes?

interesting question - we use therapeutic hypothermia in critically ill patients following cardiac arrest  commonly in the hospital - I've seen patients wake after 48h of hypothermia and have no long term effects (at least that are detectable) - not sure how things change on a cell membrane level or whether or not this has been studied in  patients

here is a link to a open access paper from the journal Circulation that discusses therapeutic hypothermia and how long/how cold we keep people - as well as a discussion of whether or not we should cool people longer and/or colder... should be useful for this question... http://circ.ahajournals.org/content/131/7/669.long


text:
Bioinformatics basics
What are the basic differences between genbank, NCBI and entrez gene?
And please tell some books and webpages where I can get more about the databases .(currently I'm using Bioinformatics and functional Genomics by Pavsner)

Unfortunately, this is not a "please hold my hand and walk me through this paper/concept/idea" site. I strongly suggest you take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question. Use Google to find websites, that's what it's there for. Go to the databases themselves, they all have help pages.

are you a university student or perhaps a graduate student? there are resources to help with this sort of thing - but it depends on what your status is - but I completely agree with MattDMo, though - this site is not what you need

Genbank is a database of nucleotide sequences that are public.
NCBI stands for "National Center for Biotechnology Information" (in the US).
Entrez is NCBI's retrieval system.
You can find more information in this article
I don't know which kind of databases you are looking for, but there are hundreds of them!
In this wikipedia article there are some of them.

This is probably what the OP was after. This answer answers the question correctly and succinctly so I'm not sure why it received a downvote other than you were setup to fail because of the off-topic question.


text:
Why don't onion root tips show mitotic stages?
It was back in the winter that we did the Onion root tip experiment in college. We were able to see wonderful stages but now in this monsoon-autumn transition the root tips hardly show any mitotic stage. Why is it so?


text:
What is meant by topology of DNA?
I couldn't find anything on internet that would give a clear-cut idea about what it could be.

Lehninger has got a good section on dna topology along with the function of topoisomerases.

Topology is the study of flexible geometries. That is, what properties do objects have when you're allowed to stretch and bend them (but not allow them to break or pass through themselves). This is the origin of the saying that to a topologist there's no difference between a doughnut and a coffee cup. Topologically, they're the same object. If the doughnut and coffee cup were made of really elastic putty, you could  remold one into the other without cutting it, or allowing it to pass through itself.
So what does this have to do with DNA? Well, while DNA is stiff on short scales (dozens of base pairs), when you get long stretches of DNA it's very flexible. You can bend and wrap the DNA up. But there's a limit on what you can do without breaking it or letting it pass through itself. (For circular DNA) You can't get knots, and the intrinsic double-helical "twist" of the DNA can't be changed.
There are various enzymes in the cells (helicases, topoisomerases) which are responsible for controlling this coiling and twisting. The way they work is to (temporarily) make a break in the DNA, pass the DNA strands through the cut, and then reclose the strands. That is, they change the topology of the DNA. This is how you get "overwinding", "underwinding" and "supercoiling"
So "the topology of DNA" is talking about the properties and geometry of DNA that it has if you treat it as an unbroken floppy noodle: how it's wrapped up and how it's twisted.


text:
Why are Natural Killer cells considered cells of Innate immunity?
Kuby Immunology says

They (NK cells) do not express antigen specific receptors and are considered part of the innate immune system.

Though
 they also have receptors for antibodies that bind to NK cells and help detect antigens or pathogenic cells that are killed by the secretions of their cytotoxic granules.
Couldn't we then call them cells of Adaptive immunity?

What edition are you using? As I mentioned in my comments to one of your other recent questions, immunologists no longer consider innate and adaptive immunity to be two entirely separate things. Cells thought to be involved in one are now seen to be involved in the other, and the processes are getting very blurred. You are quite correct that NK cells are involved in antibody-dependent cell-mediated cytotoxicity (ADCC), which is wholely an adaptive response due to the presence of antigen-specific antibodies on the surface of the target cell. Your textbook is simply incorrect.

@MattDMo It is the new edition, 7th Ed by Owen, Punt and Stranford.

@MattDMo Following your comment I have a question. I was reading Wikipedia page on Innate lymphoid cell and stumbled upon this paragraph-'The distinction between the innate and adaptive immune system focused on the innate system’s nonspecific nature and lack of memory.As information has emerged about the functions of NK cells and other ILCs as effectors and orchestrators of the adaptive immune response, this distinction has become less clear....  (to be continued in second comment)

Some suggest the definition focus more on the germline-coding of receptors in the innate immune system versus the rearranged receptors of the adaptive immune system.' What does the third line mean?

Yup! you've answered your question. The NK cells donot have rearranged receptors. Nor do they have any memory.

@Polisetty I agree with MattDMo the NK cells show immunological memory according to Wikipedia. But I don't understand the rearranged receptors. What are they?

The BCR and TCR (B cell and Tcell receptors) are formed by V(D)J recombination which accounts for their variability. This makes the receptors specific to a particular antigen. Kuby's got a whole chapter on that. Thanks for the memory thing, din't know! Anyway, found this article for nkcell memory http://www.cell.com/immunity/abstract/S1074-7613(15)00398-2


text:
How's maturation different from differentiation/activation of B lymphocyte?
I was reading Wikipedia that said $-$

In mammals, B cells mature in the bone marrow, which is at the core of most bones. In birds, B cells mature in the Bursa of Fabricius, a lymphoid organ.

So it's got the name B-lymphocyte.
My questions:
Is the transformation of Haemotopoetic stem cell to Immature B-cell called maturation of B-lymphocyte and the transformation of Immature B-cell to Mature B-cell through a Naive B-cell called differentiation/activation of B-lymphocyte?
The maturation occurs in Bone-marrow and Activation/differentiation in Spleen or lymph nodes. The whole process maturatiion + activation is called development. Am I correct?
Note: My understanding of Immature B-cell is that it is a cell in the series of B-cell development that expresses BCR (an IgM) for the first time. While Mature B cell is a B lymphocyte which after interaction with antigen has turned into either Plasma cell or Memory cell.

yup. activation is when a naive b-cell binds an antigen generally in the secondaries. maturation is in the primaries..

Initially I thought it should be the opposite. You see Immature transforming into Mature B-cell, common sense says it should be maturation but it just the opposite. Well what is differentiation and development then? @Polisetty

@Polisetty Do you mind sparing your time explaining some very confusing immunological concepts to me.? They are Isotype, Allotype and Idiotype.

Why not ask a question? Ill try answering it


text:
Books: DNA replication
In what books can I find a detailed literature on the mechanism of function of different enzymes and proteins involved in DNA replication of E. coli ?

Please have a look at the tag-wiki for book-recommendation. You have to provide more details.

Here's just the right book - Lehninger Principles of Biochemistry, 6th Ed
By David L. Nelson, Michael M. Cox.
A Google.book link to it.

Molecular Biology of the Gene
(James D. Watson
Cold Spring Harbor
Laboratory
Tania A. Baker
Massachusetts Institute
of Technology
Stephen P. Bell
Massachusetts Institute
of Technology
Alexander Gann
Cold Spring Harbor
Laboratory Press•
Michael Levine
University of California,
Berkeley
Richard Losick
Harvard University) has a detailed description of the various processes involving genetic material.
Find a pdf file here: http://tocs.ub.uni-mainz.de/pdfs/118526545.pdf

Check this online book on NCBI: An Introduction to Genetic Analysis. 7th edition

Let’s examine each of these components and see how they fit together to produce our current picture of DNA synthesis in E. coli, the best-studied cellular replication system

I used it a bunch while studying E. coli for my master degree, lots of really usefull information.

Biochemical Pathways (G. Michal, D. Schomburg) has nice old-school schematics such as this one, in addition to the text.


text:
What is the evolutionary significance of germ cell migration to gonads?
Why do germ cells have a different origin than the gonadal organs? Does it help the animals in any way?
P.S. I know it is difficult to answer whys in biology but is there any theory as why do they have different origins.

Germ cells are protected from mutations and other recombination events. It is therefore essential to keep them isolated. Germ cell segregation, therefore, IMO, happens very early during development. You can have a look at this post.

@WYSIWYG Germ cells are protected from mutations and recombination? I don't get this claim. They are not. Sure, most crossovers happen during meiosis but meiosis occur only at the very last step in the germ line.

@SanjuktaGhosh I am having a hard time with the semantic behind the post. Can you please help me out and explain how does the question differs (if it differs) from Why do we have specialized sexual organs??

@Remi.b I'm actually asking the reason behind germ cell migration. Why did animals evolve with such a different way of germ cell production. You know cells coming from a different region to the gonadal ridge instead of actually developing from the gonadal ridge(the future gonad). Has it got any evolutionary significance? Would it affect the animals if the PGCs developed from the gonadal rigde (post gastrulation structure though) itself? That's what I mean.

@Remi.b I am not talking about meiotic recombination. I am talking about transposon expansion and other non-meiotic recombination events. Plus, it is necessary to protect the germ cells from mutations. However, not much is known about how DNA repair mechanisms are highly efficient in germ cells. There are piRNAs to suppress transposon expansion. Overall, genomic instability is actively prevented in germ cells.

@WYSIWYG Could you suggest any e-book,website or paper from where I can learn about non-meiotic recombination? Besides how can somatic mutation affect PGCs?

@SanjuktaGhosh You can simply google recombination and you'll get resources. Non-meiotic recombination events include homologous recombination, VDJ recombination, transposon expansion etc. By somatic mutations I meant general mutations that can arise in any cell. Ignore the word "somatic" (it was a mistake).


text:
What does a diamond symbol actually mean in pedigree?
Does it mean a person who is neither a male or a female, a homosexual or an individual whose sex is unspecified?

I find myself voting to close a lot of your questions as unclear or homework - could you start making effort to make questions answerable and effort to answer for yourself

A simple google search gives tons of answers. Try not to ask too trivial questions just for the sake of posing a question.

I'm sorry. I'll keep it in mind.

The figures in this article show symbols commonly used in pedigrees. Squares represent males, circles represent females, and diamonds depict individuals of unknown or, for reasons of confidentiality, disguised gender. A double line between parents indicates consanguineous marriages (between blood relatives) (see Figure 3). Filled symbols represent individuals who display a certain trait, such as an inherited disease. Bars next to the symbols represent genetic loci, and different alleles are color-coded. Diseasecausing mutations are shown as stars or crosses. Symbols that are half filled indicate heterozygous individuals, but often this information isn't known.

From Wikipedia:

If the sex of the person is unknown a diamond is used

Sources:

http://www.biologyreference.com/Oc-Ph/Pedigrees-and-Modes-of-Inheritance.html#ixzz43btGJSuv
https://en.wikipedia.org/wiki/Pedigree_chart


text:
How are the two ATPs (properly 1.5 though) formed from oxidation of 1 FADH2?
Each ATP Synthase has three sites for binding three sets of ADP and Pi, so when the H+ pass through the a and c subunits are they (3 ATPs) not produced for FADH2 substrate?
Besides is the respiratory chain linked to the phosphorylation process apart from the trasfer of H+ ? How does the cell know which substrate has been oxidised and how much ATP is to be produced?

FADH2 substrate does increase the H+ gradient by 6, and so increases the ATP Synthesization "potential" by about 1.5 (6/3.3). the difference between the NADH and the FADH2 substrats are mainly the different path in the electron chain. NADH uses Complex1, and FADH2 is part of Complex2, which have different ability to to pump H+ out. (but of course there are many other differences).
About the second question, it's a really broad subject involving the Krebs cycle and Glycolysis among other subjects. it is mainly a matter of enzyme regulation. The regulation affect both the electron chain and the ATP synthase.


text:
Is there one centomere for the two chromatids in a dyad?
I have no explanation for this. It is all I have to ask.
Thank you

Each chromatid has a centRomere. A chromosome is a pair of sister chromatids (general term)... also known as a dyad in meiosis. Tetrads are the precursors to separated dyads in meiosis. Having centromeres is super important for being able to pass down genetic information in eukaryotic cells. Prokaryotes and archaea have similar structures to physically keep track of their DNA.


text:
Is complete linkage found in all four chromosomes or only Y-chromosome of Drosophila?
Male Drosophila shows complete linkage. Is it observed for all four chromosomes or only the Y chromosome?

All chromosomes. There is no crossing over in males in Drosophila. Check out the related question Why doesn't recombination occur in male Drosophila? for sources and context.

Hi @Christiaan, could you clarify your comment? I thought the OP was asking if the complete linkage in male Drosophila was for all chromosomes or just the Y, to which the answer is "all".

I don't question the validity of the answer, but the norm at Bio is to elaborate on your answer. For example, where did you obtain your answer from (references, sources)? Why is it all the chromosomes and not one? How do you know? As of now, it's a one-liner and this is generally not suitable as an answer, but more as a comment.

+1. However, it makes me wonder if this question is a dupe from your linked post?

Probably? Not sure how these things work.


text:
What is meant by electron transfer potential?
I was reading a text and came across the term. What does it mean? The sentence said 'The driving force of oxidative phosphorylation is the electron transfer potential of NADH or FADH2 relative to that of O2. '

https://en.wikipedia.org/wiki/Reduction_potential

the electron transfer potential is based on the difference in the affinity of elements/molecules to bind electrons. the affinity of the element derives from it's components as shown in the elements table, just like all other characteristics. for example, oxygen has higher affinity to bind new electron than carbon. the affinity of the molecule derives from the atoms that build it, their electric potential and the connections between those atoms.
this potential between the two elements/molecules (lets say: NADH, O2, iron–sulfur clusters) holds energy that can start a reaction which will never start otherwise.
I have tried to keep it simple. for more reading about oxidation-reduction ( reactions involve the transfer of electrons between chemical species) read TERMODINAMICS AND CHEMICAL KINETICS p.255 as suggested by @Roland.

Could you add a reference? Happy to upvote then

You should add the precise definition of electron transfer potential I think, as it's a relatively unusual term. Perhaps the best way is to describe it from the Nernst equation. Would suggest p.255 in this book: https://books.google.se/books?id=Gd1NIGrYOEoC&pg=PA255#v=onepage&q&f=false


text:
How does chromosome fusion get fixed in the population?
It's well known that one of human chromosomes is the result of fusion between two chromosomes in a primate ancestor. If we put anthropocentrism aside, it becomes clear that fusion events happened a lot of times, since chromosome count varies in different species.
Yet some people claim that while fusion event is probable, getting it fixed in the population is not, because it would require simultaneous mutation in two animals of opposite sex.
Could anyone explain in layman terms the scenario of this trait's propagation? I may only suppose that even if one parent has two distinct chromosomes and another a single fused chromosome, then two chromosomes may attach to the fused one, and then (probably) get fused themselves, thus leaving fewer and fewer specimens with distinct chromosomes in each generation. Is this a viable and likely scenario, or is some other way of propagation more likely?

Looking at this 2001 review paper by Rieseberg: http://evolution.powernet.ru/library/Scienc9.pdf (especially Box 2), drift and inbreeding are suggested ways that chromosomal rearrangements can become fixed. These forces are strongest small, isolated populations, such as populations experiencing the founder effect.
Another model discussed in that paper is the suggestion that some centric fusions (Robertsonian translocations) lead to little or no loss of fertility in the heterozygotes.


text:
What is two photon calcium imaging?
I have encountered the term "two photon calcium imaging" in a few papers.
I have tried to look in the internet but can't understand what this technique actually is.
I will be very happy for recommendations for a good internet source.
For example:

what does the "two photon" means?
how does the implement look like?
Is it sensitive to absolute voltage or voltage changes?
Does all relevant (genetically engineered) neurons light in the same color?
Is it the color that is measured or the intensity of the color?
Is the purpose of this technique single neurons or brain pathes?

Thanks!

what does the "two photon" means?

Ordinary confocal microscopy uses single photon of laser light to excite the molecule of fluorescent dye.
In two photon microscopy you use two photons, with lower energy, which cannot excite the molecule of dye on their own, but their interference in a specific place leads to summation of their energies and to excitation.
This has benefits such as decreased phototoxicity and increased precision (resolution) especially in z-plane.

how does the implement look like?
  Does all relevant (genetically engineered) neurons light in the same color?

There are two types of fluorescent dyes for 2-photon Ca2+ imagining. Since you want to measure local concentration of Ca2+, you can either use a chemical which chelates the calcium ions and changes its conformation and fluorescent properties based on that e.g. fura-2.
Alternatively, you can prepare fused protein from calmodulin ( CALcium MODULated proteIN) and some fluorescent protein e.g. GFP and transfect the cells with this product.
This means you can transfect different cells with different GFPs and get different colors. Depends on the actual experiment design.

Source

Is it the color that is measured or the intensity of the color?
  Is it sensitive to absolute voltage or voltage changes?

You can analyse fluorescence intensity changes. The derived fluorescence intensities and ratios are plotted against calibrated values for known Ca2+ levels to learn actual Ca2+ concentration. Source

Is the purpose of this technique single neurons or brain paths?

Actually, with a good interpretation of the data it can be used for analysis of both.
For more information about calcium imaging, see for example: http://www.cell.com/neuron/fulltext/S0896-6273(12)00172-9
or http://www.pnas.org/content/100/12/7319.full
or corresponding wiki articles:
https://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
https://en.wikipedia.org/wiki/Calcium_imaging


text:
what is the meaning of VIP-cre::LSL-TOM::SOMGFP(GIN) mice?
I am reading the following paper and the researchers use

"VIP-cre::LSL-TOM::SOM-GFP(GIN)"

mice (page 4) for multi cell patch clamp and

"VIP-cre::LSL-TOM and SOM-cre::LSL-TOM"

mice injected with AAV1 for two photon calcium imaging.
I have tried to look it up in the web.
I understand, for instance, that AAV1 is an engineered virus, and that CaMKII is a promotor, that TOM is a red fluorescent protein, GCaMPis created from fusion of green fluorescent protein with other peptides etc.
However, I have a dificulty in putting together the pieces and understending the whole meaning of "VIP-cre::LSL-TOM::SOMGFP(GIN)" (and the other mice types memtiond).
For example:

Take a VIP-Cre mouse. Does it mean that every VIP neuron in this mouse contains a Cre sequence in it's DNA?
What about other neurons, can they contain Cre also?
When they inject AAV1 virus to VIP-cre::LSL-TOM mice, does this mean that all neurons get the virus? including the VIP and SOM neurons?
Say I have an "VIP-cre::LSL-TOM::SOM-GFP(GIN)" mouse. I understand that VIP cells will be colored red and SOM cells will be colored green. So, why the VIP cells need the Cre promoter and the SOM cells don't?

I'll be greatfull if you could answer some of these questions, of refer me to a suitable reference. I looked a lot but the references that I find are lab references with technical details and numbers. I didn't find anything specific for this mice types that contains explanations.
Thank you!!

I think I can help explain all but your 3rd question.

A transgenic mouse will typically have the genetic construct in all cells. Unless you get a chimeric animal, which is screened for during the making of the mouse.
VIP::Cre means that the promoter of VIP was used in front of the region of DNA that encodes for Cre recombinase.  Note, the animal still has the endogenous VIP gene that makes VIP. This is an additional construct. The intent of this kind of system is to limit the expression of Cre recombinase to only the cells that would also be expressing VIP.
LSL stands for Lox-Stop-Lox cassette. LSL:TOM is the gene that encodes for tomato red protein with a premature stop in the transcript such that it never makes a correct protein (and no red).
If Cre is expressed in a cell with the LSL-TOM construct, it will recombine the LSL and remove the stop codon, thus enabling the creation of functional tomato red transcript and fluorophore (protein). Again, this construct is in the DNA of ALL cells, but the recombination event (and subsequent expression of function TOM) will only happen in the cells that are also expressing Cre recombinase. And for a VIP::CRE mouse this only happens in VIP expressing cells.

Your questions:
1) Actually every cell in the animal has a VIP::Cre (excepting blood of course or sex cells that got the non transgene allele during meiosis. This is because usually the cre genes are kept at Hets during mouse mating).
2) All neurons (and all cells; see answer 1) will contain the genetic construct VIP::CRE.  The intent is in the VIP::CRE mouse, only cells that would express VIP would express Cre recombinase.  This means that other tissues in the body that express VIP should also fluoresce red in a VIP::CRE/LSL-TOM mouse.  As an aside, all cells that normally make SOM should also be making GFP in the SOM::GFP mouse, but every cell will have the DNA transgene.
3) This question is outside my breadth of knowledge. I've done lots of work with transgenic mice, but other than looking up that that viral construct has something to do with calcium and imaging in neurons, I am not sure.
Per Bryan Krause: "...the expectation is that it will infect most if not all cells, not even just neurons, but it is using the 'synapsin' promotor which is neuron-specific (but would be expressed in both VIP and SOM cells, as well as other neuron types). Presumably the authors are using calcium imaging to detect activity across a whole mixed population but then using tdTomato to identify one subpopulation or the other, depending on which animal is used."
4) For VIP-cre::LSL-TOM::SOM-GFP(GIN).   As written, this would imply the expression of Cre is necessary to activate transcription and encoding of tomato red in VIP expressing cells. But that GFP is already active in SOM expressing cells from day one of development.
Some uses of Cre-Lox systems are illustrated here. This picture from that website demonstrates graphically what is going on with a LSL construct.
Your system has tomato red instead of lacz and is using VIP expressing cells as a targeted system.

For (3) the expectation is that it will infect most if not all cells, not even just neurons, but it is using the 'synapsin' promotor which is neuron-specific (but would be expressed in both VIP and SOM cells, as well as other neuron types). Presumably the authors are using calcium imaging to detect activity across a whole mixed population but then using tdTomato to identify one subpopulation or the other, depending on which animal is used.


text:
What is a CAG::ChR2 rat?
I am reading the paper: Pyramidal Cell-Interneuron Interactions Underlie Hippocampal Ripple Oscillations.
The authors use CAG::ChR2 rats (for example in Figure 2) and I don't know what it means.
I understand for example that in PV::ChR2 mice, parvalbumin neurons will be activated by light.
I am also familiar with types of other interneurons (Ivy, Martinotti, OLM, LTS, Bistratified, Mopp, VIP, Somatostatin...)
but I have never encountered CAG cells.
Is CAG represent a type of neuron? or, maybe it represents something else?
Thanks!

CAG is a synthetic, ubiquitous promoter which combines elements of the CMV early enhancer, the chicken β-actin gene, and the splice acceptor of rabbit β-globin. According to the researchers who created it:

The elements which constitute the pABWN vector, the CAG promoter, the weak neo unit, and the BPV fragment have only low specificity to cell types or species. Therefore, this system can be applied not only to L cells or CHO cells, but to a wide variety of cell lines. The pABWN vector should be very useful for producing large amounts of valuable proteins in mammalian cells, for changing the phenotype of host cells by overexpression of some normal or mutated genes, and for disrupting the function of targeted genes by overproduction of anti-sense RNAs.

In the paper you cite, CAG-ChR2 is used to activate all neurons in the vicinity of the light stimulation, for example in Figure 2Ab, where the panel is labeled "PYR+INT activation."


text:
What is the difference between Integrin to Cadherin?
My question is probably very basic but i couldnt get it in lecture and not from looking in the net.

What is the difference between Integrin to Cadherin.
By difference I am looking for say:

structural difference
functional difference

If i understand correctly both of them helps in cell adhesion.
But, probably in different way? or shortly, what is the difference?
Thank you!

Cadherins look like chains, that are stretched out only when bound to Ca++. They contribute to cell adhesion through adherens-junctions and desmosomes (cell-cell adhesion). They bind weakly by themselves, but function sort of like velcro, in that they make a strong junction when they are many.
Integrins can be of alpha and one beta type. Both types are used in a junction, and they sort of "claw" around the ECM. They also depent on Ca++ (and also Mg++) for correct binding. They join the cell to the extracellular matrix through aktin-linked cell-matrix juntions and hemidesmosomes. There's one alpha and one beta integrin per junction (i think) and they sort of "grip" the ECM by one of them going in the front and the other in the back of the ECM unit.
Both integrins and cadherins are transmembrane proteins, that also need adaptor proteins on the intracellular side.
For clarification:
Adherens junctions transfer the force of aktin filaments from one cell to another, using classical cadherins between the cells.
Desmosomes connect intermediate filaments between neighbouring cells.
Aktin-linked cell-matrix junctions link aktin filaments to the ECM.
Hemidesmosomes link intermediate filaments to the ECM.
Source: lectures at the university of Tromsø, Norway. Also my textbook.

A fair caveat, integrin CD103 binds to E-cadherin.

Thank you for the clearification! And I will also have a look in your book so thanks for that reference too!

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


text:
What is a unitary post synaptic potential?
I am reading the paper Cooperative subnetworks of molecularly similar interneurons in mouse neocortex and have encountered the term:
"Unitary (excitatory or inhibitory) post synaptic potential".
I know what is an excitatory (or inhibitory) post synaptic potential.
But what does the unitary refers to?
Thanks!

Does it mean a single synapse?


text:
Pearson correlation of neural responses with it's linear estimation
I am trying to anderstand the following fact from this article (page 13):
How can single neurons predict behavior
Suppose I have a linear estimation of a stimulus:
$ \hat{s} = \mathbf{w}^T(\mathbf{r} - \mathbf{f}(s_0)) + s_0$
where $\mathbf{w}$ is a vector of weights, $\mathbf{r}$ is a vector of responses responses of two neurons to a stimulus, $\mathbf{f}$ is the vector of average neural responses to the stimulus, and the stimuli (angels between $-\pi$ to $\pi$) are symetric (amount and location) around $s_0 = 0$.
Can anyone see why the following is true for the Pearson correlation (where $\Sigma$ is the covariance matrix of $\mathbf{r}$):
$$ Corr(\hat{s},r_k) = \frac{\langle \hat{s}r_k \rangle - \langle \hat{s} \rangle \langle r_k \rangle}{\sqrt{( \langle \hat{s}^2 \rangle - \langle \hat{s} \rangle^2) }\sqrt{( \langle r_k^2 \rangle - \langle r_k \rangle^2) }} = \frac{(\Sigma \mathbf{w})_k}{\sqrt{(\Sigma_{kk}\mathbf{w}^T \Sigma \mathbf{w})}} $$
Thanks!!


text:
Effect of the same caloric intake of different macronutrients on body weight
To gain weight, caloric intake > caloric expenditure.
To lose weight, caloric intake < caloric expenditure.
But what is the effect of the type of macronutrient ?
That is to say :

does the same caloric intake of carbohydrate, protein, lipid have the same effect on body weight ?
Does X amount of carbohydrate caloric intake > caloric expenditure or X amount of protein caloric intake > caloric expenditure or X amount of lipid caloric intake > caloric expenditure lead to weight gain ?
Does X amount of carbohydrate caloric intake < caloric expenditure or X amount of protein caloric intake < caloric expenditure or X amount of lipid caloric intake < caloric expenditure lead to weight loss ?

Just a warning, this would seem to be a reasonable scientific question, and there are studies addressing several aspects, but it gets to people's personal beliefs about food and body weight, which are very charged issues. I've found researchers, clinicians, public health officials, and members of the public in general have very strong opinions on this. Depending on who you ask, you'll hear the data are conclusive (on one side, or the other) and people on the other side are charlatans, shills, and hacks.

This is a hard question because you will find sources that claim that calories from protein have less effect on body weight gain when compared to the same amount of calories from carbs or fats. Likewise you will find other sources that state that a calorie is a calorie regardless of its origin and hence consuming 2000 calories of protein would have the same effect on body weight when compared to consuming 1200 of carbs, 500 of fat and 300 of protein for example.
A proposed mechanism for protein calories having less effect on body weight gain is "thermogenesis" or in order words that some of the energy from protein calories is lost when processed by metabolic pathways after consumption, but this is not globally accepted by the scientific community. Here is an article from the International Journal of Obesity that discusses the subject. I would suggest being VERY picky with the references you find on the subject since there is a lot of info floating around in the web in sites without any scientific backbone.
Something that can be assured though is that different calorie proportions origin-wise cause different results for other variables different from weight such as body composition. In addition to this, there are several studies adressing the apparent statistical find that protein rich foods increase satiety and hence facilitate body weight control; however, the latter is not related to calorie intake count but rather to other factors that decrease hunger physiologically or psycologically.


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Why doesn't Manipulated Virus for Cancer Cure Work
I'm not a biologist but I have an idea for a cure for cancer and it is very simple and probably has flaws (if it worked it probrably wouldn't be a cure for all) or is not possible but ... I'm still going to ask why because I want to learn why it doesn't work and I want to learn more in general, so you can use all the biology terms you like. The idea is essentially to use a virus and manipulate/change it (this would be mechanized if it were to be mass produced and the type of virus is unknown to me because you want one that is fast growing and goes across only specific parts of the body depending on the cancer). This virus would not have any bad parts (parts that make you sick) to it because when the virus "injects" it's DNA or manipulates the existing for copying it would instead manipulate the DNA in the cell it is going into to have growth limits and other cancer genes that are set to being back to normal and then copy itself. Eventually it would be fought off by the immune system and most of the virus would be gone (along with the cancer) because this virus would last for a long period of time (week(s)).
I appreciate anyone who answers this question because I'm sure it sounds stupid from your perspective but this is the place to learn.
Thanks,
Jackson
Note: This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.

It's called an oncolytic virus. Hint: in the future, avoid rambling and run-on sentences and parenthetical comments, and re-read your question before submitting it so it is coherent and understandable.

Okay, but my idea is different because mine doesn't kill the cancer cell because I don't know how it would tell the difference; mine just manipulates the DNA.

This is a very broad question. You've basically described viral gene therapy which is a great idea but has many complications that are yet to be solved.

What are some of the complications?

I'd first suggest reading up on what cancer actually is - a collection of thousands (or more) mutations in a cell that leads to uncontrolled cell growth. Each tumor has different mutations, and would require multitudes of individually-engineered viruses to "fix" all of them, which in many cases literally can't be done anyway, as the genome is so unstable.

@JacksonH google "viral gene therapy complications" and learn for yourself!

It is impossible that all cancer cells are infected by viruses treated. Then uninfected cancer cells grow and take over.

This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.

Since everybody else is giving you a bad attitude in the comments...
While it might work for some cancers, it is completely impractical for the majority of cancers.
SOME cancers do occur because of a specific mutation or specific set of mutations. Some genes predispose people to greater risk for certain cancers. These have a much greater chance of being treatable via viral therapy, but there are still barriers:

The length of coding material (DNA or RNA) a retrovirus can hold and propagate is limited. The mutated gene or stretch of DNA may be much larger than the length a retrovirus could potentially replace.
The retroviral material is not guaranteed to "rewrite" or "overwrite" any bad DNA. Retroviral DNA is inserted fairly randomly into the host genome with little regard for where since it is generally an entire gene meant to be read in its entirety to eventually produce proteins. You'd expect BOTH gene versions to exist simultaneously. This wouldn't end in a cure, but some middleground between cured and affected.
There are tissues where cancers develop that wouldn't be infected. Any sort of brain tumor would remain completely untouched by retroviral therapy, for example.
Targeting specific cancerous tissues while leaving surrounding or other tissues alone is a big problem, even for non-retroviral therapies. Replacing bad genes in a cancerous cell is good, but replacing good genes in a healthy cell could lead to that cell's death or -- ironically -- possibly turn it into a cancerous cell as well.

The majority of cancers are not specific mutations and do not have known genes that predispose their bearers. The majority are an accumulation of mutations across sections of the genome. As MattDMo said in the comments (paraphrased): For these cancers, viral therapy is nearly impossible. Every mutated gene would required its own retrovirus. At that point, the time and financial investments start to rise exponentially.
While I'm not one to say it's impossible (I'm not involved in the research, so if anybody who is can correct me on anything in this post, I'd appreciate it) -- it is certainly very improbable with current knowledge and methods. Every bullet point above (which isn't an exhaustive list) represents a mountain to climb on hands and knees before an "inject-and-forget" end product could be developed.
Kudos for the critical thinking and forming a working theory from the knowledge you had, but unfortunately it does break down with some more specialized information.

I would up vote your answer but I don't have enough reputation.

Retroviral or lentiviral insertion doesn't have to be random - you could load your viral particles with the components of the CRISPR system, assuming the fix you want to make is small. You could also try this method.


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Why are our muscles limited to 7 Hertz?
I have heard from a (usually very knowledgeable) friend before, that a human can only tap his fingers 7 times per second.
I generalized this to "our muscles are limited to 7 hertz"
When my wife heard this she was like "no way, I'm faster" and we recorded a video of her blinking as fast as she could (her eyes hurt afterwards) and over 5 seconds she averaged exactly 7 blinks per second.
I can't find any articles on the subject, but I did find this video of a drummer doing 1208 beats in 60 sec, setting him up at 20.13hz, meaning 10hz each hand. However if you look at his hand, his muscles are not even really tapping, they are just in a vibration (like a spasm), while holding the drumsticks, which than do all the tapping...
Ussain Bolt sprinted 100m in 9.6 seconds, with 41 steps, that's a little over 4 steps per second.
Both these are very impressive. The drummer sticks out for coordinating his 10 taps per second on each hand, alternating with the other hand, while the motion is certainly faster then our eyes can see.
So what's up with the 7 Hz speed limit? Is it a thing, or did the drummer disprove it? Could the 100m world record be beaten by another 25% when we can find a tall guy capable of doing 7 or even 10 steps per second?

Could you imagine the activity where we need higher frequency for tapping?  Touch screen games? Do we need higher frequency?

I just tabbed a key on my keyboard and got to 182 characters in 20 seconds, so there's that. Anyways, it can either be neurologically limited (i.e. how fast you can switch between the motor unit recruitment for the muscles which antagonize each other for the given moment), as well as muscularly (how fast the muscle can actually contract and relax). This last thing varies widely across muscles, depending on the type of muscle fibers (i.e. which myosin heavy chain form they contain).

This is an interesting question. Is it limited by the speed, feedback mechanisms of nerve transmission, or the compliance-inertial limitations of the muscles? It turns out that the resonance of the human body is different depending on the parts of the body, however all the frequencies are near 7 Hz.

I have timed my personal max clicks/sec on a mouse and consistently get 10+- 1 click per second.

Our muscles are not limited to 7 hertz.
You provide two examples yourself. I can provide a third: world's fastest clapper: 804 claps in 1 minute (video here), which is an average of 13.4 claps/sec -- though, you can see his pace changes so at times he's doing more than that.
What about a non world-record holding example? I can provide one of those as well: I can tap my finger 12x per second (or after 10 attempts, an average of 10.4x (SD=1.02) per second).
@Docscience's answer should help provide some background to better understand the science behind muscle limitations in oscillatory movement.

According to the book, Principles of Animal Locomotion by R. McNeil Alexander, oscillatory movements in animals are limited by an organism's nature in general to minimize metabolic energy costs. The energy capacity, inertial, compliant, and dissipative forces involved in the muscles, tendons, skeleton, and non-actuating load all enter into this cost equation.
Strictly speaking these structures are very difficult to model with any degree of fidelity, and so are often approximated by simple mechanical lumped parameter systems of masses, springs and dashpots. From these simple systems, differential equations can be written, and the frequency that minimizes cost turns out to be the natural frequency - since at the natural frequency the system has the greatest ability to trap, store and re-use energy for the movement.
Size and compliance are therefore the two parameters that matter most. Highest oscillatory speeds are able to occur in the smallest, stiffest muscles, assuming dissipative forces are small and input energy is available.

The human hand-brain reaction time is normally 100ms minimum - 300ms average, which aligns with the frequency that you talk about. There are different types of muscle movement though, and trembling type movements are very fast.
Most trembling in medicine is at 4-8 Hz from Parkinson's disease etc., but orthostatic tremor is characterized by a fast (>12 Hz) rate, which includes teeth chattering and trembling from cold.
Interestingly, your example of a finger movement isn't actually a direct muscular contraction — the muscle of the fingers sit in the forearm, and travel through a ligament and 4 joints, making the contraction indirect.
The jaw can voluntarily chatter at about 4-10 Hz, but it can tremble at well above 12 Hz.
Other muscular actions such as clapping are caused by two sets of independent and opposed strong muscles, flexing independently, which can be synchronized to act very fast at the same speed and up to almost twice the 7 Hz limit you mentioned.


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Looking for a dichotomous key to identify primates
I'm looking for a dichotomous key to identify primates by physical and possibly geographical traits.  Any format is fine (print, web, mobile app, etc.).
Other than classroom activities and genetic classification references the best I have found is on WikiBooks: https://en.wikibooks.org/wiki/Dichotomous_Key/Primates


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How to mimic / approach some animals/insects' anabolism?
This article states that some shelled animals - spiders, scorpions, crabs, worms and other creatures - have metal atoms in their claws, jaws and fangs.
I believe through anabolism, since they eat sand, soil and insects that are full of a mix of those.
For most human beings, it would seem silly to eat soil or sand, or even insects - and yet, I wonder if our bodies would be able to digest and create anabolic processes around, for example, metals, in such way that we would end up having stronger bones / teeth / hair / nails (or other things).
To a certain extent, I also wonder how anabolism isn't use to regenerate cells that become old or faulty in the body as we age or get sick (a special diet would help "regenerate" blood balance, feeble skin, brain cells, etc, if we knew what foods would turn into these cells the best by anabolic process).
This question is becoming a bit confused, so I'll end up rephrasing it: is there a document / research / map / experiences of all the foods & materials that the human body can not only digest (and in what quantities) but also how they transform into our cells (and a list of foods / materials that are NOT taken into account by anabolic processes). I.e., at what speeds they can become part of us, and how they can/could change and alter the body cells in a strengthening kind of way (not in a way that makes us sick or dead).
NOTE: I am not a scientist, just a writer, but I am fondly interested in the subject.

Teeth do have a metal - Calcium. Calcium phosphate also mineralizes in the bones.


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What is the general mechanism behind perfusion PET imaging
I understand how tracer kinetics can be used to determine binding potential but how it can be used to detect perfusion eludes me.

How PET works is more of a physics question? Can you clarify what exactly you are asking?

Alex - do you literally mean "perfusion" - like blood perfusion imaging - - - OR - - - do you mean like PET with 18O-fluorodeoxyglucose uptake imaging?


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Will bark-beetles infest the Methow Valley?
What is the Methow Valley (esp. Winthrop, WA) area's susceptibility to bark beetles?  Did the 2014 Carlton Complex wildfires increase the vulnerability due to the large numbers of dead, dying, and stressed pine and fir species in the area.  Are there ways I can reduce the vulnerability of my property, which is already in open, park-like stands?

I had trouble finding any academic or governmental references for rates of spread of Scolytids (bark beetles) in your region, but the answer to this would require speculation (i.e. prediction). Many factors, including the 'health' of the trees surrounding your home, and the connectivity of your trees to invaded areas, would aid in bark predicting whether these beetles will eventually make their way onto your property.
If your property is large, consider cost-share programs for management/prevention in your area.
See the bottom of this .gov webpage for more references. Good luck.


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Vine To Tree Root Grafting
I am experimenting with grafting multiple heartleaf philodendrons(philodendron cordatum) to the root of an oak tree(quercus). If the grafting is successful, the next step is to cut the root from the trunk, cap it, and place it in a long rectangular potter. The experiment to follow this will be to sustain the tree root with the philodendrons, and symbiotically use the philodendrons to sustain the tree root. Does anyone have experience in this type of experimental research and advice to provide?

I don't think this will work. Grafting will usually work between the same species and sometimes between the same genus. You're talking about grafting Philodendron cordatum to Quercus robur. The former is a tree from Europe, the latter a flowering plant from Brazil. They aren't compatible in the slightest. The graft will never take.
One possible route you might want to consider that may be more successful, but a lot more difficult, is using agrobacterium tumefaciens to infect a mix of cells from the two species. If you have a homogeneous mix of individual cells in culture, infect it with A. tumefaciens, the resulting gall will contain cells from both (incompatible) species. How they grow from there is unknown.


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What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?
First post here, so bare with me if I violate any etiquette or formatting rules.
Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm very interested in.  I see a highly homologous (~85% AA identity) protein in plants, and it's widely conserved.  I'm interested in eliciting the same activity of this protein in plants.  Only problem is that there's no native plant-produced ncRNA to interact with my protein of interest in the same way.  So I had an idea:
What if I introduce a transcript to plants that addresses this problem?  If the plant version of this protein interacts with this (introduced) RNA in the same way it will be really cool.  I'd like to test this hypothesis with some synthesized constructs.  But before I plunk down thousands of dollars on a few constructs, I'd like to explore any predictive or analytical tools to strengthen the case.  I'm aware the odds are against me.
Thanks!

I can't think of any predictive tools, but I think you should simplify the system as much as possible first. Instead of trying to express the ncRNA in plant, get the purified plant protein and purified ncRNA, maybe by in vitro transcription. Mix the two together and see if you can use coprecipitation or crosslinking or something to look for binding. Fluorescent anisotropy might be cool if you have a fluoremeter with polarizers, you could label the RNA with a flourophore, then measure the tumbling rate, once it binds the protein the tumbling should slow down. Use the human protein as control.

The ncRNA sequence from human may bind to the plant protein in the plant cells, but so what? You may be able to say the plant protein works as RNA binding protein, but no more than that.
Another concern is that the plant protein may not recognize the same RNA sequence to the human protein.
There are several ways to find RNA partners of RNA binding proteins.
SELEX
This method is used to find consensus sequences that your protein recognizes in vitro. Once you find consensus sequences, you can search ncRNAs from the plant.
CLIP
This is similar to Chip assay. You could find real targets of your RNA binding proteins

With my experimental plan, I plan to use a reporter transcript.  I will be able to say more than "it's an RNA binding protein".  My primary concern is precisely that the "plant protein may not recognize the same RNA sequence to the human protein" if at all.  SELEX and CHIP will likely help me in my objective here.  Thank you for your suggestions.

I would be careful using SELEX to find endogenous RNAs that bind the protein, it would probably find an RNA aptamer that binds the protein well, but there is no guarantee that the resulting RNA would actually bind in a relevant manner, or just be a novel sequence that happens to bind well. Being able to make an RNA to bind almost anything is why SELEX is so useful.


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How can two individuals of the same species have different chromosome numbers?
It is known that male drones develop by arrhenotoky, and have haploid chromosome constitution, whereas the queen bee and workers are diploid.
Thus we can see two different types of ploidy occurring in the same species. Sill the drones and queen bee are successful in mating and producing offsprings. This would require the queen to produce haploid gametes by meiosis and haploid gametes from haploid drones.
Doesn't this create a problem in defining species?

Your answer is here: http://biology.stackexchange.com/a/45372/3340

Chromosome number does not define species, otherwise the Sable Antelope, Reeves Muntjack, and Humans would all be one species.

You should read this post on the definition of species.

My question was about the defining of species. @Remi.b your post helped.

there are diverent concepts of definitions of species:

morphological species concept, distiguishes a species by body shape and other structural features
ecological species concept, distighuishes a species according to it's niche
phylogenetic species concept, smallest group which schare a common ancestor
biological species concept, a species is a group whose members can produce fertile offspring

the biological species concept is most commonly used, if we apply this on your problem, they still produce fertile offspring, so they are the same species.
If for example a mutation wil occur which causes polyploidy (more likely in plants, however it's possible in some animals). Let say the orginal species have 2n = 12, if polyploidy occurs(during meiotic error for example). We will have 2n = 24. If these species produce gametes n = 6 and n =12, fusion of those gametes will result in unpaired chromsomes, which in turn will lead to a reproductive barrière. The 2n =12 and the 2n = 24 species can only mate with each other to produce fertile offspring, so we can say these are different species.


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How is histamine useful against allergies?

Histamine is a chemical produced and stored within the body. It is a part of our immune response and is released during an allergic reaction.

Often histamine is responsible for hypersensitive response of the body towards certain specific compounds(allergens). It causes nasal congestion and pollen allergy. Also it acts as a powerful vasodilator, and causes inflammation. But is it really helpful against allergies?
I was wondering why antihistamines would be required to inhibit normal functioning of histamine, then realised that if histamine was not there, then perhaps we would not have allergies..

False premise? But if the question states anti histaminics instead of histamine, makes sense

Histamine is produced in allergic reactions. - True
Histamine is produced against allergic reactions - False
Okay. Lets get a few things right here first. An allergy is an inappropriate immune hypersensitive response. It is something, we are not supposed to have. A small harmless pollen grain, in normal people shouldn't initiate an allergic reaction.
IgE antibodies are produced against an allergen. These attach their Fc ends to the mast cell. When these antibodies are cross linked by the antigen, degranulation of the mast cell ensues which release various mediators one of which is histamine. So there is a lot of histamine produced in allergic reactions and common antihistaminics like cetirizine and terbinafine act by blocking histamine receptors thereby reducing its biological effects.
So, allergy is a bad thing. The whole IgE, cross linking, degranulation and histamine release wouldn't have happened in a normal person. Histamine isn't going to protect from allergies. It is the cause of allergic effects. Hence the antihistaminics work. You might know that if you have taken a cetirizine during a rash or severe sneezing.
So if allergy is a bad thing, what is the normal physiological role of IgE?
IgE has a role to play in the immune response against parasites where a similar mast cell degranulation process happens.
And if histamines are causing the allergic effects and allergy is bad, what is the normal role of histamine?
Histamine has several roles to play. One is that it is produces as a part of immune response by basophils and mast cells. It also is a neurotransmitter and also is important is gastric acid secretion physiology. The various functions of histamine have important pharmacological considerations while talking of antihistaminics.
Reference : Kuby, Immunology 6th Ed.


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Why is liquefactive necrosis only seen in brain?
Liquefactive necrosis is a type of necrosis uniquely observed in brain. This occurs due to breakdown of cellular proteins by the action of hydrolytic enzymes.
In other parts of the body, usually a different form-coagulative necrosis is seen.
What makes the brain so unique that this form of necrosis is only limited to brain?

According to Wikipedia citing this article, liquefactive necrosis is not restricted to brain only. NCBI books describes, how liquefactive necrosis is induced. Seems to be dependent on neutrophils. They also claim that coagulative necrosis occurs in every organ except the brain. But I just made a quick search. I hope I could help you anyway.

Liquefactive necrosis is indeed only seen in the brain in the absence of infection, but it is also seen in the case of some bacterial infections.  The reason is that liquefactive necrosis is, as you said, caused by the release of digestive enzymes and constituents of neutrophils.  Bacteria will, under some circumstances, release those enzymes, causing the cells to be devoured.
The fact that liquefactive necrosis is seen in the brain in the absence of bacterial infection is in part due to the fact that neurons have a higher lysosomal content, leading to a higher tendency toward autolysis, and in part due to a high concentration of neutrophils which swarm into an affected area.

Sources:

What happens after brain tissue dies?, PathologyStudent.com, 2012
Liquefecative necrosis, Medigoo.com, 2016
Necrosis, Cell (Liquefactive, Coagulative, Caseous, Fat, Fibrinoid, and Gangrenous), Rotimi Adigun1; Steve S. Bhimj, 2017


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What is wrong with this flower?

Today morning I was surprised to see this flower as it has four normal pale orange coloured petals and one bright red one. This is a flower of Hibiscus and all the flowers of this plant have the normal pale orange coloured petals, while this one has a bright red one.
What can cause this?

Maybe just a rare mutation?

Then why should only one flower show it? If it was a rare mutation I guess all the flowers would have one red petal. But this plant gives the same coloured flowers everyday.

Maybe an insect or fungus that affected the bud?

Could be a rare mutation next to the flower which only affects the flower... maybe sth which was induced... mutations do not necessarily have to occur in seed state etc.


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Why is it not advisable for humans to drink distilled water?
Distilled water is pure and it does not contain any minerals, so may not be advisable for drinking.
Although laboratory made distilled water is completely pure, industry made water may still contain harmful impurities.
Also there is some probability of exosmosis into body tissues which may lead to swelling.

What is your question?

As you said, distilled water is completly out of minerals/ions. The principle of diffusion is that reagents diffuse from high-concentrated to low concentrated places to reach an equilibrium. So normally, ions from the erythrocytes would diffuse into the plasma to reach that equilibrium. However, it is quite difficult for ions to pass the cell membrane which is not the case for water. So what finally happens is that the distilled water wants to dilute the ions in your erythrocytes, passes the cell membrane and the cells explode because they are too full. As consequence, you die because there is no oxygen transport anymore.

The scenario of erys exploding would necessitate substituting substantial amounts of blood plasma with demin. water.