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How many SARS-CoV-2 viruses in circulation at the moment? Mass?
How many SARS-CoV-2 viruses are in circulation at the moment? And what is their total mass?
To clarify: if there are 10 000 viruses on average in an infected human and 100 000 humans are infected the answer would be (if all viruses are in humans, which probably isn't true) 10^4 x 10^5 = 10^9 viruses.
Of course I am only looking for a rough estimate, a number that, when multiplied with 10 or 0,1 (so two magnitudes) or so, is correct.

Welcome to SE Biology. You will have read in the Tour that this site is for "questions about an actual problem you have faced" in the areas of "biological concepts, biological mechanisms behind medical conditions, and techniques in a biological or biochemical laboratory". And that the idea of the site is to amass answers to questions that are of more lasting and general interest. It is hard to see how a count of viruses "at the moment" (has it passed yet) satisfies any of these criteria. How do you propose to use the answer? Say "Wow, that's a lot!". That is really not what the site is about.

Based on all species of viruses, Everyday you breathe in 100 million viruses. There can be 1mn+ viruses per ml of blood of patients. Covid-19 diameter = 125 nm.
Perhaps it's wrong, the maths would go something like this:
1mn * 1000ml * 5liters * 400k patients = 2^12 - 2^13 sars2 viruses.
total volume of viruses =  2^13 viruses / 1^15 viruses per cm3 = 0.02 cm3
(10^7 nanometers per centimeter, 125nm diameter, gives, about 10^(5*3) viruses per cm3.)
Weight of all the Covid Sars 2 in the human population = a raindrop or a teaspoon of hydrocarbons/mayonnaise, probably less than a teacup.
Perhaps i am wrong, it's reasonable to think that the people with major symptoms contain about 1 ml of virus. 20k x 1ml = 20cm3


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Saline solution for animals
A popular "well-known fact" is that all creatures on Earth consist mostly of water (i.e. H2O). Indeed, a liquid called "normal saline solution" is just a solution of 0.9% sodium chloride in distilled water. It is generally considered the "safe" liquid to be injected into human body in relatively high volumes without any bad effects.
I know that the same 0.9% solution is also used in vet practice for at least cats and dogs. As far as I understand, that's because blood circulation structure and basic blood regeneration specs are more or less the same for cats and dogs as for humans.
But what about other animals? My wild guess is that same 0.9% solution would be ok for all mammals (probably because their blood tract is similar), but what about others? Birds? Fish? Vertebrae? Invertebrae? Animals? Plants?
If 0.9% solution is not universal, what are the other possible variants? (i.e. could you provide examples of other compositions for some other species?)
If 0.9% is indeed universal, I'd be glad to hear any pointers on why does it happen (i.e. is it related to evolution of life in Earth history, is it related to chemical composition of bodies, related to some specific cells, etc).

Not saying that it is universal, but the reason the that we use 0.9% saline is so that osmosis doesn't cause all of our cells to suddenly try to draw in water to create an equal concentration on both sides of the cell membrane. It all has to do with the "stuff" inside our cells.

Great insight, thanks! Now I just need to dig in through how cell membranes evolved and which creatures started having these "modern" 0.9%-level membranes in their cells...

Try looking into concentration of ocean water. If we have all evolved from the cells that swam the ocean there is a good chance there is something to it. Also look into fresh water fish too. If there is going to be a difference in osmosis with the 0.9% solution it will most likely be in fish.

source: Stack Exchange

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How similar do proteins have to be to trigger the same immune response?
The title really says it all. How precise or vague is the immunity we get from vaccination or from having encountered a germ before?
Is it about protein parts that are recognised if they are identical? Full proteins? Which kinds of mutations break the recognition and which don't?

What is your level of understanding of immunology? Your question — which is really quite  broad — suggests that you may be better reading some introductory account of the topic. For example some of your terms are vague or strange. "trigger the same immune response doesn't really mean anything". If you are concerned with the utility of flu viruses, for example, against annual strains, then the phrasing would be something about antibodies recognizing the same protein. And what do you mean by "which kind of mutation?" @KarlKyer is correct, but does his answer clarify things for you.

I work in genome assembly, but I'm not a biologist. So my question is posed from a sequence point of view. A virus has a certain gene sequence, this sequence is expressed as a protein (i.e. a sequence of amino acids). Which part of this sequence is recognised by the antibodies and how precisely does it have to match, is basically my question. A mutation is just a change in the sequence. Karls answer takes me most of the way, I would say.

Fine. Just wanted to check what type of answer would be appropriate.

Immunoglobulins don't recognize entire proteins, but rather,specific shapes (called epitopes). These epitopes must also be present on the surface of the invading bacteria or virus for the immunoglobulin to have access. The epitope must be exactly the same. Any change in the amino acid sequence would change the shape. But an epitope is a relatively small part of the larger protein. If the shape is the same between different proteins, it would trigger an immune response.

Thank you for your answer. I just posted a follow up question about conformational epitopes: https://biology.stackexchange.com/questions/77952/what-is-the-length-and-number-of-the-subunits-of-a-conformational-epitope

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Data for giraffe subspecies population change over the time.
Is there a historical data for the number of animals in the wild for every subspecies of the giraffe and where it could be found?

OK. It seems that I found something in IUCN website: http://oldredlist.iucnredlist.org/details/9194/0

In a recent paper in Current Biology, Fennessy and colleagues conclude that there are four species of giraffe and that their numbers are declining in Africa. Giraffes (Giraffa camelopardalis) are presently classified as one species, with nine subspecies, which are considered ‘Vulnerable’ on the IUCN Red List. The present consensus of one species divided into nine subspecies has previously been questioned (Supplemental information), and Fennessy and colleagues provide another viewpoint on giraffe taxonomy. The fundamental reason for different taxonomic interpretations is that they are based upon different datasets that adopt different statistical techniques and follow different criteria for nomenclature.
Its basically a form of evolutionary process.
Living giraffes were originally classified as one species by Carl Linnaeus in 1758. He gave it the binomial name Cervus camelopardalis. Morten Thrane Brünnich classified the genus Giraffa in 1772. The species name camelopardalis is from Latin.
The giraffe is one of only two living genera of the family Giraffidae in the order Artiodactyla, the other being the okapi. The family was once much more extensive, with over 10 fossil genera described. Their closest known relatives are the extinct deer-like climacocerids. They, together with the family Antilocapridae (whose only extant species is the pronghorn), belong to the superfamily Giraffoidea. These animals may have evolved from the extinct family Palaeomerycidae which might also have been the ancestor of deer.
The elongation of the neck appears to have started early in the giraffe lineage. Comparisons between giraffes and their ancient relatives suggest that vertebrae close to the skull lengthened earlier, followed by lengthening of vertebrae further down.One early giraffid ancestor was Canthumeryx which has been dated variously to have lived 25–20 million years ago (mya), 17–15 mya or 18–14.3 mya and whose deposits have been found in Libya. This animal was medium-sized, slender and antelope-like. Giraffokeryx appeared 15 mya in the Indian subcontinent and resembled an okapi or a small giraffe, and had a longer neck and similar ossicones. Giraffokeryx may have shared a clade with more massively built giraffids like Sivatherium and Bramatherium.
Further on researches are also being made till now!

It would be helpful to at least name the paper mentioned, or better to link to it since it is open access and available on the web.

Dear@mgkrebbs 9 its brief description you can find on wikipedia.

OK, with your answer you addressed the subspecies/species classification problem that I haven’t addressed in my question, but at this case I am looking for the historical data of animal numbers in the wild.
9 subspecies option would be best fit as I could adopt it to other variations, but I think I am talking more about perfect world solution for me.  Any source would work at this stage, for any species/subspecies interpretation.

Sure most of the sites have data related to it but depends on u that which specific data u want to choose...

@ME. To reiterate mgkrebbs comment. Please do cite the paper as "Fennessy et al. (year)" and add the link to where we can find this paper.

The table is a rework of the information that I found
on giraffe and okapi specialist group website with additional taxonomy perspective from Wikipedia page.

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Is there mismatch in injures or death numbers for carnivores that hunt during day time and night time?
Is there significant mismatch in injures or death numbers for hunters (when hunter was killed or injured by its prey), between day time and night time hunts (carnivores that hunt during the day time and night time)?

Such animals could be:  lions, leopards, hyenas, wild dogs, wolfs. Basically I am looking for such type data (if there is one) that could give me insight into  the night time hunt as a risk factor for hunter.


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How outside signals creates different chemical composition in the brain?
Scenario A:
I am walking down the street and my phone rings. I answer and I am told that my ticket that I registered last week was lucky and I won million EUR.
Scenario B:
I am walking down the street and my phone rings. I answer and I am told that my mother died in the car accident.
We have two rather different situations that have totally different “feeling” reactions in my brain. How come outside events can result in a totally different chemical composition of my brain.
Do we create certain dopamine (or any other chemical) release networks in our brain as we develop that are activated (or suppressed) by certain signaling combination?

First, of course, there is no "totally different chemical composition". The changes are very difficult to detect. In experiments with model animals, the usual method is to insert electrodes into the brain in specific regions and to monitor the electrical activity.
As to your two scenarios, it is the anticipation of reward that is most closely associated with dopaminergic transmission, rather than the consummation of reward. Schultz (2016) describes how dopamine signalling codes for a prediction error using a combination of tonic (slow but continuous) and phasic (fast and pulsed) firing patterns. A pause in tonic firing indicates that an expected reward failed to materialise. A burst of phasic firing indicates that an unexpected reward was received. These excursions from tonic firing give rise to changes in behaviour.
Thus one might expect that on receipt of your telephone calls, there may be some dopaminergic signalling, certainly in Scenario A. In Scenario B things are slightly different because you weren't expecting a reward; you simply received bad news. However, there is evidence (Matsumoto and Hikosaka, 2009) that dopaminergic signalling is involved here, also.
The cells responsible for these changes in dopamine signalling project to the frontal cortex. The receiving cells alter their synaptic connectivity in response. Successful connections are strengthened; connections producing poor results are weakened or eliminated.

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What are preparation mistakes that could make red blood cells appear crenate in isotonic solution?
Thank you for your time. I separated red blood cells from a whole blood sample purchased from a blood bank. In isotonic solution, the red cells appear crenate. I would like to know if there is anything wrong with my procedure. I used the following controls:

I purchased two samples which came from two different donors. Both samples are more than 48 hours old.
I used three different solutions to spin the blood including RMPI 1640, saline solution, and phosphate buffered saline. I used multiple solutions because the RMPI is past the expiration date.
I spun one sample at high speed and the other sample at low speed.
The first sample was delivered at room temperature, it was not on ice. The second sample was on ice. I believe the buffers and the blood sample were roughly the same temperature when I spun them.
I mixed the buffer solution with the RBCs by gently rocking the test tubes back and forth.
Thinking that the problem may be when I preparing slides, I cut the tip of the pipette in case pressure was disturbing them.
I used both refrigerator and room temperature isotonic solution when preparing the slides.
I use a spacer in the slides with double sided tape and I seal it with nail polish. I'm not sure if that should matter.

If you have any ideas as to why the RBCs look like burr cells in isotonic solution, I'd greatly appreciate it if you'd share them with me. Thank you!

Oh, the anticoagulant was EDTA.


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Can Biting Insects Detect Specific Places On A Host Body?
I'm gonna make a presumptive statement: It -seems- as though I get bitten by mosquitos and other biting insects in -exactly- the same places over and over. I mean within a few mm. Is that true?
If true, that implies that insects have a mechanism to detect certain preferred spots in order to get blood or whatever they want. (Location of blood vessels? Sweat glands?)
And if that is so, what -is- that mechanism? What are they going for? And how does this detection work?
IOW: How do they know to bite me exactly on the side of my right knee over and over and over... but never on other spots?

Lice, for example, live on the (hair of the) head, which seems specific. Some other insects bite where the skin is accessible, and that can just depends on our clothing habits.

There are at least two sources that influence patterns of behavior: the individual that is doing the biting, and the individual that is being bitten.
The example of lice in one of the comments is a good example.  Three categories of lice that get on humans are: head lice, body lice, and pubic lice.  They are related species (possibly the same species in some cases - https://www.insidescience.org/content/are-head-and-body-lice-same-species/550), but each type has their own preference for habitat and feeding.  There are all kinds of reasons for a species to have a preference, and some stick to those preferences quite strongly.
As for your mosquitoes, their absolute preferences are still not known but blood seeking insects do have their senses attuned to clues such as carbon dioxide and heat (that help identify potential hosts) as well smells and other influences on their senses.  There might be something special about the side of your right knee as far as mosquito senses go, but not every individual in a species sees, smells, hears, etc. the same way.  My brother has a gene that makes broccoli taste very bitter, but I am fortunate to not have those taste buds.  Color blindness is another example of differences in perception, but even without being color blind, what you see as red is probably not how someone else sees red due to natural variations in the patterns of sensory cells in the eye.  For a consistent pattern of behavior from the mosquitoes, in spite of individual differences we still need to consider another source of variation that might lead to this mosquito preference: the host.
If the variation of individual mosquitoes is trumped by a consistent pattern of predation, perhaps the mediating factor is the host.  Your knee could have a special smell, or other sensory flag that attracts mosquitoes.  There are efforts to understand how a mosquito's perception directs who gets bitten: http://www.scientificamerican.com/video/future-repellents-mess-with-mosquit2013-12-23/ .  Not enough is known yet about the preferences of mosquitoes to say for sure what makes your knee so good.  There is also a chance that your knee is not special to the mosquito because it appears the most appetizing.
Host behavior is another possible influence.  The knee is just far enough away from the reach of your hands.  Conscious or absentminded grooming would both be limited at that distance.  The knee may also be better than an ankle or a foot, because of what is worn or because the knee moves less than the lower leg during walking and other movements.  If you are bitten on the lateral (outside) side of your knee, this would add evidence to this hypothesis of your movement influencing mosquito behavior, because the inside of your knee more frequently brushes against the other leg.  The frequency of the inside of the knee being a safe place for a meal is much lower.
As for why it's the right knee rather than the left, there is  possibility that that is also a reflection of you, rather than the pests.  Humans display preferences in dominance for both hands and feet.  One side of your body may be selected more often than another because of you being right- or left-handed, or right- or left-footed.  This could affect grooming habits (how you swat at the bugs), how your cross your legs, which side you carry items or lean against other objects which might brush against the body, influence how well you spray yourself with bug repellent or who knows what else.  (Just for curiosity's sake, ¿are you right-handed or are you left-handed?)
In short: There's a lot of evidence to collect before we could come to a definitive answer.  There are a lot of possibilities, including that your knee may not be the tastiest spot, but rather a relatively safe spot for dinner.
For more unempirical thoughts on the relationship of insects to the lower limbs, please see: http://fishboyridesagain.blogspot.com/2005/11/bugs-and-trousers.html


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Specificity of the adaptive lymphocytes
T cells are known for their ability to bind multiple antigens, owing to the degeneracy of the recognition sites on their receptors. [I] When examining the structure of the T cell receptor, we can observe the ɑ and β chains which have a highly variable region, in their extracellular domain:

From what I understand, TCR degeneracy means that one receptor can bind to different antigens.
In comparison, the B cell receptor consists of a recognition site that contains a membrane-bound isotope of immunoglobulin. Again, from what I gather, variation in both the Ig on B cells and the TCR occur as a result of genetic recombination. [II]

Question:
Does the membrane-bound Ig in the BCR exhibit the same degeneracy as TCRs? Does variation caused by V(D)J recombination work the same way for both these receptors?
References:
[I] https://en.wikipedia.org/wiki/T_cell_receptor
[II] https://en.wikipedia.org/wiki/V(D)J_recombination
[Images] http://what-when-how.com/acp-medicine/adaptive-immunity-antigens-antibodies-and-t-cell-and-b-cell-receptors-part-2/

What do you mean by "degeneracy".

"From what I understand, TCR degeneracy means that one receptor can bind to different antigens."

Quick answer: No, individual T cells can only bind one antigen with their TCRs, just like B cells.

From the wiki TCR article: "TCRs have very high degree of antigen specificity, despite of fact that the affinity to the peptide/MHC ligand is in the micromolar range."

From the same article: "The binding between TCR and antigen is of relatively low affinity and is degenerate: that is, many TCRs recognize the same antigen and many antigens are recognized by the same TCR."

In addition to that, low affinity with an MHC-antigen complex would simply mean specificity is narrowed down - not necessarily to one antigen per receptor.

This is incredibly oversimplified, but the short answer is that both T and B cells can have degenerate recognition, though the molecular mechanisms are somewhat different.
T cells recognize linear sequences of amino acids that have been excised from their parent proteins, from 8 to 16 or so amino acids long, and that are associated with MHC proteins.  The association with MHC proteins depends on the specific sequence of amino acids, and you can think of this association as depending on a number of amino acids (let's say 4 or 5) that point "down" into the MHC.  That leaves maybe 4-10 amino acids pointing "up" that can interact with the T cell receptor.  If you search for a random set of 4 amino acids with a given spacing, it's quite likely that it will turn up several times in a large protein database; even more often if you allow some degeneracy (similar amino acids can substitute sometimes).  Therefore, yes, T cells tend to have a moderate amount of degeneracy in their epitope recognition.  However, while search a whole database may find duplicates, the degeneracy is not terrible, and the MHC binding requirement also reduces it quite a bit. Also, of course, during T cell development, TcRs that have broad and degenerate recognition of many structures are selected against.  So T cells are definitely cross-reactive, and sometimes extensively so, but in single individuals it's probably not a common thing.  (Ray Welsh and Liisa Selin have looked at cross-recognition between viruses and find quite a bit of cross-reactivity, though, so this may be understated.)
Antibodies, unlike T cells, recognize conformational epitopes rather than linear sequences.  However, just as with linear epitopes, it's not impossible for two unrelated proteins to end up with similar conformations, even with rather different amino acids.  As well, antibodies can be more or less "forgiving" in their recognition; some are extremely specific, but others can interact with a wider range of shapes.  You can imagine a "flat" antibody binding surface that is rather generic, that could interact with many different shapes. Again, B cells with broad cross-recognition are selected against during development, though not as rigorously as are T cells.

There's a lot more data on TCR degeneracy than for the BCR, but they do have a quantitative study here on CD8+ T cell cross-reactivity and they found that a single TCR was capable of responding to over 10^6 decamer peptides.

Yeah, but that's not every TcR -- that's one specific one that, because it's autoimmune, must have avoided much of the usual developmental checks already.  Probably most TcR that have gone through the negative selection process would have less degeneracy than that one.  But there's certainly still room for recognition of a large number of peptide variants.


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L-tryptophan in mammalian cell culture
Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells?
It's an essential amino acid, so I cannot fathom why low concentrations as opposed to higher ones are best. Does it have to do with carcinogenesis or some other dangerous side effect I wonder?

It is essential but it is also not required in huge amounts. I am not sure if it has toxic effects.

I just assumed it was due to feedback regulation that would affect other amino acids' production, but I really don't know. It's a good question.


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Why don't each of T and B cells make two different TCRs/antibodies, except for the class switch?
I have not been able to find any literature that clearly states this, but if I understand correctly, T and B cells are diploid.
If so, there are two sets of genomes, and if both are TCR/VDJ reconstituted, it would seem that one cell would have two different TCR/antibodies. In other words, there will be a TCR/antibody produced by TCR/VDJ rearrangement of a patternal chromosome and a TCR/antibody produced by TCR/VDJ rearrangement of a maternal chromosome.
Why doesn't that happen?

I searched for this question  and obtained the answer, which I will expand on.
There is a mechanism called 'allele exclusion' (allelic exclusion),
which means that when one of a pair of immunoglobulin/TCR genes is successfully reconstituted and
becomes a functional gene, the other one ceases to function.
Eventually, only one or the other is expressed.
For more information, search for "allele exclusion" or "allelic exclusion".
https://en.wikipedia.org/wiki/Allelic_exclusion
https://pubmed.ncbi.nlm.nih.gov/12707333/


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Formation of splint bones in ungulates
I do know that the splint bones are vestigial (reduced non functional toes in this case) , in odd and even toed ungulates. Is there any evolutionary reason of why is it so?
What were the conditions that lead to it?

what are you asking why they are reduced, or why they have not been lost completely?

@John -Why did they get reduce in the first place?

One easy way to make an animal faster (especially if it is larger than a housecat), is to make the ends of the limbs lighter, the more mass there is near the end of a limb the more energy it takes to move it and the slower you can swing it, that translates into moving slower because you cannot get the limb back into position for the next step fast enough.
Because of this reduction in the mass and number of toes in lower limb is an adaptation we see over and over again in animals focusing on running speed. We see it in dinosaurs, we see it in ungulates and artiodactyls. We see five toes reduced to three then eventually one toe, or sometimes we see a reduction from four toes to two paired toes instead.
Source

Wow! That's a really pretty simple(and awesome) logic if i think about it now! thanks =)


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Counter Staining with Safranin
After Gram Staining,
We use counter staining to find out that is there any gram(-) bacteria present on the prepared slide.
My question is-
What component in the cell wall of gram(-) bacteria is responsible for the retention of Safranin dye?
Like the Techoic Acid is responsible for the retention of CVI complex in gram (+) bacteria.
As I have just studied the staining process,any additional useful information is appreciated.
Thanks!

I find it hard to find actual literature on this, so this is just my reasoning. Safranin is a basic dye (ie positively charged). I suspect electrostatic interactions with negative charges on phospholipids in the inner membrane are responsible for its retention.

@canadianer- thanks! Your explanation helped a lot. If you can find any literature related to this, can you please post it? :)

Safranin is retained, very much like Crystal violet, by the peptidoglycans in the cell wall. However, the main difference is the thickness of the peptidoglycan layers in Gram positive and Gram negative bacteria.
Gram positive bacteria, due to their thicker peptidoglycan layer, have a higher affinity to and retention rate of crystal violet. On the other hand, Gram negative bacteria, due to a thinner peptidoglycan layer cannot retain crystal violet as well and are more likely to retain safranin.


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Vaccines against bacterial endotoxins
Today in class, there was a discussion going on about what part of pathogens(which can act as an antigen) can be used to make vaccines.
There was this point where our teacher said that bacterial exotoxins can be used for making vaccines.
My questions are-

Can bacterial endotoxins be used in making of vaccines?
If not,  then why is it so? What are the problems we face ?

There are several papers that use alkaline hydrolysis to delipidate or "detoxify" the endotoxin for use as a vaccine (1, 2, 3). The point of many of these papers is to develop a detoxified LPS (dLPS) vaccine to protect against sepsis in the pathogenesis and treatment of gram-negative infections. The detoxification is important, as the lipid-A portion of the LPS contributes significantly to sepsis. In this case you would be targeting the O-antigen or core oligosaccharide.
So one of the problems that I can see is that there are many bacterial serotypes, comprised of many different O- and core groups. I'm not aware of any vaccines with that sort of breadth. Issue two is you get an infection and you need to administer these vaccines quite fast, if not prophylactically, as adaptive immunity takes a number of days to come to speed.
It's also not clear to me whether a prophylactic vaccine to E. coli is useful to the populace at large, epidemiologically (just as an example).
The field also seems to lack clinical data on tolerability and efficacy, which is what I'd be more interested in, e.g. is it safe for humans and does it work?

So they are just under trial and aren't used as prophylaxis because 1) of the differences in core groups of the LPS of the same bacterial species. So,  speaking prophylactically , the vaccine will be effective against only one strain of that bacterial species and not as whole. 2) we still don't have any idea on the efficiency and safety of these vaccines.Am i getting that correct? Furthur, can you provide a link to the structure of endotoxin(LPS) . I really don't have much idea about the A-portion and O- part you talked about but I'm interested in finding out.

@anamikaSingh You have this idea of multivalent vaccines. For example, the conventional flu vaccine is trivalent, consisting of live attenuated bacteria from the three groups predicted to cause the most sickness that year. The strains the following year may differ due to mutation (aka antigenic drift). So it's not to say that you can't have multivalent vaccines, for example, but it's costly and laborious to produce a product against so many different serotypes. And yes, the other issue is that they don't seem to be well-tested clinically.

This is a fair structural representation: http://html.scirp.org/file/5-2270721x6.png.


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Presence of Aromatase enzyme in males : Result of Natural Selection
Males have increased chances of getting cardiovascular diseases than females ; one of the reasons might be less level of oestrogen ( which decreases deposition of low density lipoprotein LDL in blood vessels).
I know that Aromatase enzyme is produced by sertoli cells in males. It converts androgen into oestrogen.
Now ,
today my teacher said that the presence of Aromatase enzyme in males is the result of natural selection against increased chances of heart attack in males.
My question is-
1. Is the amount of oestrogen produced significant to decrease cardiovascular diseases that it can lead to natural selection?
2. Are there any evidences for the same? please enlist them.
Any help is appreciated.  Thank you!  :)

Estrogen has other functions in males; it is very misleading to attribute the ability in males to synthesize estrogen to effects on heart attack chances. The relationship between estrogen and cardiovascular disease risk is also very complicated, and current guidelines do not suggest estrogen replacement as a preventative treatment for heart disease.
A better explanation for increased male risk of heart attack might be the increased levels of testosterone, but the data on that are mixed as well.

Thanks ! The link you provided was helpful. So basically, it plays role in maturation of sperm?

Wikipedia has a list of functions of estrogen - many of these are not specific to females. On your own, you could also research the effects on males who have a deficiency in aromatase.


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What is the purpose of the AraC gene in pGLO?
The AraC gene activates in pGLO from my understanding in the presence of arabinose. Arabinose is present as a metabolite from other metabolic in the e.coli cell. Is it that there's no termination marker, so transcription continues to the GFP gene?
In addition, does AraC contain parts that are encoded 5'->3' and 5'->3'?

The AraC gene can activate GFP expression, because the GFP in the pGLO plasmid has the negative inducible pBAD promoter:
In the absence of arabinose an AraC protein dimer binds the promotor region, but does not activate transcription. When arabinose is present, the protein binds in a different way, which allows the downstearm gene (here GFP) to be produced.
According to this plasmid map I found the AraC and GFP genes are in different orientations (and facing 'away' from each other), so transcription of AraC wouldn't run over into GFP even without a terminator present.


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If someone with "XO" is one of the identical twins with the other twin as male, then what would the sex chromosome of the other twin be?
A more complete question: If someone with sex chromosome of XO is one of the monozygotic twins with the other twin as phenotypically male, then what would the sex chromosome of the other twin be?
I had heard that both XXY and XY is possible. Is it true?

"XO" (an unpaired X chromosome) is characteristic of Turner syndrome.  The Wikipedia article https://en.wikipedia.org/wiki/Turner_syndrome provides a typical image - a woman with a fairly distinctive broadness of the neck.  The phenotype is described as female, though of course gender identity can be unpredictable for anyone.
For the other monozygotic twin to be phenotypically male, the most likely explanation is a Y chromosome - a Y chromosome that was lost in all or many of the cells of the XO woman.
A set of monozygotic twins with one XXY and one XO would be very surprising - in other words, with the twins differing by two chromosomes - would be very surprising.  But nothing is truly impossible in biology.  And ... this may be such a reference, but I didn't look at the full text to make sure: https://www.ncbi.nlm.nih.gov/pubmed/27315788


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What kind of mite is this?
I found this (mite?) on my head skin close to hair. Is it a common dust mite or something else? Photographs under a simple microscope (10x objective) are below. Size is in the order of tenths of mm. Some of the hair sticking out are as long as the body. It was not that translucent enough to be well visible in bright field, only as a black spot.
Also, what could be the large round white object on the back an the brown spot to the left and right in the first picture?

Note: One month ago I was treated for scabies and my head is still itching (although scabies is supposed to not affect heads of adults). But I do not think this is Sarcoptes and I think it likely does not cause the itching.

related: How many species of mites live on the human body?


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PCR Mastermix Preparation
I am currently preparing a PCR mastermix for the first time, and have a few questions regarding the distribution. I am trying to amplify a specific gene cluster in a sample of DNA so I can use it in a cloning vector; however, I am not sure how many separate PCR reaction mixtures I should prepare in my mastermix for this purpose? Also, what is the purpose of a negative PCR reaction mixture (withouth the template DNA), as I saw a procedure recomend making one. Should I prepare the same number of negative reactions as positive, or should I prepare only 1?

A PCR Master Mix is just a way to speed up your pipetting. Instead of preparing 10 different reactions of 20ul each (for example) you prepare one reaction of 200ul and then you split it into 10 tubes. This also reduces distraction errors (it is less likely to forget to pipet once 100ul that 20 times 5ul). Also, less plastic (pipet tips) is used.
Some tips:
Given the error of some pipettes, it's generally good to count for an extra reaction every 10. For example, if you need to run 10 PCR, make a Master Mix for 11.
If you are planning to run the same PCR on different templates (which is often the case) then you don't need to add the template in your Mix.
Negative and positive controls should always be included.
The negative control of a PCR reaction is often done by substituting the template DNA with water. The negative control should not show any amplification band. This guarantees that you don't have DNA contaminants in your mix and that you primers do not amplify each other.
A positive control is a reaction that is expected to work. In this case, if your positive control shows amplification but your sample don't, you know it is not because of some component in the reaction behaving unexpectedly (Polymerase, buffer, etc..).
Let's make a practical example.
Let's say I want to amplify the same target sequence from 10 different DNA samples.
The 1X reaction looks like something like:
**PCR 1X**

Template     1ul
Primer F     1ul
Primer R     1ul
H2O         10ul
MgCl2        2ul
dNTPs        2ul
Buffer 10X   2ul
Polymerase   1ul

Now, considering the positive and negative controls, and 10% extra volume, I would prepare a Master Mix for 13 reactions. Of course, the template must be excluded.
**Master Mix 13X:**

Primer F     13ul
Primer R     13ul
H2O         130ul
MgCl2        26ul
dNTPs        26ul
Buffer 10X   26ul
Polymerase   13ul

Now aliquot 19ul in the 12 tubes, add 1ul of the right template to each of them (in the C- just add 1ul H2O) and run it!
There are cases in which you may want amplify different targets sequences from the same DNA. In this scenario, you want to include the template in the Master Mix, since it is the same for all the reactions, but you want to add the primers separately since each reaction will contain a specific set of primer to amplify a specific sequence.

Great answer! One comment: I'd say the biggest reason for using a master-mix is to reduce pipetting error due to multiple operations (pipetting 10ul once has less error than 1uL 10 times) and due to small volumes (relative error is much larger at the low end of a pipette's range).

Agree, although it's your responsibility to check the pipettes are in perfect condition.

There are four things you can change depending on how much DNA you need to insert into the cloning vector:

(i) amount of PCR reaction mixtures ("how many tubes")
(ii) concentration of template DNA ("how much template DNA in a tube")
(iii) how many cycles ("how many times will you amplify your template")
(iv) how efficient amplification is ("how efficient is amplification") i.e. ideally each cycle exactly doubles your DNA, but in practice it's almost double or sometimes substantially lower than double

Remember, 1 tube after 10 cycles ideally contains exactly as much DNA as 2 tubes after 9 cycles. Usually changing the number of cycles is the way to go. You don't need that much DNA for vector insertion, I would go with a single tube to begin with.

How much DNA do I need?

We can't help you with determining how much you need, but see how much you need for inserting into the vector; make an excess using PCR, check to see whether the PCR worked on a gel (size purification) and measure the concentration of your product. Then you take the appropriate amount for making your vector.

Negative PCR control?

Negative control is a control reaction that contains all essential components of the amplification reaction except the template. This enables detection of contamination due to contaminated reagents or foreign DNA. Here you should see exactly no PCR product - if you do, you'll have to troubleshoot your reagents!

How many separate PCR reaction mixtures I should prepare?

If you're just amplifying DNA, one tube should be enough to see clear bands on a gel. In other cases, for instance with quantitative PCR (which you aren't doing), you'd prepare replicates, so you have a negative tube, and let's say 3 experimental tubes (technical replicates) so you can average across them for better accuracy and reliability.
When preparing a master mix, e.g. for 10 reactions, prepare it as if you were making 10% more reactions (11 reactions) so that you can comfortably pipette everything. You need 100mL of a solution for an experiment? Make 110mL. This is general good lab practice - always make a slight excess of master mixes.

The number of reactions you set up depends on a lot of parameters. To answer this question you'd need particulars about the source of template DNA, melting point of primers, the taq you are using and the size of the product you want to amplify. All of these will dictate how you optimize your PCR. Have a look at the below reference
http://cshprotocols.cshlp.org/content/2009/4/pdb.ip66.abstract


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Arsenic (V) Reduction to Arsenic (III) by Microorganisms
I am currently doing research on arsenic toxicity in microorganisms, and I learned about arsenic (V)/(III) cycling. Arsenic (III) (usually in the form of arsenite) is generally 50 times more toxic to biological life; however, most bacteria (or at least some) reduce the less toxic arsenate into arsenite. I just do not understand why these organisms would reduce arsenate into something more toxic. This doesn't seem to be an accidental reduction in which the microorganism mistook arsenate for phosphate, as there are plasmids specifically encoded with genes that reduce arsenate. Why is this happening? How would this be an advantage in these organisms and not a disadvantage?

Your confusion seems to hinge quite critically on the idea that Arsenic(III) is more toxic to biological life in general. Bacteria making effort to manufacture it would suggest that it's more toxic to other life than to the bacteria making it. Can you add a source for that statement?

https://www.sciencedirect.com/science/article/pii/S2319417016000159 states that bacteria encode arsenic resistance in the ars operon.

@Armatus — Excellent ref. Why not provide a summary and go for the bonus.

You can find a great and recent review on this topic, which is thankfully also free to access, here: https://www.sciencedirect.com/science/article/pii/S2319417016000159
Arsenic resistance is ubiquitous among bacteria, they virtually all maintain the ars operon. Among Arsenic-resistant bacteria, this is not an advantage, but Arsenic was and remains a ubiquituous substance and being resistant to it confers an advantage over those that aren't; which is why bacteria that save themselves the effort aren't abundant.
The core to your answer is in the very last summary paragraph:

ArsM transforms inorganic arsenic into a highly toxic organoarsenical species that kills off by competing the bacterial species and may also be responsible for carcinogenesis in animals. Competing microbial species have responded to this environmental pressure by evolving detoxification mechanisms for MAs(III). Some produces ArsI that demethylates MAs(III) to less toxic inorganic As(III) while other produces ArsH that oxidizes MAs(III) to nontoxic pentavalent MAs(V). It is likely that all of these processes are taking place in environmental microbial communities as bacteria, archaea, fungi, and protozoans constantly fight for dominance.

Summarised in Figure 5: https://ars.els-cdn.com/content/image/1-s2.0-S2319417016000159-gr5.jpg
The reason why ArsC and other arsenate reductases (reducing Ars(V) to the more toxic Ars(III)) evolved in the first place, setting off this whole Arsenic methylation cycle, is that

they are required for resistance to arsenate, which became the predominant arsenic species after oxygen appeared in the atmosphere.

Simply put: If I can make a poison that kills you but not me, why shouldn't I make it?


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due to hypersecretion of growth hormone why only terminal growth takes place?
why only terminal growth takes place in acromegaly and gagiantism, due hypersecretion of GH?


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Is this tree poisonous?

I touched this tree on my visit to South Africa and a huge rash developed on my body,please help,what is the name of this

Welcome to Biology.SE! That picture looks like a screenshot of a previous question. Is that question yours? Consider editing it instead of post a duplicate question.


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What makes substances allergenic?
Is it possible to tell or rule out (potentially a priori) whether any given substance or compound is likely and how likely to cause allergies with high confidence, without the need to conduct experiments, e.g. by looking at its properties, e.g. solubility, molecular structure or reactivity?
From what I've heard is that generally speaking, things that we come in contact with in early years tend to be less likely to cause problems later on, but still, there seem to be differences even with food and substances that do not quite appear to be exotic, e.g. peanuts.
This question is related to these, though I'd consider it more generic.

Meat and mushroom allergies, why are they so rare?
What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?

So, the first time you're exposed to an allergen, atopic individuals generally produce a large amount of IgE antibodies, and in the case of an allergen, to that allergen. These IgE antibodies attach to mast cells. If the allergen is contacted again, they interact with the IgE on the mast cells, and trigger the allergic reaction when the mast cells begin releasing a whole host of compounds into the region: histamines, leukotrienes, cytokines, etc. There's a host of ongoing studies into genetics, heredity, and TGFß as to susceptibility. I'm unsure there's currently a way to predict it though.

You might be right, @Kendall. This could well be a trillion-dollar question. A definitive answer may establish a unified theory of allergies and produce perfect treatments and predict genetic disposition. If I had an answer, it might thus not be worth posting here but rather to file patents for anything related.


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What do biologists mean when they use the term "biological distance"?
Here is its usage.
"there is sufﬁcient genetic control to make nonmetric traits useful in anthropological work, and such variables have successfully assigned individuals from distinct geographic regions to their correct groups (for example, ... As such, nonmetric traits are an appropriate means for studying biological distances"
Source:https://www.academia.edu/5201951/Sahara_Barrier_or_corridor_Nonmetric_cranial_traits_and_biological_affinities_of_North_African_Late_Holocene_populations

I think this is more of a Biological Anthropology question, and my guess is the question could be rephrased as "What do anthropologists mean when they use the term “biological distance?”
The Anthropology Stack Exchange is still under construction so that is a dead end for now.
Pietrusewsky (2014) gives the following definition, and I quote:

Biological distance, or biodistance, is a measure of relatedness or divergence among groups separated by time and/or geography based on morphological variation (Buikstra et al. 1990).

Pietrusewsky continues with elaborating on Biodistance research:

Biological distance studies, which are undertaken to reconstruct population history and to assess ancestry, dominated bioarchaeological research during the 19th and early 20th centuries. [...] These early attempts were flawed due to limitations of the approach, which included the mistaken belief that humanity could be divided into a finite number of pure races, and the lack of adequate quantitative methods. Advances in evolutionary theory, including quantitative and population genetics, and improvements in computing and statistical procedures in the early 20th century provided a much sounder basis for measuring and interpreting morphological variation within and between human groups.

These elaborations may explain the rather defensive stature the authors take in your cited article to back up their methods, and I quote:

In any case, there is sufficient genetic control to make nonmetric traits useful in anthropological work, and such variables have successfully assigned individuals
  from distinct geographic regions to their correct groups (for example, Winder, 1981; Prowse and Lovell, 1995; Blom et al., 1998; Christensen, 1998; Donlon, 2000;
  Hanihara et al., 2003). As such, nonmetric traits are an appropriate means for studying biological distances among North African populations and the implications of
  the patterning of these distances in assessing the relative role of the Sahara Desert as a barrier to gene flow.

Biological distance is pretty much what you'd guess: how closely related are x and y based on genetic (phenotype or genotype) studies?
There is zero biological distance between identical twins. There is extremely little biological distance between family members (for most intents and purposes, none, no matter where they live). It goes on and on in this manner.

Biological distance, or degree of genetic relatedness, will be assessed by a comparison of dental nonmetric trait frequencies.1

The phrase has been used in Theoretical Population Biology for decades. Back then, they had phenotypes to measure the degree of biological distance.2 Today, actual genetic determination of kinship is possible.

Biological distance, or biodistance, is the measure of biological relatedness (or divergence) between and within human groups, living and past, based on human skeletal and dental variation.3

1 Dental Variation of Prehistoric Amerindian Populations
from Eastern Tennessee
2 Kinship, information and biological distance
3 Biological Distance in Bioarchaeology and Human Osteology

You just outran me by 1 minute!

@ChrisStronks - I saw! You gave the better answer, though, I think. :) So you got +1 from me.

Yours is great and to-the-point, +1'ed you back :)


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B Cell Differentiation
During the differentiation of B cells in bone marrow, recombination occurs in light chain and heavy chain genes to produce a single type of functional gene which determines the type of light chain and the heavy chain produced by that B cell.
Therefore, a single B cell and its generation displays a single type of antigen receptor on its cell surface.
My question is-
Recombination will occur in both the copies of the light chain gene present on the homologous chromosomes (same with the heavy chain gene).
So, the combination produced on the homologous chromosomes should be different.
Is it really so?  And if not, then how come they are identical?

There is a mechanism in T and B cells called allelic exclusion. This means that most of the times only a single allele is used by building the light chain and the other is excluded. Incomplete allelic exclusion may contribute to auto-immune diseases, because cells using two different light chains can potentially recognize both pathogens and healthy human cells1,2,3,4,5,6,7,8.


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Chromosomal pair possible in metaphase - I
There is this question which was asked in my exam.
A diploid cell contain 6 chromosomes. How many possible random arrangement of homologous chromosomes could occur during metaphase-I?
 (consider that allele for only one character present on chromosome and they are in heterozygous condition.)
Options are :
i)4
ii)8
iii)16
iv)64
Answer given is : ii)8
But my answer is : i)4
My solution :
Aa       | Aa     | Aa     |  Aa
Bb       | Bb     | bB     |  bB
Cc       | cC     | Cc     | cC
Here,  1 column represents 1 possiblity.
These are the possible combinations according to me in metaphase-I.
Am i missing something?
Please tell me where am i wrong.
PS : i would have loaded the picture of my solution but it ain't getting loaded.
Sorry for any inconvenience.
Thank you. =)

The correct answer is 8 as given by the formula 2n , where n is the number of chromosome in haploid cell.
Explanation:
During prophase 1, synapsis take place as a result of which bivalents are formed. Now each bivalent can arrange itself in two possible manner ( known as independent orientation). Since in this question there are 6 chromosomes which means 3 bivalents, the possible number of arrangement is 2 × 2 × 2 = 8
The photo here explain independent orientation in a cell having two chromosome pair. You can work this out for 3 chromosomal pair as well.
Your doubt:
As far as I can understand your doubt is that arrangement one is actually same as arrangement third ( with reference to the photo). Well, it might seem like this but if you look carefully the two non homologous chromosomes are arranged in different manner in them .. relative to each other and the homologous partner. And hence the whole arrangement is considered as different arrangements and not the same.
Thus, for 3 chromosomal pair, there are 8 possible arrangement of homologous chromosomes which could occur during metaphase-I.

The answer would be 8.
The best way to explain this would be by the formula for number of possible arrangements i.e. 2^n.
As mentioned in the question, the cell is diploid with 6 chromosomes, which means that 2n = 6 implies n = 3.
So number of possible arrangements = 2^3 = 2*2*2 = 8.
If the two homologs are A and B, mom's being A1, B1, C1 and dad's being A2, B2, C2 -
The eight possible combinations are A1B1C1, A1B1C2, A1B2C1, A1B2C2, A2B1C1, A2B2C1, A2B1C2, A2B2C2.
Hope this helps.

Yes, i get that there are 8 arrangements possible in total.  But what I'm getting confused with is it says - 'Metaphase-I '. Now,  in metaphase -I : the homologous chromosomes are still together and haven't separated yet. So,  if my one pair is let's say A1B1C1 on one side then automatically on the other side of the metaphasic plate,  A2B2C2 will be present. Same method for other combinations. So,  overall only 4 combinations are possible( Am i thinking wrong?). But,  i guess,  everyone's doing the final calculation bcz i have asked 4 teachers and they all are applying the same method.

Please point out any mistakes in my thinking. Thanks!


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Mobile carriers of Light reaction in higher plants
The hydrogen carrier PQ and the electron carrier PC are the mobile carriers in light reaction facilitating electron transfer from PS II to PS I during non-cyclic process.
My question is -

How do they move in membrane, from PS II to cytochrome for PQ and cytochrome to PS I for PC?
I do know the membrane is quasi-fluid in nature so it'll be easy for carriers to move in it but my question is how do they reach their destination? What's the driving force?
Maybe they're just arranged that way on the membrane and some change like - because of change in density (when PQ accepts the H and converts to PQH2 ; I'm not sure about the density change part) which leads to change in side on which it's present or change in anything else, they reach their target?

Is my thinking correct?


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Dominant and recessive epistasis
Can anyone clarify my confusion about that the epistasis seen in "Labradors , an example of recessive or dominant epistasis? ?
 I am not getting definite results . It's dominant somewhere and recessive in some.:(
May anyone provide me with some definite sources??
Thank you! !:)

unclear what you're asking

@rg255 ,I just want to ask -'is it an example of recessive or dominant epistasis? '   or could you please provide me with some definite sources. ..

what epistasis seen in Labradors? you need to be far more specific (did you miss something??)

I agree that the question is unclear. I personally don't know the example of the labrador and would need a reference (or a description from you) to talk about this specific case study.
The following tables are displaying all possible kind of interactions (in a haploid and in a diploid) of two bi-allelic loci. Hope that helps! source (wiki)
For Haploids (the concept of dominant epistasis does not apply)

For Diploids

it's given in Campbell biology 9th edition. ..  its like... there , in theory its mentioned E/e is epistatic over black or brown colour allele and in diagram it's given acc. To that 'e'... i. e its an example of recessive epistasis. ..   so I am pretty confused that is it an example of recessive or dominant epistasis?     Because our teacher told that its an example of dominant epistasis! !:(         anyways, thanks for the extra info. .. I didn't know this much about epistasis; )

Ok. If my answer answered your question you can check it. If not: knowing that your question will likely soon get closed. If you manage to repeat the text (and figures) of the campbell to clarify the question in time, you may get better answers. The post can also be reopened afterward. Good luck.


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Reaction centre in Photosystems of higher plants
In photosystems of higher plants, there are about 250-400 pigments (number wise) in a particular photosystem. Out of which,approx 170-180 pigments are of chlorophyll a molecules. And any one of them behaves as a Reaction centre in a photosystem.
My question is:

What are the factors and laws which decide which chlorophyll a molecule will work as a reaction centre?
What's the difference in chlorophyll a molecules present in reaction centres of PS I and PS II since they have different threshold energy. Is there any structural difference?

Someone else too had asked your question no. 2. here Photosystem 1 and 2; P680/P700; Chlorophyll a/b
The answer basically quotes Molecular Biology 4 ed. by Lodish as follows.
"The chlorophylls in the two reaction centers differ in their light-absorption maxima because of differences in their protein environment."
[I could've just commented this but I can't locate add comment option on your post. Am new here.]

Thanks Gerardo. Could you please answer a question I have put up here https://biology.stackexchange.com/questions/68190/what-is-the-primary-electron-donor-in-the-photosystem-1-and-photosystem-2


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Generating all possible conformations of an Intrinsically disordered protein
I want to simulate interaction between the bHLH-LZ domain of c-Myc encoded protein and a test ligand. Since the domain is intrinsically disordered, I want to generate all possible conformations of the IDP to run several iterations of simulation, each time with a different conformation. How can I do so? I would really appreciate if you could explain me what is the basis of these conformations and explain the concept?
Thank you!


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Molecular Logic GATE
Currently either PET-Fluorophore or FRET is used as output of the molecular/DNA-based logic gate. Likewise, in a logic gate, lets say YES GATE, you provide an input to the logic gate and in return you got fluorescence. Please help me understand what other transfer method can be used as the output. I want to develop a complex system i.e. connect multiple logic gates with each other which, definitely, cannot happen if molecular logic gate would return output such as fluorescence, can any other method be used?
Thanks in advance

You have to be more specific than this.


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Why is RAS undruggable?

Why can't mutated RAS get inactivated by GTPase?
Why don't we have any inhibitors for RAS-GTP binding?
Why is RAS undruggable?
How can mutated RAS be inactivated?

I had been researching on the topic and had a lot of doubts in the regard. Please provide me direction, as to where can I find answers to the questions and continue the research "how can mutated RAS be inactivated?"

This is not one, but four questions and all of them are quite complex - actually these are the key question to treating a lot of cancers. Can you please narrow it down?

Do you have a reference for question 3? Why do you think RAS is undruggable?

www.nature.com/nrd/journal/v13/n11/full/nrd4389.html


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Difference Junk DNA and Pseudogenes
1-Are Pseudogenes and Junk DNA both Non-Coding DNA or they are different entity? How much Pseudogenes & Junk DNA do we have respectively?
2-I read that Non-Coding DNA has functions, my question is-since we have 98.5% NON-CODING DNA, how much of them has been found to be functional?

Welcome to Biology.SE! It is expected that you will demonstrate that you have done some research on your own before asking questions here — in particular you will find answers to both your questions on this site by searching for "non-coding DNA" and "junk DNA". For details on how to use this site, please check out the tour: biology.stackexchange.com/tour and then the help pages on how to ask questions on this site: biology.stackexchange.com/help/how-to-ask. Thanks!

The ENCODE consortium classifies human and mouse genome elements to try to answer your second question.
Work by ENCODE suggested up to 80% of the genome is functional in some way. In other words, by that upper-bound measurement, there is apparently more to DNA's role in biology than just encoding genes — there's a lot going on under the hood.

Case for Abundant Functional Genomic Elements.
Genome-wide biochemical studies, including recent reports from ENCODE, have revealed pervasive activity over an unexpectedly large fraction of the genome, including noncoding and nonconserved regions and repeat elements (58–60). Such results greatly increase upper bound estimates of candidate functional sequences (Fig. 2 and Fig. S2). Many human genomic regions previously assumed to be nonfunctional have recently been found to be teeming with biochemical activity, including portions of repeat elements, which can be bound by transcription factors and transcribed (79, 80), and are thought to sometimes be exapted into novel regulatory regions (81–84). Outside the 1.5% of the genome covered by protein-coding sequence, 11% of the genome is associated with motifs in transcription factor-bound regions or high-resolution DNase footprints in one or more cell types (Fig. 2), indicative of direct contact by regulatory proteins. Transcription factor occupancy and nucleosome-resolution DNase hypersensitivity maps overlap greatly and each cover approximately 15% of the genome. In aggregate, histone modifications associated with promoters or enhancers mark ∼20% of the genome, whereas a third of the genome is marked by modifications associated with transcriptional elongation. Over half of the genome has at least one repressive histone mark. In agreement with prior findings of pervasive transcription (85, 86), ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome. [emph. added]

However, people outside the ENCODE consortium have criticised this research with strong language, such as in this article by noted critic Dan Graur:

Actually, the ENCODE authors could have chosen any of a number of arbitrary percentages as “functional,” and … they did! In their scientific publications, ENCODE promoted the idea that 80% of the human genome was functional. The scientific commentators followed, and proclaimed that at least 80% of the genome is “active and needed” (Kolata 2012). Subsequently, one of the lead authors of ENCODE admitted that the press conference mislead people by claiming that 80% of our genome was “essential and useful.” He put that number at 40% (Gregory 2012), although another lead author reduced the fraction of the genome that is devoted to function to merely 20% (Hall 2012). Interestingly, even when a lead author of ENCODE reduced the functional genomic fraction to 20%, he continued to insist that the term “junk DNA” needs “to be totally expunged from the lexicon,” inventing a new arithmetic according to which 20% > 80%. In its synopsis of the year 2012, the journal Nature adopted the more modest estimate, and summarized the findings of ENCODE by stating that “at least 20% of the genome can influence gene expression” (Van Noorden 2012). Science stuck to its maximalist guns, and its summary of 2012 repeated the claim that the “functional portion” of the human genome equals 80% (Anonymous 2012). Unfortunately, neither 80% nor 20% are based on actual evidence.

Other critics, including Sean Eddy, focus a great deal on what is called the C-value paradox: Given a genome of a certain size, if it was all functional — or a lot of it functional, as the ENCODE consortium has claimed — then it would all be under evolutionary pressure, i.e., you'd expect certain mutation rates to occur, but they don't. Evolutionary biology would say about 5-10% is functional, I believe, based on how much selection takes place and where. So those critics would say (and have had indeed said) a lot of negative things about results reported by ENCODE.
I suspect that the true answer, if there is one, depends on what one defines as functional and as evolutionarily conserved, by what means you measure it, and what the balance is between functionality and conservation. You pick your definitions and processes, and you accept the compromises and limitations that go along with those choices.
Caveat: I am a contributing author to ENCODE papers released in Nature in 2012.

thnk u very much,I m a layman bro.u said 80% of the genome is functional in some way, does it include 98.5% NON-CODING as well? or its just 80% of Coding portion of DNA?
Am I right to say There are many types of Non-Coding DNA, Junk DNA and Pseudogenes are two of them? (plz pardon my amateurish queries)

is it findings of ENCODE that Junk DNA is functional? I heard that there is no Evolutionary Biologist in their Project, is it true?

ENCODE found that a lot of the genome was transcribed, that in no way proves it is all functional.


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Flow Cytometry Channels
I did a flow cytometry experiment for the first time. I had three conditions: (1) unstained healthy monocytes (2) healthy monocytes stained with green/red (488/570) from the Live/Dead thermofisher kit (3) dead monocytes stained with the same green/red dyes.
I did those condition to know what graphs to expects, and learn the FACs process and analysis. Would appreciate it if someone can answer the following questions:

So I have two dyes in my samples and a control. Which flow cytometry channel should I use in my plots (FL1, FL2, FL3, or FL4)?
How to know the percentage of live and dead cells in each condition?
Anyone knows a free analysis software?
How practical is R to do flow cytometry analysis?

I'll amend this answer as I get details from you.
What is your cytometer, and how are the optics set up? You typically have 1-5 lasers: UV (355nm), violet (405nm), blue (488nm), green/yellow (~561nm) and red (~633nm) lasers. Your FL number, FL1-4, typically refer to a particular PMT (photomultiplier tube) and filter combination. For example, a typical FACSCantoII has a 4-2-2 setup with 4 PMT on the blue laser, 2 on the violet laser and 2 on the red laser (if you bought the device that way, there are other configurations). These fluorescence channels are set up to detect a particular fluorophore or equivalent with a bandpass filter. The base filters on FACSCanto II red laser are 660/20 and 780/60. These filter light emitted by the stained cells at a particular range of wavelengths, and you read them as 600nm +/- 10nm and 780nm +/- 30nm, for example.
You can set your software up to be FL numbers or fluorophores, but what you need to know is what filter is FL1 and so forth? Typical cytometers like FACSAria, these are FL1 = FITC, FL2 = PE, FL3 = 7AAD, PerCP/Cy5.5, etc., FL4 = APC.
So you used a live/dead thermofisher kit, please provide us also the catalog numbers.
What we want to do is take the information about your dyes and about your cytometer and reconcile them to determine what channel they should fluoresce in. 488nm looks like FITC or FL1 and 570nm looks like PE or FL2, but these look like lasers, whereas you want to tell me the dye emission to match it to a channel, using the information about your device configuration!
As for software, there are a number of good, expensive options like FCS Express and FlowJo but they're costly. See if your core or what have you has these available for you to use on-site. Otherwise, the on-board cytometer software like FACSDiva may need to suffice, and often does. I've used some of the "free" ones but they're very clunky and/or terrible to use.
R has some usefulness for high-dimensional analysis, but you need to be able to use R fluently, and you can't draw manual gates. There do exist helpful packages with good documentation like X-cyt (broad institute), though. And for visualization like PCA and t-SNE, R has a lot of documentation for flow data. Also consider R loads everything into RAM so on a slower 2-4GB computer it might have lackluster performance.
To start with your analysis, I'll ask why did you use two dyes? The LIVE/DEAD product line are reactive with free amines which present inside and outside the cell. Dying cells have more permeable membranes and take up more dye. So when you analyze the cells, everything is positive, but the dead and dying cells are 1-2 logs higher intensity of staining compared to the live population.

So the first thing any flow experiment needs are controls. You have unstained controls, FMO controls and compensation controls. The unstained just gives you an idea your morphology by light scatter, but for low-dimensional experiements can act as an FMO. The FMO or fluorescence minus-one is a cell stained with everything in your antibody/dye panel except one marker, so that you can compare against the fully-stained sample and see where to draw your gate. Compensation controls help the cytometer correct for the fact that filters pick up emission from other fluorophores than the target. You also have a biological control, which is good, because for analysis you always want to see where a clear positive and negative population lay on your dotplots or histograms. Live cells help you see where the positive and negatives are but may have a weak positive signals, and unstained cells will have a negative population that is shifted down 1/2 log or so because they dont have any dye at all. The dead stained cells will show you a strong positive signal and potentially a weak negative signal. Use these to draw your gates.
So then compensate the data electronically with your software (follow the manual), and create a dotplot with FSC-A and SSC-A on the axes. Only experience will tell how your cells look on this plot, but for reference, a blood or leukocyte sample would like like this:

You want to draw a gate around your monocytes and then create a plot based on your monocyte gate (at least gate out debris). It's also useful for further experiments to stain with a monocyte marker so you can dump everything but your target cells, so use CD14, for example, which is specific to monocytes.
On the next dotplot, make the axes FSC-A and FSC-H. This is a doublet discimination step where laser area scaling done before a cytometer run helps a lot (see your core expert). The principle here is to gate out (get rid of) cells that are stuck together:

Then you would want to look for your target cells. If they're both live/dead dyes you're going to have the same signal on two different channels, so you can probably just pick one, like live/dead green.
You can do a histogram of FL1 based on the cells kept in the doublet plot. You should see two discrete peaks on a log or bi-exponential transformed intensity axis (width basis -10 is good to use, but FACSDiva does it automatically). Width basis is a co-factor that compresses the data around 0, so negative populations get smaller and you get better resolution among the positive populations.
You would draw a bifur gate between the positive and negative peak or a range gate around the positive, and select tell the software to generate statistics to get your percentages. And you can repeat for the FL2/red dye to get those percentages, too, but both markers are looking at the same thing.
Then, apply those gates to all your samples and adjust the gates based on what the data looks like.
Please try this presentation: https://www.slideshare.net/richardhastings589/kumc-introduction-to-flow-cytometry


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How do plants that grow underground legumes/nuts distribute their seeds?
It makes perfect sense to me when plants employ some sort of method of distributing their offspring some distance from the mother plant. If the mother plant dies due to that location not being ideal, the offspring could potentially find somewhere better. Though, plants like peanut plants that grow their seeds in the same location don't make sense to me. How do their seeds travel distances and spread across land? How is this method effective enough to be passed down through evolution? It seems awfully counter intuitive to me. I tried figuring this out on google but couldn't find anything that answered this.

How do other seeding plants spread their progeny - might this still apply?

the plants you mention in your question uses bacteria to convert nitrogen to nitrate,so the plants provide fertilizer to the soil where it places the seeds.

Searching for "how do peanuts spread" lead me to http://bioweb.uwlax.edu/bio203/s2012/steinmet_vero/reproduction.htm, an excellent site where your question is answered (considering peanuts).


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Black oyster of sweet water
I have seen recently a documentary starting with introducing of the spectacular black oyster of sweet waters which imitate exactly like a prey fish in order to convey its eggs to predator fish's gills, while it had no eyes to see the form of prey fish favored by the predator fish.
The amazingness of what this creature do provokes me to ask some questions about this strange creature and know more about this odd phenomena and theories represented for evolving of such marvelous creature.
How the black oyster detect completely kind of prey fish which is favourite food of target predator fish ,and make a very detailed simillar image of it in order to deceive the target fish while it has no eyes to see?

I believe you're talking of the members of the families Unionidae and Margaritiferidae, which have a larval stage called glochidium. From the Wikipedia page linked here:

This larva form has hooks, which enable it to attach itself to fish (for example to the gills of a fish host species) for a period before it detaches and falls to the substrate and takes on the typical form of a juvenile mussel. Since a fish is active and free-swimming, this process helps distribute the mussel species to potential areas of habitat that it could not reach any other way.

This interesting study about phylogeny of these species shows that lures mimics mainly fish, but also different prey species such as insect larvae. Some species display an aspecific lure, while others show fine mimicking in order to attract a precise set of host fish species.
As to how luring evolved:

What drives the evolution of luring? Very little is known about what drives the evolution and diversification of luring, which has evolved independently multiple times. In Lampsilini mussels, luring appears to have arisen early, and the complexity of the lure has increased through the lineage. It is likely that diverse selection pressures govern the evolution of luring. One hypothesis is that luring increases the rate of prey encounter without incurring the metabolic costs associated with active search and pursuit. Alternatively, luring may present predators with an opportunity to exert control over a prey’s movement, reducing the risk of injury when hunting. Luring systems present a unique opportunity to understand signal design and evolution.

Do oysters need to see in order to evolve the lure?
No. Evolution of a body part does not require sight or will. From this blog post:

Note that [...] the mussel can’t see the fish it’s parasitizing.  In this case natural selection is literally blind. Those mutations in the mussel that make its brood pouch look more fishlike will give it a reproductive advantage over its confrères, even if it can’t see the fish it’s deceiving. Note as well that selection has “acted” (I’m anthropomorphizing here: selection doesn’t really “act”, for it’s not an external force but a process of gene sorting) not just on the appearance of the mussel, but on its behavior.  It has genes that make it wiggle its brood pouch in a fishlike manner.

The mechanism is all here:

1st step: mutations that modify the coupling of fish bites and glochidia release/mantle shape/the movement of the mantle arise.
2nd step: The bearers of favourable mutations will have more progeny and the population will have more and more bearers as generations pass.

No need of being conscious about anything. :)


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Mosaic segregation in C. elegans
How can mosaic segregation be used in C. elegans? Can it tell us where a given gene is expressed, or needs to be expressed for worm survival?


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How many Watson-Crick + Hoogsteen triple base pair combinations are there?
Are these triple base pairs the only Watson-Crick + Hoogsteen triple base pairs possible? Furthermore, are TAA and TAT mixed up? This image is from Wikipedia, so it's possible that it's erroneous.

You are correct in assuming that the image labeled TAA should be labeled TAT and the second one labeled TAT should be labeled AAT. The image should be removed from the Wiki page until it has been corrected (even so I find it unclear).
Only some of these images show Watson-Crick/Hoogsteen combinations. To answer your question of how many such combinations there are, let us first recall what a Hoogsteen base-pair is. As stated in the first diagram on the Wiki page, this is a non-standard AT or GC base-pair formed by purine rotation about the glycosidic bond and base-flipping. In the diagram I have produced by canabilizing the above I show W-C and Hoogsteen base-pairs with the difference in the glycosidic link shown in yellow overlay. Because the pyrimidines A and C in a W-C base-pair have no groups left to hydrogen-bond, the only way you can theoretically make a W-C/H combination is by ATA and CGC as shown in my diagram. Therefore there are only two such possibilities.

I am not quite sure why you want to know about WC/H combinations, other than to understand the diagram in the article, because they are not particularly important. The author of the diagram shows such combinations because they apparently occur in triple-helices of artificial copolymers, however his diagram also shows some non-Watson-Crick base-pairs, e.g. CGG and CGA (which are not examples of WC/H combinations). The molecule where most Hoogsteen base-pairs are found naturally is RNA, not DNA: e.g. tRNA and ribozymes, in regions which do not have a standard double-helical structure. In these case they can occur in combination with both WC base-pairs and non-WC base-pairs (e.g. the GG illustrated above), so there is nothing special about Hoogsteen base-pairs being combined with WC base-pairs.

What I would consider important to realize is that in the context of the DNA double-helix WC base-pairs give the most thermodynamically stable structure, but outside this context, especially in RNAs that have protein-like structures, a variety of alternative base-pairs and base-triples are structurally and thermodynamically possible, including but not restricted to Hoogsten base-pairs.


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What is difference between Incest and Inbreeding?
Are they the same? As both are related to sexual activity between close relatives.

Welcome. What have you found so far? I think copying and pasting the question title in google will deliver a result in no time.

Incest is a human concept defined by law and social conventions. For example, see a definition of the word: "sexual intercourse between persons so closely related that they are forbidden by law to marry".
A person who was adopted may have siblings who are genetically more different from them than other people they could legally have romantic relationships with. In many countries you may marry your cousin, but not your foster brother/sister born on the other side of the world.
Anthropologist Claude Lévi-Strauss pioneered the study of the universality of the notion of incest; romantic relationships with family members is culturally forbidden in pretty much all cultures around the globe. But why? One of the explanations is linked to the notion of inbreeding.
Inbreeding (mating between genetically closely related individuals) favors homozygosity, and as a consequence a certain genetic homogeneity in which there is often not a "functional" allele to compensate for the "broken" one - the consequences on physiology and mental cognitive abilities are often dramatic (see Roberts, BMJ, 1967 or this article from Stanford @ the Tech, for example); it is hypothesized that this is the reason why evolution selected behaviors that avoid the risks linked to inbreeding.

Incest and inbreeding are different concepts. Incest involves crossbreeding between close relatives. Inbreeding is a broader concept. It can be a connection between relatives or self-pollination.
UPD: This is certainly not a journal article, but..... https://en.wikipedia.org/wiki/Inbreeding

Hi, the silly girl again! We expect answers to be backed up by credible sources, preferably journal papers. In addition, the answer isn't clear - the last sentence doesn't make clear why it's different.


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What is the difference between differentiation and phenotype switching?
I am trying to model bone remodeling process and I wonder what is the difference between phenotype switching and differentiation. I am relatively inexperienced in biology. Please explain me with examples related to this context. Thanks in advance.

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

Differentiation is a process which occurs in multiple steps. A precursor cell for example a mesenchymal stem cell can proliferate (divide/multiple).  The stem cell can commit to become a progenitor cell (osteoprogenitor cell) which can still proliferate but has acquired the possibility to differentiate to a different cell type. In some cases or when specific conditions are met,the progenitor can differentiate to a pre-osteoblast and finally to a mature osteoblast.
The differentiation process require the activation of a specific transcription program and leads to large changes in the cell like morphology, size, and function. Once differentiated, the cell cannot proliferate anymore and loss the capacity to divide.
Phenotype switching can be broadly defined as any change in the phenotype like morphological change, expression of specific biomarkers, etc. In the context of differentiation phenotype switching refers to the acquisition of a specific differentiation marker usually a transcription marker like Runx2. While they might not be a large morphological change, the fact that the cell express this transcription factor indicates it is switching phenotypes and starting differentiation.
In summary: differentiation is process which occurs in multiple distinct steps. Differentiated states are characterized by a specific morphology, acquisition of key bio markers (usually transcription factors), loss of the capacity to proliferate, and a cellular specific function. Phenotype switching refers to the time frame when a cell changes from one phenotype to another; when it acquires or loss a defined morphological state or key markers.

Both differentiation and phenotype switching are terms which are used in intense research areas. Their definition will get revised in the next decade for sure. The definitions I have highlighted are what you will classically find in most publications but in reality it is difficult to define specific steps in a differentiation process because it is usually a continuous process.  Phenotype switching is even worse to define as it assumes that once classified to a category a cell does not have a dynamic phenotype: a cell which proliferate change phenotype as it goes through the cell cycle.

Thank you very much for the response. Differentiated cells lose the ability to proliferate. Does that mean they don't divide forever? Do they die?

Technically yes they should not divide. Theoretically, these cells could accumulate genomic mutation (UV, chemical environment, etc) and become cancerous but I'm unsure if this has been convincingly shown in the literature.
Yes differentiated cells can die by different mechanisms including apoptosis and necrosis, and be replaced by others cells. A good example would be neuronal cells.


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Is a female spider, well-fed by sexual cannibalism, less likely to mate again?
The Wikipedia page on sexual cannibalism (e.g. female spiders eating their mates) currently has a statement that sounds wrong to me, but I don't feel expert enough to edit it out:

An additional benefit to cannibalization is the idea that a well-fed female is less likely to mate again.

I can't see why that would be the case. Why not continue to seek a second, better, mate? Unless perhaps being well-fed makes you a slower, larger target for predators, so hiding for a while is a better tactic.
The reference given is to

Female hunger can explain variation in cannibalistic behavior despite male sacrifice in redback spiders. 9, 33–42 (1988)

A bit of searching suggests the author meant to include Behaviour Ecology as the journal name. I've only read the abstract, but it does not seem to support the statement. It suggests a well-fed female is less likely to consume her mate, which seems intuitive.
Am I right that this Wikipedia sentence is incorrect? If I am wrong, is there an explanation for the effect that I am missing?

It does appear that Wikipedia has not provided the most appropriate reference for that statement, but it is repeated in the article it refers to and that you link to, both in the abstract:

Male sacrifice may be adaptive because cannibalized males increase their paternity relative to those that are not eaten

and in the  body of the introduction:

Males that are cannibalized obtain paternity advantages compared to males that survive copulation

These statements do not necessarily contradict the other statement that a well-fed female is less likely to consume her mate, but there might be some nuance missing here in terms of mating versus mate consumption behaviors. However, the authors cite Andrade, 1996 (see below) for the second statement, and this seems like a more appropriate reference for the statement on Wikipedia:
Yes, a female spider who eats her mate is less likely to mate again. Andrade 1996 shows that males who are eaten during copulation mate longer, fertilize more eggs, and the females are more likely to not mate again after eating a mate.

Andrade, M. C. (1996). Sexual selection for male sacrifice in the Australian redback spider. Science, 271(5245), 70-72.

To be clear on my (prior) understanding: I accept that male sacrifice is adaptive - for example, because a well-fed mother is more likely to successfully produce offspring, but it isn't intuitive that the female wouldn't mate again. Your reference shows my intuition is wrong (which I celebrate. I learnt something!)

@Oddthinking Indeed, Andrade concludes that the mother being well-fed has little to do with it, because the male is so small relative to the female's mass and eating the mate does not result in more or larger eggs. Instead, the article suggests that the duration of copulation is probably the key factor. Feeding on the mate is occurring while copulation is still in-progress, so effectively she is distracted by the feeding into allowing longer copulation. It isn't clear to me what prevents future matings, but in some ways it is irrelevant because fertilization already occurred for many eggs.


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Why does arterial emboli flow in retrograde manner?
In artery blood flows with a pressure. When part of thrombus detaches it should flow along with the flow but it flows is retrograde manner.

Are you sure it does? Can you tell us where you learned this?

Yes it does. It is given in Asian edition of Robbins

I think you might be talking about Propagation of arterial thrombi.
Propagation is the increasing size of a thrombus and it occurs towards the heart, this is because thrombi are formed differently in veins vs arteries. In veins they form through the accumulation of fibrin and red blood cells whilst in arteries they form through the clumping of platelets.
https://www.thrombosisadviser.com/thrombus-formation/
Embolization is when the clot is removed from the circulatory wall and at this point it moves along with blood flow in both veins and arteries.

Yes I'm talking about propagation. But venous embolus flows along with blood flow. My question is why does arterial embolus propogate in retrograde manner instead of flowing along with the blood flow?

@KetkiShah - An embolus is different than a thrombus. What are you asking? The answer is correct that emboli flow with blood, not against.

From a bit of searching on the internet the general opinion appears to be that it is due to the fact that arterial thrombi are formed differently to venous ones.
Arterial thrombi are caused by injury to the vascular wall, causing a clot of platelets to form at that point. These platelets begin to join the clot as they hit it, causing the clot to propagate retrograde (towards the direction the blood is coming from)
Venous thrombi are caused by stasis of the blood flow, this causes the blood to coagulate at the point and gradually more fibrin and red blood cells collect onto this.

I had the same question after reading "arterial thrombi grow in a retrograde direction from the point of attachment, whereas venous thrombi extend in the direction of blood flow" from the Robbins & Kumar Basic Pathology Textbook. I think what this means is that the SIZE of the thrombus grows in the direction towards the aorta, but when it detaches it moves along the blood flow, so towards the right atrium of the heart. The reason why it grows towards the aorta is perhaps because blood is flowing towards the thrombus and the platelets get stuck on the thrombus before passing by it, so the plateles accumulate one after another. Think of it like a tube of flowing water with platelets. If the inside of the tube has some substance stuck to the wall of the tube, the platelets will sit on it before passing by it. I hope this helps!


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How does the intracellular accumulation of cyclic AMP cause edema in case of anthrax?
Edema factor is adenyl cyclase which is activated only inside the target cell. It leads to intracellular accumulation of cyclic AMP resulting in edema. How?

Welcome to SE Biology. This appears to be a homework question and you need to show that you've made an effort to answer it yourself.

@Michael_A This doesn't sound like a homework question to me. First of all, the answer is that it's poorly understood, so a full answer would require a substantial grant and a lab. Second of all, the research is right there in the question: What does edema factor do?  This is what the OP found out: what edema factor is, where it acts, what the immediate molecular effect is, and the clinical result. You may be unfamiliar with this, so it may appear to be poorly researched, but it's actually asked quite well, and succinctly, though probably by someone who's native language isn't English.

Edema factor is a high efficiency adenylyl cyclase, an enzyme that converts ATP to cyclic AMP (cAMP). cAMP is an important second messenger in many pathways, which you can read about in Albert's Molecular Biology of the Cell. In order to be an effective second messenger, it must be tightly regulated. Several bacterial toxins disrupt this regulation, by creating an excessive amount of cAMP directly (B. anthracis EF), forcing the local activator of adenylyl cyclase to stay on (V. cholerae CT), or preventing the local inactivator of adenylyl cyclase from turning it off (B. pertussis). Some of these pathways are well understood. The pathway between cholera toxin and lethal loss of intestinal fluid, as mediated by elevated cAMP, is particularly well understood. The pathway between edema factor, edema toxin, cAMP, and tissue/organ edema is not well understood, as illustrated by this lovely figure, from this review:

Note the nice question mark between Edema Toxin and Edema
It could be mediated by protein kinase A (PKA), and probably is at least partially. It could also be mediated by EPAC and the small G-proteins Rap-1 and Rap-2 (and probably is, at least partially). It could even be mediated by the loss of ATP, since the anthrax ET is so efficient at catalyzing the conversion of ATP to cAMP.


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Can supplements affect DNA? (Could 10,000% Methylcobalamin affect MTHFR genotype)
Originally titled "Could B12 supplementation affect dna test results for B12 need?" - B12 just seems like a good example question to frame the more general question of "Can supplements affect DNA?"
I recently got a DNA test done from DNAFit and found out I do not have a raised need for B12 - however - I've been supplementing with about 10,000% B12 (as methylcobalamin) for quite some time now. Been taking 10,000% every day for 5 months and like 1,000+% B12 for another 5.5 months before the increased dosage. I actually am quite dependent on my supplements, and think it's quite possible that my DNA has adapted to them, if DNA does such things. (Just looking briefly, it appears there is some disagreement as to whether DNA can change due to supplementation: google.com/search?q=CAN+SUPPLEMENTS+CHANGE+DNA )
So there's the root of the question - can supplements affect DNA - more specifically - could B12 supplementation affect the result of my MTHFR genotype (which is CC, just FTR)

What the DNAfit test does is analyse some of your genes for common variants (called SNPs - single nucleotide polymorphisms). These are hard-written in your genetic code, they won't ever change (you could in theory have mutations in some individual cells, but we can ignore that).
Taking supplements or any other environmental influences will therefore not affect these tests.
The environment can affect certain markers on the DNA, that control how active a given gene is (how strong its expressed) - this is called epigenetics. Since these markers are written on the DNA they are also potentially heritable and the two effects (the genetic code itself and the markers on it) are often thrown into one pot when some news report about 'changes to your DNA'.


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Dihybrid cross question
An experiment is set up to study two genes. The two genes assort independently and for each gene the expression of alleles involves complete dominance. In the genetic cross RrTt x RrTt, a number of different phenotypes are seen. What is the difference between this number of phenotypes and the number of phenotypes seen when the cross RrTt x rrtt is carried out?

Welcome to SE Biology. This question appears to be from an exam or quiz. Please read the guidelines for homework questions. You need to show you've made an effort to answer it yourself.

Have a look through this presentation. Let's focus on the last slide:

First, let's understand what the letters mean:
R = red allele
r = white allele

T = tall allele
t = short allele

There are two of each because the organism is presumably diploid, i.e. contains two alleles for each genetic locus, one from the father and one from the mother. In the case of RRTT or rrtt, it means the mother and father alleles are identical and the organism can be said to be homozygous ("same alleles") for these traits. In the case of RrTt, or rRtT, or rRTt, or RrtT (they are all the same, basically), the organism can be said to be heterozygous ("different alleles") for both genes.

The two genes assort independently and for each gene the expression of alleles involves complete dominance.

So we are told the alleles are completely dominant. By convention, we use capital letters to indicate dominant traits. That means that if a capital letter is present, the organism's trait will be determined by the dominant allele. A few examples of possible genotypes (left) and their phenotypes (right), to help you understand:
RRTT -> RED & TALL

RrTt -> RED & TALL

rrTt -> white & TALL

rRtt -> RED & short

rrtt -> white & short

You first make your Punnett squares, as in the picture above. In your case, one for RrTt x RrTt and one for RrTt x rrtt. You fill both in. You will know all possible genotypes to result from the cross. Now - count how many phenotypes each cross will produce! You'll be able to say which cross will produce more, equal or fewer red, white, tall and short offspring. There's your answer!
Personal tip: Always visualize to make sense of the steps. When you see the cross RrTt x rrtt, imagine a red, tall individual carrying both red/white and tall/short alleles mating with a white, short indivual carrying only white and short alleles. When you make a Punnett square, you are simply predicting all the possible different babies to come from this cross. The amazing thing is that you can predict the ratio of traits among the babies. This was a big leap in genetics!
Keep in mind you are making a few assumptions. Every time you make a Punnett square, you are assuming the laws of Mendelian inheritance apply. You are assuming that the genes assort independently (which is not always true, especially for genes which are close to each other in the genome; they could travel together when they are being mixed), are not sex-linked (e.g. "only males can become red"), that the phenotype is determined solely by one gene ("monogenic"), and that your theoretical prediction will match reality. In practice, some alleles may confer a competitive advantage (and seem over-represented when you check the offspring), or may be lethal (expected offspring would be dead and you wouldn't even see them - they would be under-represented).