text:
How does a virus stick to a non-biological surface?
Recent events has triggered an renewed interest in understanding how a virus is able to stay on a surface.
For sake of argument, let's assume we are dealing with a Corona-type virus. One can then speculate that a virus sticks to a (non organic) surface due to a London-force (a Van der Waals force) interaction between the surface and the virus Spike S protein. But I really have no idea and it's just a wild guess.
I'm looking for research and experiments on this topic but I can't find any, most likely because I am not asking Google the right question or using the correct biology language.
How does a virus stay attached to a non-biological surface?
(Are there any "stickiness" measures for this?)
PS. When I say non-biological, I mean glass, metal and plastic.

It might be useful to look into studies that have been done into colocalization of viruses and bacteria on (organic) biofilms (e.g., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993353/).

The virus never appears isolated. When it is distributed by droplets or feces that is the transportation medium. And those are sticky by them selfes.

@aggsol do aerosol droplets last days attached to surfaces even when said surface appears dry? Is it microscopic?

@aggsol That's very logical, why don't you make it an answer rather than a comment ?

@Larry Nothing is dry, check the humidity level with a device. I think it will remains attached to dried organic material maybe.

The virus never appears isolated. When it is distributed by droplets or feces that is the transportation medium. And those are sticky by itself.


text:
What is the size (diameter) of the SARS-CoV-2 virus?
You can easily find a lot of pictures of the SARS-CoV-2 virus. But although it should be trivial for an electron microscope to measure the size, I am not able to find accurate size information.
What is the size (diameter) of the SARS-CoV-2 virus?
(Why does some virus particles seem to have a different size?)

http://virology-online.com/viruses/CORZA4.htm.

Although your question is straightforward, it would be great if you could explain why this information is useful to you.

@WYSIWYG As a researcher I'm sure you can think of at least 5 reasons, but we can probably invent another 100. But I find your request irrelevant to the question, especially in the light as 2 people have already voted for closing it. So please contact me elsewhere in case you'd like to know more.

@not2qubit It is not for my personal query. Supporting the question with a rationale helps other readers understand the post better. Since our aim here is not simply help people with their specific queries but make a repository of useful information, it is always good to have some background in the posts.

It would be far more interesting to know on what grounds people are close-voting (more or less) every question I have on this SE? Apparently the common courtesy of at least explaining why they down-vote or close-vote seem completely lacking here... The perfect way to alienate just about every new user you have here.

Electron micrographs of negative-stained 2019-nCoV particles were generally spherical with some pleomorphism (Figure 3). Diameter varied from about 60 to 140 nm. Virus particles had quite distinctive spikes, about 9 to 12 nm, and gave virions the appearance of a solar corona.

--A Novel Coronavirus from Patients with Pneumonia in China, 2019
Figure 3 from that article:

Does a virus have a well defined shape? links to your answer, any thoughts?

source: Stack Exchange

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

sort: votes


text:
Cultivate snails and maintaining them alive
I found snails in my garden, I want to create a good house for them. I don't really know how to do. Sorry if this is not the good site to ask that but I don't want them to die so I'm trying to be quick.
This is a temporary terrarium for them, is it good ? What do I need to keep them in good health ? What do I need to put in the box ? Is it too small ? I will inquire all about later, I want them first in a safe place.
Thank you :)

I think you might need to put some large leaves and some water.

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


text:
Harvest honey without damaging brood cells
I want to make a homemade beehive, I want to know how to differentiate honey cells and brood cells, therefore, I'd like to know how can I organize the beehive so bees will create honey and brood cells separately. By this way, I would be able to harvest the honey without killing the larvaes :)
Ancillary issues : Do bees need cells to sleep in ? Can I populate a homemade beehive with several bees caught from my garden ?
Thank you for your attention :)

Welcome to Biology.SE. I do not think this question is really about biology (but wait to get other users' opinion). You might want to consider pet.SE and sustainableLiving.SE (or even maybe greatOutdoor.SE).

You may have better luck on beekeeping speciality site like this https://beebuilt.com/pages/beekeeping-for-beginners

I think this question is about applied use of biological knowledge, more specifically bee behavior and entomology, and should be re-opened. Closing it is to me similar to closing general questions on medical treatments or medicine, since they are "just" applications of biology/biochemistry and not "really about biology" per se. Which we do not do at Bio-SE.

In domesticated bee hives, this is usually accomplished by excluding the queen from a section of hive frames (by the size of the entrance hole), so that these frames only contain honey and no eggs/larvae.
For instance, this can be achieved using a queen excluder.


text:
How to estimate the amount of protein that are going to be synthesized?
I'm studying protein synthesis to understand how the body use the different amino acids to build proteins.
In particular I would like to learn how to (roughly) calculate the total amount of protein synthesized knowing the amount of amino acids eaten.
I think the easiest case is that of complete protein with PDCAAS value of 1. I guess that in this case the amount of proteins synthesized is equal to the amount of protein previously ingested, isn't it ?
So consider the more complex case of incomplete proteins, i.e. proteins with limiting amino acids.
For example consider raw lupins, 100g contain about 36g of proteins, with these essential amino acids:
  Amino acid   |   g in 100g of lupins
----------------------------------------
Tryptophan     |  0.29
Threonine      |  1.33
Isoleucine     |  1.62
Leucine        |  2.74
Lysine         |  1.93
Methionine     |  0.26
Phenylalanine  |  1.44
Valine         |  1.51
Histidine      |  1.03

source: https://ndb.nal.usda.gov

If I eat 100g of it, how to calculate the final amount of proteins that will be synthesized in my body ? (for simplicity don't consider the protein digestibility)
I guess the first step is to find the limiting amino acid(s) of the lupin, but how can I find it/them ?

Whatever makes you think the amount of protein synthesized is equal to (or even proportional to) the amount of protein ingested? Ever heard of urea?

I think it's impossible to estimate because of many reasons.
1) Amino acids are used not only to build new proteins in body. They can be used for other processes.
2) There are thousands of different proteins has been synthesized in cells for different purposes. These proteins differ both in number of amino acids and in what exact amino acids are included in exact protein. You have showed table for 100g lupins, for other proteins this table will be with different numbers.
3) It is impossible to estimate the needs of exact body in exact moment in exact components for exact processes. So it is difficult to evaluate the result of how what we eat will be used by body with good precision.

Thank you for pointing this out, didn't know about that. So how can all the sport dietitians give nutrition recommendations about protein intake if this cannot be estimated ?

I am not dietitian. So I express only my opinion. Recommendations is a result of simplification. General recommendations are not precise enough. They don't take into account individuality. Special recommendations are dictated by your purpose and body feedback. For such radical situation as disease, you have symptoms that give signals. For basically healthy state, you don't have good indicators. Some predictions can be made based on practical knowledge. Experienced dietitian can be more effective in predictions in specific situation. But on some level it's always trying and experimenting.

I understand, but in the case of a diet for increase muscle tissue, it is obvious that an increased protein intake is needed. As I wrote in the main question, i'm not interested in the precise quantity, but rather in an estimation. In this case (4-5 days a week of training) I guess the body needs everyday more protein than the average to build and maintain the increased muscle tissue. So, in this particular case, is not easier to estimate the protein synthesis? Should I ask in the fitness board?


text:
Pseudoautosomal regions of the X chromosome showing heterozgyosity
I've always had questions for myself about sex differentiation, mostly on account of an unusual history & puberty. I won't go into details, but needless to say it was unique.
My question is... I got results back from 23andme showing hetereozygosity at the beginning & ending of the X
I've been diagnosed as XY androgen insensitive & pseudohermaphrodite with mullerian structures intact.  Born with questionable stuff internally, only definitive thing is nothing male (no prostate, no seminal etc..)
They also did show a Y, but it was apparently missing half of it (though I've read thats not unusual for half of it to be --)
Can you have a hetereozygosity at the ends of the x and not have another x?
rs6644972   X   178624  AG
rs28475515  X   182276  CT
rs28463388  X   191998  TT
rs28669107  X   195014  CC
i6033542    X   200928  CC
rs6655397   X   201935  GG
rs7890186   X   202458  GG
i6033543    X   209741  CC
i6033544    X   215805  CC
rs28736870  X   220770  GG
i6033545    X   228250  GG
rs6603204   X   298440  GG
i6033547    X   301596  CC
rs2738344   X   310897  AA

A normal male can show heterozygosity in the "X" results of a 23andMe SNP test despite having only one X chromosome.  This is because there are very short regions at the ends of the Y chromosome, called pseudoautosomal regions, that match up with equivalent (homologous) regions at the ends of the X chromosome.
Because the pseudoautosomal regions of the Y are homologous to the matching regions of the X, the SNP results for those areas cannot be distinguished in the SNP tests, so the results appear along with the X results in "X" chromosome file.  The results in those two areas of the file can be either homozygous or heterozygous at each location.  Most of the locations in the "X" file are for  locations outside of those regions, so most of the file entries cannot report heterozygous results.

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


text:
How can a minor allele frequency be >50% (reported in GNOMAD)?
I'm receiving a data set to start an analysis. My collaborators ran GATK to find variants from sequencing data, and GNOMAD calculated the minor allele frequencies - and then I'm receiving this MAF data to start the analysis.
When I was looking at what my collaborator called the minor allele frequencies returned by GNOMAD, some of the MAF were >50% (e.g. a MAF could be 70%).
I was looking at the GNOMAD documentation and it says this: https://gnomad.broadinstitute.org/help/faf but I'm not sure I understand what it's saying. Does it make sense that a MAF can be >50%? or are the allele frequencies returned by GNOMAD just the allele frequencies of the reference variant, and extra processing is requiring to find the MAF?
p.s. I can see this question. I actually don't have the data set yet, he was just showing me it and running through what the columns were yesterday, but the column looked like this:
GNOMAD.all MAF (i.e. all ethnicities MAF from GNOMAD)
SNP1    0.75
SNP2    0.002
SNP3    0.4
SNP4    0.1

Could it be that the numbers you saw were showing the frequency as a percentage rather than a [0,1] ratio?

Minor allele critically depends on what the reference population or genome is.  And it also depends exactly how those data are sliced, it would be easier to say if we saw them.
Especially in large multipopulation consortia or aggregation efforts like gnomAD, this can be a pretty important consideration.
If your major allele is defined on something like 1000 genomes or, worse, a nation-specific population, then your "major" allele might quite often have frequency <50%.
These large data-collation efforts don't flip the major/minor allele around constantly, as that would require a significant informatics effort, and you would constantly have to track which major alleles line up with the reference genome and which don't. Probably they do update their major alleles periodically as more data gets sampled, genome builds get updated, and their curators get around to it, but it's unsurprising that at some frequency a specific population might have a minor allele at 80% or something.
It's a little more surprising when globally a minor allele is at high frequency, but it will still happen at some rate.


text:
Are bacteria repelled by self-lysis products?
Intuitively, it seems like treating your own lysis products as chemorepellants would make sense, since getting away from a place where your kind are dying would be a Good Idea, but I can't find any papers that explicitly say so. Does anyone here have insight into the behavior of bacteria in the presence of high concentrations of chemicals that are normally inside of cells?

What specific chemicals or substances are you thinking about? What would only be found inside a bacterial cell and not in the general environment?


text:
Unidentified Fish-like Microorganism from pond water
I was looking at my friends pond water and saw several Daphnia. As I was searching, I noticed a Pliomate Rotifer and some other unidentified Microorganism. It looked almost like a micro fish, with a strange patterned disk around its body

That was under 40x magnification there's another image but with the disk hidden from view.

That photo at 400x or 800x. I did notice some fast moving area near the head almost like cilia, however they were inside and didn't appear to be cilia wiggling. If anybody has seen this type of microorganism before, please do let me know! I'm not sure if it is uni or multicellular given it's size but I'd guess it's multicellular given the tail appendage and complex internals.


text:
Why does hyperventilation make you feel like you need to breathe more?
Calm Clinic claims:

"The problem is that hyperventilation makes your body feel like you're not getting enough oxygen. Essentially, it makes you feel like you need to take deeper breaths and take in as much air as possible. This makes all of the symptoms of hyperventilation worse."

As far as I know, the brain controls breathing rate by measuring the amount of carbon dioxide in the blood. So is this true? If so, why?

Hyperventilation alone does not cause you to feel that you're not getting enough oxygen. Rather, it's what causes hyperventilation that does that (thus resulting in hyperventilation.)
The Calm Clinic explains this quite well (while only mildly contradicting your quote):

During periods of intense anxiety, the body is sent into a state of fight or flight, when the brain signals to the body that danger is afoot. When this happens, you automatically start breathing quickly, as this oxygenates your blood and prepares your body to respond to a threat by fighting or fleeing. If the threat that has triggered your fight or flight response (whether real or imagined) persists, you’re likely to continue hyperventilating until you start to experience other unpleasant physical symptoms.

The focus of your question is

"...This makes all of the symptoms of hyperventilation worse." [emphasis mine]

You can hyperventilate by breathing too quickly or too deeply; either way, in people without underlying medical disorders, hyperventilation is usually caused by stress/anxiety. Anxiety makes your heart rate increase, and causes a perception of the need for more air (not the actual hyperventilation). It is often accompanied by some degree of chest tightness, which many people reasonable attribute to a problem with their heart. These things tend to cause more stress, so it's a cycle. The symptoms of hyperventilation are dizziness/lightheadedness, tingling in your hands/feet and around your mouth, and more but less common symptoms.
Under normal circumstances, hyperventilation leads to a period of decreased respiratory rate to allow for arterial blood to build up that critical buffer, HCO3.
Dealing with Anxiety Symptoms: Hyperventilation
(written for laypersons)

I meant to emphasize this sentence: "Essentially, it makes you feel like you need to take deeper breaths and take in as much air as possible."

That's fine. I hope you understand I was emphasizing that hyperventilation does not create more air hunger; the stress causing the hyperventilation does. A common symptom of anxiety is the feeling that one can't take a deep enough/satisfying breath. If this happens, a yawn will often break that cycle for a while. Yawns are wonderful things for stress. Most people can cause themselves to yawn at will.


text:
Are there any affordable devices for measuring ghrelin levels at home, similar to blood sugar monitors?
I'm interested in finding an affordable medical device that can measure ghrelin levels, similar to how blood sugar level monitors work. I understand that ghrelin level measurements typically require laboratory analysis of blood samples, making it more complex and costly than glucose testing. However, I'm curious if there have been any recent developments in this area or if there are any devices available for public sale.
I've searched online for such devices but haven't found any clear answers. Most of the information I've encountered indicates that ghrelin measurement is primarily done in laboratory settings. I'm hoping someone here might have more up-to-date information or know of any devices that have been introduced to the market.

There are some home kits, but they are professional kits. You can buy one of them if you know how to use it:
https://www.assaygenie.com/human-ghrelin-pharmagenie-elisa-kit-sbes0025/
It costs around $780.
I know it costs a lot, but there are no cheaper alternatives.
Also, I tried to find out if there are any simpler monitoring machines, but unfortunately there is no such thing for Ghrelin (at least till now).

I wouldn't exactly call a colorimetric ELISA a home kit, unless your home happens to be equipped with a 450nm microplate reader, full set of pipettes, etc. I also fixed your link to point to the human kit.

Yes, you are right. But I discussed with you what I could find out.

"What you could find out" was probably the first result of a search engine query. Everybody and their brother makes human ghrelin ELISA/EIA kits, some significantly cheaper than the one you found. Answers should have some level of personal expertise behind them, not just the ability to use a search engine.


text:
Laser in mirror experiment
Apologies if this question is very simple I performed an experiment where I would shine my toy laser at the mirror and it would be reflected.
Now here is what I tried:
I could see my laser toy , I inferred that If I could see it then external Light source must come and hit it such that it falls on the mirror and mirror reflects it back to my eye. So If I shine the laser light on the mirror in the place where my actual laser toy is I could get the laser to be reflected towards my eye.
Hence when I had my two eyes to be open light from laser toy fell on my right eye which I felt was strange. I expected the light to be in the middle because we have both eyes and the light hitting both eyes I thought would average out.
Then I closed my left eye and I could see that It fell on my right eye If I pointed the light where my eyes could see the laser.
I closed my right eye and I could make the light fall on my left eye!
So I had some questions here:
Why is it so that the images we see are inferred from the right eye for me , If we can also get images from the left eye why is right eye's image is taken to be the overall image?
What is the use of left eye in this case ?

Obligatory - Don't shine lasers into your eyes, you only have one set and run the risk of permanent eye damage!
We have dominant eyes, just like we have dominant hands and feet. This means that with both eyes open, you naturally adjust your hand/eye coordination to compensate so that your dominant eye receives the majority of the input.
A conventional test for this is to get a longish straight tube, such as that found in paper towels or Aluminium foil (AKA tinfoil) or similar (rolled up paper tube works too). Hold this so that with both eyes open you see a clear circle. Now close one eye. Now close that eye and open the other and compare. If you close your dominant eye, you will see that you can no longer see clearly down the tube, but if you close your non-dominant eye, you can still see fully down the tube.


text:
Reproduction number in SAIQR model
$$ \dot S (t)=\Lambda-\beta_1 S(t)A(t)-\beta_2S(t)I(t)-\mu S(t)$$
$$ \dot A (t)= \beta_1 S(t)A(t)+\beta_2S(t)I(t)-(\mu+\alpha) A(t)$$
$$ \dot I (t)=\alpha A(t)-(\mu+\theta)I(t)$$
$$ \dot Q (t)=\theta I(t)-(\mu+\mu_1+\gamma)Q(t)$$
$$\dot R (t)=\gamma Q(t)-\mu R(t)$$
On the above problem, where all parameters$$\Lambda, \beta_1,\beta_2, \mu, \mu_1, \alpha, \theta, \gamma$$ are known, I wanted to calculate the Basic reproduction number of the system of ordinary differential equations using next-generation matrix method(or even any other known method). However, I could not find any inbuilt function for this method. Can somebody point me in the right direction? Or can somebody help me to write MATLAB code for it?
thanks for any help.

The following derivation follows closely Vivas-Barber, A. et al. Dynamics of an "SAIQR" influenza model. 2014. I have used Wolfram Mathematica for calculations as shown below. You should validate yourself that the calculations are correct.
First, we define the state vector $E=(S,A,I,Q,R)$ and the total population size $$N=S+A+I+Q+R.$$ Solving  $\dot{E}=0$ for the trivial, disease-free equilibrium, we obtain:
$$N = \frac{\Lambda -\mu_1 Q}{\mu}.$$
Next, we calculate the Jacobian of the system at $E_0 = \left((\Lambda -\mu_1 Q)/\mu,0,0,0,0\right)$:
$$\left(
\begin{array}{ccccc}
 -\mu  & -\frac{\beta_1 \Lambda }{\mu } & -\frac{\beta_2 \Lambda }{\mu } & 0 & 0 \\
 0 & -\alpha +\frac{\beta_1 \Lambda }{\mu }-\mu  & \frac{\beta_2 \Lambda }{\mu } & 0 & 0 \\
 0 & \alpha  & -\theta -\mu  & 0 & 0 \\
 0 & 0 & \theta  & -\gamma -\mu -\mu_1 & 0 \\
 0 & 0 & 0 & \gamma  & -\mu  \\
\end{array}
\right)$$
and the corresponding eigenvalues:
$$
\begin{array}{l}
\lambda_1 = -\mu,  \\
\lambda_2 = -\mu,  \\
\lambda_3 = -\frac{1}{2 \mu }\left(\sqrt{2 \beta_1 \Lambda  \mu  (\theta -\alpha )+\mu  \left(4 \alpha  \beta_2 \Lambda +\mu  (\alpha -\theta )^2\right)+\beta_1^2 \Lambda ^2}+\mu  (\alpha +\theta +2 \mu )-\beta_1 \Lambda \right), \\
\lambda_4 = \frac{1}{2 \mu }\left(\sqrt{2 \beta_1 \Lambda  \mu  (\theta -\alpha )+\mu  \left(4 \alpha  \beta_2 \Lambda +\mu  (\alpha -\theta )^2\right)+\beta_1^2 \Lambda ^2}-\mu  (\alpha +\theta +2 \mu )+\beta_1 \Lambda \right), \\
\lambda_5 = -\gamma -\mu -\mu_1.
\end{array}$$
Rephrasing the conditions $\lambda_3<0$ and $\lambda_4<0$ as $\mathfrak{R}_0 < 1$ leads to:
$$\mathfrak{R}_0 = \frac{\alpha  \beta_2 \Lambda }{(\theta +\mu ) (\mu  (\alpha +\mu )-\beta_1 \Lambda )},$$
and a necessary condition on the parameters: $\beta_1 < (\alpha +\theta +2 \mu )\mu/\Lambda $.

Clear["Global`*"];

eqs = {
   S'[t] == Λ - β1 S[t] A[t] - β2 S[t] Ι[t] - μ S[t],
   A'[t] == β1 S[t] A[t] + β2 S[t] Ι[t] - (μ + α) A[t],
   Ι'[t] == α A[t] - (μ + θ) Ι[t],
   Q'[t] == θ Ι[t] - (μ + μ1 + γ) Q[t],
   R'[t] == γ Q[t] - μ R[t]
   };
vars = DeleteDuplicates@Cases[eqs, _Symbol[t], All];
params = DeleteDuplicates@Cases[eqs, _Symbol, All];

$Assumptions = Thread[params > 0];

Eliminate[{Total[Last /@ eqs] == 0, Ν == Total[vars]}, {R[t]}];
Ν0 = First@SolveValues[%, Ν];

J = D[Last /@ eqs, {vars}] /. S[t] -> Ν0 /. (vars -> 0 // Thread);
λ = Eigenvalues[J];

FullSimplify[Reduce[λ[[3]] < 0 && λ[[4]] < 0, Reals]]
(* β1 Λ < μ (α + θ + 2 μ) && β2 < ((θ + μ) (-β1 Λ + μ (α + μ)))/(α Λ) *)

Dear @Domen
Thank you very much. This advice and your valuable reply helped me a lot and I am now studying more closely and checking what you have said. If there is a problem, I will definitely take your and other researchers' valuable time again.


text:
Which was the first restriction endonuclease to be isolated?
I kind of have confusion between the first restriction endonuclease to be isolated and discovered.
In class XII NCERT, it says that,
"In the year 1963, the two enzymes responsible for restricting the growth of bacteriophage in Escherichia coli were discovered. One of these added methyl groups to the DNA, while the other cut DNA. The latter was called restriction endonuclease".
Now, "one of these added methyl groups to the DNA" refers to DNA methylase clearly and "the other cut DNA" must refer to EcoR1, I think?
In the next paragraph it is given that,
"The first restriction endonuclease, Hind II, whose functioning depended on a specific DNA nucleotide sequence was isolated and characterised five years later".
What I understand from this is that,
Hind II was the first restriction endonuclease to be discovered but EcoR1 the first to be isolated?
I went on many sites, but they all use these terms interchangeably.

The restriction endonuclease (RE) isolated from E. coli K strain was a type I restriction endonuclease, identified/characterized by Meselson and Yuan1 in 1968.  Type I REs are site specific, but cleave DNA randomly.
The one isolated from Haemophilus influenzae by Smith and Wilcox2 in 1968 was the first type II RE and is now known by the name HindII - the isolate they had was actually a heterogenous mixture with HindIII, for which there are no sites in the one of the viruses they were digesting, so they were able to work out the specific site of digestion for HindII, but not HindIII. Type II REs are site specific and cleave at specific sites too, which makes them useful in molecular biology, as opposed to type I REs, which aren't so useful.
EcoRI (type II RE) wasn't isolated until 1971, and was done by Yoshimori as his PhD thesis at University of California, San Francisco (see reference 27 in Roberts; ref 3 below).
Roberts (2005) a succinct history of it all3. See sections on Restriction Enzymes and Polyacryamide Gel Electrophoresis for information about the discovery of type I and II REs respectively.
Refs:

Meselson M, Yuan R. DNA restriction enzyme from E. coli. Nature. 1968 Mar 23;217(5134):1110-4. doi: 10.1038/2171110a0. PMID: 4868368.

Smith HO, Wilcox KW. A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J Mol Biol. 1970 Jul 28;51(2):379-91. doi: 10.1016/0022-2836(70)90149-x. PMID: 5312500.

Roberts RJ. How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):5905-8. doi: 10.1073/pnas.0500923102. Epub 2005 Apr 19. PMID: 15840723; PMCID: PMC1087929.

So, EcoK I (?) is the RE referred to in the first paragraph and not EcoR I. On comparing Hind II and EcoR I, Hind II was the first to be isolated (1968), EcoR I being isolated only in 1971. Am I right? Man, my teacher got me hella confused.

I could be EcoKI, but I don't know if this is actually the case; though a quick scan of the literature shows references to the Meselson paper, but whether this is related to KI itself??? I suggest you look through the literature and try looking up the history of EcoKI.


text:
How can nerves slide without tearing
While reading about an exercise called nerve glides I learned that nerves are quite inelastic. With all the nerve branches and relatively straight path how do nerves slide back and forth without stretching or snagging? My idea is they have to be located at the neutral axis (imagine your joints as beams) so that they only ever bend and never stretch. But they would have to travel directly through the center of the joint for that to be true which they don’t (except the spine more or less).

Hi and welcome. This site requires evidence of prior research (a source, link and quote). Can you please link to the site where you are getting your information? What support from reasonable sources do you have for your idea? Thanks!

Inelastic compared to what?

Muscles, skin, etc. Am I wrong and they are fairly elastic? I couldn’t find sources that really pinned down just how inelastic nerves are. I would think it would cause issues if it was less elastic then everything surrounding it.

Look at nerve placement in the body, most large nerves are close to or inside the bone thus in locations that don't  stretch much.


text:
What is the origin of the name Crassostrea gigas (pacific oyster)?
Context
I am looking for a source that reveals the origin of the name "Crasssostrea gigas". This is an oyster also known under the common names giant oyster, Japanese oyster, Pacific oyster and Portuguese oyster (amongst others).
What I've looked into so far
WoRMS and molluscabase both refer to "Thunberg 1793" page 140, but that refers to Ostrea gigas:

I did find information on the recent change from Crassostrea to Magallana (https://doi.org/10.2983/035.036.0301), but that does not refer to the origin of the Crassostrea gigas.
Question
What is the origin of the name "Crasssostrea gigas"?

Are you interested in the etymology of Crasssostrea?

Well, would be interesting as well, but ultimately I am looking for a reference where the name is used to describe this specific oyster. I.e. how "Ostrea edulis" has a reference to Linnaeus 1758, p. 699

Etymology. From Latin crassus (“thick”) + ostrea (“oyster”). Genus: Crassostrea; Sacco, 1897

As I see it, it went down like this:
1753: Linné describes the genus Ostrea
1793: Thunberg describes an Oyster as gigas and puts it in that genus
-> Ostrea gigas (Thunberg, 1793)
That is the original description and should be the original name of the type specimen.
Over a hundred years later...
1897: Frederico Sacco forms a subgenus (sottogenere) Crassostrea in the Genus Ostrea (Linné, 1753). It is not considered a subgenus anymore, today it has the rank of a genus.
So at some point, Ostrea gigas was taken out of Ostrea (this genus still exists) and into the Genus Crassostrea (or maybe into the Subgenus Ostrea (Crassostrea)).
It says here that Crassostrea gigas is a homotypic synonym of Ostrea gigas, so that also backs up that it was "just" a matter of nomenclature.
I could not find the original source that describes the basis of changing the genus. The earliest source I found mentioning Crassostrea gigas is from 1952, Adresses delivered at the Convention of the National Shellfisheries Association (page 82) and there is a reference to findings of Schaefer 1937. So if you look for that you might be able to go back and pinpoint the origin of it at some point.
The entire new Magallana Genus from 2016 (Crassostrea gigas Thunberg, 1793 is its type taxon) is also an interesting read, it seemed to have evoked quite a spat amongst malacologists.
Maybe you can find something in the Biodiversity Heritage Library that helps with your question.

@nika identifies the original description of the species as Ostrea gigas Thunberg 1793. They also identify creation of the subgenus Crassostrea Sacco 1897, which I believe, according to the rules of zoological nomenclature, simultaneously created the genus Crassostrea.
Ostrea gigas was placed in the genus Crassostrea by Gunter (1950). Previous authors had recognized O. gigas as part of the subgenus Crassostrea, but it looks like Gunter is the first to recognize Crassostrea gigas (Thunberg 1793) as belonging to a separate genus.

Awesome, thanks! It was fun looking into Crassostrea's history and it bugged me that I didn´t find the complete answer


text:
How accurate is facial reconstruction in forensics?
I’ve seen on tv where they reconstruct heads and faces from the remains of ancient people and I was wondering if anyone had a source that has pictures of maybe side by side of a facial reconstruction Vs. a picture of the actual person being reconstructed. I know it takes a long time to fully decompose but surely there’s been a reconstruction done of a recent person who’s been photographed

So, it isn’t accurate at all then. Eyes, hair, nose and mouth are the things that make a person identifiable, not just the shape of his head with some imagined details.
If you just make all those details up, you may end up with a totally different looking person. You may also get a result that is somewhat similar but that’s by pure chance.
So the rest of it is just art, not science.

I’m voting to close this question because it is about forensics rather than biology.

okkkk. I did a big project on this... and here's some of my research... let's hope it answers your question

Facial reconstruction (also known as craniofacial identification) is a method used in the forensic field.  Many people view facial reconstruction as an art instead of science.  Art is commonly portrayed as the expression or application of human creative skill and imagination, typically in a visual form such as painting or sculpture, producing works to be appreciated primarily for their beauty or emotional power.  Science is thought of as the intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment.  But where do science and art blur the lines?
WHAT CAN WE TELL FROM THE SKULL:
The skull provides clues to personal appearance. The brow ridge, the distance between the eye orbits (sockets), the shape of the nasal chamber, the shape and projection of the nasal bones, the chin's form, and the overall profile of the facial bones all influence facial features in life. Using these bones, artists and forensic anthropologists work together to reconstruct facial appearance through the process of forensic facial reconstruction.  There are many ways of telling both the approximate age, and the approximate ethnic background of the victim.  To find age, you can pay attention to the cranial suture (or the place where the cranium fuses to other bones of the skull), the size of the skull can help, as well as the teeth and the formation of the bottom jaw.  When looking for the birth gender of the victim, scientists often pay attention to the brow ridge, eye sockets, mandible, and the slant of the jaw.  Sometimes, it is impossible to tell by looking at the skull what birth gender the victim was.  In cases like this, people look to the pelvis to tell if the human has given birth, and if not, males do not have a ventral arc.  It is often very difficult to find the race of a victim if they are mixed race, or if the skull is very worn out.  However, to find the ethnic background scientists will look at the shape of the skull, the nazel root, and the space between eye orbits.
WHAT ARE THE PROCESSES OF FACIAL RECONSTRUCTION AND ARE THEY ACCURATE:
Facial reconstruction is an exacting process. The finished product approximates the actual appearance, because the skull does not reflect the details of soft tissues-eye, hair, and skin color; facial hair; the shape of the lips; or how much fat tissue covers the bone. Yet, facial reconstruction can put a name on an unidentified body in a modern forensic case, or, in an archaeological investigation, a face on history.
Today, many forensic facial reconstruction techniques are in use, including two-dimensional (drawn), three-dimensional manual and three-dimensional computer-based.  In the manual techniques, including two dimensional a cast of the skull is required, so the facial markers do not become an anomaly when analyzing the skull.  Although all of these methods are used, it is most common that a trained sculptor, who is familiar with facial anatomy, works with a forensic anthropologist and uses clay to build the facial features. The forensic anthropologist interprets skeletal features such as the subject's age, sex, and ancestry, and anatomical characteristics such as facial asymmetry, evidence of injuries (a broken nose, for example), and loss of teeth before death.
Facial reconstruction is used when the victims dental records fail to identify them, and there is no dna to pull from the body.  The process of reconstruction starts with making a mold of the unknown skull with the jaw attached and false eyes in place.  Depth markers are placed on 21 different “landmark” areas of the mold of the skull to approximate the facial tissue thickness that lay on the skull.  These tissue thicknesses are approximated from averages of other people of the same age, sex, and race as the skull is assumed to be.  Facial muscles are placed on the mold next and then the face is built up with clay to within a millimeter of the depth markers as tissue.  The nose and eye setting are very difficult to estimate due to the enormous amount of variation possible, mathematical models are used to make the approximations, the mouth is assumed to be the same width as the distance between the pupils. In facial reconstruction the eyes, nose, and mouth are mostly guess work.  Characteristics such as birthmarks, wrinkles, scars, and such are guesses at best and cannot actually be determined from the skull.  Facial reconstruction is accurate because it has been using mathematics, and calculations as such, in order to determine spaces, amounts, as well as the shapes of the face themselves.
WHY IS FACIAL RECONSTRUCTION IMPORTANT:
Facial recognition, as well as facial reconstruction is very important in the forensic field.  Both have a very important role in catching murderers, and investigating crime.  Without having a facial reconstruction, often times, you cannot identify victims.  Assuming the body is historical and for museum purposes, then without an identity it becomes very difficult to fill in large gaps of information, and time that can be crucial to history.  Also, if you can’t identify a murder victim then scientists could only look into cause of death.  Learning the identity of a deceased victim is as important to crime investigations as learning the identity of the suspect. When human remains are found, then the top priority is often to find the identity of the victim.  Police often also will look for an identity out of respect, for both the victim and the victim’s loved ones if any.  Facial reconstruction has been used ever since 1890.  Before 1890, people mostly used few facial indicators such as the shape of the frontal bone, and the remains of flesh to help identify the victim.  Facial reconstructions, can also show what injuries were sustained previous to death.
WHAT CAN WE LEARN FROM FACIAL RECONSTRUCTIONS:
Our skeleton is an extensive record of our lives. The food we eat, the rate at which we grow as a child, the injuries we sustain, whether we have given birth; all can be determined from our bones. Experts can determine sex, age, and ethnicity, relatively easily from the skeleton, with the skull and pelvis playing pivotal roles in this analysis. Later this week, we’ll be taking a more detailed look at how to determine sex and ethnicity from a skull.Teeth can reveal information about diet and a comparison between dental records of the deceased and the recovered skull is often the primary method of identification.  By looking at the scull (or any bones in fact,) you can tell childhood injuries from injuries that might have been fatal.  You can also look at bone density and other factors to tell if the victim was suffering from any diseases.  People look for the sagittal suture – the squiggly line that runs the length of the skull – If it is fully fused, the remains are likely to be of someone older than 35. After that professionals look for a second line at the front of the skull -- the coronal suture – which fully fuses by age 40. Teeth are also looked at. If they're worn down it could be a sign of a poor diet. If they're well-maintained and/or have good dental work such as fillings, they were able to afford proper dental care—another clue as to the identity of your skeleton. Oftentimes professionals consult a scientist who specializes in teeth, known as an odontologist. They can determine how old a person was at death, what kind of health they were in and what kind of diet they had.
Baby's bones begin to grow in the womb. At birth, the skeleton is partially formed. Many bones are still in "parts." The ends (epiphyses) and bony shafts (diaphyses) of long bones form separately in the womb. At birth, the ends of the long bones are mainly cartilage, with centers of bone beginning to form inside. As a child grows, the shafts get longer, and bone gradually replaces the cartilage epiphyses. Through the growing years, a layer of cartilage (the growth plate) separates each epiphyses from the bone shaft.  By paying attention to this, it is easier to tell age, and follow growth patterns to have a successful reconstruction.
Between 17 and 25 years, normal growth stops. The development and union of separate bone parts is complete. At this point, you and your skeleton are as tall as you are going to get - with many fewer bone parts than you started with.  The bones that enclose the brain grow together during childhood along lines called cranial sutures. During adulthood, bone "remodeling" may gradually erase these lines, at variable rates. Closure of cranial sutures gives general information about a person's age. It is best used with additional indicators to estimate age, or when other age indicators are unavailable.
WHAT ARE THE LIMITATIONS:
It is very hard to estimate a person’s weight and represent that with facial markers.  Since a chart of average thickness of soft tissue is used to estimate the way a person looked, if you were on the skinnier side, your head might appear a lot more overweight than usual and or skinnier.  To help determine weight, scientists look at the rest of the remains for a height.  Facial reconstruction relies on the relationships between the facial features, subcutaneous soft tissues and underlying bony structure of the skull. If there is no clue for potential identity because of impossibility to compare questioned remains with possible familiar material, in such cases one of the last chances is to recreate ante mortem appearance by face reconstruction. Many of the soft tissue thickness values are significantly different from those reported for comparable groups, suggesting that individuals from different geographical areas have unique facial features thus requiring population-specific values. This literature review attempts to throw some light on the important aspects that has to be taken into consideration while setting norms of soft tissue thickness among various populations.
Studying the unknown skeletal remains mostly becomes the only way to find out more information about individual characteristics, which could lead to identification of potential victim. If there is no clue for potential identity the most precise comparative techniques fail, because of impossibility to compare questioned remains with possible familiar material. In such cases one of the last options is to recreate ante mortem appearance by face reconstruction. Following the first introduction of reconstruction in the late 19th century, other techniques have been developed including radiography, 3D statistical model, ultrasound, MRI, CT and Cone Beam Computed Tomography (CBCT).  Facial contours were traditionally considered to be the result of positioning of underlying hard tissue followed by the soft tissue. However, current trend shows a paradigm shift from the conventional hard tissue analysis to also include both hard- and soft-tissue analysis.
IS FACIAL RECONSTRUCTION AN INTERDISCIPLINARY ART:
The skull is made up of 22 bones, 14 of those are facial and eight are cranial bones; it is a complex structure, and small variations during development and growth, together with soft tissue differences, create the enormous facial variation seen in the human population.  Artists have long been interested in the direct anatomical relationship between the skull and facial appearance.
Artist, Gaetano Guilio Zumbo (1656-1701), used facial reconstruction as an art because he believed that math and science are both forms of art.  His work can be found in the Wax Anatomical Collection at La Specola Museum, Florence, became famous for his macabre scenes depicting various stages of decomposition of the human body.  One of his most famous pieces is the head of a dead man, with facial muscles recreated in wax over a real skull.
This is the earliest surviving anatomical wax model created for didactic purposes and exhibits extraordinary anatomical precision alongside an artistic sense of horror and decay. Although we assume that Zumbo was less concerned with facial appearance than anatomical detail, he pioneered the development of scientific art and this work ranks as one of the finest examples of three-dimensional facial reconstruction.
By definition, an interdisciplinary art is relating to more than one branch of knowledge.  Facial reconstruction is often categorized as both a science and a mathematical equation.  Both science, math and art are human attempts to understand and describe the world around us. The subjects and methods have different traditions, and the intended audiences are different, think the motivations and goals, specifically for this purpose is fundamentally the same.

Welcome. Can you add sources?

Interesting essay about forensic facial reconstruction. I've noticed that forensic depictions of people from archaeological remains tend to be flattering, depicting the individual as facially attractive, whether male or female. This tendency most certainly reflects the artistic side of reconstruction.

@CaryCotterman that may have more to do with reconstructed faces always being symmetric and free of small scale flaws, which would not show up on bone. They are not going to add flaws willy nilly because it would adding things they have no evidence of, but completely lacking them makes for a more attractive face. it is the same reason a touched up photo of a model is often more attractive, touching it up is  often just removing small flaws.

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


text:
Lifespan of helper T cell
CD4+ cells or helper T cells are produced in Thymus. How long these cells live? For example, RBC live for 3-4 months.

I will respond with a "story-like" approach. You may already know some info but I want to be sure I can help you fully understand!
Unlike RBC, you are born with all the CD4+ (or Th, as I refer to them) you will ever need in your lifetime in the primary organs of the immune system -- they are already specialized and ready to be used, and this has taken place in the thymus. On the other hand, RBC get renewed through erythropoiesis every ~120 days.
In utero, the thymus and bone marrow (primary organs) now supply secondary organs (lymph nodes, the spleen, the MALT) with the various cells they’ve made (B&T). However, only 5% leave the thymus, as 95% are recognized as "anti-self" and are killed. So this would be the first "killing" of Th cells. B cells live in the peripheral layer, while T cells live in the deep lymphoid tissue and the lymphoid dullet.
The dendritic cell will "wander" into the lymph node, carrying the fragment of antigen presentation on the MHC class 2 molecule-Dendritic cell resides between the B cell area and the T cell area. Now, the first specific thing occurs in the immune response, when the T cell receptor attaches to the antigen and tells cell says to make antibodies.
Now -- as of here, we have a lot of Th (and B) cells doing nothing while the antibody is being produced. Some of the Th will be killed, while some will serve as "memory Th cells" so that the next time such an antigen is present in your body, the response will be quicker. At this point, it's hard to distinguish which Th cells are dividing, and which are dying. The average lifespan has been reported to be >17 years.
 Source: https://www.ncbi.nlm.nih.gov/pubmed/24492253
I hope I have been able to help.

you are born with all the CD4+ (or Th, as I refer to them) you will ever need in your lifetime in the primary organs of the immune system This is flat wrong. At least read wikipedia before posting misleading answers.

@iayork Hi, this is what I've learned in my immunology class in uni. I checked my lecture notes before posting this and here is a direct quote: "You are born. You have all the machinery for the immune response, but it's sleeping. When you’re born, no antigen has been involved in the making of your cells. They have been specialized by evolution. They will function later in life by antigen exposure." This is what I was taught and I apologize if it was incorrect, but please don't accuse me of posting a misleading answer. I did attempt to verify. Genuinely thought an established prof was correct.

The quote (and prof) is correct, but it doesn't say that all T cells are made by birth, just that the machinery for making them is available.

@iayork that is what I meant to imply... Everything that goes on to occur once an infection/antigen is present results from those Th cells. I go on to say that they do divide. Apologies if unclear.

You still don't get it. New T cells are formed in bone marrow throughout your lifetime. They are not all formed at birth.


text:
Protein bands not visible after sds page coomassie dye stain
I am working with cell wall protein of Candida albicans and cryptococcus neoformans but after protein extraction and run on SDS PAGE my bands are not visible after coomassie staining. Can anyone tell me how to concentrate the protein so that bands can be seen on coomassie stain.
I am using Ammonium Carbonate buffer for extraction of protein. Also, the bands are visible on silver staining.

There are many methods to concentrate protein depending on the protein itself, volume, resources availble, etc. Perhaps you could provide some more details.

I am not working on particular specific protein. I just have to extract cell wall proteins of both and run on SDS PAGE and compare the bands using a marker. I am using Sabouraud Dextrose Broth as growth media for both of them.

I have inoculated each in SDB and kept for 7 days on shaker incubator and followed by filteration. This collected mycelia is stored at -20C. then I suspended 1g of mycelia into 10mL Ammonium Carbonate and left overnight on rocker shaker. Filtered it and precipitated with methanol (1:8) followed by centrifugation and collecting pellet. Then dissolved this pellet in Urea+ DTT(minimal amount) and microfuged to get protein in supernatant. But the protein is not visible on Coomassie staining after SDS PAGE. If you could provide any protocol it would be helpful aswell.

It sounds like you already have a concentration step. Can you resuspend the pellet in less urea?

I already did in the most minimal amount possible. I dont think less than that would be sufficient to dissolve the pellet.

I have thought of using glass beads and ammonium carbonate buffer together. Instead of filteration what if we centrifuge the broth collect and wash the pellet. suspend pellet with water and glass beads with vortexing it for 15 min. then collect the suspension and add 1ml of it for 10ml buffer for overnight followed by methanol precipitation.....do you think this can work? as I am not sure about it....and if it does, when we add distilled water along with glass beads will the protein get diluted instead?

another alternative which I think is collecting the protein supernatant and preciptate it again by methanol..centrifuge it...but I dont know if this step gives any pellet.. so if pellet is obtained dissolve it again in urea+DTT..centrifuge to get the protein supernatant...but my query in this protocol is that will the earlier urea+DTT used to dissolve the pellet earlier interfare with methanol precipitation and affect my proteins?

The problem here is concentration. Coomassie Blue stain can only detect protein band greater than or near to 50ng, in this case, the concentration of your protein is too low for detection. If you want to stick with Coomassie stain, you can try colloidal Coomasie stain instead because it has a much lower detection limit than Coomasie blue (between 10ng to 20ng).
In addition, I think what causes such low protein concentration is the poor solubility of yeast cell wall. One way to get around this is to increase solubility is through chemical hydrolysis, for example using diluted sulphuric acid1-3. This will partially solubilize mannas-protein outer layer of the cell wall and help you to obtain soluble yeast cell wall products.
References:

Theodoro, S. D. S., Putarov, T. C., Tiemi, C., Volpe, L. M., de Oliveira, C. A. F., Glória, M. B. D. A., & Carciofi, A. C. (2019). Effects of the solubility of yeast cell wall preparations on their potential prebiotic properties in dogs. Plos one, 14(11), e0225659.
OGAWA, K., & MATSUDA, K. (1994). Characterization of Manno-oligosaccharides Containing α (1→ 2)-and α-(1→ 6)-Linkages Obtained from Saccharomyces cerevisiae Mannan by Controlled Acid Hydrolysist. Journal of Applied Glycoscience, 41(4), 433-437.
Peat, S. (1961). Polysaccharides of baker's yeast. Part IV. Mannnan. J. chem. Soc., 61, 29-34.

Welcome to Biology.SE! This looks like a good answer and you've done a nice job of providing supporting links. However, in the future please include the complete reference information since links can break. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. I'm also not clear on whether your "this paper" reference is to that paper or to ref 25 of that paper. Thanks!

I've converted your reference links into citations, but please check to make sure I have not make any mistakes and [edit] to correct/improve as needed.


text:
gel band contrast
Is there any way to increase the contrast of my SDS PAGE gel. I want to increase the coomassie stained gel contrast of my gel bands a little bit as it looks little less for my thesis. Ive heard that it is legal and can be done. Is there any software for it or some other way.

The bands should be a bit clearer (blue background drag in the lanes). You can try improving the protein extraction protocol. Could also be a problem with the gel. Is the leftmost lane your protein ladder?

If you are asking how to alter the image to make it clearer then your question is off-topic.

I have made a standardised protocol for protein extraction... this is the best I could get for bands as protein content is less from my sample..I dont want to alter the image just increase the overall contrast....and yes the leftmost lane is my ladder...do you have any suggestion to improve this particular image?

If this is accepted or not depends on your institution. For publications, it is usually accepted to use adjustions of color, tonal values and contrast which are applied to the whole image and which do not alter the statement of the image. These changes are not ok if for example the contrast it raised so much that weak bands disappear.
Not accepted are changes which are only made to changes to parts of the image, partial adding or removal of parts of the image. Keeping this in mind, you can basically use any software which can be used to process images. Photoshop is kind of a standard but pretty expensive, free software like Gimp also does the job.
I adjusted the tonal values of your image and raised the contrast just a little to get this:

You got there first. I also took it into PhotoShop and did an "Image>Auto Contrast" (not quite as good) but then went into "Adjustment>Levels" and with the dropper selected an area between the lanes as the white point, which gave a slightly better result.

this looks much better than my posted image..and yes it is legal over here to adjust the gel as long as we do not tamper the bands...and thanks a lot...do you think this one is good to proceed with or should I tune it a little bit more.

@Kushal That depends on your desires for the image. For me, this looks fine.

@Chris okay I'll see to it. and thanks a lot for the help and suggestions.


text:
What is the equation and mechanism of Hopkins-Cole Test reaction?
The Hopkins-Cole reaction or glyoxylic acid reaction, is a chemical test used for qualitative detecting of tryptophan in protein solutions.
tryptophan + glyoxylic acid + sulfuric acid  >  violet product
I know the chemical formulas of reactants, but I could not find the product formula and a mechanism for the reaction.


text:
Behavioural experiment on Nasonia Wasps
I want to see how two male Nasonia vitripennis interact with each other. I have been using enamel paint on their heads to distinguish them, but I am wondering if any other methods of marking them would be less invasive. Any ideas?

I’ve previously used Posca pens to mark wasps during experiments - I think that’s going to be about as non-invasive as you can get without using some kind of advanced video tracking techniques. But this was on much larger paper wasps than Nasonia which are much smaller.


text:
How does the primitive streak disappear after gastrulation?
So, I am not a biologist or anything related to the field, but this question is indirectly related to something I am curious about.
I read some articles about the role of the primitive streak in the development of the human embryo. And it says in some of them that after gastrulation, the primitive streak regress caudally or disappears. So, my question is how does it disappear, what happens to the cells that constitute it?
And this might be a little strange, but does it have anything to do with the formation of the coccyx?

Welcome to SE Biology! It can help to take the tour, if you haven't already. It would help to see direct quotes from the articles you refer to and any links/references to such articles. Have you tried e.g. a google search, and if so, what did you find? e.g. wikipedia notes that the primitive streak becomes the mesoderm, the germ layer that gives rise to all bones (including the coccyx).

I am sorry, but I have read the wikipedia page before and I think it doesn't mention that the primitive streak transforms into the mesoderm. It says that after gastrulation, it regresses (which i don't understand where the cells that disappeared have gone) and by day 20, the remaining cells constitute a midline caudal cell mass (which i don't understand what it means either). And by day 26, it has seemingly disappeared(didn't explain how did it disappear). Please if I am missing something point it to me, as I am not a professional.

Fair enough- I did not read closely, and it is not as specific as what I said. Nonetheless, it would be helpful for you to excerpt the relevant sections in your question and explain what you don't understand. I would still suggest further research, for example when I google "primitive streak cell fate" I found articles like this that have a fate map for the primitive streak.

My shot in dark (read the Wiki article): The linea primitiva establishes 1)bilateral symmetry and 2) craniocaudal axis and 3)germ layer formation (gastrulation). I suppose it serves as some kind anatomicochemical landmark which embryonic cells recognize and serves as a cue as to 1. what they should do and 2. where they should do it. Once this function is served, the linea primitiva "disappears". The only features in an adult human that corresponds to the linea primitiva are the vertebral column (structure) and the spinal cord (central nervous system).


text:
How large giant kelp can grow?
The giant kelp (Macrocystis pyrifera,
Laminariales) is the largest extant species of (brown) algae. Yet, there are many different claims about how large this species can grow. Of course, I am aware that it is quite hard to give a definite answer, but I would like to find a trustable source. Searching via google, one finds many different claims with oddly specific numbers but without any source. Let me give some examples:

The Guinness Book of World Recors states (see here) that

The longest verified specimen attained a total length of 60 m.
However, there are unverified records of even longer specimens.

Now, although the Guinnes book includes many fascinating facts about
animals and life in general, it never gives any sources, which makes it to me (at least when it comes to records in science), to a barely reliable
source. Furthermore, 60 meters seems to be quite exaggerated.

Wikipedia states

Individual algae may grow to more than 45 metres (150 feet) long at a
rate of as much as 60 cm (2 ft) per day.

again, without source, althoug later in the text they also mention
the number of 60 meters citing a textbook on Phycology (Hoek, Mann, Jahns: Algae: An Introduction to Phycology, Cambridge University Press).

The Webpage of the Monterey Bay Aquarium says here that giant kelp can grow "up
to 100 feet (30 m); 175 feet (53 m) under ideal conditions", which
seems to be a quite specific number, but again, without any source.

Does anyone have a reliable source or study on the size of giant brown algae species?

The wikipedia article does indeed have references under the "Growth" section. 8, 25, 26. I suggest you check those out and then come back with anything you don't understand.


text:
Scanning Electron Microscope images of wheat grains
I took SEM images of wheat grains but I see some granular particles on its surface and I don't understand what they are?

Is it some kind of deformation of the bran layer due to drying? Or is it the gold-palladium alloy coating which is done for SEM analysis of non-metals?


text:
How are mitochondrial ATT (Ile) start codons translated as Methionine?
In some vertebrate species, some mtDNA start codon sequences are ATT but these are translated as Methionine rather than Isoleucine. What is the mechanism for this non-standard translation?
The main example below is in a bird, blue crane (NCBI Genbank excerpt below). The NCBI data give the standard note on completion of the stop codon but there is no note about modification of the start codon. We have confirmed this ATT start codon from PCR-Sanger sequencing an independent sample. There are similar cases in other vertebrates (Aves, Squamata, Amphibia) such as ND2 in Goggia geckos (example 2 below, also independently confirmed by Sanger sequencing. In this genus the start codon DNA varies from ATT to ATA or ATC: 50/59, 6/59, 3/59). I think I have seen this in other mtDNA genes. In many other birds and reptiles ND2 starts with ATG.
Are these modifed post-transcription to ATG? If so how?
Could they reflect a variant of the mtDNA code where AUU = Met? Or where any AUX codon is recognized as Met.
Example 1. ND2 from Blue Crane (NCBI Genbank refseq excerpt)
LOCUS       NC_020572              16696 bp    DNA     circular VRT 18-APR-2013
DEFINITION  Anthropoides paradiseus mitochondrion, complete genome.
ACCESSION   NC_020572
VERSION     NC_020572.1
DBLINK      Project: 193816
            BioProject: PRJNA193816
KEYWORDS    RefSeq.
SOURCE      mitochondrion Anthropoides paradiseus (blue crane)
  ORGANISM  Anthropoides paradiseus
 gene            3970..5008
                 /gene="ND2"
                 /db_xref="GeneID:15088361"
 CDS             3970..5008
                 /gene="ND2"
                 /note="TAA stop codon is completed by the addition of 3' A
                 residues to the mRNA"
                 /codon_start=1
                 /transl_except=(pos:5008,aa:TERM)
                 /transl_table=2
                 /product="NADH dehydrogenase subunit 2"
                 /protein_id="YP_007624320.1"
                 /db_xref="GeneID:15088361"
                 /translation="MNPHAKLIFLTSLVLGTTITISSNHWMSAWAGLEINTLAIIPLI
                 SKSHHPRAIEAAIKYFLVQATASALVLFSSMINAWSTGQWDITQLNQPMPCLLLTTAI
                 AMKLGLVPFHFWFPEVLQGSSLTTALLLSTVMKFPPITILFLTSHSLNPALLTSMAVA
                 SAALGGWMGLNQTQIRKILAFSSISHLGWMTIIIMYSPKLTLLTFYLYSLMTITVFLT
                 LNTTKALKLSTMMITWTKIPTLNATLMLTLLSLAGLPPLTGFLPKWLIIQELTKQEMT
                 TAATIITMLSLLGLFFYLRLAYYSTITLPPNSTNHMKQWHTDKSTNTLIAIFTSLSAL
                 LLPLSPMILTII"

 3901 agtagagtca gctaaaaaag ctatcgggcc cataccccga aaatgatggt ttaacccctt
 3961 cctctacta**a tt**aacccaca tgcaaaacta atcttcctca caagcctagt cctagggaca
 4021 accattacaa tctcaagcaa ccattgaata tcagcctgag caggcctaga aatcaatact
 4081 ctcgccatta tccccctcat ttcaaaatcc caccacccgc gagccatcga agccgcaatc
 4141 aaatatttcc tagtacaggc aaccgcttca gcactagtcc tcttctcaag tataatcaac
 4201 gcatgatcta caggacaatg agatattacc caattaaacc aaccaatacc atgcctttta

Example 2. ND2 in Goggia (Gekkota, squamata) NCBI nucleotide locus ref.
LOCUS       KF666817                1424 bp    DNA     linear   VRT 09-SEP-2014
DEFINITION  Goggia lineata voucher MCZ R184778 NADH dehydrogenase subunit 2

The key point in understanding non-AUG start sites in mRNAs is the nature and role of the initiator tRNA.
There is a special initiator met-tRNA which differs in structure from all the elongator tRNAs in such a way that it — and only it — is recognized by the IF-2 type initiation factors (and not by the EF-Tu/EF-1 elongation factors). In a complex with the initiation factor and GTP it can bind to the ribosome at the P-site. Normally the ribosome will also be interacting with an AUG codon at the P-site, but in some cases it is not, so that initiation may still occur.

Thus, the initiating amino acid is always methionine, regardless of
  the codon, because methionine is the only amino acid with which the
  initiator tRNA can be charged.

In the case of bacterial mRNAs, it has long been known that about 10% start with other codons, predominantly GUG. This can be explained by their relative position to the ribosomal binding site on the mRNA — the Shine and Dalgarno sequence. I imagine this is what happens in mitochondria.
In the case of eukaryotic cytoplasmic mRNAs, an initiator met-tRNA complex normally scans from the 5ʹ-end, initiating at the first AUG or first the first AUG in an ‘appropriate context’. The precise definition of an appropriate context is unclear, and on can imagine that in some cases such a context pauses the ribosome at a non-AUG codon, at which initiation begins.
References
“The Biochemistry of the Nucleic Acids”, 11th edition, Chapter 12 (1992) RLP Adams et al. — this has all the older original references, but not the recent ones.
Wikipedia entry on Shine and Dalgarno sequence.
Eukaryotic scanning model: Hinnebush review (2011)
Initiation in prokaryotes and eukaryotes Londi review (2015)
Related SE Biology Answer on initiation and elongation met-tRNAs (by me)


text:
Why should all life on Earth have a common ancestor?
In principle, it should be possible for whatever happened to create life to have happened in multiple places. Out of the millions of years this could have happened, it seems odd that it didn't happen independently in at least two locations that were each sufficient to host life.
Why then does all life on Earth appear to have a common ancestor? That's weird to me.

We don't know that all life on Earth had a common ancestor. We know all observed extant life on Earth does. That's quite different. Lineages die out all the time, so if you started with life of different types it would be quite surprising if over hundreds of millions of years you would keep some of both around.

Does this answer your question? Why did abiogenesis only happen once?

do you have a source for your claim that all life had 1 common ancestor?

Not all life, all life we know of, which is mostly all surviving life. there could be millions of lines that arrose independently and did not win the competition for resources.

It's quite possible (maybe even likely) that it happens all the time, but there's no isolated system on Earth, anything new is invariably going to be small and outcompeted instantly - leaving it no time to multiply and get noticed by scientists.

One way to visualize it is to imagine that you have a pile of M&Ms on the table.  Let's say that there are 15 red ones, 5 blue ones, and 2 green ones.  Every 10 seconds you randomly select one to eat.  What is the most likely end result after 100 seconds?  Well the green ones will probably get gobbled up first, then the blue ones, until you are left with only red M&Ms.  Now imagine that your M&Ms can copy themselves and eat eachother and compete with eachother for resources, well then your whole table would probably be totally covered in red M&Ms after a while and, from the perspective of someone who only had the current state of your table to go on, it would seem that the red ones are all there ever were.  We can't say that abiogenesis only happened once, only that every living thing alive today evolved from a single common ancestor.  It's sort of like how Mitochondrial Eve wasn't the first human woman.  There were plenty of other women running around.  It's just that none of their mitochondrial DNA can be found in modern populations.  Evolution has something of a "the rich get richer" tendency.  Over time, less numerous gene variants tend to die out, while more numerous ones become even more numerous.  Run this sort of scenario out long enough and the more numerous variant often ends up with a monopoly while the others get lost to history.


text:
Fungivore that feeds specifically on spores
I'm wondering if anyone has knowledge of an organism that specifically feeds on the spores of fungi. When I attempt to research this the results are flooded with numerous examples of fungivores but I've never been able to locate any information specifically on spore consumption.
Perhaps no organisms are known to feed directly on spores but I find this surprising. It seems spores would be an excellent and abundant nutrient source for a properly adapted organism.

This paper:

Smelansky, I.E., 2006. Some population characteristics of oribatid mites in steppe habitats. Acarina, 14(1), pp.123-130.

includes analysis of the gut content of some mites, recognizing several trophic guilds including "specialized
sporovores, and (specialized) sporovores ‘feeding
on surface’ ".  These two guilds are described:

specialized
sporovores feed on a very limited set of fungal
spores including only 4–5 morphological kinds of
spores in each mite species; the guts of sporovores ‘feeding on surface’ contain unusually high portion
of pollen grains and spores of epiphytic fungi.


text:
Working in heat
What does working in temperatures of 180 degree dry heat for long periods do to the body?
Such as inside of a cooking cyclone scraping product out of it while it's still at 180 degrees.

180°C or 180°F ?

180°F while in use it gets to 250°F


text:
Please help identify this tiny bug
Starting about 2 months ago I began seeing these tiny, light brown bugs in one bathroom. I did find them outside the bathroom but in close proximity to it (on a childs wooden toy and in our picture frames on the wall). I haven't seen them elsewhere. Most of the time I'd find them dead and they die very easily. I'd find small patches of them, usually under something or behind something with less light.  Otherwise I find them just moving a long the sink and find them in the corner of the tub. I have seen them on the wall and floor too. They can move fast but most of the time are still or slow moving. I haven't experienced any bites nor my family. The amount I see has lessened since I first noticed them.
I did get a pest control company out a month ago and they said it looked like field mites. Said they were harmless, attracted to moisture with a short life span and they'd be gone in a few weeks on their own. They haven't gone away though and when I research mites I find nothing that looks like it. It's too small for my phone to focus on so I took one to work and got a picture under the microscope. It's about 1 mm in length. Also, I do have a cat that goes outside.
Geographic location = Central Virginia, USA

Lovely picture.
This is quite likely to be one of the organisms known colloquially as "Booklice". In fact this is probably one of the genus Liposcelis, which is a genus of small wingless insects within the booklouse family Psocodea. They are common pests of stored items, including books, stored cereals, dusty areas etc, as they will eat almost anything of plant or animal origin.
I think I have the right genus here because of the enlarged top joint on the 3rd pair of legs, and prominent abdomen. Compare your image with the image below from wikipedia:

(Image copyright: MAF Plant Health & Environment Laboratory, CC BY 3.0 AU https://creativecommons.org/licenses/by/3.0/au/deed.en, via Wikimedia Commons)


text:
I need help identifying the source of my contamination in my viral titration experiments
I am relatively new to what I'm currently working with and as the title suggests, I am currently having some issues with my experiment (viral titration).
So, what I have been doing is the following:

Seeding cells on a black grenedier 96-well-plate, by extracting cells from culture flasks with Trypsin, counting and diluting them to a sufficient concentration for seeding.

The day after, a virus dilution series was performed in infection medium, and the cells in the grenedier well plate were infected in different concentrations, including negative controls.

After incubation, all the cells were fixed using the reagents: PFA, Methanol, PBS.

After fixing, the plates were stained using a primary, and a secondary antibody attached to a fleurophore. The primary binds to a viral protein of interest. The antibodies were diluted in PBS, and the second one also with Hoechst. The staining was performed with standard conditions, including incubation and washing 3 times with PBS after each antibody. The plate was stored in a fridge over night before analyzing it.

The infection was visualized using a Cytation 5 plate reader.

Now, the issue Im facing is that I have kept seeing some infection flourescence in my negative controls, (which should have un-infected cells only), according to the images which showed the flourescent dye in these wells. I am trying to figure out what I am doing wrong.
I have been pipetting from lowest to highest concentration, when adding media or PBS, and used separate liquid plastic containers for the control-wells and the infected ones, to avoid contamination. I am going to redo it once again using new infection media, in case the old flask had contamination.
But apart from this, what other factors could possibly help explain why I keep seeing flourescence from the secondary antibody in my negative controls? ANY type of mistake I could possibly have been making I would love to have pointed out. Or other factors which could cause contamination in the lab.
Could PBS/the other reagents possibly be contaminated as well?
Could it be I am not washing away secondary antibodies sufficiently?
Any tips would be much appreciated!! :/

Welcome to the biology stack. Please take a [tour] and visit the [help] for more information on this site and how it works.

To answer your question we would need to know a few more experimental details - have you performed titration of these antibodies to determine that they are working as expected? Have you performed any epitope blocking experiments for antibody specificity? Are you using a block of some sort in your staining? Is the 1ry suitable for PFA fixed samples? Is the 1ry antibody suitable for native protein? What controls are you using in your experiments? You should have primary and secondary antibody controls in each plate you run. Why are you using 2 fixatives?

Hello! Let me try answering your questions:

No I havent performed any such titration but my supervisor has and it has worked before for her. She has also said blocking is not necessary. since these antibodies should be specific enough to the virus in question, but what specific type of blocking were you thinking of? I dont think a block is used in the staining, since the primary antobody is specific for a viral protein of interest, and the secondary antibody is specific to the primary.

What do you mean by "1ry"? Primary antibody? And as in "suitable for native protein", are you referring to unspecific binding to other proteins of the cells? They antibody used should be specific enough to the virus Ive been told. The negative controls used are just wells with seeded cells, that have been treated the same, but not infected with any virus. Its the same cells, treated with both the primary and secondary AB. Do you mean I should have controls that have ONLY been treated with the primary OR the secondary AB, respectively? Too see if the 2dry are specific enough for the 1ary?

good, so long as you are using her conditions exactly as she did, this should be fine. Block is used to block non-specific binding of antibodies. It is very very very common that they can bind non-specifically, depending on the conditions used. Secondaries less commonly bind non-specifically. You should have appropriate controls in each experiment you perform to ensure that you can detect these problems if they occur.

1ry = primary. Native protein is that found in cells - not denatured as in western blotting/ SDS PAGE. Many antibodies on the market will work for denatured proteins, but not native, or vice versa, or even occasionally both.  Not all antibodies work on aldehyde fixed proteins, not all on methanol fixed. You should read up on immunocytochemical staining. The controls you need to have until you are certain of your technique are to detect problems in your experimental processes....

... In your case I would recommend that you have for both infected and not-infected cells controls with primary only (tells you if you get signal with no secondary - serious problem, could be caused by many things), and secondary only (non-specific secondary binding, needs optimization in concentration most likely, could be a few other problems). I would also test fixation methods to see what works best for your samples and make sure you read the product information sheet to see what they recommend for concentrations, fixation, binding conditions.

There is no one answer to this still. You will need to work through the conditions and see what your problem is.


text:
How to define a 'trait' objectively?
I'm coming across an increasing number of papers that use trait-based approaches for risk assessment, like this one . This paper defines a trait as follows:

Traits are the physiological, morphological, and ecological attributes
  of species or other taxonomic entities, which describe their physical
  characteristics, ecological niche, and functional role within an
  ecosystem.

I've wondered about using this sort of approach during some analyses of invasiveness potential in vector insects before and it's likely to come up during a systematic literature review I'm coordinating, but I'm concerned that devising my own trait classification system is likely to introduce confirmation bias into a study. Is there either a recognised methodology for trait definition, or alternatively some sort of accepted list or classification of traits that I could use, to minimise the chances of this? Is there a generally-accepted method to correct for phylogenetic correlation?
I've tried Google but the results mostly appear to be about trait theory, which is an approach used in psychology to study human personality.

you might want to see this http://biology.stackexchange.com/questions/37143/definition-of-phenotype

I think you this paper is what you need. The many concepts of trait are discussed in the functional ecology background. But basically, a "trait" can be defined as

" 'Functional traits’ are defined as morpho-physiophenological
  traits which impact fitness indirectly via their effects on growth, reproduction and survival, the three components of individual performance." (Violle et al. 2007)

Which are not so different from the definition you posted.
Some organisms have an improved methodology to collect and measure traits, like plants. But this is not common to all organisms.
As for the method to correct for phylogenetic correlation, this is a whole different field called Phylogenetic Comparative Methods. To choose the method you need to know the kind of data you have and the question being asked.

That looks like exactly what I need for the definitions part of the question. Thanks!


text:
human gene PCR primers database
I wonder if there is a place on the internet to get PCR primers for a specific gene.
For instance, exon 15 in CFTR gene. I don't want to design myself because I am sure sombody else already did it.

Answer is, obviously, yes.
Primerbank

Here. You can search primers using accession number or Gene-ID

Note that those are primers for real-time PCR, not regular PCR.

You need primers for one exon only?  Why can't you get the sequence and flanking sequence, and put that in to primer3?
http://bioinfo.ut.ee/primer3-0.4.0/


text:
Is it possible to buy a DNA sample with a specific mutation?
I would like to test a genotyping method (ARMS) on a specific human snp (heterozygous or homozygous ).
Unfortunally, we do not have any dna samples with the mutation.
Is it possible to buy somewhere a dna sample with the mutation ?
Otherwise, can you redirect me to other solution like directed mutagenesis?
Thanks

There are many companies selling synthesized DNA, most often in the form of short oligo's. But longer pieces are also possible. What exactly do you mean when you say 'DNA sample' though?

I mean no patient with the mutation. I need a DNA with the mutation to test if my genotyping method works


text:
Simple Autosomal Recessive question by a novice genetics student
How do you figure the percentage of offspring that will be a carrier of an Autosomal Recessive gene when the FATHER is the recessive carrier and the MOTHER is not affected (normal, no recessive)?  Thank you for your assistance.

Do your cross diagram and multiply the correct combinations together:
Father: Rr
Mother: RR
Since it's autosomal:
Chance of getting R from father: 50%
Chance of getting r from father: 50%
Chance of getting R from mother: 100%
You're looking for the chance of receiving Rr, which requires r from the father and R from the mother.


text:
Why does the pulmonary artery have higher glucose concentration than the pulmonary vein?
If the pulmonary artery have higher glucose concentration than the pulmonary vein, does it mean glucose will be consumed during gas exchange?
That confused me because gas exchange is something like diffusion and shouldn't consume any glucose

So what about the red cells flowing in the pulmonary artery? And its endothelial cells?

@GrahamChiu So during the gas exchange, red cells will proceed cellular respiration as soon as it absorb oxygen?

I didn't say that

I said that because glucose will be decomposed in order to proceed cellular respiration.
Edit: I didn't know that red cells don't have mitochondria

https://biology.stackexchange.com/a/34753/22415

I still don't get it. If glycolysis does not require oxygen, then why glucose will be metabolized during breath exchange? Breath exchange seems have nothing to do with glycolysis.

Lung tissue is living and requires glucose. The answer is correct.

@nongoodnurse the answer should mention the role of the bronchial arteries. As it stands it is misleading.

Gas exchange doesn't but the cells of the tissue it occurs in do consume glucose, even the cells in the walls of the artery will consume some.  The cells in the lungs still need to be fed and only one of those two vessels has flow going into the tissue so it is the one that has to carry that glucose into the tissue.


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

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

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

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

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


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

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

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

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

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

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


text:
What makes humans feel cold?
I have seen various sources talking about the effects of oestrogen on temperature: all of them agree that it makes you cold but they seem to explain the reason differently. One states that oestrogen dilates vessels and improves blood flow to extremities which lowers body temperature but another stated that it reduces flow to the extremities by thickening the blood and a different source states that the hormone reduces flow by restricting vessels.
This leaves me to wonder two things: which of these is correct and do we feel cold because the nerves in our skin are cold (and our internal temp near constant), perhaps because blood flow to them is restricted, or because the hypothalamus is cold?

Your „neurons in skin“ assumption is the right answer. There are receptors specialized on cold perception (McKemy 2013)
They can be activated by menthol (analogous to capsaicin from spicy food activating heat receptors), that‘s why mint chewing gum feels cold, it has menthol.
However, I don’t know how these receptors work biochemically, the mentioned paper talks about changed ion transport as a direct consequence of cold, causing receptor activation and calcium signaling.


text:
How do DNA methylation canyons/DNA methylation valleys/DMCs differ from CpG islands?
Are these just both regions of the genome that are undermethylated? Is the only difference that for something to be a CpG islands it needs a high level of CpG sites and DMCs don't?
So could a 3.5kb undermethylated region of the genome be considered a DMC even though there are not many methylatable CpG sites there?
Thanks!

The level of methylation does not play a role in defining a CpG island, whereas it is central to defining canyons/valleys.
CpG islands are areas of the genome that are >200bp in length and which contain an observed-to-expected number of CGs > 0.6, and a CG% > 50%.
A methylation canyon or valley is instead an area that is >3.5kb in length and contains < 10% average methlation at any given CpG.

This looks like a helpful answer, but it would be improved by citations or links to supporting materials.

@Risk, Do you have any references to back up those numbers? I found that it sort of matches the definition of CpG island in a paper: "annotates the segment as a CpG island if it satisfies the following criteria: (1) G + C content >50%, (2) length >200, and (3) the ratio of observed to expected number of CpG dinucleotides (“CpG O/E”) >0.6". But in a paper the methylation valley is longer "> 5kb" and notes that most contain few CpG islands.

@llrs The CpG definition is taken from UCSC genomics institute here: link The definition for valley/canyon came from here: [link[(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4719427/#B1).

@Risk many thanks! I'm not sure about the second link: In the paper "Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells", (first reference from the second link) under the section "Identification of DNA Methylation Valleys" it says "These DMVs range in size from 5 kb to 68 kb and are much larger than the CGIs in these regions ". Did you meant to link a different paper?

@IIrs - Sorry I must've messed up the link. If you look in the introduction of that paper, 4th paragraph: "identified around 1,000 larger (>3.5-kb) genomic domains with low average methylation levels, termed DNA methylation valleys or DNA methylation canyons (1, 15). These elements remained unmethylated during differentiation and were often associated with developmental genes".  One of those papers is the paper you're referring to, the other one is the one I tried to link to.


text:
Facial uniqueness of some animals of the same species
Do birds of the same species ,such as each pigeon that we see in cities, have unique facial geometries (facial phenotypes) regardless of their feather ,colors, spots etc? Sometimes it is almost impossible to distinguish two pigeons between each other just looking at their facial structure and curvature of their heads.
Human face has evolved with countless of varieties such as shape of nose, distance between the eyes, proportion of mouth and the nose etc.
Billions of humans have existed so far and billions of humans will ever exist each have unique facial features.
However some animals of the same species (birds like pigeons, baby chicks, fish species like sardines and sea bream etc) look like sharing a limited amount of variations in their facial geometries therefore they become distinguishable only because of their colors, patterns etc. I know that mammals such as apes or dogs have unique faces almost  as distinctive as humans. I also know that human brain is already attuned to distinguish differences in human faces more than any other animal.
What I would like to understand whether all pigeons have existed so far and will exist furthermore have unique facial geometries like humans? Or do they all differ in millimetric level which cannot be captured by naked human eyes? Can two pigeons(or sardines) of the same species share exact same facial geometries unlike humans?  I couldn't have satisfactory answers in this subject so far. Can you please explain?

Looking forward to a good answer to this. I’ve pondered it many times myself.

Possibly a duplicate of Why do different humans look different? or Why are humans so variable in appearance.

unless you can provide a study showing greater variation in humans it is a duplicate question. humans are specialized in detected human features so we are naturally biased.


text:
A simple question about amoeba (Naegleria fowleri)
I have a very simple question about Naegleria fowleri amoeba. Some experts claim that boiling the water for 15 minutes kills Naegleria. However, I have studied somewhere that Naegleria can turn into cyst forms when the environment or the atmosphere becomes harsh to protect itself. So the question is that is it possible for Naegleria to survive boiling temperature if the water is boiled for 15 minutes at 100 degree celcius by converting into cyst form and enter the nose of human and kill the human?