text:
Immunoaffinity chromatography: avoiding damage to the antibodies from proteases
What are the possible methods to prevent the digestion of antibodies (mainly Polyclonal) by proteases during affinity chromatography?
I read some papers about doing modifications to the anitbodies:
using unnatural amino Acids
using mPEG
But, are there better options, more commercially applicable?
I am trying to find a way to purify hyaluronidase from hepatopancreas of red king crab (using polyclonal antibodies). In this case, inhibitors like EDTA, Benzamidine, PMSF don't prevent proteolysis.
These are the Hepatopancreas proteases: (Collagenolytic Serine Proteinase PC (PC—Paralithodes Camtschaticus), Collagenolytic Serine Proteinase PC 2, Trypsin-Like Proteinase A, Chymotrypsin-Like Proteinase C, Aminopeptidase PC, Carboxypeptidase PC, Trypsin PC, Elastase, Cathepsin L, Metalloproteinase)

You need more protease inhibitors, and likely higher concentrations of them too, given that you're working with extracts that are just chock full of proteases. Inhibitor cocktails like this one are available from many companies. Read the specific literature of work relating to this organ or just experiment empirically to determine optimal concentrations.

@MattDMo Thank you, but could there be other methods to isolate the anitbodies from proteases? During/before affinity chromatography?

Protease inhibitors are really the tried and true method of protecting proteins, both the ones of interest in your sample as well as those complexed to the column beads. The problem with trying to modify the immunoaffinity antibodies is that you could very easily end up altering, damaging, or completely destroying their ability to bind to their substrate. That won't happen using inhibitors. I guess I should back up a bit - are you seeing damage to your antibodies, and is there a particular reason you can't/don't want to use inhibitors?

@MattDMo Inhibitors will be added anyway, but I was thinking of other possible ways to reduce  protease activity from the crude extract before starting chromatography. Because in this case, relying on inhibitors won't be very effective, they don't work on all the proteases of hepatopancreas.

The product I linked to (I have no affiliation with the company) has a number of other inhibitors than the ones you're currently using, targeting multiple different classes of proteases. That's what I suggest you look for - a "pan"-inhibitor cocktail designed for working with difficult extracts. As for other ways of reducing activity in the crude extract: you could try using detergents or chaotropic agents, but those will also interfere with antibody/antigen binding, and so I wouldn't recommend them. You could use heat to denature, but again you might interfere with Ab binding.

@MattDMo Thanks!


text:
Could DNA replication fail in the far future?
Assuming that all environmental conditions on Earth remain the same in distant future, the tendency of nature to increase entropy would cause the chemistry and the mechanism of DNA replication to create more and more "errors".
Could these errors accumulate over time for all life, resulting in failure of replication by means known today, bringing life as we know it to extinction?
In other words, will life eventually fail to continue reproducing due to the inability to maintain its inherent state of non-equilibrium?

Hi Dennis, you've misunderstood entropy and the second law of thermodynamics. Increased entropy doesn't create more genetic mutations.

Also, the "errors" do exist, they are basically what drives evolution and what made life what it currently is.

@Andrew is not what makes this errors appear. Replication and protein synthesis are chemical proceses, and they increase the entropy. The more errors in replication, the more chemical reactions, then the more entropy.

What i say @Alexlok, is that over time, the amount of errors could make imposible the appearence of new feasible organisms, because there would be more and more chunks of useless DNA. This would happen in the very long term.  My thinking is that replication seems like a continuous chemical process, but it can't last forever. or can it?

DNA replication won't possible in the heat death of the universe, but any creaters and planets will have disappeared long before that.

The principle that entropy (disorder) must increase is true for a closed system. An organism, however, is not a closed system; it obtains energy from outside itself and with that energy can maintain order. This is referred to as negative entropy; see the Wikipedia article on Entropy and Life.

Well said. Living organisms have been creating order from disorganized stardust for billions of years, so the premise that entropy is generally increasing among living creatures is false.

But the cost is that universe entropy increases, thats what i was refering to.

Assuming that all environmental conditions on earth remain the same in
distant future, the tendency of nature to increase entropy would cause
the chemistry and the mechanism of DNA replication to create more and
more "errors". Could these errors accumulate over time for all life,

An accumulation of errors in replication over time can certainly be assumed and observed. However, these errors -also called evolution- are generally not related to entropy.
Entropy, as a statistical concept (Boltzmann), describes the population of different states, like heads or tail in a coin-flip. If you toss 100 coins, the outcome of 50 heads would correspond to the maximum entropy, while 0 or 100 heads would be the lowest possible entropy. Boltzmann also describes that higher temperatures equalize the population of different states. Too high and too low entropy would both mean death.

resulting in
failure of replication by means known today, bringing life as we know
it to extinction?> In other words, will life eventually fail to continue reproducing due
to the inability to maintain its inherent state of non-equilibrium?

If an error leads to a decreased probability of reproduction, it dies out and will not accumulate. On the other hand, in the rare instances that the error actually increases the probability of reproduction, it has a high chance to accumulate. So in general, accumulation of errors would increase the ability of reproduction.
Not being able to maintain the correct state of entropy definitely is fatal and is the natural end of life when you grow old.

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The springlike behavior of titin problem
I am currently reading a textbook (Molecular Biology of the Cell, 6th ed), and this problem on p. 170 is driving me crazy. I read through the solution given in this book but I couldn’t understand it after all.
Here’s the question:
Titin, which has a molecular weight of about 3 × 106, is the largest polypeptide yet described. Titin molecules extend from muscle thick filaments to the Z disc; they are thought to act as springs to keep the thick filaments centered in the sarcomere. Titin is composed of a large number of repeated immunoglobulin (Ig) sequences of 89 amino acids, each of which is folded into a domain about 4 nm in length (Figure Q3–2A). You suspect that the springlike behavior of titin is caused by the sequential unfolding (and refolding) of individual Ig domains. You test this hypothesis using the atomic force microscope, which allows you to pick up one end of a protein molecule and pull with an accurately measured force. For a fragment of titin containing seven repeats of the Ig domain, this experiment gives the sawtooth force-versus-extension curve shown in Figure Q3–2B. If the experiment is repeated in a solution of 8 M urea (a protein denaturant), the peaks disappear and the measured extension becomes much longer for a given force. If the experiment is repeated after the protein has been cross-linked by treatment with glutaraldehyde, once again the peaks disappear but the extension becomes much smaller for a given force.

A. Are the data consistent with your hypothesis that titin’s springlike behavior is due to the sequential unfolding of individual Ig domains? Explain your reasoning.
B. Is the extension for each putative domain-unfolding event the magnitude you would expect? (In an extended polypeptide chain, amino acids are spaced at intervals of 0.34 nm.)
C. Why is each successive peak in Figure Q3–2B a little higher than the one before?
D. Why does the force collapse so abruptly after each peak?
The solution:
A. These data are consistent with the hypothesis that the springlike behavior of titin is due to the sequential unfolding of Ig domains. First, the fragment contained seven Ig domains and there are seven peaks in the force-versus-extension curve. In addition, the peaks themselves are what you might expect for sequential unfolding. Second, in the presence of a protein denaturant, conditions under which the domains will already be unfolded, the peaks disappear and the extension per unit force increases. Third, when the domains are cross-linked, and therefore unable to unfold, the peaks disappear and extension per unit force decreases.
B. The spacing between peaks, about 25 nm, is almost exactly what you would calculate for the sequential unfolding of Ig domains. The folded domain occupies 4 nm, but when unfolded, its 89 amino acids would stretch to about 30 nm (89 × 0.34 nm), a change of 26 nm.
C. The existence of separate, discrete peaks means that each domain unfolds when a characteristic force is applied, implying that each domain has a defined stability. The collection of domains unfolds in order from least stable to most stable. Thus, it takes a little more force each time to unfold the next domain.
D. The sudden collapse of the force at each unfolding event reflects an important principle of protein unfolding; namely, its cooperativity. Proteins tend to unfold in an all-or-none fashion (see Problem 3–35). A small number of hydrogen bonds are crucial for holding the folded domain together (Figure 3–39). The breaking of these bonds triggers cooperative unfolding.
If so, I think the graph should look somewhat similar to this:

or this:

*I didn’t scale the graph because I don’t know the exact figure.
Since the protein unfolds in an all-or-none fashion, it won’t extend until it is unfolded, but it will extend gradually as it unfolds.
As it takes a little more force each time to unfold the next domain, the constant portion of the graph should be lengthened as the domains progressively unfold.
In both graphs, the extended lengths are always the same, but in graph 2 the domains get harder and harder to unfold so they require extra input of energy each time they unfold. (Thus the slope of the diagonal portions of the graph needs to be less steepened.)
I don’t know which one is correct, so I drew both.
The question is, why is my answer different from that of the textbook? Is there something wrong with my reasoning?
Any idea or answer is appreciated!

When an Ig domain unfolds, its length increases, so the force required to stretch the whole protein to a given length will decrease. Your diagrams don't account for this decrease in force.
You can think of the domains like wire coiled into the shape of a stereotypical spring when they are folded, and a straight line when they are unfolded. Stretching the coiled spring to the length of the straight wire will take a lot of force. Obviously no force is needed to keep the straight wire at its natural length. (This isn't true of unfolded proteins, but the entropic force is small compared to the elastic resistance from the folded domains)

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What's the purpose of using more than one culture medium for bacterial isolation?
What's the purpose of using more than culture medium for bacterial isolation?
Why not use just one?
If this is not generally used in isolation of various types of bacteria, I'm concerned especially with Acinetobacter spp. isolation, which grow well on blood agar and MacConkey agar.
Examples of research which include the isolation of acinetobacter spp.:

In this study, 200 (9.5%) Gram-negative, non-fermentative strains were
selected among 2108 Gram-negative isolates identified at mega
laboratories over the Suez Canal and Nile Delta regions in Egypt (1044
urine culture, 108 pus, 537 sputum, 322 blood, 23 cerebrospinal fluid,
and 74 wound) from August 2017 to October 2018. The 200 strains were
preliminary inoculated on MacConkey agar, blood agar, Acinetobacter
agar, and CHROM agar media. [1]

The samples were collected from patients of all age groups, both
sexes, who were critically ill and suspected for pneumonia, urinary
tract infection, septicaemia, skin and soft tissue infection and
meningitis. The samples were inoculated on Blood Agar and MacConkey
Agar plates under strict aseptic conditions. [2]

All the samples including bland pus, respiratory tract samples,
fluids, swabs and urine samples were surface streaked onto BA [Blood agar] and
MacConkey agar plates. [3]

https://doi.org/10.3390/antibiotics9090603
Oberoi, A., Aggarwal, A., & Lal, M. (2009). A decade of an underestimated nosocomial pathogen - Acinetobacter in a tertiary care hospital in Punjab.
https://doi.org/10.22159/ajpcr.2018.v11s2.28590

Edit:
There is one species in the genus Acinetobacter, Acinetobacter haemolyticus, which causes beta hemolysis on blood agar, however, not a single research that mentions using both MacConkey and blood agar, mentions this as the reason for using blood agar.

I think this would be more appropriate on Biology.SE and would be more likely to receive good answers there. I can migrate it for you if you have no objection.

Please do, thank you.

A good start would be to look at the purposes of each medium, and to realize that not all the bacteria that fit the category Gram neg, non-fermetative are Acinetobacter...

Were the people receiving the samples trying to urgently identify unknown pathogens? If so they would grow on several different media.

I am not sure I get your question, Do you want to isolate a sepcific type of bacterium or in general isolate most bacteria from a sample?
If you want to isolated a specific bacterium from a samples, there various "selective" media you can use. Now, I never saw a medium that is really selective, meaning other stuff will grow on it as well. But in general you can be confident that the diversity of colonies you get on these media is lower than what you get on a general medium.
If you want to isolate as many bugs as you can, well then you have to try as many media as you can. Not all bugs will like the same medium. Also there is this misconception that bacteria like rich media. This is not necessarily the case and often rich media are actually highly selective for fast growing bugs that are able to tolerate well stress, carbon overflow, and ROS/NOS.

This is a great question! We often use multiple media types for isolation in microbiology because microbes have widely different growth needs. Using various media types, we can create more than one growing environment and capture a wider range of the microbial population.
Additionally, different media can inform us about the microbial population's biochemistry. For example, blood agar plates can be used to test for hemolysis capabilities. There are a lot of media types so the purpose of each one is unique. If you are interested in learning about more specific media types I would suggest reviewing the research and identifying the main research questions.
Important note on microbial culturing: there is a large percentage of microbes that cannot be currently cultured through traditional culturing techniques. Microbiologists are advancing culturing techniques and increasing our ability to grow fastidious, difficult-to-grow, organisms. However, this is co-occurring with a greater understanding of the massive amount of microbial diversity that exists in the environment. Luckily, we now have culture-independent methods to identify microbial community populations.


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DNA sequence from the middle of a gene
Someone gives you a short DNA sequence that comes from the middle of a gene.
5'- TCTAACTGATTAGC -3'
3'- AGATTGACTAATCG -5'

From this sequence, determine the following:

Is the promoter located to the left or right as the sequence is written?
Is the sense strand the top or bottom strand?
What amino acids are encoded by this gene fragment?

The only thing I have been able to come up with, is that since this is from the middle of a DNA sequence I need to choose a frame with no stop codons.

The two segments you provide are not complementary to each other. Is this a typo or a part of the actual question?

I've edited the sequence to repair the 5' and 3' ends of the bottom strand, which are now as was shown in the original version of the question.

Gene doesnt essentially mean protein coding

TCT AAC TGA TTA GC
T CTA ACT GAT TAG C
TC TAA CTG ATT AGC
AGA TTG ACT AAT CG <<< this is the ORF
A GAT TGA CTA ATC G
AG ATT GAC TAA TCG
If the sequence comes from the middle of a gene we assume it should encode an open reading frame.
For this sequence only 1/6 frames does not include a stop codon (shown above in italics). So in standard format, with promoter to the left we can write the ds sequence as:
5'-AGATTGACTAATCG
3'-TCTAACTGATTAGC
Since this is homework I'll leave the rest to you.

Since the ORF has no stop codons, does that mean it is the template strand?

The open reading frame is the strand of DNA with the same sequence as the mRNA (with T>U). RNA polymerase makes that RNA using the other DNA strand, which is the template strand. If the dsDNA sequence is written in the conventional way with promoter to the left then the top strand is the coding strand and the bottom strand (running 3'>5') is the template strand.

Don't we want the template strand to have no stop codons? Cause when we are reading the template strand making the mRNA we don't want to encounter a stop codon.

For example if we use 3'TCTAACTGATTAGC as the template strand when the polymerase reaches TGA, it would stop right?

Or do stop codons only stop the mRNA was making proteins. It doesn't stop the DNA replication?

@itsSLO I would like to tell you a couple of things. 1. Stop codons do not stop transcription of mRNA, it will stop only the translation of mRNA. 2. Here, we are taking the sequence with no stop codons only because the question says that the sequence taken  is from the middle of a gene. So, if we take a sequence with a stop codon the mRNA from rest of the part of the gene will not be translated.

On the sequence alone, you can answer neither of these questions because:

from the sequence alone you don't know anything about the gene or the
promoter.
the same is true for the orientation
and the codons, since you don't know if the code is in frame or not.
If one base is cut-off from the original sequence, your codons shift,
and don't show the original code. The sequence has 14 nucleotides
which will not ressolve into a short amino acid sequence.

You can probably identify the gene using BLAST and then see, where the sequence is located and answer the questions. I tried to blast the sequence, but it is too short to give a definitive answer.
So the first thing, you need to do is identify the sequence (gene and the organism where it comes from), then you can do the rest of the work.

Yeah this was all that was given for the problem. Nothing else.I was thinking you can determine the frame by choosing one without any stop codons.

Thats right. Alan showed what can be done, but the rest is problematic.

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text:
Does the pyloric sphincter contract after ingesting only liquid?
At university, I was told by one of my fellow students that the reason why eating before going on an alcohol laden night out was a good idea, was because the pyloric sphincter contracted once food was in your stomach, and only let it into your lower intestines gradually. Their theory was that if you then drank alcohol, it would also sit in your stomach (with your food) and would only be let into your intestines gradually as the food was allowed through, thus slowing your rate of inebriation. Drinking on an empty stomach would conversely not cause the pyloric sphincter to contract, thus allowing the alcohol to enter your intestines at a much faster pace. However, I've been trying to find some online sources to corroborate / disprove this, and I'm having problems finding any information on it at all.
So my question is: does the pyloric sphincter stay relaxed if only liquid is consumed on an empty stomach?

The answer from CATARANTHUS looks good, but if you want to see another source of information try here.

NO IT DOESNT CONTRACT AFTER INGESTING LIQUID
1)The pyloric sphincter always remain  tonically contracted even in an empty stomach.However this tone of the pyloric sphincter is insufficient to prevent the passage of liquids to the duodenum.Thus almost all the liquid intaken in an empty stomach passes immediately to the small intestine.
2)Filling of the stomach triggers an enteric reflex that increases the tonical contraction of the pyloric sphincter.When fluids are taken then,their rate of passage to the duodenum is considerably reduced.(Although little is slowly absorbed into blood from the stomach).
REFERENCE:TEXTBOOK OF MEDICAL PHYSIOLOGY(GUYTON AND HALL)
3)As the small intestine is the seat of absorption,delaying passage to it delays large amount of alcohol absorption into blood.This not only delays its effect in the body but also fascilitates the persons capability to intake more alcohol.(This varies considerably in different persons but the central physiology is this)
REFERENCE:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1705129/

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text:
Why doesn't nitrogen diffuse into blood?
In school, I have learnt that the deoxygenated blood brought in to the Alveoli by Pulmonary Arteries contains Carbon Dioxide. And that Carbon Dioxide present in the blood diffuses into the Alveoli and squeezed out with the help of Diaphragm.
Then, why doesn't the Nitrogen present in the Alveoli gets diffused to the blood? My guess was that the blood vessels don't allow anything other than CO2 and O2 to pass through.
But I recently saw a video on KhanAcademy where Sal said that some amount of Nitrogen does get mixed with blood. Is Sal right? If yes, then why doesn't the whole Nitrogen present in the Alveoli gets diffused from there (where it is present in high concentration) to blood (where it is present in low concentration)?
To summarize,

Why doesn't the inhaled-Nitrogen present in the Alveoli diffuses into the blood present in Pulmonary Veins, similar to how CO2 present in blood gets diffused out to the Alveoli?

@GerardoFurtado So, Sal Khan was wrong. I guess you should put that as an answer so that I can accept it.

@GerardoFurtado How? Why only some?

@GerardoFurtado Okay. Thank you for your help! :)

(Alas, GerardoFurtado was never provided the link, and now his account is deleted too. Sorry, Gerardo, I didn't see your comment earlier :-P)

I like it that nitrogen came to your mind ;)
I guess in school they didn't tell you about the nitrogen at all, for the matter of simplification, because it is of no function in the body and the $O_{2}$ and $CO_{2}$ are the important gasses for biological function of breathing.
However, all of these small gas molecules are very small and generally the biological membrane is very permeable to them. That's why the cell cannot decide to let $O_{2}$ and $CO_{2}$ in and $N_{2}$ not as you suggest.
(However, the cell is able to control the permeability of these gases to some content, based on the level of cholesterol in its membrane$^1$)
The process of gas exchange is generally passive. In alveolar membrane the gas flows from the site of its higher concentration (in case of gases we talk rather about partial pressure) to the site of lower concentration. The speed of this process depends mostly on the difference in partial pressures and if you let the blood "interact" with the air in alveoles for long enough, partial pressure of all small gas molecules would come almost to equilibrium. (This happens under physiological conditions for all of the three mentioned gases)
Khan academy is right too actually. This is because as $N_{2}$ isn't either produced or consumed in the body, its partial pressure in the venous blood is similar to that in the alveolar air, and there is no force to cause its movement between these two compartments in general.

In the table you can see, that the partial pressure of nitrogen in the blood is the same as in the alveolar gas.
Picture source

@GerardoFurtado thanks, random mistake. corrected

Nitrogen is not a metabolic gas, its partial pressure is very high. No compound of blood can react with Nitrogen hence its diffusion is not possible.
its diffusion is only possible when a person is suddenly lifted from depth of ocean, such diffusion causes bubbles in blood vessels leading to death due to disease called KESHAN
THIS IS WHY WARNINGS ARE GIVEN PRIOR TO SCUBE DIVING

Please add some references explaining how you got this answer


text:
Can exercise strengthen tendons and ligaments?
Is is possible to strengthen tendons using exercise to prevent injury, for example preventing shoulder dislocation?

I don't have the background to give a definitive answer, but it would make sense if especially tendons and maybe ligaments grow stronger through exercise... otherwise the risk of tendon damage should increase sharply as a function of muscle strength. I recall having heard/read somewhere that abusers of steroids have increased risk of tendon damage due to a too fast gain of muscle strength. Maybe someone can elaborate with a better answer.

yes..It takes approximately 10 weeks of regular resistance exercise to strengthen your tendons, and it takes longer for them to thicken. You can expect up to 20 percent increase in strength and thickness of your ligaments and tendons with regular training.

Can you add some sources for your information? Unreferenced answers are frowned upon here.


text:
How effective is water purification by boiling?
Does boiling water kill all harmful bacteria, fungus etc from water, or it is just a myth and removes only few of microorganism?

To be precise, boiling water would not remove all bacteria as there are certain extremophiles that thrive at higher temperatures.
However, boiling of water is known to get rid of harmful pathogens. Boiling of water is a method of pasteurization, which means killing those organisms that can cause harm to humans.
Quoting from New York State - Department of Health >>

Boiling water kills or inactivates viruses, bacteria, protozoa and
  other pathogens by using heat to damage structural components and
  disrupt essential life processes (e.g. denature proteins). Boiling is
  not sterilization and is more accurately characterized as
  pasteurization.
Cooking food is also a form of pasteurization. For pasteurization to
  be effective, water or food must be heated to at least the
  pasteurization temperature for the organisms of concern and held at
  that temperature for a prescribed interval.

What is the difference between sterilization and pasteurization?


text:
Nutrition mineral intake method
I always wonder if rather than getting minerals from food, can I directly eat them and will they have same effect as in food,
e.g. can I eat iron filings for iron, magnesium and drink hard water for calcium?
Is there any difference between having minerals through food or directly eating metals?

Please avoid using texting language for Qs & As on the main site, I have edited to fix grammar.

To absorb essential elements, body must get them in form of stable ions.
So for calcium and magnesium, our body absorbs them from the hard water in the same way it obtains from other sources and uses them identically.
For iron, we cannot obtain iron from iron fillings because iron reacts with water and other chemicals in our body which can produce harmful effects.
For further information on absorbtion of calcium from hard water visit http://goaskalice.columbia.edu/answered-questions/calcium-hard-water


text:
What's the meaning of this notation?
In Wang et al., the authors state on page 663 at the top that

Furthermore, Bax-/- Bak-/- cells were completely
  resistant to paclitaxel-induced apoptosis.

What's the meaning of the -/- notation? Bax and Bak are proteins involved in apoptosis.

-/- means both copies of the gene (both alleles) are knocked out

I guess I need to brush up on my molecular biology, but by "both copies" you mean, both copies present during mitosis?

As chromosomes come in pairs (bar the X chromosome in males), each gene is also present twice. -/- means both are knocked out.


text:
What's the duration between the binding of adrenaline to β-AR and the first translated protein?
Binding of adrenaline (epinephrine) to the β-Adrenergic receptor leads to formation of cAMP (via G protein activation), activation of protein kinase A and subsequently to the expression of specific genes related to glucose metabolism.
How long does it take (in units of time) until translation of the first protein related to the adrenalin binding event is completed?
EDIT: I can accept a reasonable guess at the time scale (+/- factor of ten). Also, it can be also any another kind of ligand/receptor system.

This is a very interesting question. I have looked now for a while to find some references, but I haven't found any so far. I don't think that there is a definite number, as the connected processes depend on several factors. One very important is the length of the gene, for E.coli the speed of transciption was between 40-80 nucleotides per second, translation is even slower with around 20 aa/sec.

Sure it depends on a lot of things, that's not surprising. However, I haven't even got an estimate on what time scale we're looking at here. Even this would already be of worth knowing.
The numbers you gave are for a single mRNA synthetase/ ribosome unit?

The numbers come from this source.

The references in the essay are definitely useful. Still, the signaling part is missing. But so, from just estimating the signaling part to take as long as the transcription/translations parts, from ligand binding to first translated protein, how about we say we're looking at minutes?

Things can certainly vary for different ligands and different levels of cascading but these are the reactions that you may consider.

Receptor activation
Nuclear translocation (lets assume it is just a part of the receptor. You can assume secondary messengers; it will add an extra step)
DNA-binding and Transcription activation
Transcription
Nuclear export of mRNA
Translation

Finally I guess what you really want is to know when steady state is reached. This will also depend on other factors such as:

Receptor deactivation rate
mRNA and protein degradation rates
Nuclear export of activated TF
Network architecture (some networks can speed up response times). This factor can be ignored and we can consider an open loop.

Phosphorylation reactions are generally much faster than transcription/translation/translocation rates and can also assumed to be equilibrium with dephosphorylation reactions.
Nuclear import rates are also dependent on cell volumes and for polarized cells like neurons it will be much higher. The average import rate is around 0.2 - 1.2 s-1 NPC-1 µM-1(cargo) [where NPC is number of Nuclear pore complexes which is again on an average 120 ] [1].
It can be, for ease, assumed to be ~0.02 min-1 [2].
In most modeling papers the transcription rate is assumed (based on experimental reports) to be 1 per min (Average polymerase speed of ~1000nt/min and gene length of 1000nt. This can vary with gene length)
Translation rates are somewhat trickier. The translation rate per ribosome translation elongation rate is ~5 codons/sec (15aa/sec)[3] or perhaps may even be lower — 3 - 9aa/s[4] ( [3] is a more recent finding). However, the overall translation rate will be dependent on number of ribosomes (Ribosomes can be assumed to be infinite unless it is some condition like stress or starvation. By no of ribosomes I meant polysomes per mRNA, which can also vary). Also, the protein synthesis rate will depend on length of mRNA. This is one parameter that can have a broad range of values (0.6-100 min-1 × mRNA).
You can set up mathematical model (based on reaction rate equations) and calculate the response times (Depending on parameters it can be 8-20 hours). Steady states can generally reach by 8 hours (based on my own experiment. But I used tetracycline to induce luciferase). Another experiment (unpublished) using IFNγ induction caused a peak in the reporter at ~12h. I am not linking all references (you can easily look up for these). Usually, for cell culture applications, there is some sort of unsaid rule to assume 12h as a general response time to persistent stimuli. Response times are also dependent on initial conditions.
Note: Response time means the time required to achieve steady state. This does not mean the delay between signal onset and protein synthesis. Other metric that is used generally is max-peaking time.


text:
What does the "cov" mean in a velvet assembler generated contig name?
A exmaple of a contig name generated by velvet assembler:
NODE_127_length_39203_cov_244.873016

What does cov_244.873016 mean?
It sounds like coverage. Does it mean reads coverage or other statistical description of the contig?

It means coverage

covariate perhaps?

It means k-mer coverage. From the velvet manual:

4.2.1 The contigs.fa file
This fasta file contains the sequences of the contigs longer than 2 k
  , where k is the word-length used in velveth.  If you have specified a
  min_contig_length threshold, then the contigs shorter than that value are omitted. Note  that  the  length  and  coverage  information
  provided  in  the  header  of each contig should therefore be
  understood in k-mers and in k-mer coverage (cf. 5.2 ) respectively.
  E.g.  for a 500bp contig and a k-mer length of 21, the length in the
  header will be 480.

+1 for resisting the urge to say RTFM--I guess that is one of the many reasons we elected you as a moderator: impulse control.

@mdperry Haha.. I'm working on it actually :)


text:
Is it okay to scale the RNA-Seq counts after log-transformation?
On an RNA-Seq dataset, I want to apply a clustering algorithm which requires zero-mean uni-variance gene expression levels. I am wondering whether it makes sense to use "scale" function in R after taking logarithm of the counts. For microarray data, I was actually using the scale function which (as far as I know) makes sense; but this is the first time I am using RNA-Seq. I heard about "voom" normalization (in "limma" library on CRAN), but I don't really want to use that since I am not really familiar with the details.

What are the datasets; different samples? The analyses and the statistical procedures that you use depend on what kind of data you have. There are several (infinite) distributions that can have 0 mean and 1 variance. The question is, what is your expected distribution i.e. the null model. Certain data are known to follow certain models. So the question boils down to what is your data.

My data is gene expression data and the algorithm assumes a zero-mean uni-variance Gaussian distribution.

So you just have one sample? Technically, the different genes are different random variables. Moments like mean and variance are for one random variable. Comparing different genes is like comparing apples and oranges. Moreover, the expression of all genes is not expected to follow gaussian. For more details see this post.


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Interaction study of oligomeric proteins
I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system.
I have so far successfully been able to purify both the proteins using IMAC(Ni-NTA) protocol.
Further TEM analysis of the purified protein is showing the presence of oligomeric form(for each of them separately) in the purified sample.
But, how can I be able to detect or show how the oligomers of protein_a and protein_b is interacting to produce a much larger macromolecular entity ? And how can I be able to quantify that interaction ?
Any ideas regarding this issue would be highly appreciated.

Are the oligomers of a defined size? Gel filtration chromatography or native PAGE could show an interaction and give an apparent Mr of the complex.

Previous data regarding oligomer size shows that protein_a forms ~600kd oligomer(using analytical ultra centrifugation), however protein_b's oligomer size not yet known. So, I'm not sure whether native PAGE could resolve such big mw. @canadianer

Though I've never tried, there are native PAGE systems capable of resolving proteins upwards of 10000 kDa


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What is the name of classification of water, air and soil?
The definition of living organisms is all types of organisms are capable of some degree of response to stimuli, reproduction, growth, development and homeostasis.
Non-living organisms are inanimate and have stopped displaying capabilities for growth, reproduction, respiration, metabolism and movement. So what do you call air, water, and soil.
plus I am writing an assignment about environment protection. So  I am talking about how certain chemical affects the air, water(sea, and river) and soil.
So how do I classify this three thing, making them be very specific, other than non-living things, as this group is too broad.

Air, water, and the non-living components of soil, along with rock, sand, etc. are all part of the environment. They don't have a specific class or name. Of course, living organisms are part of the environment or ecosystem as well. I don't understand what your question is asking.

In ecology, non-living components can be grouped under the term abiotic factors or abiotic components. This includes water, air, light, soil, temperature, and many other qualities that describe the organism's surroundings. These are in contrast to biotic factors, which can include predators, prey, and competitors.
Abiotic Component- Wikipedia

Gas, liquid & solid are three classes in to which the majority of the matter - as generally understood - in air, water & soil would be included in.
Gases, liquids, and solids are only 3 of a multitude of possible states of matter. They are the 3 states that we are most familiar with in normal life. Air, water and soil are not broad categories of non-living matter, but is each just a mixture of matter (unless you mean pure water).
If by air you mean the gas mixture of our environment then it is a particular mixture of gases including nitrogen, oxygen, carbon dioxide, and others - or if you mean "the air outside" then it would include solids like small particles of, say, leaf debris or car-tyre rubber.
The matter that makes up living and non-living things is exactly the same and is categorised by chemists and particle physicists.
Living things are unique in the way that matter is caught up in a self-reproducing and entropy-offsetting complex system, which have evolved in to the elaborate systems of the living cell.
If by non-living organisms you mean "dead organisms" which once lived, then these can be thought of as the matter which was left when the dynamic process of life that animated the matter ceased or moved on. Simplistically, life is analogous to an eddy (or 'whirlpool') in a stream of water. Water molecules enter and exit the eddy, just like atoms enter and exit our bodies. If the currents change and the eddy disappears, the water where the eddy was still remains.
Of course the stream carries the water away quickly, rather than it sitting there as a dead organism for some time as the ecosystem recycles its matter.


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Understanding the general dynamics of protein diffusion in cell plasma membrane
Background
I am doing an undergraduate research project on the modelling and analysis of protein diffusion in plasma membranes. I am a physics and computer science student so naturally, I have many knowledge gaps in cell biology.
My understanding so far
I have been reading so many papers, but I still can't have a comprehensive general picture of protein diffusion in the membrane and what precisely that entails. From my understanding, the widely accepted model is the one with the underlying cytoskeleton actin mesh-like filaments which compartmentalize the plasma membrane. In this model then, are only transmembrane proteins affected in their diffusion by the mesh-like structure, which they sometimes touch (because the filaments are close to the inner side of the plasma membrane)? Moreover, peripheral proteins or other types of proteins, because they do not touch the actin filaments, do they just diffuse freely in a Brownian motion?
I understand that generally, proteins undergo diffusion either

freely (Brownian motion)
in a compartmentalized hop-diffusion way
or through irregular diffusion given lipid rafts (which generate concentration gradients).

Questions
But which proteins are we talking about, is it peripheral, transmembrane or else? Where are these proteins in the bilipid layer? And which direction are they diffusing, is it lateral diffusion or diffusion within the bilipid layer? Are all these 3 diffusion models going on at the same time but each affecting different categories of proteins? I can't have a clear picture of this ecosystem and would appreciate some insights on these questions so that I could begin my research with the simulations.

You might want to go to the library and have a look at Alberts „Molecular Biology of the Cell“, an older edition of which is also available on the NCBI Bookshelf. Publication-grade knowledge might be too detailed at your point of education and might not fill in the „big picture“. We know a lot more about directed processes on the cell, so read about: endocytosis, glycocalyx, secretory pathway, receptor internalization/sequestration, clathrin coated pits, etc… I mean „Brownian motion“ is nice and all, but we‘re talking about living things here ;)
For your questions:
Which proteins? Transmembrane proteins, receptors, pumps, pores, actin associated proteins, motor proteins (Myosin) etc.
Which direction? You’re looking at lateral diffusion (like lipid rafts). The bilipid layer is too thin to support anything else but lateral diffusion, since as far as I know, membrane proteins are pretty much „stuck“ at the membrane, unless they react to a signal pathway. If we‘re talking about selective pores/pumps, then movement through the membrane might be interesting to you. Also: flippase can flip lipid molecules from one lipid sheet up to the other.
Note that temperature has a big effect on cell membrane fluidity. Cells regulate the fluidity by embedding cholesterol into the lipid layer. One can measure the fluidity using FRAP (fluorescence recovery after photobleaching). That method might help you understand how diffusion in membranes works.
And yes, all the different diffusion models are going on at the same time. And so do tons of other processes. Welcome to molecular biology.


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Is Homo sapiens the only extant species of genus "Homo"?
Is Homo sapiens the only species of genus "Homo" that survived?

Some people argue that given our close relatedness Chimpanzees and humans should share a genus, which would likely be the genus Homo, meaning Homo sapiens would be one of three species in that genus. But it's not the official classification.

Is Homo sapiens the only extant species of genus “Homo”?
Yes, Homo sapiens is the only species left in the genus Homo. To be more accurate, some even consider all modern humans as being part of the same subspecies Homo sapiens sapiens. In those terms, Homo sapiens sapiens is the only subspecies left in the genus Homo.
There were other lineages before though but they got extinct.
Other Homo lineages that existed
There were other Homo lineages that went extinct. Consider the followings for example

H. habilis
H. gautengensis
H. erectus
H. neanderthalensis (sometimes called H. sapiens neanderthalensis)
H. heidelbergensis

Related posts
Here are two other posts that may be of interest to you

Does it make sense to classify all humans in a single species?
How could humans have interbred with Neanderthals if we're a different species?


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When does a jalapeño begin to produce heat/capsaicin?
I have a small Jalapeno plant in my apartment. About two weeks ago, it started producing a few flowers. In the last few days, many of them have started to turn into fruit; however, a few of the flowers have fallen off. The flowers do contain some seeds. They look rather like this:

Note this is not a picture of my plant (my flowers are white) but apart from the color it looks quite similar.
I tried munching on the seeds to see if they were hot. They weren't at all. I believe it is a common misconception that the seeds are where capsaicin concentrates, but should there have been any heat? Is there none in the seeds at all? Or was it too early in development?
Related questions: Do you think these seeds were viable at this point, or would they need to develop in an actual pepper fruit?

The reason the 'seeds' you ate weren't hot is because they're not seeds. What you thought are the seeds in the pepper flower are its anthers. The anthers are the pollen bearing parts of a flower. The unfertilized, and therefore undeveloped, seeds would be found in the flower's ovary which is at the base of the petals. The parts of a flower are labeled in this diagram.

I've tried both the seeds and the flesh of jalapeño peppers and noted the 'heat' in both but personally, I found the seeds a little hotter.


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When cancer is detectable, how many sub-clones are there at that stage?
I have read somewhere that cancer is detectable when the number of cells reaches $10^7 - 10^9$, which probably varies according to the specific tumor. At this early stage, what is the expected number of subclones of the tumor? Any references would be super appreciated!
p/s: To answer this, I tried running a simple code for a birth-death process, but my laptop freezes at $10^7$ cells. :(

Is this in humans? What is the form of detection? There are over 100 different types of cancer, so maybe pick one?

@Andrew Any example in human cancer would be sufficient. Thank you for pointing out the confusion!

How do you define subclones?

It is impossible to define subclones. But is is possible to define when metastasis. Thus, this question may be unanswerable.

@MattDMo I apologize. I was under the impression that this is a well-defined concept. I have seen some phylogenetic trees for keeping track of cancer mutation, which is why I assume they are what biologists consider subclones.


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Is there an animal venom to which humans are naturally resistant?
Some species, no matter how poisonous or venomous, have natural predators that can withstand the poison/venom. Does human also have something similar?
This question came to me after I spent an hour observing my pet black widow and looking up related materials online. I realize that some species of wasps can neutralize the poison of the black widow naturally. Hence, I wonder if humans have something similar.

Humans are resistant to some natural compounds that can be (very) dangerous to other animals, for example caffeine and related molecules, but those are plant-based. We can tolerate doses of animal-produced toxins that are lethal to other, generally smaller, animals - for example, black widow bites are rarely fatal to humans, but can easily kill their natural prey.

@MattDMo Thank you! My question aims to ask specific natural compounds that other animals/plants/etc. use as their defense mechanisms that humans can neutralize it. For example, while the black widow's venom is rarely lethal for humans due mainly to our size, we do not have something that counters it effectively. On the other hand, the yellow wasp does.

what do you mean by resistant? death? damage? what kind of damage? Humans are not resistant to caffeine, nicotine or ethanol (for example) but we do not die from small dosages. Same goes for spider bites, snake stings etc. Even too much water can kill humans.

@Hachiloni no, we are not completely resistant to the things you mentioned, but we have functioning biochemical pathways that can metabolize those compounds. I was thinking specifically of the effect of caffeine on dogs - they are much more sensitive to its effects than humans, even taking into account differences in body weight, and can be poisoned by equivalent mg/kg doses that some people consume daily via coffee or energy drinks.

@MattDMo This turns out to be a lot less clear cut than I originally thought. It seems I would need a better definition of what I mean by "resistance" as well. But I lack the background to suggest a meaningful one. I guess originally my thinking was along the line of whether humans are natural predators of some other animals. If that is so and the animals produce certain toxins, then maybe humans are immune to those toxins, just sort of a evolutionary thing.

@Paichu I think an important point you might be overlooking is that humans are generalist predators, not niche ones. When you have a situation like a venomous black widow spider and a venom-resistant predating wasp, typically the reason is that they both co-evolved in the same ecological niche, which is how resistance develops. There is no relationship like that with humans and any of our prey - we don't occupy a single niche, and didn't evolve to specifically feed on any one thing, therefore no venom/resistance mechanisms have developed.

no venoms I know of, but humans are highly resistant to maillard compounds, far more than any other animal.  they are toxic byproducts produced by cooking food, mostly overcooking it.


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Do any cells change in size or mass as mammals grow?
That is to say, are there cells that, between infancy and adulthood, get larger?  Or is all growth done entirely via cell division?  I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.

I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.

Not exactly.  When a tissue is put under stress, it can respond in four main ways:

Hypertrophy - individual cells get larger.  E.g. stressed muscle cells get bigger.
Atrophy - invidivual cells get smaller.  E.g. naturally in the thymus during development.
Hyperplasia - increased cell division to produce more cells.  E.g. mammary gland cells in pregnancy
Metaplasia - one type of specialised cell is replaced with another, usually more durable one, E.g. columnar epithelium in the respiratory tract of a smoker being replaced with squamous epithelium.

The first three responses to stress can change both cell size (auxetic response) and number (multiplicative response), meaning you can't really say that cells per unit mass stays constant throughout life.
Muscle tissue grows predominantly by hypertrophy, meaning that the muscle gains during puberty are likely to be more as a result of cells getting larger than the development of new ones.
Both auxetic and multiplicative growth occurs as the body develops.  In addition to this, accretionary growth also occurs - where connective tissues such as bone and cartilage increase in size.

This is not my field so I am sure there are other examples, but certain neurons will definitely be larger in adulthood than in infancy. There are motor neurons that connect the spine to, for example, the toes. These will grow in length as an animal grows. So, in a human infant they will be a few centimeters long and can reach lengths of over a meter in an adult.


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Do adipose cells divide in adults?
I have a dim recollection of having heard that when humans gain weight, adipose cells just get larger, rather than dividing.  True?

The Wikipedia entry for Adipocyte has a whole section on cell turnover. "If excess weight is gained as an adult, fat cells increase in size about fourfold before dividing and increasing the absolute number of fat cells present." citation

@QuietThud please consider fleshing out your comment a little and posting it as an answer.

My foray into the literature suggests that mature adipocytes do not divide. See, for example:

Lefterova, MI et al. (2009) New developments in adipogenesis. Trends in Endocrinology and Metabolism 20:107-114

In the context of looking at the possibility of stimulating the conversion of white adipose tissue to brown adipose tissue, the authors outline the way in which the expansion of adipose tissue occurs by a process in which fibroblast-like pre-adipocytes differentiate into cells capable of storing lipid droplets and responding to insulin.
It appears therefore that expansion of adipose tissue occurs by the generation of new adipocytes. Thinking of the morphology of a fully-loaded adipocyte (a lipid droplet surrounded by a narrow band of cytoplasm) it seems rather unlikely that these cells would be capable of division. The Wikipedia citation linked to by QuietThud in the comments to the OP is to a popular book on nutrition, not an authoritative source.


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How can natural selection occur at species level whilst not occuring at the individual level?
The chapter by Douglas Futuyma in 'Evolution' (Losos et al 2013, Princeton) states that natural selection can occur at the species level. Futuyma states that if natural selection occurs at the species level it does not occur at the individual level:

Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level.

But how does natural selection occuring at the species level not affect individuals? Surely any selective advantage of a particular species must occur among particular individuals of that species. For example, if Species A is selected because it is browner than Species B, this will be because individuals of Species A are browner than individuals of Species B.

could you post the word for word quote?

The quote is word for word. I've also correct a number of mistakes in my question

natural selection works in the genome level.

I think you have misunderstood the passage. Here is a larger section (found at google books):

Natural selection can also occur at the level of species, for certain characteristics enhance the rate of origin of new species or diminish the likelihood of species extinction. For instance, the number of species in lineages of herbivorous insects has generally increased faster than in closely related lineages that have other feeding habits. Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level. But individual selection, selection among individual organisms within populations, is at the center of evolutionary theory. It is at this level that selection explains most of the adaptive features of organisms.

Going through this part-by-part; the first two sentences state that lineage/species selection can occur, in the sense that species traits can enhance the speciation rate of a lineage or decrease their risk of extinction, relative to other lineages (e.g. in herbivorous insects).
He is then saying that the traits that are the target of this selection are not traits of individuals but traits/properties of the species/lineage.
An example might help to explain the point. For instance, it has been argued that pelagic larvae in sessile ocean species will lead to higher dispersal rates, which means that species can colonize new environments, and this can lead to speciation through adaptive radiation (Jablonski & Hunt, 2006). A larger range will also correspond to lower extinction rates (everything else equal). The trait might also be fixed within a lineage (so there is no variance at the individual level within-species), and if so, this lineage as a whole could have higher speciation rates and lower extinction rates compared to a sister lineage that lacks pelagic larvae.
The individuals within species will naturally have the underlying traits (pelagic larvae), but the traits that are selected at the lineage level (extinction risk & speciation rate) are not properties of individuals but are traits of the lineage/species.
He then ends by continuing with "normal" individual selection, and states that processes at this level is responsible for most adaptive features of organisms. It should also be noted that lineage selection is still considered controversial, and it has been shown that it is inherently much weaker than selection at the individual level. Personally, I think there are some very good examples of how species/lineage selection can function, but to what extent it is an important process for species and organisms is an open empirical question. If you are interested to look further, Jablonski (2008) and Okasha (2007) are two good starting points.

Nice one - I was just about to head for a google search of the text!

So if Trait A is selected above Trait B, and if all individuals of a species have Trait A, then this is species-level selection?

@luciano Not quite - its not that simple. You need to think of a lineage in the same way you would about a single species, so that the species within the lineage correspond to individuals within a species. The idea is that all species within lineage A possess trait A and all species within lineage B possess trait B. This can then lead to lineage A increasing faster than lineage B (have higher net speciation rate). That all individuals within all species in lineage A and B possess the same traits can be seen as a byproduct of this.

@luciano The traits do not need to be fixed either. It could just as well be the case that the overall frequency of something is higher in lineage A compared to lineage B, and that this leads to differential properties/traits at the lineage level.

Aha, I think the penny has just dropped. Your comment 2 above this one is what did it.

@luciano Glad I could help.

I think there is some misunderstanding there, natural selection does act on an individual and can be determined by its genes (assuming there is genetic variance underlying the variance in trait). Those with more favourable genes will have more favourable phenotypes and thus be more likely to survive/reproduce. However, (genetic) evolution does not occur within an individual, evolution occurs at the population level as the frequencies of existing and new mutations changes over time or space.
Following from your example: Two morphs of a species exist, brown and white (like the classic peppered moth), which is genetically determined, and one has a selective advantage - let's say brown. Thus all individuals of the brown morph are more likely to survive and reproduce. Over time the genes causing the brown phenotype will increase in frequency in the population and frequency of brown (white) moths will have increased (decreased).
I suspect it would be helpful if you included more of the text preceding the statement.
Edit: having seen @fileunderwaters answer, which arrived seconds before I posted mine, I see that I was right, more of the text was useful :)
So going back to the moths, an individual moth would not be able to change it's trait in response to selection.


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Plasmids for high school students?
For a final project in AP Biology, I am planning to design an experiment that uses the plasmid #170380 from Addgene. However, under availability they say "Academic Institutions and Nonprofits only".
Is there somewhere else that will ship plasmids to a high school student?

Schools don’t count as academic institutions?

No, because I am doing this for a final, it's not a district wide thing.

Have you tried putting in your school as an academic institution? If this doesn't work, try to contact their help. It shouldn't be too problematic for you to get this plasmid. As a last resort you can try looking for papers who used this plasmid in their work and write a polite email to the corresponding author of the paper if he/she can supply you with the plasmid. Usually works pretty fine.

I’m voting to close this question because it is about the definition of academic institutions rather than biology.

I'd suggest looking at the Terms and Conditions for nonprofit use, here is a screenshot of where it is on the webpage:

Look at this form that they link to for legal understanding of what they mean:

NONPROFIT ORGANIZATION(S): A university or other institution of higher education or an organization of the type described in section 501( c)(3) of the Internal Revenue Code of 1954 (26 U.S.C. 501( c)) and exempt from taxation under section 501(a) of the Internal Revenue Code (26 U.S.C. 501(a)) or any nonprofit scientific or educational organization qualified under a state nonprofit organization statute. As used herein, the term also includes government agencies.

and

The RECIPIENT and the RECIPIENT SCIENTIST agree that the MATERIAL:
a) is to be used solely for teaching and academic research purposes;
b) will not be used in human subjects, in clinical trials, or for diagnostic purposes involving human subjects without the written consent of the PROVIDER;
c) is to be used only at the RECIPIENT organization and only in the RECIPIENT SCIENTIST's laboratory under the direction of the RECIPIENT SCIENTIST or others working under his/her direct supervision; and
d) will not be transferred to anyone else within the RECIPIENT organization without the prior written consent of the PROVIDER.

All of this suggests to me that a high school would be fine, only wrinkle I can think of is whether they think that you can decontaminate any resulting materials (i.e. put it in a biohazard bag or bleach the hell out of it).


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Relationship between general pictorial representations of cells and reality
As a novice biology student, I have seen a lot of pictorial representations of cells, from a generalised basic eukaryotic cell to specialized forms.
But is it right to visualize a cell as a 3D sphere? For instance, consider an imaginary cell where I read a cellulose cell wall surrounds a cell and a flagellum is over it. Is it right to visualize a cell as a spherical hairy ball with cross sectional cut?
A Wiki image of cell

By Science Primer (National Center for Biotechnology Information). Vectorized by Mortadelo2005. - This file has been extracted from another file, Public Domain, Link
Exceptions apart, is this 3-dimensional general representation of a cell correct? Because everywhere I see 2D images. And then comes question number 2: when Hooke and earlier workers looked at cells through the microscope, did they actually cut a cell to describe its components, assuming cells are 3 dimensional ball-like structures?

Plasmids in a prokaryote have preferred locations, like near the membrane. Not just floating everywhere.

Benefiting from millions of actual photos of cell shapes of all kinds through micrography, including annotated, colored micrographs, isn't that the best way to compare? https://www.google.com/search?q=100x+magnification+cell+annotated&tbm=isch cell shapes are so varied, from sperms to eggs to bacilla and spirals and diatoms. https://www.google.com/search?sxsrf=APwXEdekgZkPlhGmqI94nl_wD5ypVBqaaw:1687346099753&q=unicellular+magnification&tbm=isch

It is right insofar as conjuring the basic image of a cell. Cells come in all shapes and sizes, to use a cliche. Muscle cells are long, sinewy things, neurons have dendrites like a spiderweb, glial cells wrap around axons like glue. So while it may be useful in visualizing the basic concept of a cell, realistically if you were to build an organism only out of these prototypical cells, it would not be an organism but a collection of amorphous tissue, if that; and it wouldn't be alive. Organisms require specialization; cells specialize. That's why pluripotent stem cells are so highly sought after, that they're able to transform and produce any type of cell needed.


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What is the easiest way to determine the species of non-tuberculous mycobacteria?
We have isolated a mycobacterium strain from patient sputum using an NTM Elite plate.
When inoculated into an MGIT tube, we observe fluorescence when observed under UV light, which means it is highly likely to be a mycobacterium.
We have assumed it is M. abscessus since M abscessus has been grown from the same patient in the past. But what would be the easiest way to verify that?
Would the answer be different if we needed to know the subspecies, like M abscessus bolletii?
We are a small lab with limited equipment, so if the best solution is to use a service provider, we would also be open to that.

From this paper [Ref. 1] as well as this one [Ref. 2], it looks like PCR, potentially combined with genetic sequencing, is a good way to go.
In the first paper, they used 16S rRNA sequences to identify samples of non-tuberculous mycobacteria (NTM), and PCR restriction fragment length polymorphism analysis (PRA) of hsp65 to determine species. This method has the advantage of running on a standard PCR setup, then sequencing products of interest as needed (either in-house or via a service).
In the second paper they used a different method - multiplex real-time PCR with high-resolution melting (HRM). This method was performed on a RotorGene 600S instrument. It's not clear whether this particular instrument is necessary, or if the method can be adapted to any real-time PCR machine. This group also sequenced some samples.

References:

Moghim S et al. Identification of Nontuberculous Mycobacteria Species Isolated from Water Samples Iran J Basic Med Sci. 2012 Sep-Oct; 15(5): 1076–1082. PMID: 23493797; PMCID: PMC3586926
Peixoto ADS et al. Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting. Rev Soc Bras Med Trop. 2020 Nov 6;53:e20200211. doi: 10.1590/0037-8682-0211-2020. PMID: 33174954; PMCID: PMC7670742.


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Is a variable domain in immunoglobulin's heavy chain different from the one in light chain?
I guess yes, there is difference in amino acid sequences of $V_L$ and $V_H$. And so we have 6 different complementarity determining regions (CDRs) per monomeric immunoglobulin as two heavy chains are identical, and two light chains are the same. Is that correct?

I think if you read up on V (D) J recombination, that will help. Try this http://www.ncbi.nlm.nih.gov/books/NBK27140/ .

You are correct. In an IgG antibody, there are a total of four protein chains — two identical heavy chains, and two identical light chains, each heavy pairing with a light to form one of the two "arms" of the molecule. Each heavy chain has three CDR regions — H1, H2, and H3 — as do each light chain (L1, L2, and L3). When the full molecule is assembled, three "full" CDRs are formed — 1, 2, and 3 — from the "partial" CDRs in the respective heavy and light chains.

from novimmune
You can see on the left the six individual heavy and light CDR loops separately, and on the right they are combined into the full CDR1, CDR2, and CDR3.
Here is a slightly more molecular view:

Thank you very much for the explanation :). The fact I missed many times in immunology textbooks is clear for me now !


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When did animals begin to "parent"?
After having a fun conversation with a friend regarding parenting, I actually had the general question arise in my mind of when did parenting actually start to take place?
But, first, I think we need to define what I mean by "parenting".  Specifically, what I am talking about is when animals decided to give birth to their young and not abandon them to immediately fend for themselves.  Instead, parenting is taking care of, and protecting children for a period of time (even a brief one) until they are grown enough to take care of themselves.
Also, I think it's worth not counting the actions of a mother or father hovering over eggs of unhatched offspring until they hatch.  True, this is a form of parental watching but I'm more interested in the general timeframe of when parents started watching over the general actions and "shenanigans" of their offspring in order to protect them from harm and to give them a better chance of survival.

Which animals are you asking about specifically? There are quite a few species and the answer will be different for nearly all of them.

Any!  Although multiple species may have started this independently, which started it first.  Generally, I'm interested in the genesis of this behavior.

Parental care
What you call "parenting" is called "parental care" and "parental care" is any investment of the parent to improve the fitness of their offspring. Parental care can take many forms from niche building for the offspring to parental feeding passing by placing plenty of ressources in the egg.
Issue with the definition of parental care
Given the vastness and eventual lack of a strict enough definition of the concept of parental care, it will likely be difficult to really know what you would consider as being parental care. Below I am suggesting two possible cases. If you were expecting to another answer, you will need to provide a nice and strict definition of parental care.
Mutation rate
Under a very broad definition of parental care, one could argue that first examples of parental care would be found in very early organisms (bacteria/archae, eventually viruses) that would at some point (for a given lineage) reduce its mutation rate to ensure transmitting a good genome to its offspring cells.
Nutrients in eggs
If you feel unhappy with me using such a broad definition, you might want to consider the first examples of parental care as being the existence of anisogamy (see here), where females (by definition) produce large eggs filled with nutrients, proteins, mRNA and other things. I doubt we know what lineage first evolved but it could be an ascomycota eventually.


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What is the function of dihydrofolate reductase in humans?
According to StatPearls, synthetic folic acid — as an artificial dietary supplement — needs to be converted into the active form tetrahydrofolate (THF) by dihydrofolate reductase.

In the cells, folic acid is reduced to THF, a biologically active
form, in a two-step process that requires two molecules of NADPH and
the enzyme dihydrofolate reductase (DHFR).

But naturally occurring folates — as natural constituents of the diet or derived from intestinal flora — are derivatives of tetrahydrofolate, (the active form), so the human body doesn’t need to convert them using dihydrofolate reductase.
If this is the case, why do humans have the enzyme dihydrofolate reductase?

Welcome to SE Biology. We find it useful if posters can support their suppositions (in this case "from what I understand") by sources, either text books or online articles. Then we can check if they have perhaps misinterpreted them. Second, we expect posters to show a little research. Have you checked what readily available web sources such as Wikipedia say about DHFR? Also notice that @user438383 has kindly corrected your spelling. However you can do that yourself by writing out your question in a word processor and switching the language preference to English.

I have now cited a source and clarified your question, which initially I had difficulty in understanding. Let me know if I have changed your meaning in any way.

Thank you @David, that's exactly what I meant. English is not my native language.

The poster’s assumption that the sole role of dihydrofolate reductase (DHFR) is to convert folic acid to tetrahydrofolate is incorrect. The enzyme is important in at least two metabolic pathways in mammals — the degradation of phenylalanine and the synthesis of thymidine.
Phenylalanine degradation
The degradation of phenylalanine to tyrosine requires tetrahydrobiopterin:

Tetrahydrobiopterin is synthesized de novo in mammals, the last stage being the reduction of dihydrobiopterin catalysed by dihydrofolate reductase:

[Sources: Berg et al. Biochemistry 5e (2002) Ch.28]
Thymidylate synthesis
Thymidine triphosphate (dTPP) is an essential DNA precursor, and is derived from thymidylate (dTMP). This latter is formed by the methylation of dUMP using N5,N10-methylenetetrahydrofolate, which itself is converted to dihydrofolate. This must be reduced to tetrahydrofolate in a reaction catalysed by dihydrofolate reductase in order to regenerate the methylenetetrahydrofolate:

[Source: Berg et al. Biochemistry 5e (2002) Ch.25]

IMO, the accepted literature position is that DHFR plays no role in the de novo synthesis of tetrahydrobiopterin (BH4), which is synthesized from GTP, where the final step (reduction of side-chain carbonyl groups) or steps is catalysed by sepiapterin reductase.  De Novo synthesis of BH4 is insensitive to methotrexate, for example. DHFR does participate in a 'salvage' pathway for BH4 biosynthesis, which allows pteridines such as sepiapterin to be converted to BH4 (sepiapterin is not thought to be an intermediate in BH4 biosyn)

Biosynthesis and metabolism of tetrahydrobiopterin and molybdopterin

Biosynthesis of tetrahydrobiopterin in the presence of dihydrofolate reductase inhibitors

*** Biosynthesis of tetrahydrobiopterin by de novo and salvage pathways in adrenal medulla extracts, mammalian cell cultures, and rat brain in vivo


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Comparison of different glassy matrices for protein immobilization at room temperature
I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials.
I am looking for a reference that will allow me to compare the performance of various matrices in immobilizing proteins at room temperature. In particular, I want to know which matrices are the best at limiting protein tumbling at room temperature.
In particular, I am interested in matrices that outperform Polylysine matrices at room temperature by a good margin, if that's possible.
I am aware that the melting point of the glassy matrices is probably a good proxy for their ability to immobilize proteins. So perhaps a reference describing the melting points of these matrices would be enough.
If this is more appropriate in the Chemistry forum, let me know.

Hmmm. I am sure that someone will have looked at it, probably in a commercial field, so there could well be difficulties finding this information with IP concerns etc for companies.


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What are monocytes with vacoules called?
I've heard that monocytes sometimes appear with vacuoles. Do monocytes with a vacuole have a name? If so, do monocytes without a vacuole have a name as well?

Well, if you’re sure that you’re looking at a monocyte, then I don’t think there is a difference in nomenclature here. But normally monocytes aren’t very phagocytic, they leave most of that to when they differentiate into macrophages.
This is further seen in blood smears. A monocyte’s cytoplasm isn’t quite vacuolated, implying that there isn’t very much phagocytosis going on; but is granular due to the presence of lysosomes awaiting fusion with phagosomes, and the lysosomes in this case are actually called “azurophilic granules”.

I think this is a helpful answer, but it would be good to include citations, linked sources, or illustrations.


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Is there an abbreviation for palisade cells?
I want to know if there are any abbreviation for palisade cells and spongy cells?
Just like there is an abbrevation for macrophages (MP).

The more common abbreviation for macrophage is actually MΦ, using the Greek letter phi.

MP isn't really an abbreviation specific for macrophages. In a paper about leucocytes, authors might use MP, but usually only after initially defining that (e.g. ...yada yada macrophage (MP) activity...). So, no. Commonly discussed things have abbreviations (EEG, EKG, EMG, CBC, HR, RR, VT, ASHD, etc.) and very specific things (e.g. CYP51A1) that are too long to repeatedly write out. MP can be "middle phalynx" and a number of other things.


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Is this a deathstalker

I want to know is this a death stalker ?

What are its dimensions? How long is the body, and how long to the tip of the tail? Where and in what sort of environment did you find it? Please [edit] your question and add as many details as possible to assist in identification. On the surface it looks like a deathstalker scorpion, but we can't tell for sure without more information.

Where did you see this? Looks interesting.


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Loss of taste and smell during a SARS-CoV-2 infection
In France the loss of taste and smell (la perte du goût et de l'odorat) is considered as one of the key symptoms of a SARS-CoV-2 infection (although googling shows that it is considered less definitive elsewhere). What causes such a loss of taste and smell?
More specifically, an infection by SARS-CoV-2 is rarely associated with nasal congestion, so one cannot blame mechanical obstruction (and it would not apply for the loss of taste). One can then think of the virus attacking the relevant sensor cells or a less direct effect via disrupting the relevant metabolic chains. I will appreciate clarifications/explanations/references.

Of peripheral interest: "There are angry ladies all over Yankee Candle’s site reporting that none of the candles they just got had any smell at all." (https://twitter.com/kate_ptrv/status/1332398737604431874?lang=en). Apparently there is a statistically significant down-hike in the scented candles ratings, complaint: No scent.

Is there really a loss of taste (i.e., no sour/salty/bitter/umami sensation) or is it just the lack of aroma because the sense of smell is gone, which makes everything taste bland? My google fu didn't give me any answers.

@Peter-ReinstateMonica Chris's answer addresses this in the third paragraph (starting "For the tasting") which refers to chemosensory defects separate from olfaction. It seems that there is true loss of taste as a physiological sense in addition to the overall perception of taste that includes smell. I don't know if there is good data on the prevalence of each, because there is some ambiguity if patients simply report "loss of taste" without further elaboration.

@Bryan Ah, thanks!

I’m voting to close this question because it should be migrated to SE Medical Sciences.

This is not completely clear to say the least, but there are some hints. Please keep in mind that there was not much time for extensive research, since this disease is still quite new. What seems clear (at least at the moment) is that most like the nerve cells (in the olfactory bulb as well as in the taste bud) are not directly affected, since they do not express the ACE2 receptor on their surface which is needed by the virus to enter a cell.
In the nose, there are two studies, which link the loss of smelling to massive damage of the epithelial cells surrounding the nerve cells. These cells have a lot of ACE2 receptors and are thus susceptible for an infection with SARS-CoV-2. An infection leads to the death of these cells, which disturbs the balance of ions for the nerve cells leading to loss of smell. Specifically this seems to affect sustentacular cells. Since the epithelial cells recover over time, smelling comes back. This also fits the description of affected people, who describe the loss of smell as a sudden event, while the recovery happens gradually.
For the tasting it is less clear, but it also seems that supporting cells (which carry ACE2 receptors) are affected. For sensing of sharp (for example Chili), which is not chemical sensing but via pain sensing, it seems that at least a part of the cells are also susceptible to the virus as they express ACE2.
Taken together this seems to indicate that important cells in the vicinity of the nerve cells are hit by the virus, causing anosmia and ageusia. It is also important to note that not all people who lose their sense of smell also lose the sense of taste.
For furter reading have a look at the references, the first one is a nice article in the scientific american, the second goes deep into the topic with a lot of nice images.
I will have a deeper look into the topic later and probably update the answer.
References:

Mysteries of COVID Smell Loss Finally Yield Some Answers
COVID-19 and the Chemical Senses: Supporting Players Take Center
Stage
Massive transient damage of the olfactory epithelium associated with
infection of sustentacular cells by SARS-CoV-2 in golden Syrian
hamsters
SARS-CoV-2 Receptor ACE2 Is Enriched in a Subpopulation of Mouse
Tongue Epithelial Cells in Nongustatory Papillae but Not in Taste
Buds or Embryonic Oral Epithelium
Real-time tracking of self-reported symptoms to predict potential
COVID-19

+1, this may be another good reference since I believe it may have been the first paper which rigorously showed the sense of smell was a distinguished symptom https://www.nature.com/articles/s41591-020-0916-2

@user438383 Thanks, I will add this in a second.

Apparently, pathological (autopsy) findings have shown "viral particles" in nerve cells. How could they possibly have entered the cells  - as it is true that nerve cells, in general, not only the cells of smell, do not carry the ACE2 receptor?

@PeterBernhard As far as I know, they have been shown on the surface of the cells. Do you have a specific reference for that?

Yours might be : "Clusters of extracellular viral particles adhering to the surface of the plasma membrane were also seen."? Here's my "German one":  https://www.charite.de/en/service/press_reports/artikel/detail/how_sars_cov_2_reaches_the_brain/

@Chris https://pubs.acs.org/doi/10.1021/acschemneuro.0c00122 Apparently, neurons, for instance, have the ACE2.

@PeterBernhard The Charite press release is interesting, as the state that they found the virus in the epithelial cells (as noted above) and also in the nerve cells. However, they also limit their own findings possibly to severe outcome patients: "It is not necessarily possible, therefore, to transfer the results of our study to cases with mild or moderate disease.” The problem is we don't know it yet in all details. We do know that the virus needs ACE2 as an entry door. I will look at the literature from time to time for updates.

"ACE2 is not present in olfactory neurons"  is in support of  your answer  ("surrounding cells" of neurons  being the only target),
https://erj.ersjournals.com/content/early/2020/07   /23/13993003.01948-2020
Interestingly, some neurons in the brain do have the ACE2. I understand that "being found in neurons" is different from "neurons carry the ACE2" . I think it makes sense to ask, if   "naked RNA"which comes as  cell debris is uptaken  by neurons and  by other body cells (in which  virus particle were  detected by electro-microscope - reference on request). Thanks!

@PeterBernhard We still don't know exactly, how this works. So far, all reports I have seen (which is most likely not complete) only report the infection of ACE2 expressing cells. However, it is possible that a part of the nerve cells carries this receptor and is therefore susceptible for the virus. More research will tell.


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What specific markers does a Covid-19 PCR test look for?
I've done a search and can't find anything as to what specifically makes a Covid-19 positive that identifies it as unique. I would expect to see something like this:
https://madridge.org/journals-admin/uploads/fulltext/MJV/images/mjv-118-t002a.gif
or
https://i.sstatic.net/423Ay.jpg
Instead I find this:
https://communitymedicine4asses.files.wordpress.com/2020/05/2020-05-07-17_38_07-covid-19-testing-what-you-should-know.png?w=624
and
https://myrepublica.nagariknetwork.com/uploads/media/PCR_20200513092900.jpg

The SARS-CoV-2 diagnostic tests that are currently in use, both serological and nasal swab, are binary tests - they either are positive or negative, like a pregnancy test. They do not (yet) report viral titre, like the first image you linked, or look at restriction enzyme "gene fingerprinting" patterns, like the second. They simply tell you if either a part of the virus is in the sample (RNA or capsid protein in the two nasal swab tests) or if your immune system has seen enough of the virus to mount an antibody-mediated immune response (the IgM/IgG blood tests).
It's worth pointing out that all of the current tests in the US are available under emergency use authorizations from the FDA, meaning they haven't gone through the usual (and time-consuming) process of full qualification and validation. That type of work needs to be done in order to develop quantitative testing ("You have a viral titre of X, compared to an average range of Y through Z."), which will likely appear in the coming months and years as the proper development work is done to support their validity.

Thank you for your answer. If I'm reading it correctly, it's not know what specific markers make a test positive, it just pops up positive?

@JohnSmith It depends on the specific test, each is designed differently.

@JohnSmith the markers are known, that's how the test is developed. For example, for the PCR test, primers are chosen for a specific unique region of SARS-CoV-2 RNA that doesn't exist in any other organism, and that fragment is amplified in the reaction. The binary answer is whether or not something amplified in a particular reaction. A quantitative answer would be something like a qPCR test where a standard curve is generated and you can then back-calculate the starting concentration of RNA. [...]

[...] For the antibody test, for example, they use a recombinant protein from the virus's capsid/envelope and run a biochemical reaction that changes color if any human IgG or IgM binds to it - it's based on the same principles as a capture ELISA. The nasal swab virus surface protein detection test is also ELISA-based, but in a different configuration. The point is that in all three cases, all of the components of the tests are known and well-characterized, but the answer they give is either yes or no - present or absent. Does that help?

To my knowledge, all of the PCR-based tests that have been authorized for diagnostics use fluorescently labeled reporter probes specific to the the SARS-COV-2 viral genome. In real-time PCR, the intensity of this fluorescent signal is measured (spoiler alert) in real time, after each amplification cycle. The fluorescent signal increases with the amount of the target sequence present in a reaction. If the signal exceeds a certain baseline threshold before a certain number of PCR cycles, the test is considered positive for that target. It really is as simple as that, but a lot of work goes in on the development and validation of these threshold cutoffs to ensure they are sufficient for sensitive detection.
What identifies the readout as unique to this virus is the design of the probes and the primer sets that go with them. These are designed to be highly specific to a given target, and are validated in silico against existing sequence databases, and also empirically against closely related organisms, or just against other things that might be present in a specimen. They should also target conserved regions of the genome that are unlikely to mutate. Most of the tests I have seen use at least two different SARS-CoV-2-specific probe targets, and at least one amplification control (often targeting a conserved human gene) to ensure that the reaction enzymes are functioning properly. But the specific regions of the genome that are targeted can vary between different tests.
Using real-time PCR saves clinical lab techs the time and effort of making gels and running the amplified PCR products out on the gel, like those in the second example you posted. This not only improves the turnaround time for testing results, but saves countless work hours for the clinical labs processing these tests, especially when you consider the scale of how many tests are being processed right now.
As with any nucleic acid test, a positive result can only indicate if the target is (or was) present. It does not provide information to clinicians about whether it is actively replicating or even infectious. But in general, this kind of testing is highly sensitive and specific when properly designed and validated.


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Difference between Condensin and Cohesin proteins?
The chromosomal DNA is stacked with help of cohesin and condensin protein in which particular manner? Can cohesin be said to form kinetochore? How would they vary exactly?
The terms are so narrowly windowed that they squeeze my brain through...!!! thank you for your kind help ^_^

Hi and welcome to bio.SE! When asking your questions, try to be as clear and provide as much information as is possible/relevant to help you get the best answer. Here, I think you need to separate your questions out a bit - you're asking about the difference in functions of the 2 proteins (cohesin and condesin), and you're also asking about cohesin's role in forming the kinetochore (related, but slightly separate). And what are you referring to when you ask 'how do they vary'? The 2 proteins? Don't be afraid to write a couple of paragraphs so that it is clear what you're asking. Thanks.

Hello sir...thank you so much for you guidance. When i said how do they vary am asking for the difference in their functioning sir as you rightly guessed. Once again thank you for your feedback and guidance.

You can edit your original question (by clicking 'edit', next to the vote buttons) to make it clearer, and tidy it up. I can do this if you would rather. Also my name is Luke, feel free to use it! :)

Condensin
Condensin I: present in cytoplasm during interphase, has access to chromosomes after prophase. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].
Condensin II: present in nucleus during interphase, involved in chromosome condensation. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].
Cohesin
It keeps sister chromatids connected with each other during metaphase and ensures that each sister chromatid segregates to opposite poles. "It facilitates spindle attachment onto chromosomes. It facilitates DNA repair by recombination." [2]

References:

Wikipedia contributors, "Condensin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Condensin&oldid=606814199 (accessed July 29, 2014).
Wikipedia contributors, "Cohesin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Cohesin&oldid=617481362 (accessed July 29, 2014).


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Are any organisms known to use meiosis I to create non-identical offspring asexually?
So, there are numerous species of animals who use parthenogenesis, but to my knowledge the reproduction is clonal. That is, the offspring are identical to the mother. Are there any documented cases where a female goes through meiosis one to produce varied cells that are now diploid and these cells do not go through meiosis two, but rather develop in to a diploid organism? It would seem an effective reproductive strategy in that it generates genetic variation without a mate (at least more-so than strict asexual reproduction). Is my logic flawed in some way?

In automixy the meiotic cells give rise to diploid offsprings. This can happen by diploidization of the haploid cell (1n->2n), which will produce homozygotes or endomitosis prior to meiosis (4n->2n) which produces heterozygotes. Examples:

Cnemidophorus uniparens : 4n->2n
Sphyrna tiburo: 1n->2n

I don't know of any case where there is fusion of similar gametes to form a diploid cell. It is difficult for two ova to fuse in natural conditions because the vitelline membrane has to be dissolved.
Experimentally a haploid ES-cell can be fused to ovum to form a progeny. Haploid ES cells undergo diploidization and when injected in blastocyst, can develop properly (Ref). In fact haploid androgenic-ES cell line had been made in this study by injecting sperm into an enucleated oocyte. These androgenic-haploid cell lines can be fused to ovum to give rise to viable offsprings.
Also see this question. Similar topic

Good to know! However, I was under the impression that Cnemidophorus lizards gave rise to clones. If I understand you (and the article) then this gives rise to varied offspring. Obviously there is no infusion of new genetic information from other individuals, but it would still seem farm more advantageous (especially in vertebrates) to produce offspring in this way, than by a mitotic mechanism. I find it odd that there don't seem to versions of automixy (that I can discern) that simply forgo meiosis II. Wouldn't this be the simplest way to generate variation and maintain chromosome number?

It is indeed surprising.. Usually the metphase-II spindle starts assembling before meiosis-I ends.. Slight delay in this process can cause nucleus to assemble¹ ² ³ and perhaps the dihaploid cell can convert to diploid.


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Are there records of monozygotic twins in which one experiences androgen insensitivity syndrome
I have given my high school biology students the thought experiment of "What would happen if a researcher induced twinning of a female zygote and then replaced one of the X Chromosomes with a copy of the father's Y chromosome". In theory you should get what would be about as close as possible to male/female identical (monozygotic twins). However, I don't believe it would be possible for this to occur in nature (feel free to correct this if I am wrong). The closest I am familiar with is "Semi-identical twins in which the egg is fertilized by two sperm and then twinning occurs. However this isn't really the same.
However, I realized that Androgen Insensitivity Syndrome, in which a mutation leads to the body not responding to masculinizing hormones, leads to a male developing as female. Is anyone aware of this ever happening? I realize it would need to occur after the zyote/morula split.
Similarly if the SRY gene (essentially the master control switch for masculinizing an embryo) has ever been transferred on to an early embryo of a pair of female monozygotic twins, essentially inducing one twin to develop male.
In essence I'm asking for evidence of physical manifestations of (near)identical monozygotic twins. Has any of this ever been done in research on other species?

This is an important question to geneticists because monozygotic twins are the only ethically acceptable way to research genetically identical humans.
I'm sure the sort of non-symmetrical fission where specific DNA coding for genes are not present or are modified to completely different phenotype in the formation of the twins probably has happened, but it incredibly rare.  In stem cells, asymmetric division has been observed frequently (warning: google doesn't like PlosOne right now).  In development, unless its actively been activated as an asymmetric division, this would be incredibly rare- this would be akin to a birth defect in a single fetus - how many cases of mixed male and female cells in a single baby. I can't even find a reference for such a thing.  Much more common are semi-identical twins, where two different sperm fertilize a single egg which may have split.  Semi-twins are still vanishingly rare - the first report was in 2007).

Such twins are probably very rare. Their existence and discovery relies on three unusual, and possibly unlinked, events: first, that an egg fertilized by two sperm develops into a viable embryo; second, that this embryo splits to form twins; and third, that the children come to the attention of science.

This might be the case you are thinking of?  In one case reported there was a gender difference.

Souter and her colleagues investigated the twins' genetic makeup because one was born with ambiguous genitalia. This twin turned out to be a 'true hermaphrodite', with both ovarian and testicular tissue. The other twin is anatomically male.

They weren't monozygotic though.  Just others from the same mother ;)
Monozygotic twins are not completely identical, epigenetic fingerprinting - including DNA methylation and chromatin DNA binding patterns (pnas - paywall) change while the fetus develops and as the child and adult age.  This can cause quite significant differences as the twins age. Epigenetic markers change the dynamics of brain development and can make a difference in the occurance of leukemia.
There are also modifications to the DNA sequences of cells, copy number variations (CNVs) are multiple (sometimes hundreds or thousands of times over) repeats of short (2+ base pairs) DNA sequences.  These also occur as the cells differentiate and divide to form tissues and organs.  Twins show significant differences there too as this is not a deterministic mechanism in development.
I can't find any references to twins showing asymmetric AIS. but the number of variants requiring this makes it sounds like its possible.  If you have a reference post it and I can have a look?
note added: this paper shows that methylation profiles appear identical at least in utero.

I am aware of the semi-identical twins (which to me is a bit of a misnomer). Also, while I share your sentiment that monozygotic twins vary (quite significantly over time) in their epigenomes, let's remember that, by definition, this is not genetic variation. My students got me to thinking a bit more about it simply because of the fascinating idea of being able to see what one would look like if they had developed as the other gender. I'm sure that it would be vanishingly rare, if it's happened, but that doesn't mean it hasn't happened...:)

@single_digit just doing my best to be comprehensive.  (The CNVs are genetic variations tho.)  It probably has happened - with 8 billion people on earth, the odds are not bad.  The article notes that such oddities are usually not reported, esp if they don't result in some defect of some kind..  cheers.


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Do we know how the different functions are selected when Wnt pathway is activated?
The Wnt signaling pathway is said to allows multiple functions:

Axis patterning
Cell differentiation
Cell proliferation
Cell fate specification
Cell migration

But how are these functions "distinguished by the cell" when the Wnt signaling pathway is activated by the receptor on the cell's surface? I mean, do only specific environment conditions (and if yes, do we know which one?) triggers the duplication of the cell, or its differentiation? Or is there a co-signalling that triggers the cell into one or the other mechanism?