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Between Cholera and Polio, which disease cannot be controlled by killing the vectors
Since Cholera affects only humans, and also doesn't have an insect vector or animal reservoir host. And Polio is a disease of the central nervous system, spread from person to person through infected fecal matter entering the mouth. Then which one of them can be controlled by killing the vector, I'm not completely sure if cholera doesn't have a vector, but if they don't, then I'll like to know if and how polio can be controlled by killing the vector.

From you description, none of these disease have vectors. A vector is any agent that carry and transmit a pathogen. So you cannot kill any vector as there are no vector to kill.

Both of these diseases do not have vectors,
Cholera is a foodborne / waterborne disease and Poliomyelitis is spread through fecal-oral or oral-oral contact with an infected person.
They both only infect humans.
Thus, both cannot be controlled through killing any vector.
The best way to prevent Cholera is to avoid potentially contaminated food and water and follow proper sanitation practices.
The best way to prevent polio is through immunisation via vaccines.
For more information:
Cholera
Poliomyelitis


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Could a man be proved positive for a pregnancy test?
From the question: Could a man be proved positive for a pregnancy test?. I don't mean if a man could be pregnant but if he runs a pregnancy test, it is possible for it to come out positive?

I agree the responses that beta-hCG is produced by both ovaries and testes. Males with testicular cancer can have elevated hCG levels, which could give a positive response with a pregnancy testing strip.

Pregnancy test, just like any test, has some non-zero false positive rate. So yes, of course a test could be positive when a man pees on it.
Pregnancy tests work by detecting the presence of a hormone called Beta-HCG. This hormone is produced by both genders but is produced in much higher dose during early pregnancy. Teenagers also produce a relatively high dose of Beta-HCG which can eventually inflate the false positive rate.
It just so happen that tumours from a particular type of testicular cancer also excrete Beta-HCG (see this blog post from the American Cancer Society). If your question arises from a personal experience, then I would strongly recommend that you talk about it with your doctor.

Yes it is possible. Pregnancy tests detect human chorionic gonadotropin (hCG), which in a healthy male can be produced by the pituitary gland. hCG consists of two subunits and the urine tests target a metabolite of the beta subunit. The levels of hCG in healthy adult males are below the sensitivity of pregnancy tests, they are similar to the hCG levels in non-pregnant adult females.
A postive test from a male may indicate a pathology that is elevating hCG. I know that hCG elevates during puberty but I am not sure whether the rise is sufficient to cause a positive pregnancy test.

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Why does it matter to predict protein structure?
And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ?
Moreover, I've read that knowing the structure of a protein helps predicting its function, but is the prediction [Structure -> Function] reliable ? Should't we predict directly the function if that's our interest (I don't mean we should not take into account predicted structure, but I don't understand why the structure IS the purpose instead of the function)
I also read the structure helps predicting affinities with other proteins and how it will bind : same question here, is this prediction [Structure -> Affinity] reliable and why don't we predict directly affinities.
To sum up a bit, I have the impression that the structure in itself is not important to know except that it is a good predictor of other protein properties (like function of affinity) and that the structure is kind of an 'intermediate' ? What am I missing ?

Structure tells you about the "hows" of the function. Just knowing the function will only answer the "what". Regarding affinity: that only works for binding reactions. What about conformational changes?

Welcome to SE Biology. New users are expected to complete the Tour to find out how the site works. (We know that you haven't, otherwise you would have a 'badge'.) Please also read the Help on how to ask questions. You will see that you are expected to ask one question at a time and that you are expected to research the topic before asking. It is clear that you haven't tried to find out about methods of protein structure prediction, or much about proteins themselves. Please do that first.

There are dozens if not hundreds of textbooks on this question. I do not feel it is suitable for the SE format. Even though some answers are present and have received upvotes, they don't even begin to answer the question(s).

How do you want to predict function and binding partners without knowing how your protein looks like? The sequence itself contains only limited information. Similar sequences might fold into similar structures with similar functions. These motifs can be used to transfer your knowledge from one protein to another, which might have similar e.g. binding abilities. But the motif might be nonfunctional in the second protein, because it is hidden in an inaccessible part of the protein due to its folding structure.
Interactions between proteins are weak compared to intramolecular bonds and dynamic. Different amino acid side chains have different characteristics (like polarity, hydrophobia etc.) which make specific interactions possible. Specific amino acids have to be accessible and while they might be far apart in the sequence, the folding of the protein brings them close together in its final shape.
Even small modifications like phosphorylation can alter the structural conformation significantly and e.g. change the enzymatic activity. Therefore, for analyzing protein function, finding binding partners or designing binding compounds (drug development), we need to know its three-dimensional structure. With the structure you can simulate binding affinity/dynamics. Scientists also try to resolve the protein structure in its different states to clearly see the differences.
Keep in mind that complex diseases can be caused by a single mutation, which exchanges only a single amino acid in the sequence but can have severe implications for protein function. Knowing the structure, the position of the amino acid and how the change affects the characteristics of the protein domain (e.g. charge), we can fully understand what's happening on the molecular level.
Since it is far from trivial to analyze the structure of a protein, predictions bridge the gap for functional predictions until the molecular structure of the protein has been reconstructed. But only with atomic resolution you will be able to properly identify interactions.
The question of how to do structural prediction might be beyond the scope of this answer. Pubmed lists around 400 papers each year on this topic. Depending on the amount of information you have about the protein or its family members (proteins with very similar sequences), you can use other known structures to predict an unknown structure:

https://medium.com/@HeleneOMICtools/a-guide-for-protein-structure-prediction-methods-and-software-916a2f718cfe

There are several reasons why understanding protein structure is useful; the most obvious is that drugs that interfere with a specific protein can be deliberately designed based on the protein structure.

Today, even though there is still quite a bit of fine-tuning necessary to perfect the process, structure-based drug design is an integral part of most industrial drug discovery programs [4] and is the major subject of research for many academic laboratories. ... The process of structure-based drug design is an iterative one ... Additional cycles include synthesis of the optimized lead, structure determination of the new target:lead complex, and further optimization of the lead compound. After several cycles of the drug design process, the optimized compounds usually show marked improvement in binding and, often, specificity for the target.

--The Process of Structure-Based Drug Design

There are three broad questions here, together covering much of the field of structural bioinformatics. I will answer each briefly but point you to a textbook for more.
Why is predicting protein structure useful?
This is actually a very good question. The standard answer here is "drug discovery", but as things stand anything other than a high quality homology model isn't particularly useful for drug discovery. I can't think of any examples where de novo structure prediction has directly led to the discovery of a drug, for example by virtual docking in a binding site, though I am willing to be proved wrong. In the future though, as protein structure prediction and virtual screening both improve, this could end up being an important application of structure prediction.
Other current uses that are more developed are: A) protein design, where improvements in structure prediction allow you to find better sequences that form certain structures and carry out certain functions (the inverse folding problem); B) exploring the evolutionary relationships and function of a protein, e.g. if a predicted structure looks like all the other membrane transporters then it probably is one too (see more on that below); and C) running molecular dynamics simulation on the structure to gain biological insights and complement experiments.
On a deeper level, scientists will always seek to answer the question of what structure proteins fold to and how they fold, because it's just such an interesting problem that is central to molecular biology. Solving it will almost certainly lead to useful breakthroughs, even if their exact nature is unclear now.
How do we predict protein structures?
By the original formulation of the problem, protein structure prediction is arguably solved. If you can find a template, i.e. a related protein sequence with an available experimental structure, then you can pretty reliably get a high quality model (less than ~3 Å RMSD). Improving a model beyond this is currently called "refinement" and this will become increasingly important as we look to get ~1 Å RMSD models that can be used in place of experimental data.
If you can't find a template you can still have a decent go at the structure, provided you can find enough related sequences. It turns out that positions in a multiple sequence alignment will covary if the residues are close in space in the structure. Initially statistical techniques were used to extract direct from indirect coupling effects, but now deep residual neural networks are showing state of the art results in this field. These developments are recent and have been the focus of news reports. The explosion of sequence data facilitates this approach, though it is still not "the solution" to those who only want to use a single sequence as input data. For pure physics-based approaches there has been limited success on small proteins, see for example here, but these methods are not in broad use for structure prediction.
Usually the input to these methods is just the protein sequence, though you often bring in other data (templates, related sequences) as part of the pipeline. We generally care about the structure at physiological conditions, which usually corresponds to the structure found in x-ray crystallography or NMR, so predictions under different conditions are not yet routine. For more on protein structure prediction, see the CASP website and have a read of their papers.
How useful is protein structure at predicting function?
Predicted structure can be used to transfer function from related structures with known function - see for example here and here.
It is not currently possible to use a predicted structure to predict the function using chemical arguments, for example by saying "I have predicted a binding site with a certain arrangement of amino acids so this must have function X". However as structure prediction improves and we have more structures and functional annotations, this is an exciting prospect.
With respect to protein-protein affinities, if you have the structure you can start to predict and rationalise the structure of protein complexes. Such predictions from structure alone (i.e. not using homology to known complexes) are not routine yet, though more data and better models will improve this. See for example CAPRI. This is clearly a biologically important area, as most proteins form complexes.
Conclusion
Sequence determines structure determines function (fingers crossed as I'm simplifying quite a bit).
You shouldn't have to know the structure to predict function/binding from sequence, but it helps, and a sufficiently advanced system would learn this anyway in order to make the connection.
Protein structure prediction is a hot research topic that currently has limited applications, but is certain to have more in the future. If anything, it has only got more interesting over the last 50 years.

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Does food lose some of its mass in form of energy during metabolism?
I had an argument with someone.
I argued that when a cat eats 1 kg of food, the sum of subsequent output (poo + pee + sweat + change of body mass) must be equal to 1 kg.
My opponent argued that the output will be less than 1 kg because a part of food is converted into energy.
Please rule.

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Possible duplicate: https://biology.stackexchange.com/questions/73288/when-you-lose-weight-how-does-the-mass-exit-your-body

Possible duplicate of When you lose weight, how does the mass exit your body?

So your opponent is claiming that your cat is a nuclear reactor?  One thing you're neglecting here is that a portion of the mass of the food will leave as CO2.

This is NOT a duplicate of When you lose weight, how does the mass exit your body? because that question explicitly says 'And please, don't suggest that it was "converted to energy"' and the answer avoids that aspect, while the present question explicitly asks about conversion into energy.  The answers are different from the point of view of a biologist or chemist versus that of a physicist.

During metabolism, the energy is released from the chemical bonds, while the atoms and their atomic mass and therefore the mass of everything what a cat eats and excretes remains the same.

@Jan - technically spoken you are incorrect

Physics answer that is a bit silly
If you want to be real technical about physics, mass and energy are the same thing, so any chemical bond that has some energy and is broken results in a change of mass (mgkrebb's estimated in a comment the final mass would be 999.999999814 g, if you started with 1 kg of protein, also known to a very precise biologist as 1.000 kg).
This is sort of a "technically correct" answer that is totally silly from the standpoint of biology, but if your opponent wants to stand by it as "technically correct" based on physics, so be it. We are talking about changes in mass that are not measurable by modern science to sufficient precision, these are only theoretical ideas based on relationships between mass and energy that can be measured on a much larger scale.
Biology answer
Since this is Biology.SE, the biology answer is that mass is conserved in chemical reactions. If you greatly simplify the metabolism of, say, glucose, to the equation:
C6H12O6 + 6 O2 --> 6 CO2 + 6 H2O
you find that the net result is that the hydrogen and oxygen atoms become water, and the carbon atoms become part of carbon dioxide (yes I am simplifying where the actual atoms end up in the biochemical reactions, just talking in terms of net changes here). Other food molecules are processed similarly, and will produce some combination of water/carbon dioxide/nitrogenous wastes. If your cat eats 1 kg of food, that 1 kg of food will become 1 kg of something else out to many many decimal places: waste solids (including anything not digested at all) and liquids, exhaled carbon dioxide, lost skin/hair, etc.
Physics answer if you just want to win the argument
If you want to still win the argument with the physics-based answer that relies on mass-energy equivalence and ignores the fact that from the perspective of biology they are best understood as different concepts, then it's just as fair to go the other way and treat the lost energy as mass, in which case you'd consider the heat lost by the cat's metabolism as mass and include that tiny tiny tiny fraction in the 1 kg and call it a day.

Though part of that 1 kg of food is indigestable bits that just get passed through.

@jamesqf That would be included in the waste solids.

I wouldn't characterize the most precise accepted scientific description as "a bit silly", but the resulting mass deficit is at present immeasurable. If you feed the cat 1 kg of protein and it was entirely metabolized, it would release about 4000 kcal of energy, equivalent to 1.862e-7 g of mass. This means the products from the 1000 grams of food would not conserve all their mass, but instead have a mass of "only" 999.999999814 grams.

@mgkrebbs From a biological perspective, measures out to 10-12 significant digits are, in fact, silly. Just as silly as using relativity when a physical system is within the bounds of Newtonian mechanics. There are too many sources of variation and error to give measurements of that precision any meaning. It doesn't make the physics wrong or not precise, of course, but chemists and biologists don't worry about those differences. Neither do physicists in most contexts.

@BryanKrause, I agree that there is no practical importance to the mass change since it is immeasurable, and therefore it should be dismissed for thinking about most problems since it adds useless detail when considering how most things work. For arguments and wagering, however, the immeasurable details do matter.

Love this answer +1

@mgkrebbs Fair enough. I'll add your number to my answer if you don't mind because I do think it's useful.

@BryanKrause, that'd be fine.

Your opponent is correct. Some mass transforms to energy; the amount is negligible.  One good  source
If you and your friend decide to do an experiment in a controlled environment and measure the masses with a scientific scale with the highest precision available today, you will see that the total mass at the beginning of the experiment and the total mass at the end are same. Because, the scale isn't precise enough to measure very very small amounts of mass.
But, this won't mean that your opponent is wrong. Because, in terms of physical laws, there will be a very small amount of change in the total mass which is the source of the energy that will be released in metabolism in various kinds like heat.
This physics.stackexchange thread can be helpful to understand the physical nature of the event..

We are looking for more extensive answers explaining the topic. You just quote someone making an assertion without any evidence behind it. What is needed to support your argument is a calculation showing how much mass is converted into energy in a specific chemical reaction. Can you provide this?

No I can't provide a calculation and this would be unnecessary as it isn't the question.

Hardin, I am trying to help you understand how this site works. @Bryan Krause has supplied just such an answer. Please read the Help on Answering Questions.

Edited my answer. Hope this helps.


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Is there a way to lyse bacteriophage with just heat?
I basically want the virus to fall apart into pieces. I want the capsid proteins to separate from the tail proteins and the DNA to all tumble out. I want all of the virus proteins, structural and DNA, simply to disassemble. If this were bacteria, I'd just use the freeze-thaw process to cause the bacteria to spill its contents into the solution it was suspended int. But apparently freeze-thaw doesn't work with viruses(?). Is there a way to do this by heating them up to a certain temperature? It is acceptable if there is a risk of proteins denaturing.

What is your end goal? What are you going to be doing with the lysed phages?

@MattDMo  I want to know if nothing more than bacterial cytoplasm proteins, Brownian motion, and time (and perhaps some ATP) are all that are needed for viral fragments and viral DNA to spontaneously assemble in an aqueous solution into complete and active viruses.

What happens when you research bacteriophage self-assembly?

@bob1 Thank you but I am not talking about self assembly of virion-like particles, or a hybrid mixture of some virus-like particles and other particles, or involving a functioning host cell.  I want to see if the assembly of the entire native virus (at least for non-enveloped viruses) can happen in vitro completely outside of a host cell, just in solution.

@edmundshelto yes... bacteriophage vlp then! What I'm suggesting you do is look at the literature and tell us what others have done, what they found, and what you plan to do. "Which Phage?" is a big part of this. This is part of the homework requirement.

the capsids of some phage, like HK97, are cross-linked and won't disassemble even if you boil them.

Of the five most common bacteriophages that live in the dirt in my part of the country, though they are all genetically quite different, all of them fall into the same general bucket as far as what temperature to use, and for what length of time. The capsomers will begin to denature at temperatures above 50-60°C (122-140°F) and can fully denature at temperatures above 70-80°C (158-176°F). The timescale is in minutes. That is about as specific an answer as I can get after extensive googling. All I can do now is collect samples, create lawns on TSA plates, isolate strains, pick plaques if and when they appear, denature the plaques at different times and temperatures within the parameters mentioned above, and test to see exactly when and at what temperature the cooked plaques fail to inoculate other colonies.


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What safe, accessible enveloped virus should we use for beginning experiments?
I need to know which virus meets the following criteria:

It has to be enveloped.
It has to have a DNA packaging scheme similar to Adenovirus (basically, sticks most of itself together then draws in the DNA like the way a human eats a noodle).
It can’t infect humans (for obvious reasons).
It has to be easily propagated, either in a microbe such as ecoli or in embryonic chicken eggs.
It has to be virus stock that can be easily derived or purchased.
It has to be BSL1 rated

Avian adenovirus met all but the sixth criteria, unfortunately.
Is there something else that you are aware of that would meet those criteria? It does not even have to be in a particular family.

While Phages (as in Acvill's answer) are probably the most tractable and safest option, another option would be insect viruses of the family Baculoviridae

Enveloped
dsDNA
Incapable of infecting humans or plants, generally species/genus specific I think
BSL-1 use in general (see classifications of some recombinant viral vectors here; note that 1* indicates parent virus containment level)
you can buy baculovirus expression systems from a range of companies and suppliers.
Easily propagable in common insect cell lines.

Consider the dsRNA bacteriophage Φ6, which has been used as a surrogate virus to study Ebola and SARS-CoV-2.

Φ6 is enveloped.
During Φ6 assembly, an NTPase recognizes pac sequences and sequentially packages three ssRNA segments into the capsid; minus strand synthesis then occurs after plus strand packaging. See figure 6 from Mindich 2004 for a helpful schematic.
Φ6 is a Pseudomonas phage and cannot infect human cells.
Φ6 is readily propagated on Pseudomonas sp. DSM 21482, which itself is a Risk Group 1 organism (German equivalent of BSL1).
You can purchase Φ6 from DSMZ.
Like its host, Φ6 is in Risk Group 1.

Not saying this isn't the right choice (because phages were my first thought too), but phi6 isn't enveloped and is RNA rather than DNA

Is Phi6 not enveloped? This paper says it is: https://www.nature.com/articles/s41598-020-79625-z

huh, I thought none of the phages were - turns out I'm wrong. Looks like only the Cystovirus genus is though.

Excellent -  thank you to everybody!  Yes this paper https://www.mdpi.com/1422-0067/19/3/790/htm also says Phi6 is enveloped.


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Is excess of potassium as strenuous and harmful for kidneys as excess of sodium or worst?
I was wondering since channels of body's cell membranes deal with potassium and sodium ions differently and considering the fact that potassium lowers blood pressure and sodium raises it :

What is the most expensive in energy for kidneys between having to excrete an excess of potassium and an excess of sodium, for a healthy person and without considering blood pressure? Which process is the longest?
I know that insulin tends to make kidneys reabsorb sodium but does glucose help the kidneys to get rid of the excess potassium in any way?
On long term, what is the most harmful for the kidneys' circulatory system considering blood pressure and in the case of a kidney failure? For tubules and nephrons?

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Genotypes in diploid/haploid cells under mitotic/meotic cell divisions
I am new to genetics , and am stuck with the following question at hand:

If $2$ cells with genotypes $(A/a)$ and $(A/a,B/b)$ undergo mitotic and meotic cell divisions respectively, what will be the  genotypes/gene compositions in the resultant diploid and haploid cells with respect to the above mentioned alleles?

Can someone help me how to proceed?

can you give a little more information - like what you think the answer might be? Is this a homework question?

@VanceLAlbaugh Not homework in the true sense. It is actually a question in one of the previous year's question paper (so I doubted to give the self study tag ) that I couldn't solve and sadly neither is my professor available , nor are my friends getting anywhere.


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Do airsacs contract and expand when birds breathe?
Something I was wondering. When birds breathe, do their airsacs contract and expand like the lungs do?
Also, if they do, do they contract and expand as much as the lungs do?
Thanks so much!

This borders on a homework question, have you tried googling avian respiration. http://people.eku.edu/ritchisong/birdrespiration.html

@John Yes. I watched several videos on the subject and read several pages. One mentioned the lungs contracting and expanding slightly, but none said anything about the air sacs.


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Reliable recipe to make DIY yeast slants
Does anyone have any good ideas on a reliable way to activate basic grocery store yeast?
I realize this is a total beginner's question.  I've built a small yeast ranch at home with my kid, and we're trying to learn how to innoculate agar'd petri dishes with home grown samples we're trying to make from basic grocery store yeast.  Eventually, want to do more advanced experiments, but for now...we're just looking for some growth.
So far, our best attempts at using grocery store yeast packets have yielded no results (i.e. no visible growth).  My best attempts to find a good recipe have lead nowhere.  I see lots of good advice on how to follow sterile procedure on making agar'd dishes and how to innoculate from an existing slant; but we thought it'd be easy to just start with grocery store yeast instead of buying a slant.
FYI -- there's obviously some kind of growth happening on the petri dishes.  When we break from sterile procedure and invite contamination; then it's clear something (not yeast) is happily growing on the plates.
My mistakes that could've lead to zero growth on the petri dishes include:
(A) Perhaps adding the dehydrated yeast to water that's way too hot?
(B) Perhaps I did not add enough wort or sugar for the yeast to feed on?
(C) Maybe i should've let the dissolved yeast ferment for a while before innoculation?
Would very much appreciate any help from someone more experienced on this.
best wishes...

You might actually get better advice at [cooking.se]. Make sure you search their site first.

Yeast grows very well in liquid. The initial innoculum from the store will visible grow (“prove”) in warm water with a little sugar.


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Skin tone of a new born just after birth
I have a question. My skin tone is light but the photographs of me as a baby show  that when i was just born, i was having an even lighter skin colour for about two years or probably more. As for now my skin tone is not the same as before. Why does this change of skin tone happen in the first place? Also, is it possible to get back to that same skin tone as i was, when i was a baby? Also, another follow up question, talking on the matter of skin tone, there are alot of factors that come into picture to make the tone like the location and the amount of sun rays we recieve, beside obvious genetics. So i wanted to ask can a change of location from place of birth to another completely different location, (possibly other side of the globe) can bring about a change of tone? Thanks.

Skin color in humans is mainly determined by a pigment called Melanin. Melanin is produced by cells called melanocytes present in the epidermis of the skin. Melanin production rates are determined both by genetic and environmental factors. Melanin controls the amount of ultraviolet radiation (from the sun) that penetrates the skin and while UV radiation can assist in the production of vitamin D, excessive exposure to UV can damage health. This is why the amount of sunlight a person receives can control the amount of melanin that is produced in their body. Sun tanning occurs when a person receives more sunlight than they usually do, increasing the melanin content in their skin.
As Wikipedia quotes:

[skin] start[s] out pale in infants and turn darker as the skin is exposed to more sun. All human babies are born pale, regardless of what their adult color will be. In humans, melanin production does not peak until after puberty.

This is likely why your baby photos show you as pale-skinned.
As for your last question, while a change of location can obviously affect skin color (sun tanning is an example), it is also affected by genetics. If you change location while very young, there is a big chance that your adult skin color will be different than what is expected using genetics. As noted above, melanin production peaks at around age 30, so the location you were at age 30 would most likely affect your skin color. Again, slight variations such as tanning and becoming pale will be noticeable after a location change. However, this topic is very hard to study and there is not much evidence regarding my hypotheses. It is merely an educated guess that I took after studying present evidence.
I would recommend checking out the Wikipedia article to learn more about this.

Thanks for your answer!


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Does rotten food produce methane gas?
If we put a meal into the food storage container, does it produce methane gas while it is getting rotten or what else types of gases it produce?


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Does endocrine noradrenaline stimulate sympathetically innervated cells?
Cells that are innervated by the sympathetic nervous system, does endocrine noradrenaline target the same receptors on them? Are they dually activated by both nervous and endocrine noradrenaline?

Welcome. Is this a homework question?

Nope. Norepinephrine happens to be both endocrine and neuronal, technically the endocrine circulation should reach same receptor sites as the neuronal. Was interesting. Asked.


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Why do some karyotype graphs contain 46 pairs of chromosomes?
The human genome consists of 23 pairs of chromosomes. Two copies of each pair connect to each other at the centromere. Normal karyotype graphs should look like this:

But some karyotype graphs contain 46 pairs of chromosomes, such as this one:
Why is this the case?

They both contain 23 pairs of homologous chromosomes (and... yes as Luis suggested the first one is male and the second one female).
In Figure 1 each chromosome is composed by 1 chromatid, while in Figure 2 each chromosome is composed by 2 chromatids. This is probably because the two pictures were taken at different stages of Mitosis.
In Figure 1 the picture was taken probably in anaphase, while in Figure 2 was probably taken in or before metaphase.
You might want to search the internet to check the difference between chromatids and chromosomes and to read something about the cell cycle and mitosis.


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Thermodynamically, how did the first cell arise?
Living cells are biochemical systems that constantly perform chemical reactions. One of the important consequences of these chemical reactions is the capacity of a living cell to replicate itself. The daughter cells will also constantly perform chemical reactions.
From an evolutionary perspective, new cells always arise from old ones via cell division. The first cell on premordial Earth must be readily performing chemical reactions in order to replicate. A raft of biochemicals must have for some reason aggregated to form the first cell and begin chemical reactions.
An important effect of highly orchestrated chemical reactions inside a living cell is that biological order is maintained, at the expense of increased entropy in its surroundings. However, this observation is an effect of cellular organization and activities, not the cause.
I feel thermodynamics is important in explaining how a raft of biochemicals came together in the first place to organize the earliest cell, and how these biochemicals started to engage in highly orchestrated chemical reactions. Then, what is the exact theory?

I'm a little bit unclear on what you're trying to ask. There is a whole literature on this subject, which is normally termed abiogenesis. What is it about the standard textbook explanations of abiogenesis that you need help to understand?

Simple question. Simple answer. Nobody knows.

For a provocative paper and a great introduction to this topic, see Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics, where the importance of irreversibility and autocatalysis/self-replication is emphasized.

The first amino acids
For how life arose from no life, the Miller-Urey Experiment demonstrates how in primordial Earth conditions, a spark in the atmosphere (analogous to lightning) could have initiated synthesis of the many of the same amino acids (and amines) life uses today.
My understanding was that the spark broke some bonds between the gases (and water vapor) in the air, allowing atoms to re-bind in new combinations to make amino acids.
Here’s a 25-Page Biographical Memoir from the NAS on Stanley Miller, page 3 is where they start discussing this experiment. Miller published this experiment in the early 1950’s, in which he identified 5 amino acids. However, NASA and others revisited the same experiment and discovered Miller under-reported amino acids present, a result from the limited equipment available at the time. They have found 14 amino acids and 5 amines. Miller’s vials from an unpublished experiment of similar nature produced 22 amino acids.
In addition, amino acids have been found on meteorites, suggesting that they are capable of spontaneous synthesis.
The first replicating life
There is a lot less known about this, as we’re still researching it now. Not only this, but there are currently several different going theories.
Keep in mind, the Central Dogma of molecular biology describes genetic flow as DNA—> RNA—> PROTEIN.
The reason why there are different theories (and so many models within them) around the chemistry-to-biology (CTB) transition does not lie in which monomer is more likely to synthesize spontaneously, rather it is almost literally a chicken-and-the-egg situation. Everything is a precursor for everything.

Proteins are made by amino acids, which are polymerized by metabolic processes. Proteins are made by other proteins, and directed/coded for by RNA.
RNA is made by the monomer building blocks of ribose (sugar), phosphate, and a base (A, U, G, C). The bases are biosynthesized from metabolic pathways. RNA is elongated, and read by proteins.
Metabolism is driven by proteins and largely by ATP, which contains the nucleobase adenosine found in RNA (& DNA).

Protein first
Since amino acids are the monomers of proteins, it is a likely (and simple) possibility that a spontaneous reaction bound amino acids in the right order and configuration to create the first protein that enabled life. This protein’s function could likely be to polymerize/elongate amino acid chains into proteins.
This theory is supported and demonstrated by this study, which suggests that the first “protein” catalyzed the elongation and proper folding of other amino acid chains, including creating more copies of itself.  0.3% of the possible permutations of monomer sequences give a “protein” the elongation capability described, which though small, is an exciting possibility considering the age of the Earth and timeline of life. What’s more, polypeptide formation does not require as much precision as RNA synthesis, as speculated characteristics of proteins and amino acids comport with the computer modeling shown by the study.
Though this theory seems to contradict the central dogma, we must keep in mind that thermodynamically the reactions occurring at the origins of life were spontaneous, so the “pattern” of genetic flow present in most life might not be a direct indicator of “what came first.” This is supported by the existence of prions (pathogenic proteins), and the fact that simple organisms don’t always use mRNA to synthesize proteins (alternatively, they use “nonribosomal peptide synthetases”).
The limitation of protein-first models is that proteins don’t really “work backward” into RNA. Though nucleic acids acids contain components of amino acids from their biosynthesis, the are pretty different molecules.
Some models suggest this protein-first theory, AS WELL as an RNA first theory (see below). The idea is that self-replication of biological molecules started with proteins, but nucleic acid-based “life” also evolved, seperately. RNA self-replication probably took longer to reach, but outcompeted protein “life,” explaining today’s life as well as providing an explanation for the above limitation.
Organisms can “uptake” other organisms and incorporate them into their own cells. 2 commonly-cited widespread examples include organelles mitochondria and chloroplasts, both thought to originally be independent prokaryotes themselves.
RNA first (aka The RNA World Hypothesis)
Some theories suggest RNA came before functional proteins. In fact, this has been the de facto theory, because we had no mechanism to explain how proteins could self-replicate - something that has recently been demonstrated. In addition, this follows the central dogma, and would explain not only the development protein synthesis but also genetic information storage (the latter of which cannot be directly explained by the protein-first theory alone).
An idea behind this is that some RNA was able to auto-synthesize the first RNA-replicating enzymes. This sounds like a catch-22, but this study had found some RNA strands when joined can self-create an enzyme that replicates itself - the literal chemical makeup of this enzyme are RNA-oligonucleotides.
However, these RNA fragments in the lab have been take from existing ribozymes, so they may not be an accurate indicator for the first, spontaneously-created enzymes.
Limitations from and only RNA-first model stem from the fact that currently RNA synthesis/replication processes are detailed, intricate, and fragile. The chances of spontaneous reactions alone creating this process seem minuscule (though as mentioned earlier life took a LONG time to develop).
Until recently, another cited limitation concerned the fact that no known organisms replicate RNA. However, some viruses manage to code for RNA-replicated proteins, and (as mentioned earlier) RNA’s capability of self-replication has been recently discovered, be it in a lab setting.
Other theories
The last main debated theory concerns metabolism. This idea suggests metabolic processes occurred before the first life form, since many metabolic processes known today synthesize amino acids and nucleic acids from chemicals in our diet (how our body make the building blocks).
However, such a huge part of what makes metabolism today possible is driven by enzymes, which are proteins. Because of this, all of these processes would have to be dramatically slowed down in rate to mimic spontaneous reactions in primordial conditions, and on top of that there would have to be an explanation for how energetically unfavorable reactions in metabolism would occur. Most of these energetically unfavorable reactions in current metabolism harvest the potential energy in ATP, which longhand is adenosine triphosphate. The molecule adenosine is also used as one of the bases in nucleic acids, which at some level inherently contributes towards to the RNA World Hypothesis.
Primordial amino acids (that have not been retained in today’s life) serving as the hidden first building blocks of life is not an uncommon theory. However, this concept rarely stands alone - it typically contributes to either the protein-first or RNA-first theories.
Proto-RNA theories propose an unknown “stepping stone” molecule like RNA. Evidence of this inherently will be limited.
Some ideas cite a meteor or space rock on which life was present collided with Earth, transferring life to Earth.

Once self-replication AND translation (RNA-protein) have been established, Darwinian evolution can explain the rest.

Additional resources
How Structure Arose in the Primordial Soup (Quantamagazine)
Life’s First Molecule Was Protein, Not RNA, New Model Suggests (Quantamagazine)

What simple organisms use "nonribosomal peptide synthetases” to syntheisize proteins ?

All organisms replicate RNA, do you mean self-replicate RNA? the big advantage of the RNA world hypothesis is the entire RNA to protein translation process is made of RNA components. both ribosomal subunits, tRNA, Its all RNA. proteins are made by RNA not proteins, they are modified by other proteins. you also may be interested in more recent work on self-replicating self-catalyzing RNA. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943892/


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Endospores contact with surfaces
I am currently studying endospores-forming bacteria. To be specific B.subtilis. I noticed that the formed spores have strong contact "grip" with the surface it is forming on. For example, when they are formed on an agar plate you have to scrape them off it. where is this attachment coming from? is this some type of enzyme or protein? or is it something else?


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How to create long term stock for Bacillus subtilis?
I am trying to create a long-term stock for Bacillus subtilis (Bacterial glycerol stocks). I have looked online for guides and step-by-step tutorials and I found that they don't say where the sample originally comes from.
In my case, I am using Bacillus subtilis subsp. subtilis (ATCC® 23857™) pure from the supplier bottle.
What is the proper procedure to create a long-term stock for Bacillus subtilis using this product?

I worked with B. subtilis WB800 and just used 50% glycerol / 50% LB. I imagine the same would work fine with wild-type.

Do you add the bacteria in the LB before mixing with the glycerol?

No I would prepare the glycerol/LB mixture and autoclave it then create the stocks from log-phase (approximately) plate cultures.

@canadianer Wouldn't you want to use liquid cultures as the source so you can count the number of cells? Or does B. subtilis not grow in suspension? I come from the world of eukaryotic (mostly mammalian) cell culture, so I honestly don't know...

@MattDMo They certainly do grow in liquid culture, but I’ve never used one to make glycerol stocks. Perhaps some do it more carefully than I do but, in my experience, this method was sufficient for my application (protein expression). I imagine mammalian cells are a lot more finicky.

@canadianer Can you turn your comments into an answer so that I can vote it up?

@jakebeal Sure thing, although I’m not sure how helpful it was.

I worked with Bacillus subtilis WB800 and just used 50% glycerol / 50% LB. I imagine the same would work fine with wild-type. I would prepare the glycerol/LB mixture and autoclave it then create the stocks from log-phase (approximately) plate cultures. This method was sufficient for my application (protein expression).


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When Bacillus subtilis form spores vs die?
In my understanding:
sporulation in Bacillus subtilis involves the differentiation into two cell types, the endospore, and the mother cell. The endospore coat is a multilayered shell that protects the bacterial genome during stress conditions and is composed of dozens of proteins. However, I also read about how Bacillus subtilis could die.
Q: When do Bacillus subtilis cells die vs form endospores? Also, could there be dead endospores?

Minor correction first: Bacterial endospores don't result from one cell differentiating into a different cell type. An endospore is not a cell type, but rather a protein structure that first forms inside of a mother cell, carrying all of the necessary machinery and genetic material to remain viable outside of the mother cell and eventually form a new cell when it encounters the right environmental conditions. In a sense, it's more like a mother cell becomes an endospore through the process of sporulation, which (with any luck) eventually becomes a new vegetative cell through the process of germination.
Bacterial endospores tend to form when cells encounter environmental stresses (like lack of nutrients, changes in pH or temperature, etc). Generally speaking only a portion of bacterial population will sporulate under a given set of conditions. However the remaining cells don't necessarily die right away. They may remain viable for quite some time, depending on how much and what type of stress they are experiencing.
Sporulation efficiency (the percentage of cells in a population that sporulate) is governed by a number of different environmental and genetic factors. Some organisms require specific nutrients or vitamin cofactors to sporulate efficiently. Others may require a specific pH range temperature. And different strains of a given organism can have wildly different sporulation efficiencies, making it hard to provide a very specific answer to your first question.

Q: When do Bacillus subtilis cells die vs form endospores?

The broad answer is that cells sporulate when they encounter the proper environmental cues in a medium containing all of the required nutrients in the correct amounts. And the ones that don't form spores don't necessarily die (it's not often an either/or scenario). You can look at a sporulation protocol for B. subtilis to get an idea of what makes them sporulate (see page 9 of this document).
Because sporulation requires time, vegetative cells will simply die if you assault them with something that kills them fast enough, or otherwise prevents sporulation from happening. But in most environments (outside of a lab), bacterial populations are heterogeneous and will likely already consist of a mixture of spores and vegetative cells. So when you try to kill them with something like that only kills vegetative cells, like a solution of ethanol, you are simply killing off the vegetative cells, leaving behind a preexisting population of spores to germinate and grow when conditions change again.

Also, could there be dead endospores?

Yes (assuming you consider endospores to be living). In practice, and population of dormant organisms will have some members that are no longer viable. Spore stocks in long term storage will slowly lose viability over time. There's also a lot of basic and translational research on how to most efficiently and effectively kill bacterial spores, especially those of sporulating pathogens in sensitive environments like hospitals or assisted living facilities (the answer is bleach. It's always bleach).


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How to get Bacteria to attach to an Object?
I have cultured Cyanobacteria (in a media) in a beaker. I want that bacteria to attach to a cloth (e.g. Carbon). My current method is using a syringe to slowly push the bacteria to one side of a cylindric tube and exist through the other end. The cloth is placed stationary inside that tube throughout the process.
Is there a way to get more bacteria to attach to the cloth? (e.g.maybe adding something to the cloth)

Why do you want them attached to the cloth?

I am doing a study to see how long can I help the bacteria live in the cloth and I want to store as much bacteria as I can.

I wonder if you could try this membrane filter technique, but replace the membrane with a fabric of your choosing.

You might also be interested in these CDC Biofilm reactors, if your cyanobacteria are biofilm formers.

Thank you, I will read about them and see.

You're thinking in terms of making them attach to your cloth, but they want to be attached - there are more nutrients and it is safer.  Make sure they have enough light, but not too much, and their nutrients.  They may be attaching and growing, but just not as fast as you expect.
It is also possible that your strain of Cyanobacteria has lost the ability to attach.  If it has been maintained in liquid culture for many generations, any bacteria attached to the wall of the container were selected against.


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Why are some bird hybrids fertile?
So, we all know that hybrids are infertile, that's the definition of a species, but how come some parrot species can interbreed and still be fertile. For instance a military macaw and a blue and gold macaw can have offspring that are fertile and can breed to make further hybrid macaws. These two species are definitely different species and not sub-species. How is this possible?

Minor comment - not all hybrids are infertile. 'Hybridisation' can occur between two e.g. breeds of the same species and can therefore produce fertile offspring.

Yes I know that sub-species can interbreed to create fertile offspring because they are in fact the same species. However, military macaws and blue and gold macaws are separate species and therefore should not have fertile offspring. Although thank you for clarifying in case it wasn't clear in my original post

"hybrids are infertile, that's the definition of a species" is not accurate - it may be a definition but certainly not the definition (and completely fails for asexually reproducers). Remi's answer at https://biology.stackexchange.com/a/39669/27148 is a good related read.

Yes but that still doesn't really answer my question. Macaws reproduce sexually and therefore still come under that definition of a species. I'm not trying to argue I've done so much digging to find an answer to this and just can't.

@RowanBlackwell-Cronie Did you read the answer I linked?

@Bryan Krause yes I did, and whole I found it interesting, I understood it as stating that whilst similar species might never normally interbreed, e.g a bird with blue feather and a bird with red feathers, but if they did they could create viable offspring. However I interperated this as meaning that those birds were actually of the same species in order to do this? But there have been cases of very different bird species creating fertile offspring. Which is what I can't understand. Please correct me if I'm wrong here

@RowanBlackwell-Cronie No, the birds in the situation Remi describes would still typically be described as different species based on their reproductive isolation, even if hybrids are actually fertile. That's the whole point of the post: the weakness of definitions of "species".

Ohhh right. Thanks for clarifying. I'll do more research into this


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In terms of Prions is there a possibility, that other proteins apart from PRPC could be misfolded
This is as from research PRPC seems to be the cause of all Prion related diseases. Thank you

Can you please provide citations for your claim? Use the [edit] function to modify your post.

Please write a question as a question. A title is a title not a question. Take care to make clear the context of your problem and the research you have done to answer it yourself. Currently that is lacking.

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. Please start by clarifying if you are only interested in human disease. In addition, we expect you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). See also this sites criteria for "homework", which can even apply to questions not assigned as homework. Thanks!

There are many prions other than PrP; it is often helpful to e.g. read wikipedia for these cases.
For example, there are many yeast prions that are not homologous to PrP https://en.wikipedia.org/wiki/Fungal_prion.
But even in humans there are a number of other proteins that form amyloids and are described as "prion-like" even though they aren't the canonical protein: https://en.wikipedia.org/wiki/Prion#In_other_diseases


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How do we regulate the production of proteins when designing plasmids?
I think it should be no surprise that I, as many others, am interested in the new COVID-19 vaccines being developed. In my region of the world there are two mayor candidates. One is mRNA based and one is, as far as I understand, plasmid based.
I have a passable understanding of the mRNA based vaccine.
I also know what a plasmid is, and how it is transferred between cells, but my understanding is otherwise limited.
As far as I understand we want the plasmid to be "unlooped" and grafted onto our target cells DNA. This, as far as I reckon, should enable the cell to produce whatever protein the plasmid coded for. In vaccines this lets us device anti-measures (vague because of my lack of knowledge) against the virus... But, how do we regulate the production of these anti-measures? Can we include a "regulator" for the production in the plasmid, so that the modified cells only produce the proteins when the virus is present? Or do we just let the cells continuously produce the anti-measure proteins, regardless of their necessity?
My main interest here lies in where the permanency of the vaccines induced changes lie. With the mRNA vaccine I understand that the permanency lies in the regulated immune system, with other cells being otherwise unchanged after the mRNA decomposes. Regarding the DNA/plasmid vaccine I'm still unwise.
Thank you for your time, and happy holidays.

The DNA vaccine does not "graft onto the target cell's DNA" or change its genome in any way whatsoever. That's a common misconception and line of attack for anti-vaxxers, and is completely false. Nothing personal against you, I just wanted to emphasize that fact.

Thank you. Can you elaborate on what it does do instead? My question stems from the fact that it is hard for me to find information on this subject on the internet, and while I appreciate your negation of my false understanding, it is in not the negation alone I seek but a correction which includes the correct understanding.

I was waiting for someone who had the time to flesh out a real answer, and I'm still hoping someone does, but the quick and dirty answer is that all expression plasmids have an upstream regulatory sequence (before the protein-coding region starts) that includes one or more promoter elements. These elements attract and bind cellular transcription factors which help initiate transcription of the coding region, which is then translated into protein. Typically this process happens continuously until the plasmid is eventually degraded - it doesn't depend on the presence of virus.


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Why do microarrays require a priori knowledge of the genome?
Reading this paper they said this:

Contemporary microarrays emerged in the wake of genome sequencing
projects for one obvious reason: arrays require a priori knowledge of
the query genome

Why do you need a priori knowledge? Thanks.

How do you think people know what sequence to put on the probesets?

There is  a bit of ambiguity in the term of "microarrays", which is currently mostly used to relate to "microarrays" that detect nucleic acids through their sequence-mediated binding (see excellent answer below from Pascal). While much rarer, there would also be "microarrays" directed at other chemicals, such as proteins binding antibodies: https://en.wikipedia.org/wiki/Antibody_microarray

If the query genome is unknown, a microarray cannot be made for a target species. Microarrays have DNA fragments of what you want to amplify on them. Those fragments must be known.
From nature:

DNA microarrays are microscope slides that are printed with thousands
of tiny spots in defined positions, with each spot containing a known
DNA sequence or gene.

From wikipedia:

Scientists use DNA microarrays to measure the expression levels of
large numbers of genes simultaneously or to genotype multiple regions
of a genome. Each DNA spot contains picomoles (${10^{−12}}$ moles) of a
specific DNA sequence, known as probes (or reporters or oligos). These
can be a short section of a gene or other DNA element that are used to
hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called
target) under high-stringency conditions.

This answer consists of two quotations, neither of which is an answer to what in my opinion comes under the heading of "questions that show insuffiient thought to be worth answering". You state that "Microarrays have DNA fragments of what you want to amplify on them". This is incorrect. 1. There is no amplification "on" the fragments. — the cDNA generated from the mRNA may be regarded as amplified. 2. They are not DNA fragments. They are synthetic deoxyoligonucleotides. Please edit your answer such that it is is clear and correct.

Some good clarification. Maybe @David, you might consider editing the Wikipedia article.


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When do Blue Jays form their crests?
I've noticed that not all Blue Jays appear to have a crest. I know that at certain times the crest may be down and less visible, but I notice in most images of juvenile Blue Jays they don't appear to have a crest. I'm curious if the crest forms later on or if Blue Jays are born with a crest?

Short answer
It seems like blue jays form their crests as adolescents, after their first post-juvenal molt before their first winter.

Longer answer
The top of the head of a bird is called the pileum, with the very top called the crown. As far as I can tell there is no particular distinction between "crown feathers" and "crest feathers", rather the presence of a "crest" is because the crown feathers are longer and stand out from the rest of the head.
Juvenal plumage
Blue jays born with their natal down will molt within the first two weeks to get their juvenal plumage. Dwight (1900) is quite descriptive of the juvenal plumage, but does not mention any crest, only that the pileum is a "flax-flower blue separated from the blue-tinged white forehead and white superciliary line by a narrow black line".
Crown feathers are longer after the first prebasic molt, forming a crest
The first prebasic molt refers to the (partial) loss of the juvenal feathers. Bancroft & Woolfenden (1982), examining young birds captured in Florida, found 8% in the first prebasic molt of the crown/head area in the first half of August, 89% in the second half of August, 78% in the first half of September, and 54% in the second half of September. So it seems most birds are getting through this molt by mid-September.
Dwight (1900) writes that "young birds become practically indistinguishable from adults" around this time and that compared to the juvenal plumage, bold mine:

the blue of head, back and wing coverts now distinctly barred with black and much brighter, and the crest feathers longer

I haven't found mention of crest feathers rather than crown feathers in descriptions of the juvenal plumage, with one exception I'll get to below, so I'll tentatively say that a blue jay forms its crest as part of this first prebasic molt in which the first winter plumage is evident.
Blue jay crest in behavior
The crest position of blue jays differs across behavioral contexts, ranging from erect to pressed against the head. Conant (1972) mentions the crest specifically as part of several different postures/behavioral contexts (parentheses are my paraphrasing):

In neutral posture, the crest and plumage are relaxed

While a Blue Jay is asleep, the crest is relaxed and the body plumage is usually fluffed

(while "investigating"): the crest is fluffed

(during "mild aggression"): the crest is fluffed

(during "intense aggression"): crest is fully erect or ruffled

(during avoidance/submissive posturing): the crest is relaxed or sleeked

(during "courtship feeding solicitation"): the crest is relaxed or sleeked

And finally, the one section that makes me a little uncertain, Conant (1972) describes the "nestling alarm freeze" behavior of nestlings when their nest is disturbed or they hear an alarm call:

The crest and body plumage are sleeked, wings closely appressed to the body, and tail closed.

My guess is that she's using "crest" here to mean the crown feathers, and just referring to them as the "crest" since that's the word used when describing the other behaviors that primarily involve birds with adult plumage. However, it raises a bit of doubt and perhaps the other descriptions missed that there is also a crest in the juvenal plumage, hidden in the alarm/sleeked position under the watchful presence of predators scientists. Dr. Sheila Conant is now Professor Emerita at the University of Hawai'i at Manoa; one could ask her, but I think it has been awhile since she studied blue jays closely.

Bancroft, G. T., & Woolfenden, G. E. (1982). The molt of scrub jays and blue jays in Florida. Ornithological Monographs, (29), iii-51.
Conant, S. (1972). Visual and acoustic communication in the blue jay, Cyanocitta cristata (Aves, Corvidae). The University of Oklahoma.
Dwight, J. (1900). The sequence of plumages and moults of the passerine birds of New York. New York Academy of Sciences.


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What are the effect of radioactivity on grey wolves in Chernobyl?
I am doing some research about the effects that radioactivity has and is having on grey wolves in Chernobyl and more particularly on their genetics, but maybe also looking at the populations in the area as a whole.
I was wondering if anyone has any knowledge or resources they could share. It would be great!

Is there evidence that the radiation has any effect at all?  Other than keeping most humans out of the area, of course.

Sorry I forgot to point out that I am not only researching the effects that radiation has on wolves now, but also on wolves that were present in the area not long after the disaster. Surely the radiation should have caused genetic mutations in those wolves.


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If aging is caused by "DNA Damage" why is the process of aging generally similar between people?
When I hear the phrase "DNA Damage" I imagine completely random changes in the DNA of a person's cells. If this is the case, then it seems like every person would age differently depending on what happens to their DNA. But that is not what we see. In general people age in very similar, predicable ways almost as though it was programmed into the system.
Is it just that most random DNA changes result in cell death and that most of aging is just having fewer healthy cells in any given tissue?

Hi Mark. Welcome to Bio.SE. DNA damage is one aspect of ageing. Ageing was definitely not programmed into the system, and in fact is probably entirely plastic. See here for more about ageing: https://www.youtube.com/watch?v=-hCkVHioBVA Crucially, we have not lived longer than about 30 years old during evolutionary timescales. I'd also challenge the idea that we all age similarly.

It's worth pointing out that processes causing DNA damage are not necessarily random. Telomere shortening in somatic cells, for example, seems to be controlled mostly by deterministic factors. Likewise, somatic cell mutations, which probably occur stochastically (not necessarily at random), can affect fitness at the cellular level, and therefor persist or accumulate in predictable ways that affect cell proliferation and/or survival.

People do age differently.  Consider perhaps the most obvious signs, like grey hair or baldness.  Some peope go grey (and men start to lose hair) in their 40s or so.  Others can hit their 70s with a full head of hair that has only a few streaks of grey.

https://biology.stackexchange.com/questions/98428/biochemistry-of-ageing-new-discoveries I think as is said there ageing has to do with dna changing structure more than code. But also sunburn seems to leave same traces on people, for some reason. Great question though

Nit that clear to me tbh @jamesqf. There are epigenomic chanfes, mutations due to methylation ,UV, ROS, telomere shortening, some energy troubles with the mitochondria too..


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Why are disaccharides less reducing than monosaccharides?
My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?


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Why are cells in blood smears undetectable after absorbing moisture?
I'm a student learning how to prepare blood films and today I was curious about something, so I performed an experiment.
After preparing a thin blood smear and drying it (no staining), I took a look under the microscope (at a total magnification of about 200X... I have a cheap microscope). Even though it was zoomed out, the red blood cells were easy to distinguish. The cells were clear but they had dark edges.
Then, I blew some hot air onto the same slide, causing the dry smear to absorb some moisture. Then I let it dry once again.
I observed the same slide under the microscope once more, but this time, I could barely make out the red blood cells. They were certainly still there, but their features/borders were extremely hard to make out and distinguish.
I'm wondering what causes this. Are the cells absorbing moisture and thus changing their morphology? I couldn't find any answers online, so I thought I'd ask here.

It might be helpful if you are able to post a picture of what you're seeing, however, it sounds like the blood cells are lysing.
The water you introduced to the cells through the moisture in your breath is likely creating a hypotonic environment, causing the cells to intake a lot of water and then lyse, causing their appearance to become atypical.


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Why is African hair different in texture to European or Asian hair?
Most Africans with the exception of Ethiopians and Somalians have relatively kinky/coiled hair. The texture is very different to that of Europeans or Asians. Why is that?
I've heard it has to do with the shape of the hair follicle which is flat but also the thickness of the hair itself. Is this true?

As this article details, the texture of hair is influenced by many aspects of the hair follicle, primarily the follicle shape (curved or not, angle relative to scalp), distribution of particular cells within the follicle, and the coordination of cellular activity in the follicle (symmetrical or asymmetrical activity).
The article also confirms, as the question recognizes, that a great variety of hair textures are found in all parts of the world, so that categorizing hair by country or continent of origin is specious.


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How does the position of hydroxyl group in a nucleotide monomer affect the dehydration synthesis of nucleotides?
In dehydration synthesis of nucleotides, the hydrogen atom from the 3' carbon on the deoxyribose sugar of one nucleotide reacts with the hydroxyl group on the phosphate group of another nucleotide to form water. As the water molecule forms, a new covalent bond comes into existence between the two nucleotides.
Hydroxyl group can be in different positions within the phosphate group, for example:

I'm wondering if different positions of the hydroxyl group have an impact on the dehydration synthesis between nucleotide monomers. For example, when the hydroxyl group is at the bottom, will the dehydration synthesis occur at all? Also, when the hydroxyl group is on the left, does the spatial structure of the sugar-phosphate backbone have a spatial shape different from when the OH group is on the top?

You need to keep in mind that simple chemical structure drawings like these do not at all reflect reality on the atomic scale. The 2D electron from the "double bond" is shared among the 3 O atoms (except the one on the right, AFAIK), as is the proton from the hydroxyl group. Everything is floating around in quantum probability clouds, not permanently fixed in one specific position in rigid bonds. The other thing to keep in mind is that a phosphate is a tetrahedron in 3D space and can rotate pretty freely, allowing the dehydration reaction to occur in any conformation.

Wherever the hydroxyl group is; the result is the same I think. The phosphate has oxygen arranged in a tetrahedron around it.
In cells the hydrogen is not attached most of the time. For example the triphosphate on ATP is a weak base with a pKa of about 6.6. Cytoplasm usually has a pH of about 7.2, so an ATP molecule is only protonated (very approximately) 15% of the time.
https://en.wikipedia.org/wiki/Polyphosphate#Acid-base_and_complexation_properties


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Contradiction between random molecular collisions and regulated cellular processes
A cell is a chemical system, consisting of billions of molecules, ions, and atoms. These chemical species are constantly engaged in chemical reactions.
Physics gives the impression that chemical species concentrated in a tiny space, such as a cell, are randomly moving and colliding into one another. Any chemical reaction can occur only if the correct reactants collide with one another and get transformed into a raft of products, under exergonic conditions.
It appears that motions and reactions for biochemicals inside a cell are random and unpredictable. However, cell biology is all about highly regulated and coordinated cellular processes, including transcription, translation, vesicular transport, replication, gene regulation, and so on.
Since each of these cellular processes relies on specific biochemicals to undergo correct chemical reactions, it now appears chemical reactions inside a cell are much more predictable and controlled than what physics might suggest, and so are motions of biochemicals.
How do I reconcile these conflicting ideas about the nature of cells?

Short but relevant: https://biology.stackexchange.com/a/104417/59521

"Random" quantum events don't look so random at the chemistry resolution. I think you are conflating the colloquial concept of random to a very special definition of random used by quantumn physticists. Holistic medicine practioners do a similar thing with the special term "energy".

I’m voting to close this question because it makes an assumptions about randomness that are not necessarily true.

Short answer: Unlike the physical model you're describing above, the reality is that localisation of biomolecules in the cell isn't a passive process, instead molecules are actively concentrated where they're required to be by a variety of different mechanisms.
long answer: I think possible 'missing pieces' of this picture which may help you reconcile these ideas are compartmentalisation and intracellular localisation, which extends beyond just the nucleus and membrane-bound organelles.
It's often the case that the constituents required for biochemical reactions are concentrated locally in compartments which facilitate the "collision" of relevant components to progress the reaction. Some examples would include liquid-liquid phase separated compartments or membrane-less organelles (https://www.sciencedirect.com/science/article/pii/S0960982217311090 and https://www.frontiersin.org/articles/10.3389/fmolb.2019.00021/full are some good overviews).
Scaffold proteins also help in this regard (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117218/)
Another example would be the idea of spatially localised transcription hubs where all of the components required for gene regulation and transcription are located in proximity (https://www.scienceopen.com/document_file/6fe11e52-baf9-4ee7-97be-72f3444d1e04/PubMedCentral/6fe11e52-baf9-4ee7-97be-72f3444d1e04.pdf). A specific example would be nuclear speckles (https://academic.oup.com/nar/article/45/18/10350/4101253).
In terms of intracellular signalling it's often the case that molecules involved in cascades are localised in close proximity at the cell membrane (https://pubmed.ncbi.nlm.nih.gov/16467194/). Receptors which sit at the cell membrane but act as transcription factors when active (e.g. nuclear hormone receptors) are actively imported into the nucleus on activation and other signalling molecules are similarly trafficked in an active, directed process (https://cellandbioscience.biomedcentral.com/articles/10.1186/2045-3701-2-13).
Ultimately, most biochemical processes are compartmentalised or otherwise localised through diverse but active mechanisms to facilitate life, as opposed to molecules floating and randomly bumping into each other as you get in a cell-free solution.


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What will happen if mitochondria had a structure like lysosomes?
I wanted to know an explanation how the structure of mitochondria affects its function. Therefore, how would it turn out if its structure is like the structure of lysosomes, what is going to happen?

Mitochondria are double membraned organelles with an outer membrane which is a rod-like shape, and a convoluted inner membrane (Figure 1).

Figure 1
On the other hand, a lysosome is a single-membraned vesicle containing digestive enzymes, with no internal structure. Its function is to keep these dangerous enzymes in a compartment.
The "purpose" or "role" of the mitochondria is to do cellular respiration to provide energy (as ATP) to the cell. To do this, the mitochondria have many respiratory complexes (groups of proteins which make respiration happen) embedded in their internal membrane (Figure 2). As you can see in Figure 1, this membrane is convoluted with many folds; this is to increase the surface area of the membrane to have more space for respiratory complexes.

Figure 2
Moreover, these complexes pump out H+ ions into the intermembrane space. The fact that there is this thin intermembrane space allows for a buildup of H+ concentration which is crucial for ATP production (through the action of ATPase). This process is called chemiosmosis and you can learn more about it here as a starting point. A lysosome with only one membrane does not have an "intermembrane space", so this buildup in concentration cannot happen.
If you would like to learn more about mitochondria, I would recommend reading Power, Sex, Suicide: Mitochondria and the Meaning of Life by Nick Lane.


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Why does the DNA of Bacillus subtilis not contain DNA families of 20-37 members?
I am reading the book "Molecular biology of the Cell, 6th edition" and in chapter one page 18 the following figure is included

I am presuming this figure represents all genes within the Bacillus subtilis, which makes me wonder: why are there no families with 20-37 genes? There is a group for 4-19, and one for 38-77. What happened to all sizes in between?

You would need to read the original paper on which this figure is based. Do you have access to Nature? If not I can send you a reprint, but I don’t think this is a question about biology, but one of arbitrary data selection.

@David that may be the case, but to the OP that distinction cannot be easily known. So although an answer to this post might in fact point out arbitrary data selectivity as the cause, I think the question is otherwise biological in nature and therefore OK.

Based on the paper (open access) from which this figure was adapted, the 38-77 group consists of 5 gene families with 38, 47, 57, 64 or 77 members. In contrast, there are 284 “families” with 2 members, 91 with 3 members, 42 with 4 members, 25 with 5 members, etc. This is clearer in the original figure:

Thus the larger gene families are outliers and there simply exists no gene families in B. subtilis with 20-37 genes (at least by the methodology of this paper).

Very useful to see the original image and now that I know that there are also gaps within the groups given by my textbook the single gap between 19 and 38 seems a lot less extraordinary


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Preserved flowers in epoxy resin
I want to cast flowers in resin. The problem is that everyone is casting dried flowers in order to prevent the moisture from fresh flowers evaporating while the resin is curing and I need to cast fresh flower. I tought of freeze dried flowers but could not find any company that could do it in my country nor online shop where to buy in europe. I am thinking of castin stabilized roses which are dehydrated first and the soaked with glycerin, propyl glycol and som dyes for colors. I wonder  if the glycerin with propyl glycol will evaporate with the higher temperature during the resin curing process.


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Any kind of online "molecular modeling playground"?
I'm wondering if anyone has ever made a tool to try out new molecular modeling/simulation algorithms, where the tool itself handles the "boring" tasks of loading PDB files, building chains of amino acids from sequence so that the atoms can later be assigned coordinates by user scripts, rendering rotatable graphics in 3D, etc., but where the user can then write scripts that loop over the coordinates, do some kind of math, and then modify the structure. That way you could experiment with new force fields, integrators, etc. Something like TurtleToy does with plotter graphics.
There are obviously molecular modeling tools with scripting capability, but quite a few have licensing restrictions and also they are commonly intended as ways of splicing together existing algorithms and modeling "recipes" in new sequences. The actual simulation code is often "buried" deep in complex codebases and spread across multiple files that must be compiled together just to get something working. Clearly something like an energy minimizer written in for loops in a language like Python won't compete in terms of speed with GPU-accelerated parallelized C++, but it can be written completely from scratch to test out completely new algorithms, and if seamlessly integrated with a rendering component that accepts redraw calls from in the script, it's a quick way to visualize "what is this doing to my protein structure?" in real time as you single-step through your algorithm (and the rendering overhead probably makes speed a moot point there anyway). That way if you want to quickly see "how does my method compare to the existing ones in CASP" or something, you have a "playground" to try it out.
If I'm looking for this I'm sure others have too, so I'm wondering if it exists. An even potentially more interesting feature would be the ability to execute scripts as "filters" over the PDB, something like "Find all sequences of length 5-20 amino acids in the PDB for which this expression evaluates to "True", align them using the following transform, and plot them in this canvas". But I can see where the PDB might not like people doing this as it could bog down their servers from all the fetches, so this may be a bad idea. But allowing people to operate on their own PDB files would obviously not be a problem if the tool were around.


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How to assemble three 60mer nts by pcr?
Good morning,
I am new to molecular biology. The question might be silly but i would like to know the answer. I have three 60mer single strand synthetic oligonucleotide. Namely Tag 1 - 3. My goal is to assemble these three together by pcr. So i designed two primers having overlap of 18nts from each tag 1 and tag 2 and then Tag 2 and tag 3 ( i mentioned the orientation of my primers). What is the best way to assemble. I read about PCR- based two-step DNA synthesis. But i would like to know more about this.
If you have any questions please feel free to post. Thanks and looking forward for your valuable answers
[]

In order to assemble your TAG oligos by PCR you will need to redesign your primers so they are complementary to the TAG oligos as DNA polymerases work by adding nucleotides to the 3' end of a DNA strand.
Your design would look like this :

Now with this design you won't be able to assemble everything together as TAG-3 complementarity to primer 2 only presents 5' ends to be extended, which your DNA polymerase can't do. So you can either order the entire reverse complement of your TAG-3 oligo or design a primer 3 that would anneal at the 3' end of TAG-3 to amplify TAG-3.
With all these parts, you should be able to assemble everything in a single reaction, but depending on your downstream process you may have to purify the product of interest as the single reaction will generate intermediates (1, 2, 3, 1+2, 2+3).

Really thanks for your explanation. So i have to redesign the primers that should share  complementary with tag-1 and tag-2 (not reverse complement right). I will assemble first tag-1 and tag-2 and then i will go for tag-3 with my product.

You should order the reverse complement of your primer 1 and 2. Let's say that your TAG-1 sequence is 5'-attgcctg-3' and TAG-2 sequence is 5'-TAATTGCC-3'. So far what you have ordered as primer 1 is 5'-ctgTAA-3' but you need the reverse com 5'-TTAcag-3'

Awesome. Once again thanks.

@Rengaraj If this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered. If you have >= 15 reputation points, you may also upvote the answer if you wish. There is no obligation to do either.

I would suggest using Gibson assembly. I am not an expert but this is the kind of problem that it is designed to solve. Probably there is some way to do this by PCR but I expect that it will be quite finicky.
See this quote from that page (my emphasis):

Tip: “Stitching” Fragments Together using Oligos
When you need intervening sequence between two PCR products, one method is to “stitch” together several oligos. This technique is especially useful for introducing promoters, terminators, and other short sequences into the assembly and is used when the part to be inserted is too long to include on overlapping PCR primers (>60 bp) but too short to make its own part (<150 bp).
Please note that the way to design the “stitching” primers and the amounts of them to include in the Gibson reaction are different than with normal PCR primers. The details are published in ( Nat Methods 2010; 7:901-3 ).
Tip: Number of Fragments Assembled Simultaneously
Multiple fragments can be assembled in one reaction. However, some labs have observed a sharp decrease in success rate when assembling more than 5 fragments at a time.

Update
It looks like there are people who argue both that Gibson is impossible with short fragments or that it works fine. There is more information on this here and here and here. Due to the relatively complex nature of your reaction, I think that Gibson might save you time. But other people linked there do claim that PCR works better.
Update 2
GaelC's answer above has better/more specific methodological advice on PCR assembly.

I agree with Gibson assembly but i read that it is not suitable for short fragments such as 60-mers.

@Rengaraj see update

Exactly, these are the posts i went through. First i will check by PCR assembly, if it did not work i will order the Gibson assembly kit. And i have a doubt? the way i designed the primers are fine or correct? or should i have to change anything...

@Rengaraj I think that GaelC's answer is good if you choose to go with PCR.

NEB's tech support is fantastic. If anyone has the answer about Gibson assembly of shorter sequences, they would.


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How to incerase the efficiency of co-immunoprecipitation?
immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i could see enriched pattern in the IP pull down (lane 1 and 2). but the main problem is that i can same pattern in the control also. I am using my lysis buffer for the washing also (2 times washing with lysis buffer 10 mins at cold room followed by 2 times with 1X pbs). I am Using Mag Strep "type3" XT Beads (Incubation 4 hours in cold room with beads).

Lysis buffer:
20mM HEPES-KOH pH 8
15 -per glycerol
150mM KCL
0.2 per NP40 (I reduced to 0.05 per)
1 mM DTT
1X protease inhibitor cocktail

Can anyone help me with this. Should i change the washing buffer what about the stringency. What are the other factors that could increase the efficiency of the co-IPs. I am trying to optimize the protocol. This is human cells.

What are you doing your Western for - your IP target protein or a known binding partner? Please give identifiers for your different proteins (i.e., Protein X, Protein Y, etc.) and indicate what exactly the samples, IP antibodies, and WB antibodies are in each lane. Or is this an image of a stained gel? Please label molecular weights as well, it's possible you're just staining heavy and light chain.

The gel is silver stained. I know my protein (70kDa) but i am looking for the interaction partners (which i am interested). It is a streptavidin pull down. I have given only the experiments only. From the left to right first two lanes reduced NP40. 3rd to 6th lane reduced   0.2% NP40.


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Is it possible to use two forward primer and one reverse primer?
I have eGFP and the gene fragment i assembled by pcr.The next step is that i have to join my fragment fragment into 3'p end of the eGFP.I have three primers FP1 is forward primer for eGFP, FP2 has overlapping between eGFP and my fragment. RP1 is just revcom of my fragment 3 prime sequence. How can I assemble this by pcr. is it possible to mix all the three primers together with GFP and my fragment.

Well, technically yes but no. Why yes is because on paper this looks simple enough but think about the technicalities. Your FP1 and FP2 will have different TMs, meaning the temp required to make the complete fragment with FP1 and RP1 will be different than to the MP of FP2. Effectively when the temp for FP2 reaches it might cause FP1 and RP1 to detach.Or the opposite might happen, where FP1 and RP1 are attached whereas FP2 might not.
Another problem I could think of is that as the PCR is cycling, the difference will lead to random length amplifications if at all you get any. The maximum amp product you might see will be of Frag-2.
If you want to fuse such fragments, I suggest going for OE-PCR (Overlap extention PCR).
This is a highly effective method to join two pieces of DNA using PCR. the concept is similar to what you have proposed.
Look at the wiki page- https://en.wikipedia.org/wiki/Overlap_extension_polymerase_chain_reaction

This image also explains the process...

Thanks for you explanation. For Overlap extention PCR i need more primers or overhangs in the fragment right. But i don't have the overlap in my fragment instead i have it on my primer. Is it possible to do by Gibson assembly?

@Anteres I don't see what you mean by "technically yes". It is simply not possible to achieve the fused fragment by the three primers proposed by the op.

@gaspanic - correct, it can't be done by the PCR as designed. It could be done with a fairly simple blunt-ended ligation of the two products. Though in that case I would do the PCRs individually rather than in 1 tube. The OE-PCR is the correct procedure for this, or simply put it all into a GFP-vector in-frame with the GFP.  I can't think of many applications where you would need a naked GFP-GOI construct without promoters, RBS etc.

The ultimate aim is to integrate my fragment into the 3' end of the gfp plasmid. The plasmid has all the essential features. I thought i can assemble gfp and my fragment by pcr then i can incorporate into the plasmid. Is that wrong?

What do you mean by the 3' end of the gfp plasmid? Is GFP already in the plasmid, and all you need is to insert your second fragment downstream of GFP? In that case your primers FP-2 and RP-1 should be sufficient, assuming that you have appropriate restriction sites near the 3' end of GFP.

The reason why i am doing this, to preserve all the restriction site.

In order to get a good response I think you will need to post a new question clarifying what you have and what you want to achieve. The comments section is not the right place for this.


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colocalization by IFA?
I have done IFA (immunofluorescence assay) previously but i targeted only one protein or i tagged my endogenous protein with GFP/RFP then i performed IFA. I want to do the IFA in parental cell line (HEK cells). My aim is to show the two proteins are co-localized or not?

Protein-1 (secondary antibody Mouse)
Protein-2 (secondary antibody Rabbit)

How can i co-localize two different proteins in the same sample? Which primary antibody do i have to add first?  can any one please suggest me something?

If you search the web or Google Scholar, you should be able to find plenty of examples of colocalization protocols.
In general, though, for each target you're going to want to have an unstained control sample (you can use one for all targets), a secondary-only sample to look for non-specific background staining, and a single-color sample (primary plus secondary). Then, you'll have a sample with both primaries and both secondaries. You always add the primaries at the same time, and the secondaries at the same time.
As you start getting into higher numbers of colors, you'll also need an FMO (fluorescence minus one) control for each color so you can test for signal bleed-over from one channel to another. This sample will combine all the colors except for one.

Thanks for your answer. It is really helpful. one more important question i have. Is there any way to do the RNAase treatment in IFA? I suspect if my protein of interest co-localization RNA based?

@Rengaraj yes, it is possible, although I haven't done it myself. Here is a ResearchGate discussion (with references) on how to do it.

@Rengaraj, also, if this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered. Since you have >= 15 reputation points, you may also upvote the answer if you wish. There is absolutely no obligation to do either.


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Why do huskies have markings above their eyes
[1.         Dogs in Antarctica pulling sleds

It's not just Huskies,  Many breeds - Rottweilers, Dobermans, Bernese - have them.  Others like German Shepherds may or may not have them as part of their coat color variation.

You may be able to get better answers at [pets.se].


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Coacervater were more like Viruses or Cells?

The answer considers them as first formed living cells as they were precursor of life. But they had no lipid bilayer nor any cellular organization, shouldnt they be more like Viruses ,or like Prions and Viriods ??

Do not post text as graphics on this list. It discriminates against people with visual disabilities who use screen readers. This is a homework question and should be tagged as such. You need to put more effort in before an amended homework question would be acceptable. For a start, a reference to "coacervates" is necessary. I for one have never heard of them

@Astrolamb - please do not provide answers-in-disguise as a comment, it deters other users from answering. I have removed your comment.


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Why I don't feel pain when I press the skin on my knee and elbow?
Does the muscle on our knee and elbow have some speciality ? Why are we unable to feel any sort of pain when I pinch it ? I also did it with my Mom and Dad and result was same .

I think the skin is what you are pinching, and its mostly dead skin. I could really find a valid source though. Sorry

There are no muscles (except smooth muscle in the skin) under the skin at the knee or the elbow. You are pinching skin, not muscle.

There is several types of nerves in the body.
Some nerves are specialized in sensing cold or hot temperature, some other to cuts and cell damage and others feel pressure and touch.
The answer to your question is that the nerves in your elbows and knees have less pain detectors and are in fewer number, thus with they are less sensitive.
Here's a funny little poster on BBC: Can you pinch yourself without it hurting?