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Why are venomous mammals and birds so rare in comparison to reptiles and fish?
Why are venomous mammals and birds so rare in comparison to reptiles and fish?

Metabolic reasons? Morphology? Selection pressures?
Why are not all reptiles venomous but many are?
Why are platypuses venomous?
Is there a difference between venomous and poisonous?

one question at a time.

The last question is a whole different topic.

Does this answer your question? Why is venom more common in fish and snakes than other vertebrates?

Short Answer

See Why do some bad traits evolve, and good ones don't?

Evolution of venom is complicated and full of convergent events.

Our awareness and perception of venom production is biased toward recognition of chemicals as human-impacting venoms, and the full scope of venom production and their various ecologies have not holistically or thoroughly been studied.

Venom vs poison: both are toxic but their delivery sytstem differs: "poison" is ingested/inhaled/absorbed and "venom" is injected [by teeth, sting, spine, claws].

Sources: NPs.Gov, Australian Academy of science, Natural History Muesum

Long answer
I definitely want to point you toward one of our most linked posts on this website, Why do some bad traits evolve, and good ones don't?, as it mostly answer your otherwise nearly impossible-to-accurately-answer question. However, I'm going to provide a bit more nuance by pseudo-answering your questions with some comparisons between two of the groups you asked about (reptiles vs mammals) and a number of citations to try to demonstrate how "messy" (complicated) this answer might be to answer.
You're correct that a number of reptiles are venomous -- about 1/5 of snakes for example. According to National Geographic approximately 600 out of 3,000+ species of snakes are venomous. But it's not just snakes; Gila monsters and other non-snake "squamates" also are known to produce venom. This would suggest that production of venom is possibly a fairly early trait to evolved in squamate evolution. Still, it turns out only a single clade of reptiles is known to commonly produce venom(s).
According to Wikipedia:

Recent research suggests that the evolutionary origin of venom may exist deep in the squamate phylogeny, with 60% of squamates placed in this hypothetical group called Toxicofera. Venom has been known in the clades Caenophidia, Anguimorpha, and Iguania, and has been shown to have evolved a single time along these lineages before the three groups diverged, because all lineages share nine common toxins.[24] The fossil record shows the divergence between anguimorphs, iguanians, and advanced snakes dates back roughly 200 million years ago (Mya) to the Late Triassic/Early Jurassic,[24] but the only good fossil evidence is from the Middle Jurassic.[25]

Citations: [24]: Fry et al. 2006. "Early evolution of the venom system in lizards and snakes". Nature 439(7076):584–588. doi:10.1038/nature04328. [25]: Hutchinson et al. 2012. "Tikiguania and the antiquity of squamate reptiles (lizards and snakes)". Biology Letters 8(4):665–669. doi:10.1098/rsbl.2011.1216

Fry et al. (2005) shows us this "venom clade" visually in figure 1 of their paper:

Figure 1 copied from Fry et al. (2005)
Let's contrast with mammals.
According to Ligabue-Braun (2017):

There are four mammalian orders with known venomous representatives, as recognized today. These comprise solenodons and some species of shrews (Order Eulipotyphla), platypuses (Order Monotremata), vampire bats (Order Chiroptera), and slow lorises (Order Primates)

Fitzpatrick et al. (2022) provide the following to aid in viewing this phylogenetically:

 Figure 1 copied from Fitzpatrick et al. (2022)
This phylogeny suggest less conservation of this venom trait. Knowledge of these species confirms that their venom appears to be unrelated evolutionary.  Schendel et al. (2019) writes (my emphasis):

Venoms are one of the most convergent of animal traits known, and encompass a much greater taxonomic and functional diversity than is commonly appreciated.

Venom systems have evolved independently more than 100 times in an extremely wide range of taxa that includes at least eight separate phyla (see Figure 1)

In summary, as seen from Figure 1 below copied from Schendel et al. (2019), what we do know about the evolution and ecology of venom is quite widespread across the animal kingdom and quite messy (complicated) for exploring:

 Figure 1 copied from Schendel et al. (2019)
In addition to this point, we actually are still not fully aware of the full scope of the many toxins in the animal kingdom. Schendel et al. (2019) also point out that our perception of venom presence is biased due to a focus on venoms that impact humans vs. a broader ecological context:

Venoms and toxins have thus been primarily characterized using human and other mammalian tissues and receptors. An exception to this is the targeted screening of venoms as sources of novel insecticides [15,16,17,18], which typically rely on a limited number of pest or pest-related insect species. Nevertheless, most toxin pharmacology is based on species that are ecologically irrelevant and/or represent only a fraction of the taxonomic diversity targeted by the venomous animal in nature, which likely affects the perceived ecological role due to differences in toxin activity in the model and the ecologically relevant species

So, if I read this correctly, one way to summarise your answer is that in some sense venoms are more common in mammals as they evolved venom at least four times +/- independently while in reptiles it evolved only once?

This is one of the best answers I've read on this site. Love it!

@MartinModrák actually, no, you've read this incorrectly. It's not more common in mammals. The point of my answer is that the evolution of venom in animals is a complicated story. There is no "one" trend that likely explains/answers the OP's question other than individual stories of natural selection and chance. Thus, why I start the answer with a link to the trait question which discusses natural selection of good/bad present/not present traits


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Problems reading my gel electrophoresis result
This is an image of my gel electrophoresis result.
I used the alkaline lysis method to extract E. coli plasmid and put it on gel electrophoresis. Based on what I had learned, I expected to see a band of nicked plasmid, a band of supercoiled plasmid and a smear at the positive end due to DNAse that was not completely removed.
However, I can't identify which band is which in my result and the smear from 200 to 1000bp having 3 bright bands is confusing me.
Could you please help me identify the forms of plasmid present in this result?

What plasmid are you trying to isolate, which size do you expect?

source: Stack Exchange

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

sort: votes


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Why people carrying the same SNP doesn't have the same Promethease report
I'm a frequent user of Promethease to run health analysis based on MyHeritage SNP data dump.
I ran two people through Promethease and both have the same SNP:
rs4307059 (T;T)
In one report we see an Elevated Autism risk and in the other report we don't even see this SNP mentioned.
Does anyone ran into this same problem?

counterbalancing snips that reduce autism risk/lower some polygenic score?

Are the two VCF files from the same testing company and did they use the same version of the test?

Welcome to Biology.SE. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. In particular, this question seems like would be a better fit for [Bioinformatics.SE], but please do not crosspost, instead request migration. This site is intended for questions about biological process or mechanisms, but your question seems to be entirely about a software product and is thus off-topic for this site.

can you migrate it please?

I can't migrate as I am not a moderator — you can request migration of this question by flagging your post for moderator intervention and explaining what you want and why. ——— Also, if you want to notify a poster who isn't the original poster you need to @ them (e.g. @ppaulojr).

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


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I am conducting an experiment with oil eating bacteria. However, I am struggling to find a method to check how much oil they cleaned?
I am experimenting to determine the optimum conditions for microbes to break down motor oil. The conditions I am going to test are different pH levels to resemble freshwater pH and saltwater pH. I will be using the chemical NaCl to adjust the salinity of the solution.
I have researched and found that one method is using a standard plate count. To just count the bacteria after incubating them for a few hours with the oil and pH concentration. The greater the number of bacteria, the more oil was degraded.
But my professor wants me to measure exactly how much oil is degraded by the bacteria to make a distinction from how much oil was at the beginning to how much is left at the end of the experiment.

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. In particular, it appears that you are looking for methods to quantitate how much oil is present in a solution? If so, that isn't really a biology question. In addition, it is generally true on SE sites that you are expected to show evidence of prior research. For both of these reasons your question is may be closed or downvoted.

You could measure and test just one component of the oil. Perhaps make sure that the oil is the only energy source for the bacteria. Measuring oil degradation or actual consumption?

Centrifuge out the oil and weigh it?

is the oil a purified hydrocarbon, or a commercial motor oil which can consist of up to 30% additives including various detergents, surfactants, friction modifiers, corrosion inhibitors, etc. In either case, a hexane wash (or two) of the spent media (after harvesting cells) would likely removed most of the residual oil, but it's hard to say how much of the additive package might be left behind. Make sure to use an appropriately sized separation funnel. Probably also want to work with an analytical chemist to quantify residual hydrocarbons compared to the inputs.


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What type of bacteria can I use to break down motor oil for a high school biology experiment? Any suggestions where I can find this bacteria?
I am experimenting to determine the optimum conditions for microbes to break down motor oil. The conditions I am going to test are different pH levels to resemble freshwater pH and saltwater pH. I will be using the chemical NaCl to adjust the salinity of the solution.
I have researched and found companies that provide oil-eating microbe powder. However, there is no information on what type or strain the microbe is in the power.
I'm failing to find information on what type of microbe would be best for this experiment and additionally where these types of microbes are supplied.

hit number one on google https://response.restoration.noaa.gov/about/media/who-thinks-crude-oil-delicious-these-ocean-microbes-do.html after searching for:bacteria that breaks down oil ,you can do a search for the different bacteria mentioned in the article

If you have the time, run an extra replication using dirt from a place where oil has been spilt for many years.


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What is the best way to stack parafilm wrapped petri dishes?
I have several petri dishes that are individually wrapped with bemis parafilm.  As space is somewhat limited, I've begun stacking them on top of each other, however in doing this the wrapping for each plate will sometimes get stuck to the wrapping on the other plates.  Is there a good technique or separator or tool or something I can use to both efficiently store my plates and not jeopardize their parafilm seal?

Thinner strips of parafilm.

Is a sheet pan rack/"speed rack" a possible option? Or would that take up too much space for the number you need?

Yea that would take up too much room.  If I had plenty of space, I would just have them all laid out.  Considering trying to use 6"x6" wax paper for hamburger meat to separate them.  Kind of need to vertically store them and access them daily to track growth progress.

Do you need to individually wrap them? We used to just store a stack of them in the plastic bag the stack came in, resealed with tape at the end.

Our lab uses food-wrapping-foil to seal agar petri dishes instead of parafin. We buy a rool at grocery store an cut the rool with sharp knife into cca 1.3cm wide minirools which we than use. It is cheaper than parafin and food-wrap comes sterile from production. Never had problem with plates sticking to each other when stacked.

Guess it depends on how long you need to store them. Sometimes I've put them in a refrigerator-sized plastic tupperware container with a sealing lid. Didn't last quite as long as parafilm, but kept them from drying out long enough for my needs.

I ended up getting the 6"x6" wax paper for hamburger meat and putting a sheet between stacked and wrapped petri dishes which prevented them from sticking to each other.  Their footprint is now bigger but it works.  I could cut the sheets down or probably get smaller ones if I really wanted though.
Above there are some interesting other solution suggested like saran wrap and other methods of storing them that may work for some other use case.  As I need to document my dishes progress regularly they get handled at least daily so 'extra' or a thick application parafilm is used to make sure they stay tightly sealed.


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Lab device to periodically, automatically transfer zooplankton between containers
I need a device to periodically draw a sample of transfer small aquatic organisms from one container to another without crushing/killing them.  Each sample would be on the order of 10ml.
My sketch of an idea is below.  It would use a pump to pull the sample from the source container into a reservoir through one check valve and pump it into the destination container through another.
I believe I can build it out of a peristaltic pump and commonly available check values, , but I'm worried that zooplankton won't fit through the values.
I'm also curious if there's a better and/or off-the-shelf solution for doing this kind of thing.

As if feeding predators in the second tank? Perhaps a "Fraction Collector".

There are multiple kinds of check valves such as ball valves.

@DKNguyen I've spent some time looking and I can't find any that useful for the small volumes I need other than those used in aquariums (which might work).  I'm new at this, so maybe I don't know which suppliers to check?  Any suggestions?

@PolypipeWrangler Yes, that's exactly what I'm doing.  The fraction collectors I see online don't look suitable.

Mcmaster Carr maybe?

If zooplankton are small, a dripping tap might work. Or in the predator tank have a screen (permeable to zooplankton only) and let them live there.

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.


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why do spirogyra turn brown after formation of zygospore?
in the sexual reproduction of spirogyra, the reproductive parts of the 2 spirogyras come together to form a structure called zygospore. after this formation spirogyra turns brown. why is it so? i want to know the reason of colour change only

Can you provide a reference for this happening? Are you sure this is actually something that happens naturally versus an experimental manipulation (e.g., staining)?

my professor asked me this. He said this happens and that no one has been able to answer this. i was thinking the reason is death

"I said so" might be good enough for your professor, but it's not sufficient for this site. We expect questions to demonstrate prior research, which includes evidence that a thing happens before asking "why".

i am sorry for the inconvenience but he is not a very good teacher


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database of Animals/insects which would contain their queriable geographic location?
Is there a database of Animals/insects which would contain their queriable geographic location?
I would need to perform a rather simple query, such as Animals of <Location>, where Location is some well-defined geographic area such as Elephant Nature Park - Thailand.
So far I have found multiple lists on Wikipedia and other webpages, however they seem to be quite incomplete as their intersect is quite small. Moreover, I have found EOL (Encyclopedia of Life) collections but they appear to struggle the same way.


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Is Mallow toxic to livestock or is it only Parviflora that is?
Thank you for your time.  I have a question about toxic plants.
Mallow plants.  Specifically, my horse (while up in North Central Arizona for the Summer) had access to (and ate, unsure how much), Malva Neglecta (identified in a fb plant identification group from photos).  I have found plenty of evidence of Malva Parviflora being toxic to livestock, depending on quantity consumed. There is a write up about several horses in Australia that died from ingestion and others got rapid onset laminitis.  Link: https://pubmed.ncbi.nlm.nih.gov/27341541/#:~:text=Reason%20for%20performing%20the%20study,euthanasia%20after%20ingesting%20the%20plant.
Should I assume both plants are toxic since they are from the same family, or is it possible only the parviflora is toxic and the malva benign?
The reason for my question, is that my horse has developed some hoof soreness issues over the Summer, and I am wondering if the mallow plants could have been an additional factor, along with too much toe sole being removed when trimmed, a very rocky pen, and a particularly wet monsoon season this year.
I posted in a vet group, but got no answer.  I think many of them just don't know.

According to Livestock Poisoning plants of Oregon (1969!) it "should be regarded with suspicion".  To quote: "Another species of cheeseweed or mallow occurring in our area is Malva neglecta Wallr. (Fig. 57), and it, too, should be regarded with suspicion". But, I suppose, that in itself is not very informative.


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Why is it so that phloem parenchyma is absent in most monocots?
I am currently studying anatomy of flowering plants and came across this statement in my textbook:
'Phloem parenchyma is absent in most of the monocots.'
We learnt that the main function of phloem parenchyma is to store food material and other substances like resins, mucilage and latex. Do monocots have some other structures for the same purpose? Why is it that they lack these type of cells?

@MaximilianPress I did look up as many Q and A forums as I could (posting questions only after thorough research) and mostly the answers I saw didn't actually explain the reason and instead wrote it down as a fact. Answers on Quora especially , were very vague and not that helpful. I'll edit the question accordingly , thanks.

@MaximilianPress please don't recommend users look up info on such disreputable (and low quality) sites such as Quora.  -_-

@theforestecologist fair enough, deleting comment.


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What is my original skin tone i.e. my genetic skin tone with minimal/ subtle sun tan?
When I was younger (about 2-3 year old) I had a lighter skin color and now I have a darker skin color ( currently 19 years old ). Now as a teen I have became conscious about my skin issues ( including sun tan). I have recently started using Sunscreen in the hope to get closer to my original skin tone but I don't want to keep any false expectation so I want to get an idea of What my original skin tone could be like i.e. my skin tone with minimal/subtle sun tan ?
I searched through internet to get the answer and found a convincing answer on Quora but I don't trust the source also the answer mentions some facts that I've never heard of so I'm posting this question here.
Quora Answer
Here's the summary of the answer for a quick perusal:-

Most children born of darker skinned parents are lighter in color. Both because the melanocytes take some time (mostly) to really start working. Also after a while they stop protecting babies from the sun with a cloth, and let the sun change things.
So I would say your ‘real’ color is what it was at six months of age. Of course, your sun tanned skin is not ‘unreal’ either, but it is different. I believe the six months of age answer is what you are looking for.

Welcome to Biology.SE! While we encourage new users to be active and ask questions, we also recommend that duplicates are not posted. This question seems awfully similar to this one, and if the existing answer for that answers your question, kindly close or delete this question. Ensuring that duplicates don't exist guarantees a more organized website that users can navigate easily. If the link I shared answered your question, please don't hesitate to upvote the answer (and/or the question)!

@Zo-Bro-23 I read that question earlier before posting this one but these are different questions the one mentioned by you ask "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?" whereas I'm confused about " What my skin tone is in first place ?" How do you find it the same ??

I get it now; you're right that these questions are different. My bad, sorry!


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Is taking antimalarial drugs a confounder when exposure is "having sprayed insecticide in the house" and the outcome is "malaria infection"
Morning all,
I am curious as to whether the concept of confounding applies in the following situation: Specifically I want to know if "taking antimalarials" is a confounding variable.
The exposure being investigated is "having sprayed insecticide in the house in the last 12 months", and the outcome is "infected with malaria".
Also, would it make a difference if the drugs were taken for preventative purposes rather than curative?
Thanks
T

To determine whether "drug" ("taking antimalarials") is confounding the relationship between "sprayed" and "infected", first you would have to investigate empirical evidence or your intuition regarding the relationship of "drug" with either of the two. Next, consult the back-door criterion. If you, like me, believe that "drug" does not affect "sprayed" but does affect "infected", then it is a collider and you should not control for it.

Hi, thanks for your response. I believe "drug" is associated with "sprayed", yes, as both are preventative measures (a prophylactic drug, that is), but not a causal association, no.  Would that make it a collider, then? I am still working on the DAG - getting myself a little confused with this back-door criterion.

It appears that you have to clarify the relationship between "drug" and "sprayed" in your head. If one affects the other --either directly or indirectly-- and you want to examine the relationship between "sprayed" and "infected", then you need to control for "drug".

Hi vkehayas, thanks for coming back to me on this. Yeah, the relationship is somewhat confusing. As a prophylactic drug, such as is used in an MDA campaign, the association is really just that, an association, not one causing the other. It just so happens, that a person who sprays their house is more likely to also participate in the MDA campaign, and so take the drugs. As a curative drug, however, getting malaria might induce persons to 1) take curative drugs, and 2) start spraying their house - but here they are both caused by malaria.

But, not spraying could cause malaria, which in turn causes someone to take the curative drugs. But, here, I believe curative drugs are an effect, which rules it out as a confounder.


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Structure of pores of tinder fungus
I’m interested in various natural structures: fractals, packing, hyperuniformity etc.
Here is photo of pores of tinder fungus or Fomes fomentarius:

The pore distribution is neither hexagonal packing nor purely random.
I see strange patterns like large circles.
Is there any information on the pore geometry?
What is the pattern?

I've had a rummage around on google scholar and there's some truly bizarre papers out there related to this fungus, but nothing like what you're asking. The folks on our [bioinformatics.se] site may just have access to resources not listed. Perhaps you could try there.

You do have to remember that our brains are very good at finding patterns even if there aren't any. It looks fairly random to me, but I have no data to back that up. I don't even know how you would go about a randomness analysis in this case.

A vague idea popped into my head, a suspicion that the [astronomy.se] site might have knowledge of software that could perform exactly the kind of analysis you're looking for. I've no idea how to phrase the question to be on-topic there mind you. Same goes for our [dsp.se] site. In fact, having glanced at their site, I'd bet on the latter.


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Copyright free species image database
I assume that there are several websites with licence-free photographs of animals, plants, fungi, etc. (properly identified at species level, of course), but I have not been able to find them. Can you tell me which sites you know of?
Thanks in advance!

I’m voting to close this question because it is not a question about biology, but a general question about resources showing no evidence of any attempt of the poster to find the information for himself.

It depends in part by what you mean by "licence-free photographs".  Many photos are available which are free to use if one credits the author and/or references the license terms.  If you mean free to use in any way without restriction, that is (in the U.S. at least) ones in the "public domain",   I'm not aware of sites that have only public domain photos and identify by species.
However there are sites where one can find such photos (at times).  Specifically, one is "commons.wikimedia.org".  To search for such photos there, one has to do a qualified search.  One way is to go to the search page, select "Search in: File" from the list of "namespaces", and search for the species name along with the quoted string "work is in the public domain". You'll then have to check the "File:" page of one you might want to use to assure it's in the public domain for the country you want to publish it in.


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Why instects aren't blinded by Sun?
Insects have compound eyes with very wide field of view, but when they're in sunlight some of ommatidium would be directly facing the Sun. Doesn't that damage photoreceptors?

Why do you think insect eyes are not damaged by sunlight?

@BryanKrause that is not an answer to my question. I don't know, if I knew the answer I wouldn't be asking a question, they cannot blink so they need to look at Sun. And if they go partially blind then what's the point of having compound eye looking almost everywhere when half of it will be useless later

It doesn't make much sense to ask a why question unless you have evidence that the thing you're asking why actually happens. How can anyone answer "why" for something that isn't true?

@BryanKrause So they go blind? Then why they have initially such wide range of view if insects are gonna be partially blinded

Their photoreceptors are going to be damaged if exposed to enough UV light, yes. I think you're making poor estimates of how much a given receptor is actually pointed directly at the sun, though. Also remember that most insects live short lives.

Your question interested me, I've posted: Does the Ogre-Faced Spider regenerate part of it's eyes daily? which I thought might interest you.


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Can house pets show signs of zoochosis?
Animals in captivity can show mental problems, it's been observed in zoos and aquariums. Very limited area can negatively impact animal leading them to such things like over-grooming pacing or even self-mutilation.
Could house pets that are kept indoors all the time, like for example cats, shows signs of zoochosis or other mental problems?
Source

Yes. Zoochosis doesn't seem to be an accepted term in the scientific community yet, however, this sort of thing is known as stereotypic behaviour, so unless you know that term, you would have trouble finding any scientific reports. As far as I can tell these behaviours are a often a result of boredom and stress.
It is very common in household pets, particularly those on the intelligent end of the scale, like parrots.
Many sources (e.g. AllAboutParrots.com) will tell you signs to watch out for in parrots that are bored - it often results in destructive behaviours, including self-mutilation (usually plucking feathers, but also gnawing on limbs). This has also been scientifically studied
Cats exhibit this sort of behaviour, particularly if weaned or taken away from their mothers early (<12 weeks). They can also exhibit obsessive-compulsive behaviours
Dogs also show stereotypic behaviours, particularly when not walked regularly.
Farm animals exhibit stereotypies, you can even see it in chickens and you can even breed to select against some of these behaviours.
I think it is safe to say that most animals that are kept confined and a non-stimulating environment will experience some form of stereotypical behaviour, whether we recognize it or not at this point in time. Certainly for those species we interact with a lot we can see it frequently.


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Primer Optimization for full length gene amplification
I need your help. I have sequences of my desired gene (WRKY TF) from RNA seq data (it was a denovo assembly performed on agave sisalana). Now i need to amplify full length of that gene for which I designed degenerate primers (from 1st nt of gene to the end) . However, I am unable to get the desired band. My gene size is 1000 bp but the bands I am having after PCR amplification is near to 1000 bp (around 800-700 bp) but not exactly 1000 bp.
Please help me to sort this issues..
Note: Please find the gel pic in the attachment. ladder used is 1 kb

If you have the full sequence, why are you using degenerate primers?


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Are there any species whose descendants can meet their ancestors from 100 generations back?
I.e. Humans can sometimes meet even their great-great-grandparents, but are there any species that can be alive at the same time as their great-great-……-great-grandparents? I imagine it would be those species with a long lifespan and an early age of first reproduction.

Do the species have to be animals?  Many trees would seem to qualify.  Then there's the Greenland shark: https://www.newscientist.com/article/2100823-worlds-oldest-vertebrate-is-a-shark-that-may-live-for-500-years/

I’m voting to close this question because it comes under the category of “idle amusement” rather than being a real problem in biology faced by the poster.

@David: Is it an official rule, that questions must relate to a "real problem in biology faced by the poster" ?

@KaPy3141 I quote from the [Tour] "Focus on questions about an actual problem you have faced. Include details about what you have tried and exactly what you are trying to do." And in the Help on  Asking Questions "are more than just mindless social fun"

I take it that questions must not be motivated by the reactions or interactions they cause. I think I get it!

Yes, cryopreservation works quite well for many species, including multicellular animals. So you can freeze the ancestor and wait until the descendant is there, then unfreeze them. A good recent example in the news would be the Siberian worms that woke up after being frozen in permafrost for a very long time.
Cryopreservation is routine in laboratories, to freeze ancestors and compare to descendants; see the Long Term Evolution Experiment. It doesn't work well for every organism of course. In principle it might work for humans.
Some bacteria will sporulate, and in spore form they can persist for thousands of years theoretically. They don't even need cryopreservation. There are other organisms that do something similar as well.


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Do some animals have a tolerance to the negative effects of inbreeding?
Are some animals more or less tolerant to inbreeding? By tolerant I mean do they have a genetic mechanism that allows them to inbreed and corrects for issues introduced through this? When I started searching for this I quickly ran into theories on how inbreeding is avoided but did not find information on whether some animals have genetic mechanisms that make them less likely to get negative effects from inbreeding.

Can you expand on what you mean by genetic mechanism? Do lethal recessives that prevent development and thus prevent offspring count?

@kmm I hadn't considered that, I was thinking of more of a self-correcting technique that would prevent to many occurrences of the same genetic markers from being chosen or just a level of fault tolerance where the critical mass of bad combinations is higher than most other vertebrates.

@kmm I'm not very well versed in biology but I was looking for something similar to how TP53 works in humans and elephants to prevent bad DNA copies. I was curious if such a mechanism existed in some animals at conception to prevent the negative mutations of inbreeding. I'm not sure if such a parallel mechanism exist but I figured if they can correct for bad copies that it would be possible to correct for too many pairs being duplicates or rather not enough entropy. Again sorry a lot of my terminology is a mix of computer science and what I remember from high school biology.


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Why is movement of water through cell walls considered the apoplast and symplast pathway?
Why would the movement of water through cell walls be considered the apoplast and symplast pathway? I understand why it's considered the apoplast pathway (as the water is moving through a non-living part by diffusion) but should it not be considered symplast since that is only for when water moves through living structures? Thanks in advance.

Your question could be a bit more clear, but I think you are referring to this-

The apoplast is the space outside the plasma membrane consisting of intercellular spaces where the material diffuses freely; it includes parts such as the cell wall and intercellular spaces.

The symplast consists of the cytoplasmic network of plant cells interconnected by plasmodesmata.

I suppose, in the motion of the upper stream of water (as indicated by the blue arrow in the diagram) you can see that to enter the symplastic pathway, the water has to first pass through the apoplastic pathway, in a sense. That is, it cannot 'teleport' directly into the cell's protoplasm, it has to pass through the cell wall.
Hope that clears things up.


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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?
I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19.5 kDa) with an N-terminal His tag and a TEV cleavage site between the His tag and the N-terminus of the domain. The purpose is to study the properties of the domain in isolation, but without any tags that might interfere with its function. Using the His-tag will make for easy purification, after which the tag can be removed with TEV protease, leaving only a glycine at the N-terminus of the domain, which will not affect my experiments in an appreciable way.
The way I've gone about doing this is to use a forward primer that, after the restriction site and start codon, contains the sequence which codes for the his tag followed by the TEV cleavage sequence, followed by the first 6 codons of the domain sequence. The reverse primer contains the final 6 codons of the domain sequence followed by a stop codon and restriction site. These primers are used to amplify the target domain sequence from a plasmid that contains the full protein sequence, but with the N-terminal cleavable tag attached. The plan is then to clone this DNA insert into a pET21b vector to transform into DH5alpha / BL21 cells.
However, it seems like I'm having problems during PCR amplifying the sequence of the domain from the template DNA. After cloning my purified PCR product into the pET21b vector, and successfully transforming into DH5a cells, sequencing the section of the cloned plasmid with the insert revealed that the insert DNA consisted of only the forward and reverse primer sequences on the ends, sandwiching a single alanine codon. Put another way, the inserted sequence reads as (His-tag)-(TEV cleavage site)-(First 6 codons of domain)-(Single Ala Codon)-(Last 6 codons of domain). This would mean all my cloning steps were fine, but the insert DNA was copied incorrectly during PCR. If it were just the primer ends, I'd think there was some sort of overlap between the primer sequences, but there is that one alanine from the domain template DNA (alanine is the next residue after the first 6 in the domain sequence). A weird result, and I'm not sure where to begin troubleshooting.
My question is, is there anything that I'm doing in this procedure that might stand out as particularly problematic that would cause this issue? Or more generally, is there a better way to put a TEV protease-cleavable his tag on the N-terminus of a protein? Any advice would help, even if it's just to point in the direction of useful references or protocols, and I'm happy to clarify as needed. Thanks!

I don't think your approach is problematic, I think it's just a  PCR technical issue. Have you run your PCR product on an agarose gel to check it ? How have you purified you PCR product : column, gel extract ? Can you add the primers sequences ? What I can envision so far is that your primers may have Tm to far apart.

I hadn't run a gel on it, but I used a Qiagen pcr cleanup kit (mini eppendorf column). The primer sequences are: Fwd: TAAGCAGAATTCATGCACCACCACCACCACCACGAAAACCTGTATTTTCAAGGCCTGGATTATAGACCAGTG
Rev (reverse complement, 5'->3'):TGCTTACTCGAGTTATACTGTTTTTGTGAAGTACAG

Welcome to Biology.SE! Please [edit] the above information into your post (comments are ephemeral and often overlooked — as such they should not be used to convey information important to understanding the question). ——— Note that you should always run a gel to check the size of PCR products — knowing the size (and number) of bands produced could be key to answering your question. In addition, it could be helpful for you to post the target (template) sequence — a (cryptic) primer binding site is one of many possible explanations for your result. Thanks!

Ok, so if you haven't run a gel I would do that first and as mention by @tyersome you should always do it so you know what you're working with. In the meantime if you could share the target sequence it would help us check if there is something happening there. Thanks.


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Rapid generation advancement in Maize breeding
Maize (Zea mays L.) is one of the important crops and its acreage is increasing considerably especially in Asia and Africa.  The common production system in tropical and subtropical climates is rain-fed. From the “Mendelian era” of nineteenth century we have now reached the stage of “Genomics era” in twenty-first century where several new tools and techniques are available to understand the genetics of traits and accelerate the breeding process. I want to induce early flowering in commericially grown Maize to reduce the life cycle of the crop. Any method to fast track the generations of the breeding cycle in Maize. Is Rapid generation advancement method established for Maize crop? It will help to reduce the normal crop life cycle which is 120-150 days to 60-70 days so that in 1 year 3 cycles of the crop can be grown.

Depending on what you want, a 60-day generation for maize has been established with some lines suitable for research ("mini-maize"). I doubt that these lines are agronomically interesting, so if your goal is to breed these with the idea of developing germ plasm for production they may not be useful. If, however, your goal is to do research and determine variants useful for introduction into an agronomic background, then it may be useful. It looks like there are related strains optimized for gene editing.
If you are mostly just interested in traditional breeding in a fixed line, then there are a variety of environmental conditions that can accelerate flowering in most plants. The main issue is that these conditions may interfere with your phenotyping regimen or with desirable outcomes such as yield.
There is additionally significant natural variation among maize types (some apparently with <60d flowering time, which seems surprising to me). Possibly using one of those early-flowering cultivars as a starting point or founding parent could be interesting.


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What is this red little cocoon like creature here?
I found this bug here outdoor on the wall of my backyard. I’m in California.
Red and looks like a cocoon, notice some tiny dots on its back. About 1cm.
Does anyone know what kind of insect is this? Seen it there for a few days now.
Thanks

"Seen it there for a few days now" On the exact same spot or was it moving?

On the exact same spot!

This looks like a lady beetle pupa.  Given the appearance and your description of it's size, my guess would be of Harmonia axyridis.
Here'a link, with a picture of another pupa about half way down the page: https://edis.ifas.ufl.edu/publication/in361. This species has a diversity of colorations, both on the adults and the pupa.
Here's an example of another pupa of what is most likely the same species (from https://bugguide.net/node/view/410817/bgimage):


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Atom or Cell? Which is the basic unit of life?
As it is said that everything in this universe is made up of atom and molecules and atoms is called the building block of matter. But then why the cell is called the basic unit of life, why not atoms?

What do you think distinguishes "life" from "not life"?

I think you have a misunderstanding of the term unit as used in unit of life. Unit here refers to the smallest building block that is somewhat complete and operational in the relevant context (here: life).
Cells are called the units of life because all life we know is composed of cells. (There are some borderline cases like viruses, but even those rather resemble a cell than an atom.) On the other hand, if you cut a cell in half, it is certainly not operational or alive anymore.
You wouldn’t call atoms units of currency, even though all coins and bank notes are made up of atoms (ignoring digital currency for the sake of the analogue).


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SARS-CoV - relative size of the spike protein
I was given the task of determining the percentage of the S-protein of the SARS-CoV relative to the total of its proteins from the attached image. However, I have been given no explanation of the image, and with a physics background, I simply do not understand it. Can someone please explain to me how it would be possible to solve the task from the given image (i.e., explain the image).

I'm not going to give you the final answer, because this is still a class assignment, after all, but I'll give you some tips. What you are looking at is a Western blot of whole-cell extracts from a cell line called Vero, either on its own (vertical ane 9, from numbering across the bottom) or infected with various viruses carrying specific genes, as indicated. Lanes 1-7 are from Vero cells infected with the BHPIV3 viral vector (a live-attenuated virus that can carry genes from another organism). Lane 1 is just the viral vector itself, with its own proteins. Lanes 2-7 are from cells infected with the viral vector carry certain genes from the SARS coronavirus. Lane 8 is from cells infected with SARS-CoV itself (so it carries all the previous genes). The numbers along the far right side are molecular weights, in kilodaltons.
A Western blot is performed in three parts - 1) separating the protein samples (whole-cell extracts) by molecular weight (size) in an SDS-PAGE gel by using an electric field, 2) transferring the separated proteins to a membrane, also using an electric field, and 3) using some sort of probe (usually a specific antibody) to determine what is present and in what amount. In this case, two antibodies were used. The lower, narrow image shows the samples probed with an antibody that recognizes the HPIV3 F protein, which is present in all the BHPIV3-infected lanes, in relatively equal amounts. This can be determined because the size/intensity of the different bands in each vertical lane is directly proportional to the amount of that protein present in the original sample.
The upper part of the image shows the extracts probed with an antibody that evidently recognizes the SARS S, M, and N proteins, but apparently not the E protein (as Lane 6, with the SARS-E virus, is blank). Using this information, you can now determine which bands correspond to which protein.
Keeping in mind that Lane 8 contains all the proteins from the SARS-CoV virus, while the previous lanes just contain certain ones as labeled along the top, you should now be able to use ImageJ to answer the question. I will give you one hint - there is much more information present than you need to answer the question. You actually only need 4 (well, maybe 5) of the lanes. I'll leave it to you to figure out which ones.

Thank you for your very elaborate answer; it helped a lot. One question. You say that lane 8 contains all the proteins from the SARS-CoV virus, but that I need 4-5 of the lanes to answer the question. But if lane 8 contains all the proteins, could I not get an estimate of the relative amount of the spike protein from this lane alone?

@Physics101 You need the other lanes to tell you which band the S protein is, and to tell you which (if any) bands are background artifacts. The E lane is also important, as it affects how you report your results.

Okay, thank you very much.


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What does does a blood sample tell you about an individual's identity?
I am working on a fiction/mystery scene where blood is found in a particular character's residence but the character themselves is missing. I would like to understand whether the law enforcement/forensics team are realistically able to identify if the blood belongs to the missing character, without having a prior blood sample or DNA of this missing character? If not what details are they able to learn from the sample eg. gender, age, physical characteristics etc?

I'll add a full answer later, but sex, some physical characteristics (e.g. hair, eye, skin colour) and ethnicity can be determined (not perfectly) using DNA from blood.

@user438383 thank you very much, looking forward to your full answer.

The forensics team would also use other sources of DNA found around the house, like hairs and skin cells, to confirm (or not!) that the blood is from the person who lives there. You can also take samples from this character's relatives to establish if the blood came from someone related to them.

@MattDMo very helpful, but if there's other people (or even one person) who visit(s) on a regular basis then their hair, skin cells etc would also be there?

@FrontEnd there would, but the majority would likely be from the resident. They would do things like look at the hair under the microscope to see if it matches the occupant, take DNA samples from the bed, a toothbrush, comb, or towel, that kind of thing. It wouldn't be just one sample, they'd take dozens. If one of the visitors is a romantic partner who sleeps over regularly, then it might be a little more difficult, but forensics people have lots of tricks up their sleeves. There are lots of accessible sites out there that explain aspects of criminal forensics, you might want to look them up.


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What are evolutionary reasons for humans' limited regeneration abilities?
As far as I understand (I am not a biologist), a ability of a species arises during the evolution if:

It increases reproduction chances
It is not too energy expensive
It is physically possible

At the same time, if a human loses his/her hand/eye/tooth/almost anything, it won't regrow. However, if such regeneration was possible

It would definitely increase reproduction chances, because it would make it much easier to survive (or maybe something even more direct, like reproduction of sexual organs)
Ability to regenerate isn't supposed to require any energy until the moment such regeneration is needed (and, therefore, energy spending is justified)
It seem to be indeed physically possible, at least for some organs (Wikipedia provides examples of species who can regenerate their teeth, body parts (tails) or even lungs)

This seem to be strong reasons why this ability should have been gained during the evolution, but this didn't happen. Why?

I think the claim #2 (energy) requires more detailed examination of what regeneration involves. Also, the ability to regenerate is rather an exception than a rule among animals, so singling out humans is rather anthropocentric.

In order to understand limits of evolution of regenerative abilities you must understand the molecular biology of embriogensis including the main genetic players.
https://journals.biologists.com/dev/article/147/14/dev190629/224370/Mechanisms-of-human-embryo-development-from-cell
You should appreciate the complexity of embriogensis! Obviously, this puts enormous constraints on evolution.


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What is the meaning of harboring cryptic in below sentence?
Tissue culture became more widely used at this time because of the introduction of antibiotics, which facilitated long-term cell line propagation, although many people were already warning against continuous use and the associated risk of harboring cryptic, or antibiotic-resistant, contaminations [Parker, 1961].

I’m voting to close this question because it is off-topic (english language usage rather than biology as defined in the [help]) and demonstrates a lack of the expected prior research — an internet search would have turned up relevant definitions for both of these words.

The natives are more friendly here

Harbouring, using harbour as a verb and in this meaning containing/hiding (see 3rd and 4th definitions at Harbour)
Cryptic = hidden/difficult to find - this is how the word is often used in biology, particularly zoology.

So it means containing hidden contamination.

Yes, that is correct.


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Why doesn’t heart have smooth muscle tissues?
Smooth muscle tissues are involuntary. And so is cardiac muscle tissue. So why doesn’t heart have smooth muscle tissues like most organs?
I know that they are visually different (branched vs non-branched, striated vs non-striated) but how does that affect the heart?

Striated muscle contraction is synchronized by the structure at the individual fiber level, this also produces a lot more force. They also have a faster recovery time than smooth muscle. Presumably the heart needs that higher power, synchronization, and/or quick response to pump blood under high pressure. I would put money on synchronization at the individual fiber level being the main factor, but I could find no definitive study, possibly because the effects can't easily be separated.
https://journals.physiology.org/doi/full/10.1152/advan.00152.2018
https://www.ncbi.nlm.nih.gov/books/NBK526125/


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What is the difference between cuboidal and columnar epithelium (other than their shape)?
The difference between squamous and cuboidal/columnar epithelium is clear. Squamous is used for filtration and diffusion while cuboidal/columnar is used for absorption and secretion.
But if both of them are used for absorption and secretion, what is the difference? Why would there be two different tissues that have the same function?

I hope this helps..https://pediaa.com/what-is-the-difference-between-cuboidal-and-columnar-cells/. If you still face any issues, let me know I'll give a detailed answer.

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please consult the [help] starting with [ask] for details.


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Structure coordinates in PDB file
How the atoms-residues-amino acids structure information prioritized? Specifically, I am trying to understand how the first atom is identified since it does not seem to correspond to the first amino acid in the sequence. I assume it's based on the structure but is it bottom to top, left to right and such. Thank you.

Welcome to SE Biology. I have provided an answer to what I think is your question, but it would have been better if you could have referenced a PDB file so it was clear what you were referring to. And what do you mean by bottom, top, left and right? These terms have no meaning in relation to protein structure.

The atom numbered 1 in a PDB file is the most N-terminal atom visualized by the structure determination — the most N-terminal amino acid, the co-ordinates of which are presented.
If the X-ray diffraction (or whatever technique used) does resolve the first amino acid, then it will, in fact, be the first amino acid. The following is an arbitrary example from 4LI3 (chain X):
ATOM      1  N   MET X   1     100.329 111.822  35.431  1.00 66.81           N
ATOM      2  CA  MET X   1     100.845 110.803  34.526  1.00 67.85           C
ATOM      3  C   MET X   1     101.961 111.361  33.646  1.00 71.14           C
ATOM      4  O   MET X   1     102.979 111.840  34.153  1.00 77.28           O
ATOM      5  CB  MET X   1      99.722 110.256  33.648  1.00 61.70           C
ATOM      6  CG  MET X   1      98.581 109.621  34.412  1.00 66.53           C
ATOM      7  SD  MET X   1      97.327 108.947  33.300  1.00 82.23           S
ATOM      8  CE  MET X   1      96.071 108.440  34.463  1.00 69.80           C
ATOM      9  N   ALA X   2     101.754 111.288  32.331  1.00 67.01           N

If the X-ray diffraction does not resolve the first amino acid, or if the structure is of a fragment of the protein that does not contain the first amino acid, then the co-ordinates of the first amino acid are not listed in the file and ATOM 1 is from the most N-terminal amino acid. The following is an arbitrary example from 1BTE (chain A), starting at amino acid 7:
ATOM      1  N   GLU A   7      15.888  47.505  13.150  1.00 34.63           N
ATOM      2  CA  GLU A   7      14.455  47.789  12.947  1.00 33.53           C
ATOM      3  C   GLU A   7      13.538  46.900  13.794  1.00 29.91           C
ATOM      4  O   GLU A   7      12.342  46.832  13.476  1.00 30.54           O
ATOM      5  CB  GLU A   7      14.084  47.715  11.461  1.00 37.16           C
ATOM      6  CG  GLU A   7      14.284  46.356  10.821  1.00 41.38           C
ATOM      7  CD  GLU A   7      14.124  46.366   9.313  1.00 43.82           C
ATOM      8  OE1 GLU A   7      12.959  46.323   8.849  1.00 46.10           O
ATOM      9  OE2 GLU A   7      15.151  46.420   8.600  1.00 45.51           O

(Knowledge of the first amino acid is from nucleic acid sequencing.)


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Detecting multiple compounds on a lateral flow immunoassay – is this a case of monoclonal vs polyclonal antibodies?
I am working on developing lateral flow immunoassays for drugs of abuse and needed some advice on detecting multiple drug compounds in one immunoassay.
As an example, an existing LFIA on the market tests for amphetamines, and detects the following compounds as positive at varying levels:

d-Amphetamine
d,l-Amphetamine
l-Amphetamine
3,4-Methylenedioxyamphetamine (MDA)
β-Phenylethylamine
Phenylpropanolamine
Tyramine
p-Hydroxynorephedrine
(±)-Phenylpropanolamine
p-Hydroxyamphetamine
d,l-Norephedrine

These compounds are all tested in one test strip — not multiplexed; the presence of any one of those compounds above the cut-off level will cause the single test strip to show a positive.
I don't quite understand how antibodies work and have a few theories:

Polyclonal antibodies have been used on the test line, which means all these compounds are detected
A mixture of monoclonal antibodies have been used, to detect all these compounds
These compounds are all chemically similar enough to be reliably detected with a single monoclonal antibody

Which of the above would be correct? Or am I misunderstanding this entirely and the answer is something different?

Background: I worked for a number of years as a product scientist for a fairly well-known antibody company, designing and producing polyclonal and monoclonal antibodies from several species.
Of your three theories, any one of them could be correct. Polyclonal antibodies are the cheapest, easiest, and generally fastest way of producing antibodies to a particular target, and I would imagine that they're used pretty extensively in LFIAs and other clinical immunological tests. However, polys have a major limitation: reproducibility. Animals' immune responses can change over time, even with regular booster immunizations, so it can sometimes be difficult to maintain the exact same specificity and sensitivity over multiple lots or batches, especially if you have to change animals. One way around this is to make very large lots, but they may end up degrading over time, even if kept at very low temperatures.
One way to get the recognition of multiple epitopes that polyclonals have with the epitope stability that monoclonals have is to make a "multiclonal" mix of monoclonal antibodies. This could be anywhere from 2 to a dozen or more clones, depending on the number of targets you're trying to analyze.
A single multiclonal antibody is also possible in this circumstance. While a monoclonal does only recognize one epitope, that epitope could be rather general and exist on multiple molecular configurations. An example of this type of antibody is Cell Signaling's Phospho-Akt Substrate (RXXS*/T*) rabbit monoclonal antibody (clone 110B7E). Instead of recognizing phosphorylated Akt/Protein Kinase B, this clone recognizes its phosphorylated substrates that have an Arg-X-X-pSer/pThr motif in them. It has been shown in tandem mass spec studies to bind to hundreds of unique peptides with this motif.
In the context of this particular question, it is perfectly reasonable to believe that the mixed amphetamines LFIA could rely on a single clone that recognizes a generalized "amphetamine-like" epitope that is present in all of the molecules listed, but (hopefully) not in other chemicals that are not drugs of abuse.

In general, monoclonal antibodies are used as primary antibodies and conjugated to the nanoparticles due to their ability to bind specifically to a single epitope of an antigen (1). Even a small change in the structure of the epitope can affect the binding to antigen, so this automatically makes your last statement impossible because a single monoclonal antibody can only recognize one epitope of the same antigen (2). In contrast, polyclonal antibodies are mostly used at the test band because they can recognize a host of antigenic epitopes, meaning that they are able to recognize highly similar compounds that vary in a single or small number of epitopes, making them ideal for generating signal for detection (1,2). But keep in mind that use of polyclonal antibody can also lead to increased risks of cross-reactivity (false positive result) (1,3).
Resources
(1) Qriouet Z, Cherrah Y, Sefrioui H, Qmichou Z. Monoclonal Antibodies Application in Lateral Flow Immunochromatographic Assays for Drugs of Abuse Detection. Molecules. 2021 Feb 18;26(4):1058. doi: 10.3390/molecules26041058. PMID: 33670468; PMCID: PMC7922373.
(2) Neil S. Lipman, Lynn R. Jackson, Laura J. Trudel, Frances Weis-Garcia, Monoclonal Versus Polyclonal Antibodies: Distinguishing Characteristics, Applications, and Information Resources, ILAR Journal, Volume 46, Issue 3, 2005, 258–268, https://doi.org/10.1093/ilar.46.3.258
(3) Reschly-Krasowski JM, Krasowski MD. A Difficult Challenge for the Clinical Laboratory: Accessing and Interpreting Manufacturer Cross-Reactivity Data for Immunoassays Used in Urine Drug Testing. Acad Pathol. 2018;5:2374289518811797. Published 2018 Nov 21. doi:10.1177/2374289518811797

This is not correct, especially your bolded statement. It is perfectly possible for a single monoclonal antibody to recognize multiple targets, even if they are composed of different amino acid sequences (in the case of protein targets) or atoms, in the case of small molecule targets. Any one of the OP's proposed mechanisms could be correct.

@MattDMo if this is the case, I would accept that comment as an answer – that there isn't enough information to tell which is the case.
Certainly would appreciate any other feedback to improve the question.


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Has life on Earth explored the entire space of genomes?
Recently I came across a 2008 article, the authors of which argue that in fact the space of protein sequences is not as large as it might seem, and that life on Earth has most likely already explored this entire space (maybe before the appearance of eukaryotes).
Dear experts, can you explain what this means?
That life on Earth has already explored all the possible space of genomes, and all possible living organisms that are generally possible have already appeared? But after all, only the human genome consists of about 3 billion base pairs, and all possible combinations are a gigantic number, how could life explore them all, not to mention other genomes? And if life before eukaryotes tried every possible genome, then how did other life forms with a different genome come about?
I'm confused, please help.

The idea that all possible living organisms have already appeared is readily disproven, by for instance plant breeding.  Just with flowers, we see things like artificially-induced polyploidy, and interspecies hybrids that only survive because of things like embryo rescue.  WRT that 3 billion base pairs, note that in addition to the combinations, you can make it 3 billion +1 and get a new set, then repeat with 3 billion + 2 &c.

The article argues about protein space, which is orders of magnitude smaller than genomic space.  1) There are 20 AAs for 64 codon sequences. 2) Proteins average 300-600 aa depending on the organism (source); note that this is much larger than your cited article's claim of <100aa, upon which their math is dependent 3) Only a fraction of most organisms' genome codes for proteins

@Punintended How many orders of magnitude is the space of proteins less than the space of genomes?

@ArmanArmenpress To compare the two, you'd need to make approximations for both. The amount of work in that task depends on your assumptions/approximations, and would likely be a paper (or two) in its own right. A constraint like "stability" will depend heavily on your precise definition, and since proteins and DNA have different chemical properties (and therefore stability), stability constraints on one will manifest quite differently in approximations of the other. Eg, "stability = 6 months at 4dC" will give very different results for different proteins, never mind comparing it to DNA

@Punintended Thank you. That is, it is not known what proportion of all possible genomes are stable.

The answer to this question is very much no. Genomes are of arbitrary length and structural organisation (i.e. ploidy), so there isn't a fixed number of 'slots' that different base-pairs could inhabit (like e.g. rolling a dice). As a consequence (and as jamesfq mentioned in the comments), no matter what genome you have, you can always add additional levels of complexity. Take for example the human genome which is approximately 3.1bn base pairs long; you could reconfigure it by adding or removing a base-pair (also known as indels) indefinitely.
That's not even considering the total number of combinations of base pairs at each position in the human genome, which is 4^(3.2e9), which is so astronomically large that it's not even worth entertaining that all  those combinations could have occurred in nature.

There's a significant difference between "possible genomes" and "stable genomes", as the latter constrains protein sequences. As an easy example of the latter, for organisms following the central dogma of DNA -> RNA -> Protein, at minimum the genome needs to encode sequences for replication, transcription and translation

a) yes that makes it more clear, b) agreed. but the question didn't really specify (to my reading) whether or not the genomes were viable or not, but I'll edit that in to be clear.

@Punintended That is, life on Earth has explored all possible stable genomes?

@user438383 Is it known how much of the genome can be functional and stable?

@ArmanArmenpress - you mean how many combinations of nucleotides end up being stable? Not sure myself, I think that would be a hard (but interesting) question to answer.

There'll be a large difference between "chemically stable" (mostly energetic?) and "biologically stable" (proofreading, error correction, replication?).  What do you mean by "functional"?  Even with rigorous definitions, as user438383 says, it'd be hard/interesting to answer

@user438383 it seems to me that the answer to this question is generally impossible. Indeed, for genomes with different numbers of base pairs, the number of stable combinations will be different.

@Punintended: Seems like it very much depends on how you define "stable".  Logically, any functioning genome must at a minimum be stable enough for it to hang together long enough for the organism to reproduce.  OTOH, if it's not somewhat unstable, it won't mutate, and evolution becomes much more difficult.


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How is the possibility of beneficial mutations ensured in the genome?
To ensure natural selection and variability, the genome must have a structure in which the occurrence of beneficial mutations has a high enough probability. But how is this ensured? The space of possible genome configurations (even if we are only talking about "used" regions) is enormous. And the subspace of useful configurations is most likely negligible. That is, the likelihood of a beneficial mutation is extremely small. In this case, how does the genome provide the opportunity for beneficial mutations, which, in turn, provides for infinite evolution?
I want to add that I myself am an ardent supporter of the theory of evolution, so the question is no trick.

I think you might find this useful reading - it should answer some of your questions http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/EWNRG07.pdf

OP It is not. @user438383 If you could compose an answer summarising the key points of the paper you cite, I think that would make a useful contribution to SE Biology.


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What are the prospects in synthetic biology, especially in the introduction of biological computers?
One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I have read a large number of articles on this topic, and in almost all of them the logic gates are made of DNA or RNA inside bacteria. What are the prospects? For example, are there developments that imply the construction of logic elements and microcircuits directly inside the cell: DNA encodes the necessary proteins that are synthesized and assembled into logic gates and other components in the cell?

I wonder why people put a minus without any explanation?

1 downvote is from me - people aren't obliged to explain why they downvoted. I downvoted because, whilst certainly interesting, your post doesn't ask a question with an objective, fact-based answer. 'What are the prospects' is quite open-ended and will encourage opinion-based answers. If you have a specific quesiton about synthetic biology, I'd encourage you to focus on that. Thanks.

@user438383 a specific question: are there developments that imply the construction of logic elements and microcircuits directly inside the cell: DNA encodes the necessary proteins that are synthesized and assembled into logic gates and other components in the cell?

@ArmanArmenpress If you can formulate more specific and less opinion-based questions, I would encourage you to ask them as separate questions, rather than asking them in comments.

What are the prospects? For example, are there developments that imply the construction of logic elements and microcircuits directly inside the cell: DNA encodes the necessary proteins that are synthesized and assembled into logic gates and other components in the cell?

Yes, there is an entire literature on this called "genetic circuit design", which Brophy and Voigt 2014 introduce nicely. Xiang et al. 2018 provides a discussion of developing biological computers. Karkaria et al. 2020 provides an excellent overview of what this field has accomplished, what the current challenges are (such as metabolic load and non-orthogonality of parts), and how they might be tackled by having community (distributed) circuits.
For a school assignment I performed a rudimentary citation analysis of the genetic design literature (Seilis 2020). While it isn't publication-quality work, and certainly isn't peer-reviewed, you might find some interesting papers are cited there.
In terms of logic gates, you'll find that both unary gates and all sixteen possible binary gates, and many others, have molecular implementations. And in terms of prospects, they could be used for monitoring and control, production of medicine and goods, and literally run molecular experiments, among others. I recall Xie et al. 2013 constructed a circuit that when put in non-cancerous cells did nothing, but when put into HeLa cells would trigger apoptosis.

Might be worth mentioning that computation is possible without every logic gate type. In fact, the minimal set of logic gates requires only a single type-- either NAND or NOR. These are called "universal logic gates", since they can be combined with themselves to produce any other logic gate. In practice this is often very convenient in that it allows for device construction with only one process, rather than many different processes (one per gate type).

The functional completeness of certain sets of boolean functions is worth mentioning because it motivates the intuitive idea that we could program a system to do whatever we want within the physical limitations of the system.

One of the physical limitations that prevents us from just using compositions of NAND or NOR everywhere is the non-orthogonality of parts. Unlike in a silica circuit where identical parts would have isolated behaviour, solution chemistry leads to things dispersing  across the cell. To have two independently-acting NAND/NOR gates one would have to implement them using different interactions to prevent undesired behaviour. This is one of the challenges discussed in Karkaria et al 2020 among others.


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aneusomy vs aneuploidy
Simple question: aneusomy vs aneuploidy - what's the difference?
I tried google and PubMed, but although there are articles talking about aneusomy, I wasn't able to find a clear definition contrasting the two.
I have no formal genetics training, so sorry if this seems trivial!

Can you quote definitions for each term from the citations you've found to clarify what you don't understand about the difference between the terms?

The suffixes -somy and -ploidy mean different things. The suffix -somy translates to "body" and in genetics typically refers to an individual chromosome. Ploidy level, on the other hand, refers to the full chromosome complement.
For example, most human cells are diploid - they have two copies of every chromosome. The number of chromosomes in a diploid cell is 46. Now, if there was an extra of one of those chromosomes, we would have a trisomy of that chromosome (e.g., Trisomy 21 refers to having an extra chromosome 21, but still has only 2 of every other chromosome). If there was one extra of every chromosome, that would be called triploidy (this actually does happen in plants).
Aneuploid comes from the word euploid - which refers to the "true" amount of chromosomes that should be in a cell. If something is aneuploid (i.e., not-true), there is something wrong with the amount of chromosomes. Aneusomy would refer to the chromosomes, while aneuploidy refers to the chromosome set.
This article from NCBI gives a good overview of aneuploidy, but also monosomy, trisomy, etc.
This page from Khan Academy may be a little more non-biologist friendly.
In my experience I have encountered "aneuploidy" much more than "aneusomy" as a descriptor. It may be that in certain fields of genetics one is more relevant or common than another.


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What do decomposers eat if they break down complex substances and make it available for producers?
I have a doubt for which I haven't found the exact answer.
Decomposers break down complex substances into simpler substances and make it available for producers. But what does decomposers get (or eat) in this process.
Answer with an example would be appreciated.
Thanks in advance!

Homework questions are off topic unless you show an attempt to answer it on your own.

There is stored energy in complex substances: that's what the decomposers use.  For instance, if you've ever made bread, you'll have seen yeast decompose sugars & starches (complex substances) into less-complex CO2 and ethanol, using the energy released to reproduce.


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What is the minimum Ct value that you would consider indicates no gene expression?
I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR.
Looking online I find several different sources suggesting different values that indicate high, low, and no gene expression. Some say that Ct > 35 = no expression, others say > 40 = no expression.
Where do you draw the line with Ct values and why?

I find that reaction chemistry often determines the upper range of usable Ct values. With intercalating dyes (SYBR), Ct values >~32 can start to blend with NTCs, but a melt analysis can help you tell if it's a true signal or not. With fluorescent probes, I generally count any Ct with decent technical reps, but in principle, a well designed reaction with good amplification efficiency should have single-copy Ct values at or below ~38 cycles, making quantitative interpretation of higher Ct values dicey (especially if you haven't established the linear range of the assay).

Can't you just do a negative control and use that to calibrate?
Alternately, run the DNA from your PCR on a gel with a positive control indicating expression. Literally zero expression should mean that the correct band never comes up even after 40 cycles or whatever. And if you do see a band even in a negative control lane, that means that you have contamination and you should probably do something about that!
I think it's also reasonable to use those thresholds that you mention.
Overall, what I'd say is that PCR (and particularly Ct type values) are finicky and while the basic amplification is robust, there are tons of factors that affect the kinetics of your amplification curves. That's why it's so important to run controls in every qPCR run- you are correcting for all the weird batch effects of your reagents, primers, etc. in your master mix.
Every primer set will have slightly different kinetics, and so will every enzyme, so if you want to be really rigorous you would establish a threshold for every possible methodological permutation and reaction setup. However, that's a lot of work. I'd rather just run the final product on a gel and say yup or nope- it should be pretty obvious.

Thanks for your response. You're right, I definitely should have used a negative control. Unfortunately its too late now (I was doing an undergrad project and my time in the lab is up so i'm just left with the data).


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Does cytoplasmic streaming cause passive organelle movement in animal or fungi cells?
In plant cels there is a current debate about whether or not cytoplasmic streaming, which is thought to be driven by the force of myosin motors transporting cargo along actin filaments, can cause organelles to move by passive advection.
I want to know if this is a genuine means of transport in other eukaryotic kingdoms, and not just passive movement of small molecules, but actual organelles?

I believe that fungi use cytoplasmic streaming to transport organelles to the tips of their hyphae to extend them. I haven't heard of cytoplasmic streaming in animal cells but it might exist.

If you look at
http://en.wikipedia.org/wiki/Melanosome
you will see an example of this organelle being transported in animal cells.
Is this what you mean? or are you looking for unbound organelles being swept along by a current?

Thank you for answering, and yes I mean unbound organelles.


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How does protein knockdown allow a phenotype to be observed?
I am trying to understand how AID2 technology works.
I came across an article that says "Protein knockdown using the auxin-inducible degron (AID) technology is useful to study protein function in living cells because it induces rapid depletion, which makes it possible to observe an immediate phenotype".
Can someone please explain in simple terms how one could make inferences about the phenotype based on protein depletion via AID2.

Here's a starting point for some research: "Auxin-Inducible Degron System for Depletion of Proteins in Saccharomyces cerevisiae"  PMID: 31503416 PMCID: PMC6741457 DOI: 10.1002/cpmb.104 One way to study protein function is to see what phenotype you get without that protein. That can be difficult if the protein in question is essential for the cell to grow or survive. This system allows you to grow cells normally, then at a time of your choosing add auxin and trigger the cell's own protein removal system to get rid of the protein of interest.

Phenotype is defined as the observable physical properties of an organism (organism here includes things like cultured cell(s)).
If you knock out the protein of interest you may observe a change in the function, behaviour etc. of the object you are studying via the methods you are using to look at that system. For example, in terms of proteins you might be looking to see how removing a certain protein affects production of a metabolite to investigate which pathways are being for production of that metabolite.

Yes, the "phenotype" is just what you observe, no "inference" involved.


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How can I purify the RNA from polyribosomes on microtubules in mammalian cells?
I've found some old papers that used triton-x-100 to fractionate cells and obtain the cytoskeleton fraction which includes polyribosomes. I'm assuming this is still the best method for isolating microtubules and associated RNA?
Does anyone know a good method/protocol for purifying the mRNAs associated with microtubules from cells? Would really appreciate tips for a simple way of doing this

I am not sure if this is the best way, but if you have a defined fraction which contains your RNA of interest, I would probably simply do a Phenol/Chloroform extraction.


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Best way to predict the effects of deletion mutations on protein function?
I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of these mutations on the final protein?
I am looking at AlphaFold but papers have found it is no good at predicting protein stability change (ΔΔG) based on point mutations, and AlphaFold answer one of their FAQs by saying "AlphaFold has not been validated for predicting the effect of mutations".
So... what is the best method for predicting effects of mutations based on sequences?

Not sure, but look into Rosetta or DynaMut. Obviously, actual experimental validation is the best. Are there known deletions in related species or the same species (ExAC, gnomAD, ClinVar)?

I would suggest looking at the sequence conservation of the protein domains / sequence positions of interest.
One such tool that is oriented towards human genomics is CADD. This tool can provide a score predicting how damaging a mutation at the position in question might be.
But in the absence of a convenient interface, you could generate a sequence alignment yourself of homologous proteins and compute the conservation (similarity or identity) of the position across such homologous proteins.
Unfortunately I am not sure that these methods will make you feel much wiser, they will largely be useful for saying that one area of a protein is more important than another, they will not necessarily tell you much about the functional changes in the protein.
It is of course always a good idea to look at the domain annotations of the protein in question, e.g. mutations in the active site of an enzyme may affect activity, mutations in a DNA binding domain are more likely to affect DNA affinity, etc.
Uniprot is one place where you can investigate both of these at once to some extent.


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If I want to study protein translocation with RFP as a reporter should I fuse it to the C or N terminus?
I want to identify the whereabouts of the signal sequence (signal peptide) on a coding gene and I want to infer this by using RFP or GFP fusion and visualising the location of the fluorescence. Can somebody please explain how I might go about this (in layman terms) and how fusion to the C terminus vs the N terminus would alter the results.

What research have you done on your own to try and answer this?

I have been reading a textbook on protein localisation/translocation and looking through the literature but I think I have hit a mental block. I must be missing something.

Well, do you want to track the signal peptide or the main protein? Depending on your answer, that's where you put your [R|G]FP.

I want to track the normal localisation of a protein of interest. I just want to use the fluorescent tag (fused to the protein) so that it is expressed in the organelle its signal sequence specifies under normal conditions - i.e. I want to know its subcellular location.

In relation to above, is your signal peptide cleaved after the protein arrives at its destination or not? If it isn't, you'll have to think of another way to do your experiment.

It is more of a thought experiment than a real one. I am just simply trying to understand how fluorescent tags can be used to discover the localisation of a protein that is known to contain a signal sequence.

For the purposes of this answer, we'll assume that we're working with Aquaporin's Localized Protein, or ALP for short. It has an internal cell membrane localization sequence at its N terminus which gets cleaved by a signal peptidase upon correct localization.
What will happen if we put GFP onto the N-terminal end of ALP, separated by 6 peptide flexible linker sequence? Assuming the signal sequence (SS) still works (and this is not always the case!), after translation the GFP-SS-ALP fusion protein will be shuttled to the interior of the cell membrane, where it is inserted into the membrane and the SS cleaved. This now leaves free GFP, which is soon degraded. Looking at fixed cells under a microscope, you'll see diffuse cytoplasmic staining, meaning you can't really localize it to a specific region. Fail. This process is called "grad school".

Source: biotium.com
However, you keep going. You express C-terminal GFP-tagged ALP, again with a short linker, and end up with SS-ALP-GFP. The same process occurs: translation, transport to the inner cell membrane, anchoring, and cleavage of the SS. So what's different? The GFP is still attached to ALP, and viewing under the microscope will show mainly membrane staining.

Source: biotium.com

I got a good laugh at that grad school bit

Thank you for your response, this makes a lot more sense now. I appreciate it!


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How does auxin-inducible degron technology make it possible to observe an immediate phenotype?
I am having trouble understanding this paper, which says

Protein knockdown using the auxin-inducible degron (AID) technology is
useful to study protein function in living cells because it induces
rapid depletion, which makes it possible to observe an immediate
phenotype.

How does protein knockdown allow immediate phenotypes to be observed in general, and specifically using AID technology?

I don't think the sentence is trying to say that protein knockdown allows immediate phenotypes to be observed in general. Rather, inducible knockdown does. What is your understanding of inducible knockdown mechanics (steps taken by researcher and expected effects)?

My current understanding is that inducible knockdown (in this context) is the use of a ligand (e.g. auxin) to control the speed of proteolysis of a given protein target. I want to understand why this is used and exactly what the purpose is? I am not so much interested in that paper itself, I just want a basic understanding of how the AID2 system works

In the future you should [edit] your questions rather than reposting substantially duplicate versions of the same question.


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Did animals primarily evolve to differentiate UV-rich sky from UV-poor substrate OR did they evolve to see visible light?
I read two things that appear to contradict each other.

The reason humans only see light in the visible spectrum is likely related to the transmission of light waves through water: most infrared and UV is absorbed by water while the range of light we see transmits very well through water, since we evolved in the sea it makes sense that we evolved this way.

The basal colour sense in all animals is UV and a green (or mid-wavelength) sensitivity. These are used to differentiate the UV-rich sky (or open space) from substrate which reflects UV poorly.

How can UV be a basal colour sense of all animals when all animals supposedly evolved in the sea and thus evolved to see light primarily in the visible spectrum?

What makes you think that the sense of vision cannot evolve further? This happened between 400 - 500 mio years ago, which is a long time, even if you think in evolutionary timespans.

I know vision can evolve further, it's just that the the two points were presented as explanations for the initial evolution of colour vision in all animals. One predicts UV is one of the primary spectral sensitivities to evolve, the other predicts it is only visible light since UV isn't transmitted well through water.


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Does cytoplasmic streaming exert a force on the cytoskeleton itself?
In plant cells, cytoplasmic streaming is though to be driven by the force generated from active transport of myosin-cargo complexes along actin highways. Does this force also act on the actin filaments themselves? Does it contribute to the movemement of the cargo along these filaments?


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Where do garbage flies come from?
I want to know the origin of those very small insects/flies which we see over kitchen garbage or when some surface is wet for some time. Where do they come from? Who actually reproduce them?

I suppose that they reproduce themselves. How a new garbage bin becomes infested with them is a good question - probably because they already live nearby, eithe rin other garbage bins or everywhere, but in less noticeable concentrations.

But I have seen them even when there are no nearby piles.

As I said - they are everywhere... not sure what is the question then.

Not spontaneous generation: https://biology.stackexchange.com/a/97165/16866

“All things bright and beautiful all creatures great and small…”

Q-> Origin of Insects/flies and Who reproduces them?
A-> Eggs laid by adult female flies.
Q-> Where do they come from?
A-> Nearby sewage, society waste-disposal areas, drainage systems.
The very common flies such as - Musca domestica and fruit flies often feed on rotten kitchen food, overripe fruits/vegetables, human excreta, animal dung. They prefer food that is either in liquidy or soluble in their saliva. Water is also required by them as they're also living creatures after all. Other food sources can be milk, sugar syrup, meat broth, etc.
Since dustbins are a food source for such insects, these are the perfect places for breeding as well (their babies also need nutrition). Female flies from near by sewage or locality waste disposal area often lay eggs on the home-based garbage and organic material. Eggs of flies are hatched within few hours and one can see a sudden increase in the number of flies around their bins.
In the daytime, when they are neither hungry nor breeding and prefer resting, that time they are seen in non-waste areas such as walls, floors, ceilings, clothes, etc. These resting places are nearby of their feeding places only.
For more info- Check https://www.who.int/water_sanitation_health/resources/vector302to323.pdf

Another major source for these flies is produce that is brought into a house, which may have fly eggs laid on it already.
While you aren't likely to eat maggot-filled fruit, it's quite easy for waste (e.g., peelings, cores, rinds) to end up sitting for long enough for the eggs to hatch in a trash can or down an imperfectly cleaned garbage disposal.


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What controls the growth of a body?
Everything in our bodies is made of cells - bones, muscles, brain, blood. How do cells know how to build a body? Granted, each cell has a blueprint of the whole body in its nuleus, the genome. Does that help the cell know where it is in the grand scheme of things and how it should behave (divide?) for the end result to look like a human body?
If someone told ten million people to form the word "Help!" that's 100 miles wide and each person got the exact blueprint of what the end result should look like, I don't think the aliens would see a convincing message in a few months or maybe even years.
If those people are to finish their task in any forseeable future, they need some kind of a feedback loop. For instance, they could build an app that showed everyone's position on the map, so they could say "Hey, that blob looks like they're trying to be the dot in the exclamation mark. I need to move 400 meters to the south-west if I want to join them."
Do cells have similar feedback loops? Or am I too naive to think that individual cells have any say in how our bodies are built? If it's not the cells, then what is it that controls the growth of our bodies making sure we don't grow a second head and everything works in perfect harmony? Obviously, this doesn't work 100% of the time - that's when we get cancer or Siamese twins. But it works most of the time.
How does the body do it? What and where is the conductor of this billion-cell orchestra?
I am not a biologist, so please be condescending. After all, the question What controls the size of breasts? got a decent answer. I don't see why mine shouldn't.

Welcome to Biology.SE. Unfortunately this is not a good question for this site because it is too big. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book (or this case an entire library) that answers your question, you’re asking too much. To get some idea of the size this field of research you can search on this site for the tag 'development', which is relevant to your question (currently >200 questions). IMO, if you have a strong interest in this subject you should start with the basics and work up to this very big question. ...

... I have found Khan Academy to be a good way of getting a quick introduction to an unfamiliar (or mostly forgotten) subject area (I used them to relearn the basics of calculus). There are also many free textbooks available at the NCBI Bookshelf. Other reading you might find interesting includes this — try searching for "developmental-biology for computer-scientists" to find similar material. Hope that helps.

so basically you want us to sum up all of embryology for you? note the question about breasts is about a specific tissue. your question is far too general there is no conductor other than your DNA each tissue is controlled in a different way by different gradients and feedback loops. try starting here https://en.wikipedia.org/wiki/Embryology

The answer to your question is huge and still evolving, involving whole fields of scientific research.
The general process of how cells develop macro-structure forms is known as morphogenesis. Within that realm of study, the science of "evo-devo" (evolutionary and developmental biology) is closely tied to the question that you've asked, as it turns out that the molecular basis of body-plans and how evolution works are closely tied together.
I would recommend that a good place to start is the popular-science book "Endless Forms Most Beautiful", by Sean Carroll, which provides a nice introduction, overview, and good intuitions for the non-biologist to start to understand what is known about this topic.

acapellascience's youtube channel has a song called evo-devo that nicely summarizes Carroll's book.


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Can you calculate the coefficient of inbreeding (F) without a family history?
Apologies in advance, this question may be completely obvious.
Say, I didn't have a family tree for two individuals. Could I calculate their coefficient of inbreeding? If not, is there a good proxy for it or an alternative way to calculate it?

Yes.
These days inbreeding coefficients are generally computed from observed gene frequencies, not from pedigrees.
From this review:

Inbreeding coefficients are defined in terms of the
probability of identity in state of different pairs of genes.
Here the probability of identity in state is simply the
probability that two genes are of identical allelic type.

Thank you very much. One further question. How expensive would it be to calculate the coefficient of inbreeding for a random couple? I'm an Economist and this isn't my domain of expertise.

@anonymousquestionbio1994 It really depends on the degree of precision that you want, density of information, extensibility, etc. I suggest doing some background reading on the topic of experimental design in the field: https://www.frontiersin.org/articles/10.3389/fgene.2020.00870/full, https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-12-16-0425-RVW

Thank you again! Will certainly be reading this!


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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?
I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 mins. Smolen oscillators as described in Stricker et al 2008 A fast, robust and tunable synthetic gene oscillator  seem like something I could use, however, I'm not sure if I should, I am new to oscillators.
Please let me know what kind of oscillator you would recommend for a 2-20 min period time, preferably robust. Any other relevant information or recommendations are welcome. The intended system is Synechocystsis 6803 but initial work may be done in E coli.

I believe that what you are aiming to do is not possible with the mechanisms that you propose.
In most transcriptional and translational genetic circuits, the limiting factor for switching state is dilution or decay rate.
This is because genetic regulatory networks directly control rate of production, rather than concentration.  Thus, even if your oscillator instantaneously switches on and off (which it won't), your ability to turn off an enzyme depends on the rate at which its concentration decreases.
Degradation mechanisms in the cell do not operate at the time scales that you're looking for (see, for example [1],[2]), so you need to depend on dilution. E. coli at full stretch goes at about at 20 minute division time, and even the fastest doubling organisms (e.g., V. naturiegens) max out at around 7-10 minute doubling time. That gives you a half-life, not complete removal, so if you want an enzyme to be mostly off (not just decreased some), then your target times are simply not achievable with genetic regulation.
When cells need to regulate protein activity on these tighter time scales, they generally regulate protein state rather than protein concentration. This is more difficult, but if you really need to hit such tight times, I recommend that you look into such mechanisms. Alternately, do you really need to modulate this quickly?

I see. I understand the limitation my approach has. Thank you for your detailed answer. I'm actually not sure what period we're looking for, will have to check that out through mathematical modelling. I'll look into what you mentioned.
Enzyme 1's product (P) has a feedback inhibition effect on Enzyme 2, and we want to separate their concentrations in time. Are oscillators a good approach or would placing Enzyme 2 under transcriptional control of a P sensitive transcription factor? Any other approaches you can think of?

Oscillators is a very interesting idea, if you can afford a longer time-scale. Available oscillators are fragile, though, so doing that would likely entail significant focus on the oscillator. You could also use transcriptional control or try to do spatial separation (e.g., two separate strains) if the product can be exported.