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How to calculatie frequency of recombination between two genes based on their coordinates in ENSEMBL?
I have two genes:
https://www.ncbi.nlm.nih.gov/gene/326619 and https://www.ncbi.nlm.nih.gov/gene/326620
both are mapped to chromosome 13. First is at position 23944778..23945232 second is at positions 23940920..23941369. Is there a way to compute approximate recombination rates between the two based on position? I need this for predicting efficiency for maintaining stable linkage between genes for a mouse cross.

I would strongly recommend consulting a mouse recombination map. Hopefully no need to compute anything, as you should be able to just look up recombination rates between named SNPs.

Here is one mouse map publication.
Here is another one.

I'd suggest taking a look at those and figuring out if they have the information you need.


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Is this tailed butterfly a coral hairstreak?
I spotted this butterfly feeding on some lantana in Fort Worth, Texas.  It looks exactly like a coral hairstreak, but it has these two tails (?) on its hind wing, whereas I thought coral hairstreaks had none.  Is it just a slightly unusual specimen, or is it some other butterfly?
Thanks to @tyersome for the suggestion to estimate the size.  I'm bad with estimating sizes, but it was a small butterfy, with its height (from the flower to the tip of its wing) perhaps more than my thumbnail but less than the diametre of a US quarter—maybe 2 cm.

Welcome to Biology.SE. Your question looks good, but it may be helpful to add an estimate of the butterflies size. Not an expert on this, but to me the 'coral band' looks very reduced compared to a typical Coral streak — combined with the tails I'd guess this is a different species.

@tyersome, thanks!  I have estimated the size (perhaps 2 cm high).

Oh my goodness, you just posted a picture of my favorite butterfly! It's not a coral hairstreak.

It's a Gray Hairstreak Butterfly (Strymon melinus).
It can have one, two, or even three "hairs" on each wing. How much coral is on the wing varies, as does the amount of coral on the antennae.
Hairstreak Butterflies Identification Guide

That is certainly it; thanks!  I thought 'hairstreak' was an idiosyncratic name for the coral hairstreak, but it seems to be part of a theme.  Do you know why hairstreaks are so called?  (One might guess it's after the hairs that you've mentioned, but the coral hairstreak doesn't have those, so I am confused!)  I also don't know how to tell that these things on the wings are properly called hairs, rather than tails ….  Any further light you can shine would be much appreciated.

@LSpice - You're right to be confused. Until I saw your question, I didn't know Coral Hairstreaks didn't have a hair. Hairstreaks are actually named for that "hair"; most of them have it. If you'd like to see it from a different angle, try ere. So cool! And I agree; swallowtails aren't called swallowhairs... but "gray hairstreak" is purely descriptive.

@LSpice - Btw, that's a beautiful photograph! I have tried many times to photograph one, and have never come close to that.

Thanks for the clarification, and the compliment!  The age of basically-free digital photography has upgraded me from "no pictures ever come out" to "fortunately, I can throw away 20 or more pictures that didn't work out for 1 that did."

I got a picture of the wriggling behaviour described in your link, though it didn't come out as sharp:  https://i.imgur.com/g8pxeOJ.jpg .  I see a lot of these butterflies on my local trails, so I'll have to see if I can get a picture from below!

source: Stack Exchange

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

sort: votes


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Bladder size based on child height/weight
My son is 10 years old, but weighs 24kg, which is quite little for his age.
Is it correct to estimate his bladder volume based on a formula using age? This seems to be a generally accepted way, for example: (age + 1) * 30 = volume in ml.
I would assume that a smaller and thinner child will also have a smaller bladder?

Obviously there are more factors involved than just age. But age is easy to use even if it's wrong. Very much like how BMI ignores a bunch of other stuff about people.

May I ask why you are asking this question? There are studies that answer this, and it's most important in the pediatric population because of kids with urinary tract issues. At which point is it related to height more than weight? Because obviously it's not linear.

Personal medical questions and health advice are off-topic on Biology.SE. We cannot safely answer questions for your specific situation and you should always consult a doctor for medical advice.

@anongoodnurse I'm asking to be able to discuss further with a urologist. I'm not convinced with their judgement by age, because my son is in the lowest 10 percentiles for weight and in the lowest 25 for height his age. Nonetheless, she is convinced this does not matter for his bladder size and required volumes. I'm not looking for a big discussion, but it did make me wonder if there are studies saying otherwise.

Ah, in that case, it's personal medical advice, but it's easy enough to Google, esp. if you use Google Scholar.

Well, I'm not looking for advice actually, just wondering. Because, I'd assume, smaller body, smaller organs, larger body, larger organs. I'm wondering if my assumption is correct. I did come across these studies yesterday, but I don't know enough about the subject to be able to interpret correctly: https://www.academia.edu/resource/work/12317425, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2062747/

So, to clarify further, I'm obviously consulting a doctor for this, and won't use any answers as medical advice. I'm just wondering, as an outsider, if organs are larger in larger children of the same age?

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


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Identify grasshopper species
I found this grasshopper on a house door in central Italy. It did not move for the whole day. I can tell it's a grasshopper, however I am unable to determine the exact species.
Size: ca. 6cm
Feel free to ask if you need any more information / details.

Identifications questions should include: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible) — photos must be uploaded (not links); and 2) habitat information. Please [edit] your post to include this essential information. Not in particular that without at least one picture or a very detailed description this is impossible to answer.

Sorry, I thought I had uploaded the picture. This is the only one I have as I am no longer there.

Unlikely to get a full ID from that photo - too dim to make out markings and not enough views to get morphologic features.


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What insect is this? I spotted it on a wall in a bedroom

This is the closest distance & the best photo resolution I could get from my handphone.
I discovered it on a wall in my bedroom.

Could anyone identify what insect is it?
Why the insect is in the bedroom?
How do I prevent this insect from staying in the house?

Thank you

Welcome to Biology.SE. Identifications questions should include: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible); 2) the location (e.g. country and region — the more specific the better) where you observed this organism; and 3) an estimate of the size of the organism. Please [edit] your post to include this essential information after checking to see whether a similar question has already been answered. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.

"Why [is] the insect... in the bedroom?" sounds a lot like "Why did the chicken cross the road?"


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Is there a reference brain sample for the RNA-Seq data in the Developmental Transcriptome tool from the Allen Brain Atlas?
I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain.

I have read the official documentation as to how the RNA-Seq data for the Developmental Transcriptome was generated and analysed. In the documentation, it says that they used postmortem human brain specimens from a range of different developmental stages (embryonic, early prenatal, early mid-prenatal, late mid-prenatal, late prenatal, early infancy, late infancy, childhood, adulthood).
The heatmap showing the gene expression levels across the different brain samples was generated from the RNA-Seq data. I know that heatmaps show the gene expression levels in a number of samples (e.g. treatments, disease) relative to a control sample.
However, when showing the gene expression levels across the different brain samples they used, I was wondering if there is a reference brain sample that was used? E.g. they are comparing gene expression in other brain samples relative to the reference brain sample. I have read the documentation and there is nothing mentioned regarding this.
I was wondering if anyone who has used the Developmental Transcriptome tool before knows whether the gene expression levels are compared against a reference brain sample? Any insights are appreciated.


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How fast is dopamine released in the brain?
Dopamine is released when one anticipates a pleasurable event says https://www.psywww.com/intropsych/ch09-motivation/pleasure-and-pain.html.
"People with more sensitivity to ritalin rated higher on Depue's positive emotionality index. "When our dopamine system is activated, we are more positive, excited and eager to go after goals or rewards, such as food, sex, money, education or professional achievements," according to Depue (Lang, 1996)/
Dopamine is associated with anticipation of sex, drugs, drinking, getting money, winning competitions, and religious worship. Religious worship? Yes, Previc (2006) summarizes the relevant research showing "dopaminergic activation as the leading neurochemical feature associated with religious activity." Dopamine is apparently a marker for the purusit [sic] of enjoyment of any type."
Is it released instantly like adrenaline, or more slowly?

Dopamine is a neurotransmitter and released from synaptic ends via transporters. Such a release happens within milliseconds; the time present Dopamin needs to move some tens of nanometers.
Adrenalin is a hormone produced by the adrenal gland, which needs to distribute through your body. This is several orders of magnitudes slower.

Within milliseconds of what exactly. I was thinking of the start time being the time a person decides to go to a bar and drink some alcohol, or to be more objective, the time someone hears a friend says, "What about going to bar now?". Also, does dopamine come with a recognizable sensation, like adrenaline or endorphin?

I am referring to the speed of release: The time the neural end needs to release Dopamine after receiving the electric signal. It seems you are interested in control of Dopamine synthesis/degradation. Unfortunately, I can't confidently answer such a question. Maybe edit your question and someone will answer it in this regard.

"control of dopamine synthesis and degradation" seems like a promising search string for me. Is it that a certain type on neural end (which I take to mean the first half of a synapse) always uses dopamine as a neurotransmitter to trigger the second half, and then the residue of dopamine then drifts around the brain modifying how other synapses behave in such a way that the brain becomes more pleasure seeking? Or does work some other way? Or has this not yet been worked out by science?


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Is it possible to "triangulate" the location of a termite colony in a horizontal space using light sources as attractive bases?
So we have termites and I noticed that one of the can lights in our subfloor (the 1.5 foot vertical space between our first and 2nd floor) was a lift off point for many swarms. I put some tape over the can light and was able to catch the swarmers each time they did it. The termite guy wouldn't touch the area (useless good for nothing) because it was an "electrical" area and out of risk or harm I had to remove the can light first before he can investigate the area. Left before we figured out how to open it (I wish I was good at this kind of stuff... took less than 30 seconds once you understood the trick to remove it). In any case, the termite specialist says since the colony has spread in between the floors he can only offer tenting since other methods will be ineffective but he also knows we are an attached home and that means the only way we can do anything is if all neighbors agree to the tenting of which we are all unable to do at the moment due to a long story I won't get into here. In any case, I've been endoscoping the heck out of the area... plenty of other things I found in there except termites, I was wondering is it possible for me to "triangulate" the nest source?
It seems like that specific can light has a direct line of sight to the colony because all the swarmers go straight for it and none other. I was wondering would it be possible for me to place three different light sources in the space and see which ones will trap the most termites and maybe use that information to zero in on the nest location. Anyways, a bit of a wild idea but maybe its possible. I already know that triangulation and trilateration are useful if you are at your own location so that would mean the nest needs to be known but maybe there is something I am missing where I could locate the nest using light sources and traps and wait until swarm season. Anyways just a thought..

Perhaps better in the Biology Stack.

Please explain. Why would you think that? I feel like Biology would have something more about how to identify species or the anatomy of animals - not how to locate a nest/colony for extermination. Pest control seems very much a DIY topic.

Because termite behavior under changing lights conditions is not Home Improvement…

Termite behavior is better asked about on Biology.

Interesting question and reasoning tho. Try the three lights thing and post an answer to your own question.

My approach with termites is to spray every possible place with poison . We get the type that build tunnels to the ground so I have a pretty good idea where they are . I have had them in the garage twice as they are common here .  Apologies for the political incorrectness of insecticide.

Thanks for the comment! Wish I had the same problem, unfortunately they are in the area that doesn't touch the ground - we believe they are drywood termites and yours sound like subterranean termites. Subterranean termites create those tunnels and come from the ground so that is a great tell!


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RNA-Seq: Is it conventional to use a threshold RPKM value to determine if a gene of interest is expressed in a sample?
I am interested in finding out at what stages of development a gene of interest is expressed in the human brain. I am using the Developmental Transcriptome tool from the Allen Brain Atlas to find this information. The heatmap showing the gene expression levels across the different brain samples (taken from donors of different ages) was generated from RNA-Seq data.

From the official documentation on how the RNA-Seq data for the Developmental Transcriptome was normalised, RPKM (Reads Per Kilobase Million) were the gene expression units that were used in the RNA-Seq data analysis. The gene expression values were then transformed into a log scale (log2 RPKM) for easier visualisation on the heatmap.
From visually looking at the heatmap, you can see at which stages of development the gene of interest is expressed, with brighter colours (light blue, green) indicating a higher level of expression compared to dark blue regions of the heatmap. However, I do not think that visually looking at the heatmap colours is an unbiased way to determine at which stages of development a certain gene is expressed.
I am completely new to analysing RNA-Seq data. This might be a basic question, but is it a convention/practice in research to use a "threshold/cutoff" RPKM value to determine whether a gene of interest is expressed in a sample? E.g. If a sample has a log2RPKM above the threshold value then you consider that gene to be expressed at a sufficient level.
Any advice is appreciated.

Please specify what"sufficient level" means. You are trying to convert something that is continuous into a binary — IMO this makes unsupported assumptions. 2) This also assumes the level is a constant! 3) Is your gene of interest protein coding? If so, to really know whether the expression meant something you would need to do something like show it was also translated and then confirm that the protein meant something — e.g. by observing an effect after preventing the protein from acting at that stage. ——— Bioinformatics is great, but it is not a substitute for wet experiments ...

The proportion of reads containing the mRNA of your gene is all what RNA-seq can tell. What else do you expect from it? The relevant cutoff probably depends on the function of the protein, and the exact methodology of the RNA-seq experiment.

possibly a better fit for bioinformtics.stackexchange.com. I think that the real question here is about what the "limit of detection" (LOD) is for bulk RNA-seq of some depth. One example of an assay doing something similar is here: https://pubmed.ncbi.nlm.nih.gov/29929942/. There are some statistical procedures used to estimate this LOD, which would ideally include a spike-in control of standards of some kind. RPKM is hard because it is an inherently relative/compositional measure; LOD RPKM will vary from expt to expt based on e.g. depth.

I checked and your resource's documentation does contain information about data processing and spike-in controls, I'd suggest consulting that: https://help.brain-map.org/download/attachments/3506181/Transcriptome_Profiling.pdf?version=1&modificationDate=1382036562736&api=v2


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Why do tumours need stem cells, when they can generate their own telomerase?
In the molecular biology of the cell (6th ed), it is stated that:

Some cancers seem to be organized in a similar way: they consist of
rare cancer stem cells capable of dividing indefinitly, toghether with
much lager numbers of dividing transit amplifying cells that are
derived from the ancer stem cells but haave a limited capacity for
self-renewal. These non-stem cells appear to constitute the great
majority of the cell population of some tumorus (p.1121).

Although in an earlier segment, however, we can read that:

Human cancer cells avoid replicative cell senescense in one of two
ways. They can maintain the activity of telomerase as they
proliferate, so that their telomeres do not shorten or become
uncapped, or they can evolve an alternate mechamism based on
homologous recombination (called ALT) for elongating their chromosome
ends. Regardless of strategy usedd, the result is that the cancer
cells continue to proliferate under conditions when normal cells would
stop (p.1100).

How do we interpret these two passages? Are some cancer cells incapable of lenghtening their telomeres, and is it these types of tumours that can't persist without cancer stem cells? Or are cancer stem cells beneficial in some other way to the tumour (such that a tumour stem cell might differentiate into several types of tumour cells, which might be suitable for different environments)?
I understand that having cancer stem cells that proliferate at a slower pace than regular cancer cells might be beneficial for withstanding things like chemotherapy. But what's being emphaphized is not their capacity for survival, but their greater ability at self renewal?

Be careful with thinking that tumors have wants and needs; these are descriptions of what happens, not statements of how things need to be.

Sure, I could have rephrased that in another way ("Why tumour cells which aren't stem cells have a limited capacity for self-renewal?"),

Isn't that a tautology?

This is like asking why there are multiple forms/mechanisms of dementia when "one would suffice".
To save this from being just a trivial comment, note that the mechanism of elongation differs between cancer types, likely depending on the types of cells involved:

Despite being present in a minority of cancers overall, the prevalence of ALT in cancers is not uniform, with cells of mesenchymal origin being more likely to rely on ALT for telomere elongation. Indeed, certain cancers, such as osteosarcomas and cancers of the central nervous system, have rates of ALT positivity approaching 90%, eluding to possible mechanistic reasons for ALT development. The most likely cause of this distribution is that, in contrast to cells of epithelial origin, cells of mesenchymal origin are more likely to have more stringently regulated telomerase expression, reducing the potential for telomerase-mediated telomere maintenance.

Are tumors cells vulnerable, as healthy stem cells, to DNA alteration?

My professor claims that cells go into senescence due to multiple reasons, and that many cells stop dividing after a set number of divisions, despite having ample telomeres and no appreciable DNA damage. He claimed that tumours (counterintuitively) often work in this very same way, so that cancer cells need to be able to differentiate back into cancer stem cells for the cycle to reset itself.
I'm not really qualified to determine who is right. I'll post this answer and let people vote for what's more reasonable.


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Can you name this spider?
Found this spider in my bathroom in central London,UK. I’m convinced it’s tropical. I’m probably wrong. My kids are very curious. Many thanks!

Welcome to Biology.SE! Please [edit] your post to include an estimate of the size of the organism and if possible photos from different angles (e.g. from the side, front, back, and below)  — this will improve your chances of getting a good answer. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.

Can you name this spider? -- how about Kevin? ;-)

here is a famous one https://www.youtube.com/watch?v=Isvqg90LhqM&list=PLG1oNzlyjHd5CeafD9-SKuWvsEbWGaBcR

This is a false wolf spider called Zoropsis spinimana:

It is found all over Europe, including the London,UK area:

A photo gallery and distribution map of user-submitted observations of Zoropsis spinimana can be found here:
https://inaturalist.org/taxa/127112-Zoropsis-spinimana

Without a sense of how big this spider exactly, but based on the width of the grouting, I'm guessing body length of about 15-18 mm (0.59 - 0.71 in). This, along with the colouration and long palps would most likely make it Eratigena atrica also known as the Giant House Spider.
This species is widespread in Europe and parts of North America, so not of tropical origin. They are harmless to humans and like to live in cool dark environments, such as under houses, in caves etc.

This is NOT Eratigena: the carapace markings are not Eratigena, the leg markings are not Eratigena, no visible spinerrets, the abdominal markings are not Eratigena, the eye arragement is not Agelenid.

@JimN Thanks. I have almost no knowledge of spiders at all, so I welcome your comment and answer.  Wolf spider was my second guess, but the dimensions I could find were all much smaller than I could estimate.

Hi Bob, While the Tegenaria House Spiders would normally be a good guess, this one has some noticeable points of difference.  Eratigena and its cousins have a rather 'blocky-looking' cephalothorax, with a broad, light-colored central band flanked by darker edge bands.  This has the more shield-shaped pattern similar to the North American Dolomedes tenebrosus Fishing Spiders and some Wolf Spiders.

Also, the abdominal pattern is quite different.  If you look at Eratigena and its relatives, the pattern is rather lacy, not too unlike the Amaurobius-type Ground Spiders, with a chevron patterning at the back.  This spider has a dark somewhat triangular mark at the front of the abdomen, rather like many familiar Wolf Spiders, and does not have the obvious dark/light chevrons you'd expect from Eratigena.

@JohnRobinson Thanks, very interesting. I'm not an arthropod person at all, nor from North America, so ID is a challenge from half-way across the world, but always willing to learn.


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Why do people get headaches after oversleeping?
I've tried a web search, but the results are mostly non-scientific advice on good sleep etc. One link provides some explanation, but I have not noticed them providing links to that referenced research:

Getting too much sleep is actually a common headache trigger.
Multiple explanations exist for why exactly this happens, but
scientists have dug into some research on this connection. Serotonin
disruption
Some research suggests that oversleeping has effects on
neurotransmitters in your brain — particularly on one (rather famous)
neurotransmitter called serotonin. ....

What is current status of scientific research for such phenomena? Please provide links to studies etc.

I don’t think the place for this question is Biology, but it may well be appropriate on SE Medical Sciences.

Maybe I better rephrase, but I am interested in biological underlying mechanism of pain from oversleep, AFAIK it is not considered a decease, so I posted here.

Doesn't happen to me, so I suspect one also needs to ask what genetics are involved too. It seems circadian rhythm disruptions are suspected as the cause in such cases.

More recent review https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381824/

It may not be a disease, but headache is a medical condition. that I would consult a medic rather than a biologist about if it affected me. SE Medical Science considers the science underlying medical conditions.

Is there data to suggest that this is a common/universal phenomenon?

Headache (by any cause) is still a frustratingly not understood phenomenon from a neuroscience perspective.

Is it even possible to get too much sleep?  As opposed to the more common use of "oversleeping" as not getting up in time for work, school, or whatever - in which case your body probably needed the sleep.

@jamesqf, internet finds entries from search for headache from oversleeping - that is sleeping too much (as they say).


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Why is "mutual search" of some disadvantage/loss of power? (in Darwin's The Descent of Man)
I read a book "The Descent of Man" from Charles Darwin. What is the reason for the following statement?
"It would be no advantage and some loss of power if both sexes were mutually to search for each other."
I know that in most species it is the male having an active role in the search of a partner to mate, but Darwin provided no fact in supporting the quoted statement about the disadvantage of mutual search.
Mr. Darwin died 139 years ago, so his books became a public domain (70 years after his death). Here is a link to a pdf file:
The Descent of Man - Charles Darwin
There it is page number 273, in the pdf file page number 322, in the lower half.
EDIT: The explanation provided on Wikipedia, that I just found, is the Batemans principle. It says that the females are "more valuable", because of greater time and energy they put into producing offspring, compared to that of the males. Hence, the males compete for the females.

I’m not sure what exactly Darwin was getting at, but the answer to why males perform the search (generally speaking) seems to me to be the same as to why there isn’t mutual searching.


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How have some cancers "evolved" to be so aggressive and treatment-resistant?
[In this post, I may ascribe agency to processes, inanimate objects or microorganisms: this is rhetorical, I know they don't "intend" anything. I will also use "evolution" in a fairly loose sense of "learning" (again, rhetorical agency) to overcome obstacles to survival].
Assumptions:
Cancers are caused by mutations of cells, and "successful" cancers are caused by mutations that result in a, sometimes literally, killer combination of

Suppression of their own apoptosis
Invisibility to the immune system or resistance to immune attack
Ability to co-opt biological resources such as bloody supply so they don't starve

The various "types" of cancer that we know and give names to are the end-points of available "mutation pathways" that cells can take to get to such a "successful cancer" state. Because lots of mutations result in cancers that don't "work" for some reason (e.g. immediately shut down by an immune response), they just don't result in a noticeable tumor. Therefore, we end up with a discrete set of "familiar" cancers, each representing a different path, and their frequency related to how likely it is that path is hit (i.e. how many mutations needed, etc).
Some cancers, the malignant ones, happen also to spread very effectively, though this is not specifically required by the above success criteria, so we also see benign tumors which don't spread but still can be said to "succeed" in that the cells survive.
Once mutated, cancers are presumably fairly genetically static within a single case, otherwise we'd see a storm of cancer variants developing within patients over a relatively short period as an evolutionary arms-race took place, much like the race between antibiotics and bacteria.
However:

Some cancers have quite "advanced" mechanisms for spreading1
Some cancers are extremely resistant to human treatment

The question:
How did these "dangerous" cancers becomes so dangerous?  A dangerous cancer seems to be "fully capable" of effective spread in the first instance, rather than undergoing a complex evolutionary battle with the host's own anti-cancer abilities or some exogenous treatment.
Furthermore, even cancers that "succeed" can't effectively propagate themselves like bacteria, because they're always in the same body2. If anything, cancers that do not kill the host should be selected for, since people with genes "near" dangerous mutation opportunities would be less likely to reproduce effectively3. So (naively, since it's clearly not the case), if people do evolve such that they can get cancer4, cancers would tend towards being both benign and generally non-life threatening.
Even if they do somehow "evolve" to spread and threaten the host (as they indeed evidently have), why are they then also often so good at evading non-host treatment?
It seems like two warring armies (host vs. cancer) that have evolved together using hand weapons, evenly matched for centuries. The cancer invents the crossbow (mutates) and starts to win the war. Then, aliens (doctors) suddenly turn up with UAV surveillance and cruise missiles (imaging and treatment) and side with the host, but the cancer still wins much of the time, even though they're facing an Outside Context Problem that by rights they have no innate ability to counter.
So what results in these cancers being so adept at spreading themselves without some adversarial evolutionary process (à la bacteria vs. antibiotics)? Furthermore, how are they so often also resistant to human-directed treatment? Is it just because the human treatment is crude (i.e. not so much aliens but a large but unruly peasant milita that often doesn't really help that much)? Is there more "evolution" going on within a single cancer patient than I imagine?
Expansion in response to comments: if my assumption that the cancer cells are not usually "evolving" once formed is indeed incorrect: is that evolution then usually the cause of treatment escape? And does that mean that treatment-escaping cancers are freely evolving, in that they could take a number of case-dependent paths to escape (as opposed to the original recognizable cancer "type" which took one of a limited number of available mutation pathways through the fairly static environment of human biochemistry to become that cancer in the first place)?

For example, the use of matrix metalloproteases to escape into the bloodstream, the use of cytoskeletal locomotion and various other highly specialized mechanisms that I would normally associate with a long and involved adversarial evolutionary arms race on a far longer timescale than one patient's cancer progression
Certain transmissible cancers like in Tasmanian devils notwithstanding
The obvious mechanism for this is they die or become critically disabled before having children, but it could also be disadvantageous for elders to die too early, especially for humans, when they assist in rearing their own descendants
Perhaps as a by-product of some otherwise-advantageous genetics, like sickle-cell anaemia and malaria resistance, where the occasional lethal downside of in a certain percentage of people is outweighed by the statistical benefits.

"Once mutated, cancers are presumably fairly genetically static within a single case" this is not always the case, and varies from tumor to tumor. The reason cancer is cancer in the first place is because of genetic instability (mutations) that either overcomes normal regulatory processes like DNA repair and cell-cycle checkpoint pathways to grow uncontrollably, or constitutively activates tumor promoters like growth factor receptors, thereby forming a tumor (in solid tissue cancers - blood cancers often don't form tumors). Once those negative regulatory pathways like DNA damage repair [...]

[...] are compromised, mutations continue to accumulate, which leads to further genetic instability and more mutations. This can lead to both metastasis and escape from previously (mostly) successful treatments, but it can also lead to complete dysfunction inside individual cells and cell death.

Here's an interesting and potentially relevant paper that I saw presented at a journal club recently: Cycling cancer persister cells arise from lineages with distinct programs. Tumor heterogeneity at the metabolic level accounts for some cancer cells' ability to withstand treatment and proliferate. Great question, btw

Cancer being 'dangerous'
I define 'dangerous' as reduces survival of patient significantly. In my experience, cancers become dangerous, if one can't remove the tumor. This happens if it starts spreading (metastasize) or start infiltrating surrounding tissue. In order to do so, cancer has to 'digest' extracellular matrix (e.g. the stuff that holds cells together as connected tissue).
Each cancer has its own mechanisms, allow me to illustrate this in one example, multiple myeloma:
Multiple myeloma degrades surrounding tissue (bone), because doing so directly yields a massive survival benefit. Bone is a huge storage for TGFβ, a growth factor, so myeloma cells get a huge growth boost from mining away bone tissue. To do so, myeloma cells upregulate metalloproteases (MMPs, enzymes that shred proteins). They can do that, since myeloma cells have a mutated form of the NF-κB, a transcription factor that can upregulate a shit-ton of genes (including MMPs, and also growth and survival genes).
So you see, all these mechanisms are focused on maximizing the expression of survival and growth genes. Becoming untreatable in the process (and hence 'dangerous') is simply a "side-effect".
Other cancer types infiltrate surrounding tissue, since their fast increase in size has made them starve for oxygen (hypoxia & angiogenesis). They secrete signals for blood vessels to grow into the tumor and provide oxygen. This can also make a tumor "untreatable" since they cannot be removed, without risking irrepairable blood loss. But you see, this is also just a "side effect" of the tumor maximizing survival.
My point is, the "danger" of a tumor is not a direct consequence of the evolutionary armsrace towards huge growth and survival. It just happens as a side effect, since cells are stupid and can ignore the needs of surrounding tissues.
About Tumor spreading
I got two disagreements.
These spreading mechanisms do not have to be "advanced". Sometimes one requires just one dysregulated transcription factor (NF-κB) to induce MMP expression (ref1, ref2). And given their rapid mutation rate, cancer cells populations are very heterogenous and hence provide for a huge functional plasticity, so even 'advanced' mechanisms are possible.
Degrading surrounding tissue does provide a success criterium, like I said, myeloma benefit from mining growth factors (TGFβ) from bone, or from degrading surrounding tissue to provide room for blood supply.

Cancers that do not kill the host should be selected for

Sadly, this is incorrect. Most humans get cancer after the reproductive age. In other words: Cancer happens when you're old and already had children, so it did not prevent you from having children. That's why cancer is not that much of a selective pressure today. It would be, if e.g. a large proportion of teenagers/young adults would get cancer, but that's simply not the case.
About Cancer Resistancy
Cancer resistance to treatment often times is a side-effect of them upregulating survival factors and downregulating apoptosis factors. In other words, the drug is damaging the cancer-cell, but the cancer cell simply doesn't know how to die.
Of course, the treatment kills a lot of cancer cells, but resistant ones remain (e.g. using ABC-transporters to pump the drug right out of the cell). And I gotta say: Most classic chemotherapeutics out there are simply very very ineffective.
I hope that I could answer your question somehow. I am sorry for not providing references for each point. If you want some sources on specific points, I can look through my papers and see if I can provide something.


text:
What other sites do non-competitive inhibitors bind to apart from allosteric sites?
I learned competitive inhibition and non-competitive inhibition.
My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites.
I thought 'somewhere on the enzyme apart from active sites' refers to allosteric site. Because allosteric means changing shape and non-competitive inhibitors do change the tertiary structure of enzymes. However my teacher said this is wrong -- non-competitive inhibitors do bind to allosteric sites but they also bind to some other sites as long as they don't bind to active sites.
So, I am wondering, apart from allosteric sites, where else can non-competitive bind to? Or, is my teacher wrong?

I think your teacher is more than a little mixed up. A competitive inhibitor, for example, can bind to an allosteric site (and not to the active site at all): all that is required is that the binding of the inhibitor prevents the substrate from binding to the active site. See part (e) of this diagram, for example.  My thoughts on such issues are recorded here, and I won't rehash them. But IH Segel is excellent on (reversible) enz inhibition (quoted in the above ref)

The fact that a competitive inhibitor need not at all resemble the structure of the substrate is one of the things that so impressed Monod

Does this answer your question? Identifying type of inhibitor from $K_m$ and $V_{max}$

@user338907 that is an answer! Very well done.

Here is a helpful excerpt from the lecture notes for Introduction to Molecular and Cellular Biology at Columbia University, taught by Lawrence Chasin and Deborah Mowshowitz (emphasis mine):

Re: noncompetitive vs. allosteric inhibition: noncompetitive inhibitors bind to a site other than the active site and render the enzyme ineffective. Allosteric inhibitors do the same thing. So, how are they different? And, in what way can we apply the Michaelis-Menton equation to our understanding of allosteric inhibitors? For instance, can we quantify what happens with the presence of an allosteric inhibitor, or do we just have a qualitative understanding?

I agree that at a simple mechanistic level non-competitive and allosteric inhibition appear the same. There are several differences, however. Allosteric inhibition generally acts by switching the enzyme between two alternative states, an active form and an inactive form. It usually works by binding to a sites in a specialized subunit of a mutimeric protein, and thus binds at several sites. The more inhibitor that binds, the more then can bind, and vice versa with substrate. The kinetics are thus complicated, being cooperative, and non-Michaelis Menton, and are beyond the scope of this course. So a qualitative understanding is all that is called for here. Allosteric inhibition is designed into the proteins and represents an important physiological process.
Noncompetitive inhibiton is more of a catch-all for non-physiological inhibition that does not compete with substrate for substrate binding to enzyme. In that, it is defined (and named) from a negative point of view. As described in your texts, a non-competive inhibitor may bind to a non-substrate site on a protein and distort it to the point of non-functionality, and adding more substrate will not alleviate this inhibition. Or, as in the example I used in lecture, it may simply block a catalytic site without interfering with substrate binding, an example that is more distinct from allosteric inhibition.

In addition, note that an allosteric inhibitor may display alternative kinetics in reference to substrate binding, as described in this NIH guide:

An allosteric inhibitor decreases activity by binding to an allosteric site, other than or in addition to the active site on the target. This interaction is characterized by a conformational change in the target enzyme that is required for inhibition. These conformational changes can affect the formation of the usual enzyme-substrate active site complex, stabilization of the transition state, or reduce the ability to lower the activation energy of catalysis. Figure 1e and Figure 2a are classical examples of allosteric inhibition. As such, an allosteric inhibitor may display a competitive, noncompetitive, or uncompetitive phenotype with respect to substrate binding.

(+1) I think the first part of your answer and the last part are using two very different definitions of 'non-competitive inhibition'. The NIH site (which I agree with) distinguishes between competitive, uncompetitive and non-competitive inhibition. C and Mowshowitz seem to be unaware of uncompetitive inhibition and use the term 'non-competitive in a  archaic way to cover everything that is not competitive. But even working within the (correct) NIH definition, there is a problem:  what Cleland and his school refer to as 'non-competitive', European kineticists tend to call 'mixed inhibition'

For Cleland, see Enzyme Kinetics and Mechanism

I hate to sound naive, but I always thought that the active site of an enzyme encompassed both the substrate-binding site and the catalytic residues. So if an agent inhibits an enzyme by irreversibly chemically modifying a catalytic residue, it would seem to be both non-competitive and acting at the active site. Of coarse it is crass stupidity teaching this stuff about inhibitors to school children (and most undergraduates) when the emphasis should be teaching them what we know about catalysis and it’s regulation.  I prefer to talk about poisons and regulators.

@David couldn't agree more. Putting hard semantic borders around scientific concepts often just leads to confusion when students (inevitably) find exceptions to the definitions. An archetypal question on this site seems to be "My professor said X is the case, but my textbook argues Y. What's true?"

@user338907 it seems you have thought this through more than I have. Indeed, this is a concept that I've always found a tad confusing myself. My personal understanding of allosteric regulation has always been that allosteric factors tend to be endogenously-produced regulators with concomitant sites for activity, whereas "noncompetitive" regulators can be exogenous factors or poisons. Though my understanding certainly has its flaws

@David I think the terms 'competitive, uncompetitive, and non-competitive refer to reversible inhibitors. But of course, an irreversible inhibitor  may give rise to a Lineweaver-Burk plot that looks 'strictly' non-competitive (a plot such as this) because irreversibly killing the enz could give rise to a LB plot where both the slope and y-intercept is changed to the same extent (ie no apparent change in Km) , for the reasons that you give. Kineticsts (used to) delight in pointing this one out!

To try and 'tease out' the non-competitive/mixed inhibitor confusion.  (All of the following refers to reversible inhibition). Let's analyze the types of inhibition by the patterns produced on Lineweaver-Burk (1/v vs 1/s) plots: (i) A competitive inhibitor affects the slope but not the y-intercept (no effect on Vmax) (ii) An uncompetitive inhibitor affects the y-intercept but not the slope.  So far so good ...

(iii) The Europeans refer to the situation where both the slope and intercept are changed to different extents as 'mixed' (reversible) inhibition and the 'special' case where both the slope and y-intercept are changed to the same extent as 'non-competitive' inhibition. The LB plots will intersect on the x-axis (see here, for example). (iv) But Cleland  refers to all cases where both the intercept and slope are changed as 'non-competitive' inhibition and the case where both are changed to the same extent merely as a special case)


text:
Hive building animals
Many species of animals build nests to live in. However, a beehive is a structure built by Homo sapians that houses Apis mellifera (or a related bee species). Are there other species of animals that build hives, i.e. that build structures designed to house a species different than their own.

Not specifically to nest other species, but I know there are ant species who colonies the nests of other species of ants e.g. Dino ants in Brazil.

Probably not in the spirit of the question, but there are species of ants that farm fungi.

What you're referring to is called metabiosis:

a mode of living in which one organism is dependent on another for
preparation of an environment in which it can live.

Examples:
The Goby and the Pistol shrimp. youtube video
The video shows these housemates cooperating, the goby, with its capable vision keeping watch, the shrimp, pushing sand and detritus from the shared burrow. This extends to keeping watch whilst the goby feeds - waggling and snapping it's claws as a warning if a potential predator shows, the goby bringing back food to the burrow, the shrimp eating the leftovers. In times of hardship the shrimp will eat the bodily waste of the fish.
Hermit crabs:
Their non-calcified abdomen makes their adoption of a marine snail-shell obligatory. As time goes by, with growth, they will seek-out a bigger or more suitable home, competing and combatting (rather carefully not to expose their vulnerable parts) until a compromise is found - usually on the terms set by the largest or fiercest crab present (youtube video BBC).
The dresser crab (decorator crab) (But this is stretching the definition a little):

newscientist.com 2015 Fair usage
These decapods show discretion, camouflaging their appearance with whatever is around, sea anemones, weed, a sea urchin as above or increasingly, human made detritus (youtube video). Using their spikey shell to immobilise their covering. Though in this case there is no strict dependance, the anemone is thought to benefit by food particles being stirred-up by the crab during feeding and passage.

The goby+shrimp is the best example. The snails unwittingly give their shells up to the hermit crabs when they die, so it is not an "intentional" act on the part of the snails.


text:
Why does mitochondrial DNA have a high mutation rate, even though the mitochondrial function is highly conserved?
My understanding is that genes that are functionally important are more highly conserved. The DNA coding for ribosomal RNA is one example of that. I was surprised to find out that mitochondrial DNA had a high mutation rate. I'm mostly concerned with metazoan mitochondrial DNA, and more specifically, animal or mammalian mitochondrial DNA.
I've tried searching why exactly that is, and so far, from what I understand, it could be:

the lack of DNA repair enzymes in the mitochondria
the production of free radicals in the oxidative phosphorylation process leading to more point mutations

But how would the cell with these somatic mutations (or embryo with inherited germ line mutations) survive then? Are these mutations only passed down in the non-coding regions on the mtDNA, and the coding regions are indeed highly conserved?
I've also read that:

the high mutation rate refers more to the shifts in gene order on the chromosome
critical genes in the mitochondria migrate to nuclear DNA

I think I could be missing some understanding of wobble base pairing in the  mitochondrial translation system, or some quirks of the bacterial DNA, etc. I've hoping for a relatively complex and in-depth explanation of this. Thank you.

Could you please give a source for your statement about the rate of mutation in mitochondrial DNA. Also your assumption about importance and conservation — cytochrome c comes to mind as a counter example.

This is one example: Sen Xu, Sarah Schaack, Amanda Seyfert, Eunjin Choi, Michael Lynch, Melania E. Cristescu, High Mutation Rates in the Mitochondrial Genomes of Daphnia pulex, Molecular Biology and Evolution, Volume 29, Issue 2, February 2012, Pages 763–769, https://doi.org/10.1093/molbev/msr243
I would be happy to learn about why that assumption is wrong for cytochrome c as well. I'm looking in general to understand why mutation rates can be high for a highly conserved structure.

I'd put the reference in your question. Be careful. Your question referred to highly conserved function, not structure. Cytochrome c is a protein whose function is conserved through many species, but large sequence variation has occured, outwith the residues crucial for function.


text:
Why don't viruses cause wounds?
A simple mental model of a viral infection is that an infected cell emits a lot of virions and eventually dies. The emitted virions have a chance of infecting other cells. Nearby cells are at a higher risk of infection.
Based on this model, if one cell in my nose gets infected, I would expect a large part of my nose to be destroyed, as the infection spreads and destroys more and more cells in the same area.

This does not happen! I survived a number of infections and still have my nose. Why?
I know there are "flesh eating" bacteria. Why isn't this the norm for infections? Does a common cold virus or SARS-CoV-2 not infect a lot of cells within the same area?

Sorry for the childish question. I'd truly like to learn the answer. https://biology.stackexchange.com/questions/93782/what-fraction-of-human-cells-gets-infected-during-a-viral-infection says a virus may infect around 0.3% of the cells in the human body. That could still be a visible piece out of my nose!

If you’ve ever had or seen a cold sore, that’s a viral wound. There are others, but not a great deal, and the reason is explained below.

Cells which are infected release interferons which, among other things, inhibit protein synthesis in nearby cells. This reduces the susceptibility of nearby cells and is likely one of the reasons behind tissue infection not perfectly matching your model.

How thick do you think your nose is, in cells? How many cells deep would a virus have to "dig", starting from the inside of your nose, until it popped out on the face side of your nose?

Faulty premise.  Viruses certainly can and do cause wounds.  Measles, Ebola, Herpes, Smallpox... the list goes on.  All of them causing horrible lesions, pustules, and nasty suppurating wounds.

A virus does not destroy that many cells before it is exterminated by the immune system or before the host dies.
Perhaps even more crucially, viruses typically target a very specific type of cell — those on the inner mucal surface of the nose in the case of cold or flu, those of the gastrointestinal tract in the case of stomach viruses, CD4 immune cells in the case of HIV, etc.
Update
As an example of how much time it takes for a virus to eat a noticeable wound, one could take the extermination of the immune cells by HIV - although it does not look as a physical wound, it is one, in the sense that enough of the specific tissue is destroyed to cause a life-threatening condition. It takes about a decade(!) - from the initial infection to the immune system failure.
On the other hand, the lethal effect of typical respiratory viruses is typically via obstructions of the respiratory ways due to inflammation or secretions resulting from the immune response, or via creating suitable conditions for a more serious bacterial infection.

Thank you! This makes sense. So the key is that the targeted cells are sort of rare? Even if the virus kills all these cells in my nose, the loss is invisible? I have no idea what my nose is made up of. But there are parts that I think are largely made up of one type of cell. (Muscles, brain.) Do viruses cause macroscopic damage in those tissues?

@DanielDarabos I think the point is that there are cascading secondary effects that cause more damage once a small number of cells are destroyed directly by the virus. Analogy: if you're stabbed, the wound is just a small hole, but you can lose much blood through it.

Another example of a possible local 'wound' is the anosmia (loss of sense of smell) that occurred frequently with early variants of covid.  There's evidence suggestive that entry, infection and death of sustentacular cells (which support the olfactory receptor neurons) could be a major contributor to anosmia and thus a very specialized wound that, while not visible, has a directly notable side effect.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488171/

@DanBryant A very relevant example, thank you!

"it does not look as a physical wound" *look like

The innate immune system is remarkably good at providing a first line of defense.  Viruses don't just march into your body uncontested.  They basically have to fight for every square centimeter of ground they claim, and even then, it's a race against time before the adaptive immune system pulls facial recognition on them and sends out hit squads which targets them directly.
That means that viruses aren't necessarily able to infect all of the cells in a particular area of tissue.  While viruses have some defenses against immune systems, their very simplicity limits the tricks they can use.  Flesh-eating bacteria, being much larger and more complex, have more tools at their disposal when it comes to attacking host tissue.
Kurzgesagt has some really good videos on the immune system:

Tiny bombs in your blood - the complement system
How the immune system actually works

The complement system, in particular, is especially interesting, because it's basically a free-floating chemical warfare system which passively protects virtually every part of your body 24/7.  No signalling molecules or specialized immune cells are necessary for it to start interfering with foreign invaders.

Square centimeter seem huge

@theonlygusti: Change to square micrometre then.

"Flesh-eating bacteria, being much larger and more complex, have more tools at their disposal when it comes to attacking host tissue." One of which being producing toxins (I suppose a virus theoretically could have genes that cause your cells to produce toxins, but they can't produce anything directly).

Smallpox, now eradicated, caused severe lesions. In those who survived: the lesions often turned into scars.

Welcome to Biology.SE. Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site and then [edit] or delete  your answer accordingly. In particular, note that answers should directly address the original question and are much more likely to receive a favorable response if they include supporting references (primary literature is best). A critique should be posted as a comment below the post, not as an answer.

The other answers cover our immune system and the likelihood of viruses surviving it.
Regarding your missing nose:
Do you know how big skin cells are?
Do you know how many need to vanish to leave a visible defect?

As a visual aid, have a look at Genetics Education Site of University of Utah.

A typical skin cell is about $30$μm² - that is really really really small.
Some math:
Using these numbers we can estimate how many cells need to die for a 1mm² defect:

$1$ mm² holds $1.000.000$ μm²

That fits about $33333$ skin cells.
To remove your nose though we need volume - so:

$1$ mm³ holds $1.000.000.000$ μm³

Assuming$^\bigstar$ square-ish skin cells, each cell is about $\sqrt[2]{30}^3 = 165$ μm³ "big".
A $1$ mm³ "hole" has $1.000.000.000$ μm³, that are about $6.06 * 10^6$ square-ish skin cells for a defect that I regularly make while shaving.
And all those damages are constantly under repair by your body.
Summarize:
The danger of you losing your nose from a viral infection is negligible. They tend to spread out and not stay localized, are constantly battled by your immune system and efforts of your body to repair/remove damaged cells.

$^\bigstar$ not squarish - but for simplicity's sake we'll go with that

I'm not sure this really addresses the thrust of the question. I interpret it as; "a virus that initially infects the nose can do enough damage to kill you. How can that much damage occur without the initial site of the infection being totally destroyed." (The answer really being that viruses don't fully conquer one area before moving on but cause small amounts of damage all over the place)

Those huge numbers have no meaning for exponentially multiplying things like viruses...

(1mm)²/(30μm)² = 1,111 not 33,333 are you assuming that the skin cells are 30μm by 1μm? (I mean, they aren't going to be square either, but they presumably aren't that narrow)

("losing" (not loosing - near "The danger".)

@PatrickArtner I can't edit to make that correction (30um²  area rather than the currently 30um) to your answer as it's only one character


text:
Please, help identify this sea worm

It was found in Malta, in a puddle by the sea.
It left a lot of tiny hair on the shoes (which we removed thoroughly without touching them).
I didn’t have any coins with me so I put keys for scale.

Apparently a "bristle worm" , there are many kinds. When I had salt water aquariums, there were at least 3 varieties in the gravel that were introduced with "live" rock.

Looks like a Mediterranean Bearded Fireworm (Hermodice carunculata).

 Source: The Malta Independent
From Wikipedia:

Bearded fireworms are usually 15 centimetres in average length, but can reach up to 30 centimetres.

Each segment has a pair of parapodia, a structure for locomotion, clusters of stinging white bristles, and red or orange gills all in bilateral position.

You can see this post from the Malta Independent warning people who hang out in tidal areas in Malta about this polychaete worm -- it's bristles can inject a neurotoxin which can cause intense irritation/burning and possible nausea and dizziness.
Also, FYI, the whitish elliptic shape on the second body segment closest to your keys is the mouth. See here for some images of this mouth in action!

@Thomas. Thanks for accepting my answer -- hope it helps! Please consider upvoting, too :)


text:
DNA Design for Multi-Site Restriction Enzymes
I have to use the SacII restriction enzyme, which requires multiple recognition sites to efficiently cut DNA, for a DNA assembly. From my understanding, multiple copies of DNA holding only a single restriction site can still lead to digestion through bridging interactions between molecules and enzyme. However, this appears to require digestion optimization I would rather avoid. Can I place two SacII sites in tandem on my insert DNA to enhance my digestion? How far should these be spaced to allow efficient enzyme interaction between the sites?

You've got a very nice answer from @acvill, but for future reference the NEB website is a good first place to look when you have questions about the specifics of RE usage (and for many other enzymes as well).

Hi @tyersome, that's where I started but they are not clear on design.

In its active form, SacII (also called Cfr42I) is a homotetramer that must bind two copies of its recognition sequence in order to efficiently hydrolyze its substrate.1 Upon binding two sites on a single molecule, the interstitial sequence is "looped out" and cleaved. The efficiency of cleavage is a function of the length of the intervening sequence due to the sterics of DNA bending (see resources concerning the persistence length of DNA 2 to better understand the energetics at play). One study on the effects of DNA tension on the cutting frequency of two-site restriction endonucleases (including SacII) suggests that the optimal loop length is hundreds of bp.3

In each case the DNA template contained multiple recognition sites for the enzymes being tested with separations ranging from ≈200 to 1,000 bp, predicted by theory to be favorable for looping.

A different study notes that EcoRII, another two-site enzyme, can cleave its target with as little as 10 bp between the 5′-cytosines of its two recognition sites.4
As an alternative to designing a construct with multiple SacII sites, you could supplement your digestion with a dsDNA oligonucleotide containing one SacII recognition site.3

...stimulation of activity upon addition of short oligonucleotide duplexes containing the recognition sequence has been reported for Eco57I, HpaII, Cfr9I, and SacII. Such stimulation provides evidence that an enzyme complex can bind in trans (i.e., across two sites on different molecules).

If you go this route, I would recommend first incubating SacII with your construct for some time, then add the oligos and continue incubation. This way, SacII will associate with the cut site on your target, and you will reduce the frequency of events where SacII binds and cuts two oligos at once, which would reduce the available oligo concentration and possibly lower your target cleavage efficiency.

References

Gasiunas G, Sasnauskas G, Tamulaitis G, Urbanke C, Razaniene D, Siksnys V. Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res. 2008 Feb;36(3):938-49.
Manning GS. The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys J. 2006 Nov 15;91(10):3607-16.
Gemmen GJ, Millin R, Smith DE. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force. Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11555-60.
Reuter M, Kupper D, Meisel A, Schroeder C, Krüger DH. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J Biol Chem. 1998 Apr 3;273(14):8294-300.

Thank you @acvill! I think I better go with the dsDNA oligos in this case, it's a shame Benchling doesn't highlight these enzymes.

@JEJS I've updated my answer with a methodological tip.  I hope your experiment goes well.

Oh great thanks @acvill!

Update for future reference: I actually had no problem with standard digestion conditions being 1ug DNA (~170 pmols) to 1ul SacII. However, I did leave digestion for 16+ hours which I imagine to be critical.


text:
Do human lungs have more protection against smoke compared to other animals?
Our ancestors have used fire for more than a million years. Wood smoke is not good for the lungs, but our ancestors were depended on fire. Especially in colder regions of the World like in Europe, where people would have been sheltering in closed spaces like caves or tents, the exposure to smoke would have been significant. I've been in Arctic regions and been inside tents used by indigenous people. They use woodstoves inside tents, and while there is a chimney, the concentration of smoke inside is huge. After a while your eyes start to burn.
So, the question is whether after tens of thousands of generations living in such conditions our lungs have evolved to neutralize the damage done by wood smoke to some degree?

Although I am not aware of any scientific evidence regarding the emergence of more smoke-resistent lungs in humans compared to the past, this can by no means be imputed to the "evolution of lungs". This is not how natural selection works. Rather, hypothetically speaking, nature may have selected humans with particular genetic traits that made their lungs more resistant to smoke, and therefore gave them a survival advantage compared to humans that lacked such trait.

I attended a lecture about an adaptation on the aryl-hydrocarbon-receptor gene that's present in all humans but not present in any other extant primates. This receptor senses dioxin (among other things) and triggers a response from the immune system, so they definitely hypothesized a link to our relationship with fire, especially indoor cooking fires. Wish I remembered more about what the actual phenotype of the adaptation was.

That would be nice, but just reflect on the damage smoking does. Chronic bronchitis, chronic obstructive pulmonary disease, different cancers. How in heaven’s name would we know the answer to this question since other animals are not similarly dragging on cigarettes?? (That’s one thing you can research; animals were in fact forced to smoke. We’re they more or less likely to be injured by smoking?)

@anongoodnurse good point, but you have to compare the average human lifespan for most of our existence with the average ages when smoking-related morbidity and mortality become a significant issue. Most of our predecessors likely died from other causes long before the effects of smoke inhalation became a health issue for them.

@MattDMo - I agree that most ancient humans died of “other causes” before smoke inhalation became an issue. The OP would have a different idea. However, smoke is more of an issue in the younger populations than you might think. In kids, it’s related to ear infections, asthma and other problems. If we have developed better lungs, I’d hate to see how earlier humans fared.

I don't know the answer. It may be human lungs are anatomically different than other species' or diverged evolutionarily to be substantially different or more resilient to particulate entry or deposition. They may also be different physiologically, say with respect to clearance mechanisms of particulates that are captured and removed. Soluble particulates are largely cleared by pinocytosis and insoluble ones by mucociliary movement ("ciliary escalator") and this may very well be different between older and modern humans. I think it would be difficult to demonstrate this definitively though.

From a population lineage point of view, I can understand the hypothesis that multigenerational, repeated, endless exposure to smoke may have affected the gene pool by removing the one extreme end of human variation selectively, one that had hypersensitive lungs or issues with clearance of particulates from the lungs. We think the same for those who couldn't run away quickly enough, or spot or hear danger, or store fat reserves for the winter, so why not for smoke tolerance? Of course, whether it happened to a degree enough to have contributed to changing the gene pool is an open question.


text:
What is harvest mortality and how is it calculated?
My background is not in biology, however for the work I'm currently doing, I am reading some papers in ecology and the term "harvest mortality" appears. I could not find the meaning of this term or an equation explaining the way it is calculated.
Can someone please define the term "harvest mortality rate" in the context of wildlife ecology and sustainability, and also provide a formula explaining the way it is calculated please?

“I am reading some papers in ecology and the term "harvest mortality" appears.” — could you please link one or more of the papers that use that term?

"Harvest mortality" usually refers to the proportion of a population that is killed by humans for economic purposes (e.g. birds or terrestrial mammals that are shot by hunters, fish caught in nets or on lines, trees cut down by loggers, etc.). For a specified population and time period, it will be something like (number harvested/total number alive at time 0).
The first hit of this Google Scholar search for "harvest mortality" is by Solberg et al. They describe a complicated procedure for estimating the number of moose of a given age and sex alive in a given year. Basically, they add up the reported number of moose shot by age and sex in each year, combine it with estimates of the non-hunting mortality by age and sex, and do the accounting to back-calculate how many animals of a given age/sex must have been alive in a given year (they do the book-keeping up to a maximum age beyond which few animals survive).
Once they've done the hard part, estimating the total number of moose of a given age that were alive at the beginning of a given year,

The  age-specific  harvest  mortality  was  calculated
as the annual number of moose harvested divided by
the annual number of moose present in the respective
age groups.

Solberg, Erling Johan, Anne Loison, Bernt-Erik Sther, and Olav Strand. “Age-Specific Harvest Mortality in a Norwegian Moose Alces Alces Population.” Wildlife Biology 6, no. 1 (2000): 41–52. https://doi.org/10.2981/wlb.2000.036.


text:
How to customize the output of my BLASTP output form
I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with -qseqid -sacc -qlen -slen -length -nident -pident -evalue -stitle and I want to set the evalue less than 1e-10. Here is my code :
#!/usr/bin/env bash
blastp -query Trinity.fasta.transdecoder.pep \
    -db swissprot \
    -outfmt "6 qseqid sacc qlen slen length nident pident evalue stitle" -evalue 1e-10 1>Predict.txt \
    2>wrongPredicted.err

However this is the first several lines of output I got in the txt file :
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E0  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964D9  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P53472  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoskeletal 1A; AltName: Full=Actin, cytoskeletal IA; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P92179  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E1  400     376     376     363     96.54   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E2  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P69004  400     376     376     364     96.81   0.0     RecName: Full=Actin-15B; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   O17320  400     376     376     361     96.01   0.0     RecName: Full=Actin

The problem is that all the evalue is 0.0 for some reasons, cuz what I want is something like this :
TRINITY_DN8_c0_g1_i1 Q5ZKK7 283 788 64 53 82.81 1e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q7ZVV1 283 782 64 53 82.81 3e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q1RMT1 283 782 64 52 81.25 6e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q5RA62 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q60HG1 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3

The 8th column should be valid evalue. Need some help! Thank you!

Very low e values are rounded to zero, so that’s a valid output.

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0 is a valid e-value. It is the strongest e-value you can get.
the sequence identifier in a FASTA file (and thus what BLAST uses) is "everything up to the first space". If what you have behind "::" is indeed useless, you should remove it from your query before submitting it.

FWIW, my lab makes SequenceServer, a powerful graphical interface for running BLAST. It enables you to run BLAST in the cloud or on your local computer.

Good answer, but three links to your own application? Really!

Hi @David - Sorry I didn't mean to cause offence. I'm quite proud of what our app has accomplished: SequenceServer helps me and 1000s of others perform and interpret BLAST analyses every week. Anyhow, I've removed 1 of the 2 links to the app.


text:
Why are there otoliths in the otolithic membrane of the saccule and utricle but there aren't in the cupula in the semicircular canal?
I know both of the 2 systems work quite similar the first (saccule and utricle) detect linear acceleration and semicircular canals play the role of angular acceleration detectors. I wonder if there is a functional reason for which there are no otoliths in the cupula. Why are they important in the otolithic membrane but not necessary for the cupula ?

In the ampulla of the semicircular canals, the flow of the endolymph is blocked by the gelatinous cupula into which the hair cells protrude. Thus, during circular motions when the endolymph is accelerated in the semicircular canals, the pressure on each side of the cupula will be different and hence results in some displacement of the cupula, which the hair cells may then detect. When the rotation stops (or the rotation speed is constant), the axonal firing rate of the hair cells will return to the firing rate at rest.
In the maculae, the gelatinous layer is not blocking any canals and hence it isn't displaced effectively by fluid motions as the cupula is in the semicircular canals. The role of the otoliths (which are heavier than the surrounding fluid/tissues) is to cause a temporal displacement of the gelatinous layer during linear accelerations, which happens due to the temporal motional lag between the otoliths and the sensory epithelium with the embedded hair cells. During head tilts, there will also be a displacement of the gelatinous layer, because of the gravitational pull on the otoliths, and the hair cells will then continue to fire their axons at increased/decreased rates (depending on the tilt direction) for the duration of the head tilt.
Thus, the method for displacing the cupula/gelatinous layer is slightly different between the maculae and semicircular canals, and in the semicircular canals, there isn't a need for otoliths to make this happen.
The book Neuroscience edited by Purves et al is a good resource on this.

Great first answer Michael, especially liked the description of the physics aspect. Welcome to biology. (From review)


text:
Can blood transfusion help to fight cancer cell?
First of all, I'm not a biology student or have sufficient knowledge of biology so I apologize if this question appears silly. Let's say patient A has cancer cells and a healthy person B has the same blood type as patient A, by using a blood regulator device to regulate the blood between A and B, will the white cell in patient B recognize the normal cell in patient A as foreign cell and attack it? Is there a chance the white cells of person B recognize the cancer cell in patient A as a foreign cell and attack it?
So far what I understand as below from internet
At early stage white blood will detect cancer cell but as the cell evolve, the white blood cell will no longer recognize the cancer cell as foreigner cell which enter the escaping phase, in this phase the cancer cell start to growth without obstruction. However, I am not able to find article like the membrance wall constitution for different people so logically if it is similar, the white cell will not recognize normal cell in both people as a foreigner cell, correct me if i'm wrong but a cancer cell that enter the escaping phase may not treated as normal cell in person B due to difference membrance wall constitution? If this is true, then can this method use to save patient with cancer especially for family members that willing to use a blood regulator device to constantly regulate the blood between both hence regulate the white blood cell of person B into A to fight cancer cell? If this work, this can also use to save patient with Covid at critical stage where an immune person can regulate the blood between both people as if lending the person immunity system to fight covid infected person?

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site 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. Our goal is not simply to be an answer site, but rather a site that promotes self-learning with some expert help along the way.

White blood cells have antibodies that target specific proteins on the surface of different cells- this is why blood transfusions need to occur with the same blood type in each patient. (If this were to happen, your body would produce antibodies to attack the foreign blood cells.) To address your first question, as long as the blood types are the same, the cells inside of patient B's blood will not attack any of patient A's blood. Even if patient B had a different blood type as A, if his blood was introduced into A's bloodstream, a healthy amount of B lymphocytes (these are cells that stem from bone marrow and differentiate to create new antibodies) would need to be introduced along with it. Otherwise, the cells would not have the capability to create antibodies that are compatible with A's blood. However, doing this wouldn't really be a good idea, as this would cause an indiscriminate attack- all of A's blood cells would be attacked. And to answer your second question- after cancer cells get past a certain stage in their development, they lose important proteins that the body uses to identify them. In other words, they sneak past its immune system and begin to spread. The escape phase is a direct result of this- the tumor begins to metastasize throughout the body and the body fails to stop it. To be frank, there is very little to do here- the issues with the blood transfusion method are detailed above. And to address your final statement about Covid- from what I understand, this is mostly correct. If you may remember, people with antibodies often donate their plasma to be used in other patients. However, the key part of this is that the blood cells are not the useful part of this transfusion. The antibodies are. It isn't a matter of blood transfusion- it's a matter of antibody transfer. For the most part, however, your logic is correct. I could help you a little more if you linked the websites that you researched. Thanks.

Would you edit this answer so it's not a wall of text that breaks people's eyeballs, also, adding references to support your claims. Please take our [tour] and refer to the [help] for guidance as to our ways. Welcome to Biology.

https://news.cancerresearchuk.org/2019/02/28/science-surgery-why-doesnt-the-immune-system-attack-cancer-cells/ this is the article I refer to but that is from the perspective of immune system A couldn't recognize the cancer cell. If the same cancer cell that enter escape phase in A put into healthy person B,C,D and so on, there a 100% chance it escape the immune system of all these healthy people?


text:
What protein(s) bind together the calcium carbonate tiles in abalone shell to give it strength?
The articles that I've been able to find on the structure of abalone shells mention that they consist of calcium carbonate plates connected by proteins, but don't name the proteins. These proteins are key to the shell's strength. What proteins connect the calcium carbonate plates to give the shell its strength? What other proteins are they related to (if any), both structurally and phylogenetically?
I searched via DuckDuckGo using phrases such as "abalone shell protein", "abalone shell structure protein" and "abalone shell structure calcium carbonate protein". The best match I found on proteins was "In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix"; while it names many proteins, it doesn't identify their function.

What did you find when you googled “what is the protein found in abalone shell?” Using this phrase got me a very interesting article.

@anongoodnurse: I used DuckDuckGo. Updated question includes search terms. Looking over "Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell" now.

The article is quite interesting, but seems focused on identifying proteins for their shell growth function rather than tile binding (the proteins may have both functions). This is ambiguous in parts, since "bind" is also used for CO₃ crystal growth.

Pif-80 might be one protein identified as potentially binding plates in that it hypothetically "binds in vitro to calcium carbonate crystals" (rather than binding CO₃ molecules together), according to another study (Suzuki et. al., "An acidic matrix protein, Pif, is a key macromolecule for nacre formation", 2009). The proteomic analysis article also describes some proteins as fibroin-like, which could be involved in the shell strength.

The article also mentions even other species in the same genus have vastly different proteins in their shells, which means the question might be too broad at the given taxonomic rank.

In that paper alone, you have 14 proteins listed. They were identified by tandem MS (fractionated proteins isolated from crushed shell). Does that paper answer your question in part? I also recommend looking at a more recent one where some of the same authors more recently (in 2018 as opposed to 2010) identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer, in a different abalone species. A total of 448 proteins were found. Would that satisfy your question?

@SPr: Unfortunately, no. I'm not only interested in the proteins in general, but the proteins with specific function (as described in the question). The more recent one you mention is also the paper I linked in my question. Neither of the two papers identify with certainty the proteins that connect the CO₃ plates for strength.

I see. It is difficult to identify proteins with specific niche functionality ("carbonate plate-connecting") by MS/MS. That method is designed to identify isolated proteins, and in this case, the entire shell was isolated. I hope you will find your answer, but it's possible it doesn't exist. Seemingly, the group interested in this research did a whole shell extraction in 2018, and I can't find anything relevant since. I think the protein motifs and domains discussed in the two papers we link here may provide hints. Plate connecting protein(s) must have domains that can interact with carbonate.

@SPr: Pif-80 and the fibroin-like HasCL10contig2 & P0025F23_658 (mentioned in "Proteomic Analysis ...") are the best candidates at this point.


text:
Hodgkin huxley neuron not spiking consistently for currents greater than threshold?
Hi I am currently studying physics at the undergraduate level. As part of my final year project Ive got to implement the HH model and investigate certain types of behaviour.
My issue is the following.
I understand that for $I_{inj}>I_{thresh}$ we should expect action potentials that spike at a regular frequency.

Here I've got an input current that seems to generate 2 initial spikes however no further spikes are generated. Is this physical? The presence of the initial spikes must mean that the input current is greater than the threshold, but we do not see consistent spikes across the entire stimulatory current.
Increasing the current slightly gives the expected behavior:

Is this an error in the code or is this a real physical phenomena?
EDIT------------------------------
Following Bryan Krause's suggestions, here is the full picture with the gating variables.
Case 1:
Stimulus current with amplitude 35 mA with period 100ms

Case 2:
Stimulus current with amplitude 37 mA with period 100ms

Case 3:
Stimulus current with amplitude 500 mA with period 100ms

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@tyersome I believe I have shown my attempt at an answer  by providing the second example as going by the HH model, that is what I believe should have also been observed in case 1.

What are the equations this model is solving?  Your case 1 looks like a strongly damped oscillator in the voltage, whereas case 2 looks like an oscillating solution. If you have a nonlinear damping constant, that could explain the difference between case 1 and 2 qualitatively.

@AtmosphericPrisonEscape The HH model is quite a famous standard model in neuroscience.

This is happening due to sodium channel inactivation. Some relevant sources:
https://en.wikipedia.org/wiki/Ball_and_chain_inactivation
https://www.st-andrews.ac.uk/~wjh/hh_model_intro/ (I guess this link is broken for some people? works fine for me as-is; see the links before and after instead, then)
https://neuronaldynamics.epfl.ch/online/Ch2.S2.html
In the HH model, inactivation is sometimes referred to as the "h-gate" based on the parameter they use for this inactivation, assigned the variable "h".
Sodium channel inactivation changes the action potential threshold and can even prevent action potentials completely. The easy way to understand this is that inactivated channels aren't available to participate in the positive feedback loop of an action potential. Because of this, it's not quite correct to think of a constant threshold for action potentials for a given cell/model. Instead, there is a threshold for any given holding potential or recent history of the membrane potential. Most often, you'll be concerned with the threshold at the resting membrane potential, but if you apply a constant external stimulus (or if you trigger a lot of action potentials in sequence without enough time spent at hyperpolarized or resting potentials) then the number of available sodium channels is not the same as at rest.
I would suggest a couple things...first, try other steps, too! What happens if you use an even bigger stimulus? Second...plot out the HH gating parameters m, n, and h as a function of time, not just the voltage.

Ive added a few more cases to my original question. Based on your answer I can't understand why case 3 and case 1 look identical.

@Vishal Look at the h-gate! Compare h before the first stimulus to after the first action potential (or first couple, once the APs stop).

Your St. Andrews link is dead.

@AtmosphericPrisonEscape Works fine for me.

I cant access the St. Andrews link either…
With regards to the h gate behaviour, I can see that h is quite close to 1, which makes sense since the neuron is hyper polarised. I’m not sure what to take away other than h is high when the neuron is hyperpolarised and low when the neuron is depolarised.

@VishalJain h is only close to 1 at rest; later in the pulse, it is less than 1. In the first case, it's low enough that the threshold has shifted so the stimulus is no longer superthreshold after the first spike, and h continues to decrease (more inactivated).  In the second case, there is enough of a relaxation of the h gate during the hyperpolarization between spikes. In the third case, the stimulus is too strong and the h gate never has a change to reopen; h stays low and so there are not available sodium channels to open.

I don’t get why the neuron seems to come to a resting potential at V = 0 after the first spike in case 1, but got case 2 (with just a small increase in the injected current), the neuron properly hyperpolarises in between action potentials.
Looking at the gating variables values all make sense when you look at the corresponding membrane potential at that time step.
EDIT: reading the previous comment it seems as though that tiny increase in current was enough to give the h gate enough time to relax to properly reset?

@VishalJain It's not just the membrane potential that matters, but also the state of all the gating parameters. In both case 1 and case 2, there is never a time that the h gate makes it all the way back to 1; it looks like it recovers to around 0.9 in both case 1 and case 2. Case 2 has a strong enough stimulus to still trigger an AP with only 90% of the channels available; case 1 doesn't, but the subthreshold depolarization is sufficient to cause even more channel inactivation (h continues to decrease over time).

Ok it’s starting to make sense, last question on this and I think it’ll click.
I can accept that in case 1, we provided a stimulus that was super threshold when the cell was at rest, however once stimulated it was no longer large enough to generate further spikes.
However,  if you look at my original image where i provided an image where we had 2 such initial spikes, how can you explain this? Here we clearly simulated the cell once when it was at rest in a hyper polarised state and again once while the stimulatory current was being applied, however then we stopped generated spikes.

@VishalJain You can see in your "case 1" that there is kind of a mini-spike; it's enough for some voltage gated channels to open and depolarize the cell a second time, but not enough for a full positive-feedback spike. By the third such "event" it's even weaker. Same thing happened in your original case 0 except the stimulus was strong enough to make the second spike, but you do see that the second AP is a little weaker than the first, and the third fails. All of this is best understood by thinking about how many sodium channels are available, aka "not inactivated", aka "h".


text:
Is lysozyme present in the lysosome?
Is lysozyme present in the lysosome? I cannot find anything about this in the literature.

@infinite if you have got your answer, feel free to self answer it. Self answer are always appreciated and it also help future readers.

lysozyme is not a lysosomal protease and the pH optima is too basic for the function in the lysosome we can conclude that lysozyme is not present in lysosome.

This is not the type of answer required on this site. Lysozyme is either present in or absent from lysosomes. An acceptable answer would refer to papers in which the enzyme was assayed in different cell compartments. Statements that it is not a protease (we know that) and that it has a basic pH optimum ( what, precisely?) do not allow us to conclude anything about its subcellular location.


text:
Do plants originate from a single cell
I read the generalization that life originates from a cell, and from my understanding animals, they originate from a single cell, produced as a result of sexual reproduction. And then life begins to develop from there on. But when it comes to botany, I stumble upon this doubt because of plant seed varieties. During any stage of seed production, can the seed be designated as having come from a single cell. Can i use the following generalization and correct me wherever i am wrong.
every life is made of cells, and every life comes from a single cell

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nice of you for helping me with the terms, i will look up and get back. So my question is supposedly looked down upon as being vague, and ill-researched ?

In a nutshell, that's correct. The homework help section states: *What is a homework question?... ... A question that addresses a basic biology concept that may seem trivial to biology professionals" among other things.  You might also want to look into plant cloning and things like coppicing and stolons and compare to sexual reproduction.

Obviously a plant has to come from a single cell, because cells can only multiply by division, so at one point there must have been a single cell. In plants the germ cell is called an "ovule" and it is a single cell.

Or, as Rudolph Virchow famously put it in the 19th century: omnis cellula e cellula (“every cell stems from another cell”).

plant single cell phase is caled plant gametes.

You are actually right by saying that. The embryo of a seed is a single cell that germinates after several cell division and differentiation resulting in to a whole plant.

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In addition, to what David pointed out your answer is misleading. Most plant embryos consist of many cells and germination is often (if not usually) triggered by environmental factors and has no direct connection to cell division.  ——— NB:From "How do I write a good [answer]?" in the [help], Answer well-asked questions. Not all questions can or should be answered here. Please delete this post as it is both inadequate and encourages the posting of questions that are not appropriate for this site — please see the [tour] and other [help] pages such as [ask] and [answer] for more information.

Bro, most life on earth start drom a single celled condition called the zygote. And it is applicable to most plants also ( I say "most" because biology is full of exceptions and pretty much most of the time, we can generalize ).

Welcome Adithya. Please take our [tour] and refer to the [help] for guidance, you'll find that we need answers. to be supported by references and citations, you can improve your answer by [edit]ing those in.


text:
What is the difference between Haploinsufficient and Autosomal Dominant mutations
I have been reading a paper that classifies genes in different groups by the type of disease-causing mutations. The categories of mutations (alleles) it gives are:

Haploinsufficient
Autosomal dominant
autosomal recessive

I was wondering what is the real difference between haploinsufficient and autosomal dominant.
As far as I know, a Haploinsufficient gene is the one that one copy LoF mutation produces the phenotype. This seems to be exactly the same as an Autosomal Dominant disease???
Can someone give me an example?

Genes can be haploinsufficient, but genes cannot be autosomal dominant, only mutant alleles can be dominant or recessive.  If m/+ has a wild type phenotype then the mutant allele ‘m’ is recessive (recessive to the wild type allele ‘+’).  However if an m/+ heterozygote has a mutant phenotype then the mutant allele is dominant (dominant over the wild type allele ‘+’)
Dominant alleles are usually, but not always, GoF (gain of function). If a gene is haploinsufficient then a heterozygote with a LoF mutant allele over wild type, m/+, has a mutant phenotype, and is dominant but is not a GoF. The classical test is when you have a deletion or deficiency of the gene, and still have one good copy, but still get a mutant phenotype.
The autosomal dominant alleles you refer to then have to be GoF, either hypermorphs, antimorphs or neomorphs.
In the model organism, D. melanogaster, the genes Ubx (Ultrabithorax) and N (Notch) are both haploinsufficient, because a heterozygous deficiency of either of those genes have their respective mutant phenotypes.  Examples of autosomal dominant mutations in humans are the classical oncogenes, for example the mutant ras gene alleles that cause bladder (and other) cancers.

In human genetic diseases there are in fact autosomal dominant mutations which upon detailed molecular analysis turn out to be loss-of-function alleles of a haploinsufficient gene.  Autosomal dominance is a pattern of inheritance defined by a phenotypic pedigree, it is not a molecular mechanism underlying biological function.  Haploinsufficiency, on the other hand, is a description for dose-sensitive genes where two copies of the gene are necessary for a wildtype phenotype.

Haploinsufficiency would be like a red and white allele making a pink flower.  If the red allele were totally dominant, a flower with one red allele would look exactly the same as one with two red alleles

In your example, if the red and white alleles are both dominant gf (gain-of-function) mutations, then what you have described, a flower where both phenotypes are present, is called codominant.  A classic example of codominance is in the mating type locus of the baker’s yeast S. cerevisiae. a/a diploids, alpha/alpha diploids, and a/alpha diploids each have different phenotypes. I believe Ira Herskowitz wrote a small review article about this as an example of codominance.

Typically, a white allele would be a loss of function; the pigment doesn't get made.  A pink flower is pink because it makes less red pigment than the flower with two red alleles.

The question is about the difference between haploinsuffieicny and complete dominance.  Yeast mating types are neither.  Co-dominant situations are neither.