Bacteria in our colons During my education in Iran, until now, which I must say that I'm graduating high school this year and will go to college next year, our biology book has said that there's some bacteria in our colons and those little cells live there and use the celloluse of our food and because mostly they are anaerobic they produce methane or hydrogen and hydrogen sulfide and so on and sometimes they are the reason of the smell of our farts. Also they produce little amounts of B and K vitamins which is good for us and also, by using cellulose they make the rejection of feces better and easier. Anyway I wonder that where do these bacterias come from? I mean are they with us since birth? Then it means they come from our mother's body but, wait how our mothers have them? But maybe they are not there since birth and they come to colon from the food we eat during our life, but why don't they die in stomach. Even if we think that they go there by eating food, passing stomach easily, what if we don't eat the "food that can have those bacteria", then could it be possible to some humans don't have those bacteria? But they can't have a good release of feces.

It has been demonstrated that there are common patterns of microbiome composition evolution during life. In general, the diversity of microbiota composition of fecal samples is significantly higher in adults than in children, although interpersonal differences are higher in children than in adults. Much of the maturation of microbiota into an adult-like configuration happens during the three first years of life.

As the microbiome composition changes, so does the composition of bacterial proteins produced in the gut. In adult microbiomes, a high prevalence of enzymes involved in fermentation, methanogenesis and the metabolism of arginine, glutamate, aspartate and lysine have been found. In contrast, in infant microbiomes the dominant enzymes are involved in cysteine metabolism and fermentation pathways

evolution of the vertebrate gut microbiota :

Multi-cellular eukaryotes have existed for at least a quarter of Earth's history, or 1.2 billion years. Thus an already long history of interaction between multi-cellular lifeforms and microbial communities preceded, and likely shaped, the evolution of the vertebrates. The legacy of ancient associations between hosts and their epibiotic microbial communities is evident in the present day effects that the gut microbiota exerts on host biology, ranging from the structure and functions of the gut and the innate and adaptive immune systems, to host energy metabolism. Host responses to microbial colonization are evolutionary conserved among diverse vertebrates including zebra fish, mice and humans

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664199/

"the human body is made up of about 10 times more microbial cells than human cells . Further, there may be millions more microbial genes than human genes in this human+microbiome system (which is often thought of as a human ‘superorganism’), and it is the ways in which these microbial genes interact with the human host that describe their ultimate role in our health. Scientists now believe that infants are sterile (meaning free of microbes) in the womb and receive their first inoculum of microbes from the mother during natural childbirth. This inoculum goes on to colonize the newborn and initiate a succession of events leading to the development of the child’s own microbiome. The newborn relies on this maternal vaginal microbial inoculum and the additional inoculum of microbes from mother’s breast milk for microbial colonization of all exposed surfaces in and on the infant’s body (e.g., oral, nasal/airways, gut, urogenital, skin).2 This is a dynamic process in which microbial abundances increase from effectively zero at birth to over six orders of magnitude (that’s more than a million times!) within just the first few weeks of life, with wide swings in the microbial membership of these communities until the microbiota largely stabilize in composition and numbers after approximately three years of life."

http://www.actionbioscience.org/genomics/the_human_microbiome.html

you can read about Gastrointestinal Tract Microflora here:

https://www.ncbi.nlm.nih.gov/books/NBK7670/

and normal flora :
https://www.ncbi.nlm.nih.gov/books/NBK7617/


What is the normal duration of human sexual intercourse? Wikipedia is saying:

  Men's typical ejaculatory latency is approximately 4–8 minutes

How the researchers measured this? How did they know if the test subjects weren't suffering from premature ejaculation?

And is this measured from the start of erection or from the start of penetration?

First, "premature ejaculation" is a matter of definition. Here is an authoritative source. From the American Urological Association's news site, a 2008 notice:

'The ISSM [Int'l Soc. for Sexual Med.] has defined premature ejaculation as “a male sexual dysfunction characterized by ejaculation which always or nearly always occurs prior to or within about one minute of vaginal penetration; and, inability to delay ejaculation on all or nearly all vaginal penetrations; and, negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy.”'

The main author of the ISSM paper was Sharlip. Sharlip ID, Hellstrom WJG, Broderick GA: The ISSM definition of premature ejaculation: a contemporary, evidence-based definition. J Urol, suppl., 2008; 179: 340, abstract 988.

If this is the threshold for PE then it is not a stretch to say that almost anything else is within normal limits. If "typical latency is 4-8 minutes" then 1.5 minutes would be near the low extreme of normal.

I think the issue of stress is at least as important as duration. If something isn't bothersome it never becomes a medical issue.

A nice study involving 491 men is reviewed here. The mean IELT (intravaginal ejaculatory latency time) is 5.4 minutes. As you can see from the graph on the site, most of the results are contained in the first few minutes with a tail of longer times to the right.

The original source for that information is MC Waldinger et al. A multinational population survey on intravaginal ejaculation latency time. Journal of Sexual Medicine 2005 2: 492-497. This also addresses your question about the timing of measurement--it's post-entry.

An expert in this area could update my information but it's a recent average so I don't think things have changed much.


Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends which provides 2 phosphate groups. But there are still 2 nicks in the vector product! How are these normally repaired ?

The nicks are not repaired during preparation. Instead, the vector (which is circular, despite the nicks) is transformed into the host where it is repaired by endogenous mechanisms, likely through base excision.


What is a inhibitory tone when talking about neurons? In this SE answer: Could an "overactive" brain increase the chances of Alzheimer's Disease?

user @nico used the word inhibitory tone What does that mean?

More examples of it used:

http://www.ncbi.nlm.nih.gov/pubmed/18234887

http://www.cell.com/neuron/abstract/S0896-6273(11)00479-X

Neurons communicate electrochemically. That is, when a signal arrives to a neuron it fires a series of electrical signals, called action potentials.
Action potentials are depolarization events that propagate along the neuronal membrane, down to the neuronal terminal.
The terminal of a neuron is (with some exceptions) in contact with another neuron, via a structure called synapse.
When the depolarization arrives at the terminal, it allows the entry of calcium, which then mediates the release of a chemical substance, a neurotransmitter into the synaptic space. Finally, neurotransmitters act on the postsynaptic neuron, by binding to specific receptors on its cell membrane and can either stimulate it, in which case the postsynaptic neuron will fire more and release more of its neurotransmitter or inhibit it, in which case the opposite happens.

The textbook example of a stimulatory neurotransmitter is glutamate, and the inhibitory one is GABA1.

In various areas of the brain certain neurons are constantly receiving inputs from GABAergic afferents. This means that those neurons are constantly receiving a GABA stimulus that inhibits them, and are thus under a constant inhibitory tone. This will prevent their firing until a sufficiently potent stimulatory stimulus arrives or until the inhibitory tone is somehow released (for instance if the inhibitory GABAergic afferents are themselves inhibited by some of their own afferents).

1note that this is not always true: GABA can also be stimulatory in various situations


Chromosome size without heterochromatin Im doing different analysis of the human chromosomes and diffent loci, however when using different databases, the heterochromatin structures are not part of the human genomes. I know that heterochromatin is a more dense structure within the DNA and stained differently and are not part of the different reference genomes.

However all the information regarding the human chromosome sizes, I can find all includes the heterochromatin regions.

So i would like to know, is there anywhere i can find the length of the human chromosomes without the heterochromatin structures?

Thanks for your time and help.

There are a couple of caveats that need to be addressed before answering this question:

We don't know all of the regions in the human genome that can be heterochromatic. In some cases large chunks of heterochromatin are simply missing from the genome assembly. For a somewhat outdated but still informative review of the topic see here.
Which regions are heterochromatic differs from cell to cell. For example, I would recommend reading about the differences between constitutive and facultative heterochromatin at wikipedia.
Heterochromatic regions of the genome are very important biologically and not taking them into account could be a mistake, though it depends on your motivations.

The human genome project initially estimated that 92% of their original genome build is euchromatic, 2.85 Gbp total. However that original genome build has been substantially updated. That estimate is close enough for many purposes, probably. But we've learned a lot about genome structure and biology since that time.

We do have a lot of data that is highly correlated with what we think of as heterochromatin. The UCSC human genome browser has a lot of information about chromatin modifications (I would look at the ENCODE analysis section here). In principle you can make educated guesses about regions of heterochromatin based on chromatin modifications. This will be somewhat noisy, and you will have to make decisions about which cell types are relevant, as they will have somewhat different regions.

For more information about which chromatin modifications might be relevant, you might start looking here. You will likely need to analyze some data yourself to find a more precise answer.


Why are low temperatures lethal? Why can't we (human, or even unicellular organisms) withstand low (body) temperatures (5 - 25°C). I have a limited background in chemistry and biology, so this might be obvious, but not to me.

I know that low temperature reduce the speed of chemical reactions, so any creature cold enough should just perform slower? Or are there any other cold-induced effects that prevent certain reactions? (a reaction requiring more energy to happen, would still happen, but at a lesser rate, right?)

And, supposing a bacteria/virus/small&simple organism was subjected to low temperature (above freezing, but low enough to stop working), what would prevent this organism from booting up again when subjecting to "normal" temperature?

Low temperatures change the speed of different chemical reactions, throwing delicately balanced systems out of balance. How resilient a creature is to temperature changes is largely a function of how complex it is, and how buffered it is against this kind of change.

Tardigrades as kmm mentioned essentially can't be killed by cold, surviving down to almost absolute zero (absolute zero ≈ minus 273.15°C). Most unicellular organisms can be frozen (especially if frozen quickly or cryoprotected with something like DMSO) and revived later without any change. Most strain libraries of bacteria are kept frozen for cost reasons. Even human cell cultures can be frozen and thawed, even though some of the cells will die. (If even 10% of your cells died you as a person would probably die, so freezing is off the table unless you are very clever indeed.)

Humans and most mammals are pretty sensitive to temperature changes, even though reptiles are not. Most fish are cold-blooded and are adapted to cope with the relatively cold temperatures, but the human heart is not well adapted to even relatively warm temperatures. The atria and the ventricles of the heart stop communicating below 27°C (80.6°F)or so, and below 20°C (68°F) the heart can stop beating entirely. Nerves are complex systems, and absent regulation systems in the nerves themselves to compensate for the changes in temperature, they can stop firing completely. A simple heart can run with less sophisticated orchestration, and is, therefore, more resistant to temperature change. A complicated heart involving the coordination of the atria and the ventricles to produce effective pumping action is affected much more strongly by the drop in temperature.

So, in general, more complicated implies more vulnerable to temperature changes. There are exceptions, however. Bears can hibernate and drop their core body temperatures without any ill-effects, so it's possible to adapt to. Fish deal very well with cold temperatures if exposed gradually, and some fish could live quite happily in a slushie, salinity notwithstanding.


What can I see with a microscope at what magnifications? I'm 26 and where I grew up the schools were complete crap so I've never really used a microscope much or learned much about them. And I want to learn some science and look at some microscopic things, like organisms in water, how tiny  bugs or dirt looks up close, blood cells, and whatever else there will be to discover.

So my questions are about magnification  and what I will be able to see at various magnifications. How much magnification would I need to get a detailed look at tiny insects like a gnat or tiny aphid? Or to see microscopic organisms in water, or our blood cells, or the fibres in my microfiber glasses cleaner. And If i was looking at stuff like blood cells, or food, would i be able to see anything like viruses or diseases? (And as an extra question, any good books for self learning about microscopic organisms like that?)  I was looking on amazon and found 500x max up to 2500x max, and would like to be able to see living microscopic organisms if possible.

You'll be able to see something that is 1 micrometer as a slightly formed (meaning you can decide whether it's more oblong ore more round) dot. So any structure that is bigger than that can be better observed. Unfortunately, viruses are far smaller, and many interesting cel organelles are too.

Also, many things (like parts of cells) are not visible until they are stained. There are many stains that are suitable for beginners (others are quite toxic or teratogenic). I'd recommend buying a book from 1970 or before (no re-issue), because many stains and chemicals are nowadays deemed too dangerous (although they are not that dangerous if used in amateur-microscopy volumes) and normal light microscopy technique has not changed since then.

With a used microscope from a reputable manufacturer (inquire beforehand whether the tubes are of a standard size so you can get replacement oculars etc.) you are on a good way. Schools and universities will sometimes purge their stock, which is where you can make incredible deals.

Get a microscope with mains-fed light, ideally LED. Some 'tricks' like Dunkelfeld are very interesting to use, but require a good light source and non-broken iris.

Also look at the table, it should have a smooth, no-hysteresis (meaning if you go left, and then right, there should be no 'slack' to take up before the picture moves the other way) x/y platform, ideally with a measure attached.

Total magnification is ocular*objective, and many microscopes offer the possibility to attach a camera, either additionally or as replacement ocular. that is a great thing, as you can take pictures and zoom in (real magnification will not change, but still, some things are easier to see that way) or later tweak the colors or contrast.

Depending on whether you mainly want to look at things that can be put between two glass slides (cells, bacteria, small parts of insects, ...) or at 3D things (insects, flowers, minerals) you can either buy a two-ocular microscope or binocular (3D) or a one-ocular microscope.

Objectives and oculars are small tubes with many lenses built into them - this means humidity and even rot can slip between those, so be sure to check used material (especially from learning institutions) for clear pictures.


How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function? I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283.

An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable and concrete information (e.g. catalytic sites, motifs) that explain this annotation from that link?

The endonuclease is controlled vocabulary. In this case, it looks like GO actually cites UniProt as the source for the endonuclease keyword.

With the Uniprot url, whenever you want to see where the information comes from for the annotation in Uniprot, type /publications after the ID. For example: http://www.uniprot.org/uniprot/Q13283/publications


Is it possible to Interpret Nerve Signals As to Where They Are Going In The Human Body And What Their Task Is? I have recently watched some anime, (yes, anime, probably a huge cause to lots of questions asked on the internet), and it got me thinking. We can intercept nerve signals throughout the body, but could we interpret their task, as to whether they are meant to contract or relax a muscle, and their destination, as to which muscle they are meant to travel a signal to.

Extra Inspiration:
I have seen an article by Chris Brooker about the theory of intercepting optical nerves to benefit augmented reality, so it got me thinking, what if we could intercept all nerves in one go, the brain, but I realised, that's a stupid idea, they travel to the brain all over, so the next best location was the Central Nervous System (The Spine).

On top of Anime super inspiration, and some articles which helped further my theory, I thought more and more about how nerves travel around the body as impulses, so I theorised maybe they use different currents or charges to travel to different parts of a body, which brings me to my conclusion, is there anyone who would be willing to carry this experiment out? And then give me the results? If this is true we may be able to make a huge breakthrough in the virtual department, even if incorrect it can still be a starting stone for a new hypothesis.

However this entirely bases on the idea that all nerves start from one point on the cns, however the start to this would be to gain a test subject and patch a circuit into a nerve. on the circuit would be an ammeter and a voltmeter, and then have the subject move the muscles connected to the nerve.

The second step would be to find a lone point in the cns where all nerves touch or cross paths to identify the Sweet Spot (( ͡° ͜ʖ ͡°) I named it myself) and differentiate different nerves for different purposes.

Keep in mind this would be no small discovery, this would help engineer a better future in the virtual department, however this is only a small part to this, imagine being able to truly see or hear without the help of heavy machinery, or be able to walk with actual legs again, or be able to play catch with family again as this would engineer the greatest part to prosthetic engineering where we could actually move lots of different gears as if we contracted or relaxed a muscle.

If my hypothesis is completely off as my science is incorrect than please let me know. I currently do not have the facilities to go further into this as I am still in High School ((̿▀̿ ̿Ĺ̯̿̿▀̿ ̿)̄), and am busy with studies, but I hope I am correct and thus would have contributed to science which can help thousands of people everyday.

Please contribute to this topic even if it is criticising it.

Thanks,
IbnJalal

I agree with previous comment from com.prehensible but I would like to change the emphasis ever so slightly.
Its great that you 1. get inspired by experiences you find in the world 2. you think about them and 3. you reach out to other people to check if your ideas are correct. This is basically how any scientific project starts.

I don't think that an informal tone is detrimental to serious and precise scientific discussions on any topic, quite the opposite, so I wouldn't worry about talking about animes or high school. Ask away and as you talk more and more with people with the same interests your language will automatically change to reflect more precise and specific objects/subjects.

Nonetheless, and to the point of the previous commenter, I'll try, instead of general statements of form, to point out some specific things you might want to look at in order help you think about your question:

A precise statement of your hypothesis is a must. You almost make a precise hypothesis about different charges and currents. A lot is known in terms of neuronal communication, both at the single cell level as at the group level. I would start from the wiki entry on action potentials it might help you understand exactly how neurons "talk" to each other. Also it might be useful to have a more specific insight on how these cells are physically organised. Again the wiki on the CNS is a good place to start.
You should have a specific idea of a particular experiment that would allow to you to test your hypothesis. Thinking about the experiment will require you to know what is possible and what is not. Usually animes, movies, and books are quite a bit more advanced in terms of what is nowadays possible, hence the word "fiction" in science fiction. Thinking of an experiment also allows you to operationalise your hypothesis, which is science speak for deciding exactly what you will measure and how. This will tell you if you can answer your question as you stated it and is super important to plan an experiment.

If you have these 2 things i.e., a good idea and a doable experiment that would answer your question the hard part is done!
Well... then you will probably need time and money, but that is a different problem altogether...

Answering your question though, yes, it is possible to interpret nerve signals, both in terms of their targets or downstream areas, as in terms of information content they might relay in order to accomplish a particular task. There is a whole field of Neuroscience that studies neural coding and its trying to solve how neurons transmit messages to each other or how they can encode information in general. However looking at the signals by themselves is usually not enough and people are very careful about the particular behavior that is going on while these signals are being recorded, basically it turns out that one needs context to properly interpret the messages that are intercepted.

Good luck :)


Plasmid in the nucleus and gene expression If we insert a plasmid into a human nucleus that contains exact copy of gene and all relevant promoters to produce some human protein,  will the cell create functional protein from that plasmid only when the cell needs it?

I am not talking about inserting DNA to some chromosome. Inserting separate plasmid to the nucleus (transient transfection).

If you transfect cells with plasmid then these plasmids need to go into the nucleus (otherwise they wouldn't be transcribed). Getting the plasmid either happens during cell division (when the nucleus is not present) or by adding a signal sequence to the plasmid which induces the import into the nucleus through nuclear pores. The SV40 sequence is an example of such a sequence.

If you have the right promoter present on the plasmid, you can basically express any protein in the cell (unless it's toxic). The promoter either needs to come from the organism from which the cells are or has to be something universally activated like the CMV promoter (from the cytomegalo virus).

A good example for this is the expression of green fluorescent protein (GFP) which originates from jellyfish and can be expressed in cells to make them glow green (from here):

Untransfected cells or cells transfected with an empty plasmid (without GFP) don't glow.

Targeting specific cells or control the specific activation of genes only in one cell type is possible. For both you need sequence (and cell specific) promoter sequences which either allow the nuclear import (see reference 1-3) or the expression from a cell type specific promoter (see reference 4).

This has been done in the liver of mice in which the ApoE has been knocked-out. The expression of the human ApoE gene with a specific promoter led to the correction of the hypercholesterolemia the mice were suffering from. This needs a lot of knowledge on the promoter as well as on the other transcriptional regulation elements in the specific gene (see reference 4).

References:

Cell-specific nuclear import of plasmid DNA.
Tissue-specific and transcription factor-mediated nuclear entry of
DNA.
Progress and prospects: nuclear import of nonviral vectors.
Sustained liver-specific transgene expression from the albumin
promoter in mice following hydrodynamic plasmid DNA delivery.


How to protect my mounted insect specimens from ... insects? I have a modest collection of insect specimens that I caught, prepared, mounted, and dried myself. I'm entirely an amateur collector, so my procedure may be causing me this trouble now, but here's how I preserved them.

Killed in the freezer
Placed in a sealed container on a dry platform, with a 50% isopropyl alcohol solution under it. This lets the specimen thaw and remain moist, while the alcohol prevents rotting.
Kept in container for two to three days.
Stretched over foam and held in place with paper and pins.
Kept on stretching board for three weeks.
Placed in a consumer grade display box.
Stored in a dark, dry closet.

It's been a while since I worked on this hobby, but I do like to pull the collection out from time to time and admire it. Today, I was surprised and disappointed to find that some of my best specimens have been turned to dust by a small caterpillar type bug. There are live bugs in my display case, eating my bugs!

I've had these for years without issue, and now I find this. What can I do about it? How can I keep this from happening again? Should my preservation procedure include some other step? How are they even surviving? There's no moisture in there at all!

I'd rather not put something toxic in my display case, as I like to take them out and examine them without the glass in the way. I don't want to be exposed to toxic things every time I look at them. I hope there's some effective, cheap, and safe thing I can do. I've become rather proud of my collection, but it's disheartening to have worms eating them before they've even eaten me.

Here's some pictures of the devastation:

That stain on the right used to be a specimen.

The big pile of dust there on the left used to be a praying mantis. I don't even know what the pile on the right use to be.

This beetle's entire insides have been eaten.

This horsefly looks like it was mounted a hundred years ago.

Apparently moths and butterflies don't taste very good.

The culprit! This little guy and his pals are responsible. You can see exoskeleton sheddings all throughout the other pictures.

I ran into the same issue when collecting bees in a hot, humid environment.  As arboviralstated, freezing is a great way to help with the infection but keep in mind:

It may not kill all of your pests
It will not keep your specimen from future pests
It may damage your samples

From the USDA website, you could pretty cheaply use paradichlorobenzene or naphthalene:

  Two of the most widely used fumigants are paradichlorobenzene (PDB)
  and naphthalene, both of which are obtainable in balls or flakes.
  Never mix PDB with naphthalene as they react chemically and produce a
  liquid that may damage the collection. It should be noted, that most
  major collections are now moving away from the use of solid fumigants
  because of health concerns and in some jurisdictions, it is now
  against regulations to use some fumigants.

That being said, I used a combination of freezing and then naphthalene (moth balls).  It's cheap and anecdotally pretty effective for my purposes.  I also didn't access my collection frequently once established, so the health concerns were less of a worry for me.

Definitely worth mentioning that there has been talk that using naphthalene  or PDB may damage DNA and hurt DNA extractions on down the road, but this is demonstrably false.  That being said, keep in mind these chemicals still pose some heath effects - especially with prolonged or occupational exposure - such as poisoning and carcinogenic risk.


Can one derive COVID-19 risk from a cheap consumer genetic test like 23andme? Studies have found genes associated with a significantly higher risk of severe COVID-19, some of them claiming it to be 1.6 times the general risk.
They mention genes at markers such as rs35044562, rs1129183, rs679599192 to be significant.
Can people use the raw data from a consumer-grade genetic test like 23andMe to assess their risk, at least theoretically? The raw data has many gaps and the markers and their positions may not be included in the data. Can one then look at markers at positions close by, or at other markers? Does a more rare genotype imply higher risk?
Articles

https://www.nature.com/articles/s41586-020-2818-3
https://www.biorxiv.org/content/10.1101/2020.11.02.365551v1.full.pdf

I suppose the answer is 'theoretically yes, but don't trust the results much'.
The 23andme genotyping array is very useful for ancestry testing, but much less useful for clinical diagnostics. I have worked in the past for Genomics England (an arm of the NHS in the U.K. which performs genetic diagnostics for rare disease). There, the samples were sequenced to very high coverage and underwent extremely stringent quality control checks which were being constantly updated. If you want to interpret a variant in a clinical sense, you have to very sure that you get the right genotype.
I believe that the details of how 23andme performs its variant calling and quality control are proprietary and therefore I would never trust their variant calls for any kind of clinical diagnostics, and neither would any clinician I know. This doesn't mean 23andme results are invalid - they are very useful and pretty accurate for testing ancestry, but they are not valid for clinical diagnostics. If your risk calculations hinges upon a few SNPs of relatively large effect size (such as BRCA), then you want to be very sure you make the correct variant call. You simply do not get this assurance with 23andme.
Secondly, like you mention, many of the SNPs you refer to aren't covered by the 23andme array. The effect size of a particular SNP on a trait is calculated for that specific SNP only. Extrapolating the effect size for one SNP in a gene to another, nearby, SNP in the same gene is likely to give you innaccurate results. In fact, the same SNP in the same gene can have pretty different effects in different people (https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/febs.14080 caused by the environment, pleiotropy).


False positives in TAP - MS experiments Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments?
Particularly the Acs1 protein (Acetyl-CoA synthetase) seems to be a protein I often see in a TAP-MS experiment so I am starting to think it is a false positives but I can't seem to find a good paper or website where it is mentioned as a commonly found false positive interacting protein.

Any insights will be helpful.
Thanks.

The common repository for affinity purification (CRAPome) contains the results from many tandem affinity experiments and scores them based on their presence in control purifications.
The database can be found here. I did a very quick and dirty comparison of the frequency that human ACSL_1 (Uniprot ID; P33121) and GAPDH were detected in control purifications. The graphs shows that ACSL_1 is not a frequent contaminant (detected in less than 5% of GFP control purifications) whereas GAPDH is frequently detected in control affinity purifications.

You can submit your tandem affinity experiments to the CRAPome and it will  provide quality scores for your hits. It's very well thought out and not difficult to use. You might want to try it if you're still .


Has it been enough time for evolution through simple natural selection? Let first state that I understand natural selection. I am not asking if evolution happened. I see evolution as a fact, but I do not assume the current theory of natural selection as fact.

I wonder if there has been enough "time", or number of generations, needed to create enough mutations that lead to the known genetic complexity of all species today (or even just until dinosaurs), since the Last Universal Ancestor.

Is it possible to prove, or estimate this time?

Note: There was obviously enough time for evolution to occur. My question is if, the known mechanisms of mutation and theory of natural selection, are enough to justify the evolution in this amount of time.

The evolution to the current state of life on earth has occurred through some 3.8 billion years. During this time it has gone from the most basic forms of life, simple self-replicating units, to the complex beings we see today. Evolution, the process of change within a collection of units, is caused by 4 factors, mutation, selection, drift, and gene flow. So firstly, the current state is not thought to just be the result of natural selection but instead a result of all the mechanisms of evolution.

Selection can itself be subdivided in to two types, natural and sexual selection. Therefore "natural selection" does not even contain all types of selection. Selection is not a simple process, but occurs in a very complex manner, simultaneously affecting the many levels upon which selection can act (nucleotide, gene, organelle, cell, organs, organism, population, species, ecosystem etc.).

There are a number of things to consider when discussing whether enough time has elapsed for the mechanisms of evolution to produce the variation we see today, a primary concern is quantifying how much variation there is in the world that has evolved. Here are some other factors which would determine the likelihood at arriving at that level of genetic variation:

Mutation rates (per generation)
Generation times
Offspring per generation (affects the number of potentially new lineages per generation)
Genome size (number of potential sites)
Complexity and strength of selection
Population size (affecting drift and the efficacy of selection)
Genetic admixture/inbreeding/potential gene flow
Recombination rates
Social structure
Environmental variation

These all vary wildly in contemporary populations and would also have varied in ancestral lineages too, this makes it, in my opinion, near impossible to even get a rough estimate of how likely our current state of variation evolved via the known mechanisms of evolution. But there is a simple answer, all variation you see today arose from simple life and evolved in the last 4 billion years via the four known mechanisms of evolution - which, in part, includes natural selection. The proof is in its existence and the absence of other possible (plausible) mechanisms.

To illustrate the complexity of the problem and the high likelihood of these mechanisms leading to substantial genetic variation (this is highly unscientific):

I'd suggest a very conservative estimate of just mutation rates and time since life began (3.8 billion years, Last universal common ancestor [LUCA]), using approximate human mutation rates (175 per generation and 25 years per generation = 7 bp mutations per year), would suggest a single lineage from LUCA to now could have had some 26 billion mutations, an average of 8 mutations per site in the human genome (this would assume constant mutation and generation rates, and starting genome size of 3 billion BP in LUCA - obviously completely ridiculous, but it's just an illustration and assumes evolution purely by drift and mutation).


Why is epinephrine not part of the somatic nervous system? I learned that the adrenal medulla releases epinephrine, which is a vasodilator of the vessels that lead to the skeletal muscle.

I also learned that somatic nervous system only uses Achetycholine as its hormone (not epinephrine).

I also learned that the somatic nervous system controls skeletal muscle.

So, why is epinephrine not considered a part of the somatic nervous system hormones, if it is controlling the skeletal muscle? What is wrong here?

You are confusing different functional systems. Epinephrine released by the adrenal medulla circulates in the blood and indeed dilates the blood vessels in skeletal muscle. This ensures that enough oxygen and nutrients are available for the muscles to perform in a fight/flight response.

The somatic nervous system utilises acetylcholine not as a hormone but as a neurotransmitter. It is not released into the blood but only into the tiny (about 10nm wide) gap (synapse) between the nerve cell's axon terminal and the next nerve cell or muscle cell respectively.

This release by the somatic nerve cells causes an electrical potential in the muscle which makes it contract.

In summary:

The somatic nervous system controls the muscles because it stimulates the contraction which makes e.g. your arm move. Epinephrine released into the blood by the adrenal medulla serves to ensure the muscles have the blood supply they need in a stress response (e.g. a dangerous situation).

Along with muscular blood vessel dilation, epinephrine in the blood for example also stimulates the heart to beat faster and stronger, and dampens down mechanisms involved in digestion - essentially it does everything necessary to allow a quick escape or a strong fight.


Can I elute my GFP-tagged protein off anti-GFP antibody using a peptide? I would like to perform a modified co-immunoprecipitation assay using a GFP-tagged protein.  We are going to bind the tagged protein to anti-GFP antibody then bind that to protein A/G beads, however we want to be able to selectively elute the tagged protein off the beads.  I know that you can elute a FLAG tagged protein off of M2 anti-FLAG antibody by adding excess FLAG, so can I use the same approach with my GFP tag?  If so, does anyone know a commercially available GFP monoclonal antibody who's epitope has been mapped so I can use excess epitope to elute my protein?  Or possibly a source of recombinant GFP?

I found a paper that describes a method to purify GFP fusion proteins using affinity chromatography: "Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography" (1). Unfortunately I don't have access to the full text, so I can't check how exactly they elute the GFP fusion protein from the column. They describe a specific monoclonal antibody they use, there should be information on how to obtain it in the paper.

Abstract:

  GFP has often been used as a marker of gene expression, protein
  localization in living and fixed tissues as well as for protein
  targeting in intact cells and organisms. Monitoring foreign protein
  expression via GFP fusion is also very appealing for bioprocess
  applications. Many cells, including bacterial, fungal, plant, insect
  and mammalian cells, can express recombinant GFP (rGFP) efficiently.
  Several methods and procedures have been developed to purify the rGFP
  or recombinant proteins fused with GFP tag. However, most current GFP
  purification methods are limited by poor yields and low purity. In the
  current study, we developed an improved purification method, utilizing
  a FMU-GFP.5 monoclonal antibody (mAb) to GFP together with a
  mAb-coupled affinity chromatography column. The method resulted in a
  sample that was highly pure (more than 97% homogeneity) and had a
  sample yield of about 90%. Moreover, the GFP epitope permitted the
  isolation of almost all the active recombinant target proteins fused
  with GFP, directly and easily, from the crude cellular sources. Our
  data suggests this method is more efficient than any currently
  available method for purification of GFP protein.

(1) Zhuang R. et al., Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography. Protein Expr Purif 2008, 59(1), 138-43


How does a higher channel density increase speed of propagation of an Action Potential? If there is a higher density of sodium channels then there will more Na$^+$ flux in the cell. So it's like trying to pass more material through a pipe and therefore the speed of action potential (AP) propagation will be more. This is what comes to me intuitively, but I am not sure about my answer.

Can anyone explain in better words, how the speed of an AP increases with increasing channel density?

As @another'Homosapien' mentioned in the comments, the reality is actually the opposite:  action potential speed is inversely proportional to channel density.

In other words: lower channel density increases speed of propagation of an Action Potential.

If you decrease the density of ion channels, you increase membrane resistance. This results in less "leakage" of cations, which allows voltages to spread farther and thus reduces the number of action potentials that need to be generated. This results in increased conduction velocity.

 Long Answer

It's important to note two things about action potential propagation:

Each action potential takes time to occur.
The charge (i.e., voltage) that is created dissipates with $ \uparrow $ distance.

In fact, we have equations to calculate both the time a voltage change takes to occur and how current flow decreases with distance.

You can read more about the mathematics behind this and passive membrane properties in general here and here.

Importantly, these equations rely on two constants: length and time.

The time constant, $\tau$, characterizes how rapidly current flow changes the membrane potential. $\tau$ is calculated as:

$$\tau = r_mc_m$$

where r$_m$ and c$_m$ are the resistance and capacitance, respectively, of the plasma membrane. (See this previous answer for an explanation of resistance and capacitance. )

Importantly, these variables partially rely on membrane structure.

c$_m$ (the capacitance of the membrane) decreases as you separate the positive and negative charges.
r$_m$ (the resistance of the membrane potential) is the inverse of the permeability of the membrane.

The higher the permeability, the lower the resistance.
Lower membrane resistance means you lose ions quicker and therefore signals travel less far

But why? This is where that length constant becomes important. The length constant, $\lambda$, can be simplified to:

$$ \lambda = \sqrt {\frac {r_m}{r_e + r_i} } $$

where, again r$_m$ represents the resistance of the membrane and r$_e$ and r$_i$ are the extracellular and intracellular resistances, respectively. (Note: r$_e$ and r$_i$ are typically very small).

Basically, if the membrane resistance r$_m$ is increased (perhaps due to lower  average "leakage" of current across the membrane) $\lambda$ becomes larger (i.e., the distance ions travel before "leaking" out of the cell increases), and the distance a voltage travels gets longer.

 Why am I telling you all of this??

How are the time constant and the space constant related to propagation velocity of action potentials?

The propagation velocity is directly proportional to the space constant and inversely proportional to the time constant. In summary:

The smaller the time constant, the more rapidly a depolarization will affect the adjacent region. If a depolarization more rapidly affects an adjacent region, it will bring the adjacent region to threshold sooner.

Therefore, the smaller the time constant, the more rapid will be the propagation velocity.

If the space constant is large, a potential change at one point would spread a greater distance along the axon and bring distance regions to threshold sooner.

Therefore, the greater the space constant, the more rapidly distant regions will be brought to threshold and the more rapid will be the propagation velocity.

Sooo....

If you decrease the permeability of the membrane (i.e., if you prevent ion pumps from moving ions in/out of the axon), you increase the resistance of the axon membrane, which allows for the voltage created in the action potential to travel farther before dissipating.

By allowing the voltage to spread farther before necessitating the generation of another action potential, you reduce the time it takes for signal propagation.

In other words, if you decrease the number of ion pumps, you increase  membrane resistance (r$_m$). This causes voltage to spread farther and thus reduces the number of action potentials that need to be generated. The result? increased conduction velocity.


What are the effects of removing CD4 receptors? If the gene for the CD4 receptor was removed, would the person's immune system work normally?  Could a new artificial receptor be substituted in place of CD4?

Could HIV infection be prevented in this way?

The CD4 receptor is vital for the proper functioning of the immune system. It is found not only on T-Lymphocytes, but also on macrophages and dendritic cells. Its function on T-cells is to stabilize the interaction between the T-Cell receptor and the MHC Class 2 (often known as HLA II in humans) antigen complex on antigen presenting cells and improves the affinity dramatically.

CD4 is also vital for the activation of Helper T-Cells (2). It is needed in the signaling which occurs in the thymus that selects for CD4+ T-Cells. If you were to delete CD4, you are, in effect destroying the adaptive immune system in humans, as there would be no CD4+ produced. In this situation, you would not get activation of B-Cells or Cytotoxic T-Cells, and the immune system would only be left with its innate defenses to protect it. This is found in diseases such as Severe Combined Immunodeficiency and can only be cured with early bone-marrow transplantation.

A better target would be the CCR5 receptor. This receptor acts as a coreceptor for the interaction between GP120, the receptor on the surface of the HIV capsid and the CD4 receptor. People who have a mutation in the CCR5 receptor are resistant to the most prevalent isoform of HIV, as the interaction is necessary for the capsid to fuse with the plasma membrane of the CD4+ cell.

See this article about the CCR5-∆32 mutation. HIV Resistant Mutation


Does class switching occur both in B cells and Plasma cells? I understand that the cell class switches to change the type of immunoglobulin it is producing. The B-cell produces the membrane bound B-cell receptor (BCR) while the plasma cell produces the the secreted form of Ig, the antibody. Now, the isotypes are different in their constant regions and I'm assuming switching only matters if it is an antibody. (differences in avidity, permeability, antibody receptors, etc.)

How would a B-cell receptor (membrane bound Ig) even benefit from class switching? Does class switching even happen in activated B-cells? Or is it a process limited to plasma cells? I read up that BCR also has the 5 isotypes.

What are the specific chronological milestones at which class switching happens in plasma cells and B-cells (if it does)?

Short Answer : B-cells class switch to become Plasma cells in the germinal centre of the lymph node.

Long Answer :

There are two important concepts addressed in the question. One is the Immunoglobulin structure - isotype and membrane/soluble type. And the other is the germinal centre B-cell paradigm. Understanding both the concepts are a prerequisite to understand the answer to the issue.

First of all, immunoglobulin synthesized by the lymphocyte can either be membrane bound (known as the B-cell receptor (BCR)) or soluble antibody. After gene rearrangements, the B-cell (still immature) begins to produce membrane bound IgM/IgD. This continues even in the mature B-cell. The membrane bound Ig or mIg has an extra sequence (refer image) on the carboxyl end adding a few hydrophobic amino acid sequences so that it gets anchored well in the hydrophobic part of the membrane. Also at the end is a series of hydrophilic residues involved in downstream cell signalling.

Class switching is process that leads to a change in the isotype of Ig that the cell is producing. Class switching involves excision of DNA which implies that the cell can not revert back to producing the Ig once it used to. The sequence of the gene segments on the heavy chain gene hence becomes important.

When there is a first time exposure to an antigen, the mature B-cells follow a classical paradigm to T-cell dependant antigens, which is shown in this picture below.

Class switching occurs in B cells that are participating in a germinal center reaction, after the naive B-cell has been activated by antigen and a cognate T cell. There also is germinal centre independant class switching that we ignore here.

After a B cell has undergone somatic hypermutation and class switching of its immunoglobulin gene, it may or may not be positively selected to differentiate into a plasmablast. Plasmablasts proliferate rapidly before terminal differentiation to plasma cells, which secrete affinity matured, class-switched antibody. So in other words, class switch recombination is largely restricted to activated, germinal center B cells. These B-cells class switch, as one of many processes to produce soluble antibody producing plasma cells.

Plasma cells and B-cells aren't just one and the same. B-cells undergo a series of processes to form the plasma cells which are also different in morphology.

As already has been mentioned, it should be remembered that class switching involves excision of the intervening DNA between the rearranged VDJ exon and the constant exons being switched to, meaning that they are deleted from the allele. Thus, a B cell that has class switched from IgM to, say, IgG would delete the IgM and IgD heavy chain exons on that allele, and would be restricted to IgG (or IgE and IgA, which lie downstream).

But then, if the B cells bearing IgM had already class switched (to their possible downstream counterparts), how can the primary immune response be IgM dominant? How could IgM antibodies come from class switched plasma cells?

This is because, this whole germinal centre spectacle takes time to happen and in the meanwhile, there are extrafollicular mechanisms of antibody production in place in extrafollicular foci in the spleen or in the medullary cords of lymph nodes. Since antibodies that are develpoed in a germinal centre dependant manner (IgG) are from somatically hypermutated cells, they have more affinity to the antigen than IgM produced by germinal centre independant plasmablasts.

BCR generally has only two types, mIgM and mIgD. If there is a class switch, they turn to soluble antibodies (IgG/IgA/IgD).

Secretory antibody here refers to soluble antibody that is exocytosed from the WBCs, not the IgA that is found in bodily secretions.

Reference, Picture credits :

  Nature reviews immunology, Germinal centres: role in B-cell
  physiology and malignancy
  Kuby Immunology. 6th Edition
  Immonological reviews, Extrafollicular antibody responses


How to design internal primers? I have sequences of the Cytochrome c oxidase I (COI) from several populations of Peringia ulvae (Mollusca; Gastropoda; Littorinimorpha; Hydrobiidae). I need additional COI sequences from a specific population. When using the same primers and PCR protocol as for the other populations, I do not get any PCR product for the specific population. My PI suggested me to design internal COI primers for Peringia ulvae. How can I do that? Should I use the COI sequences from the other populations?

If you are not getting amplification, there are multiple things to visit before you want to design internal primers. You should try troubleshooting your PCR reactions before designing and ordering internal primers. If you are doing the PCRs wrong, it is likely you will run into the same problems again with internal primers.

There are excellent guides to trouble shooting PCRs - Just a google search "Trouble-shooting PCRs" should give you a lot of material to go through. This is from NEB, but there are several others, each manufacturer having their own, so you could refer to one of whose reagents you are using.

Primers generally give good reads from the 5' end for about 600-700 bp and after that the quality of base calling deteriorates, so if your target amplicon is above 1500bp or so, you would need internal primers because the 'external' primers would give you good sequences for only 1400 bp or so (600-700 bp from both directions, for fwd and rev primers). So internal primers can be used to sequence the regions that cannot be reached by the main (external) forward and reverse primers. The published papers from where you are using the external primers will most likely have the internal primers if CO1 is long enough to require internal primers.

Otherwise, you would need to align the existing sequences from the other populations, and look through regions of the alignment that are conserved which could act as potential priming sites. There are other issues to be taken care of before you can consider a 'conserved region' a 'priming site' and go ahead and order primers. Again there are excellent primer design tutorials available, just a google search away.

Let me know if any parts of the answer are not clear, or sound like jargon and I will do my best to simplify it for you. However, I would strongly suggest troubleshooting the PCR first - for e.g. trying a gradient PCR to find the optimal annealing temperature.


How long can human tissue last without blood? I've heard it said various times that the body's tissues will begin to necrotize after being cut off from the blood supply for only a few minutes, but that can't be true.

A few years ago, I woke up one morning and apparently I'd been sleeping just right so that the main artery to my left arm was totally pinched closed, because it was completely numb.  Not just "arm's fallen asleep", either; I had no mental control over the entire arm and no feeling in it.  I could lift it up with my right hand, and it would fall back down immediately when I let go of it, and I didn't feel anything when it landed on the mattress.  It kind of freaked me out at first, but in just a few minutes I felt the "pins and needles" feeling of circulation returning, and it was 100% back to normal within less than an hour.

Given that I had presumably been sleeping on it like that for several hours, and yet I somehow didn't end up with a dead, useless arm that needed to be amputated, I know from personal experience that tissue doesn't die within a few minutes.  So how long does it really take?

As EMT (Emergency Medical Technician) instructors will tell you now, when wearing a tourniquet, you have about four hours to get the injury to a vascular surgeon and get it cared for appropriately. The rule therefore is four hours. However, the common thread I see in most sources is that about an hour and a half is the longest you want to go without blood flow to a limb.

As far as what happened to you, it sounds more like the limb simply fell asleep. When a limb falls asleep, it is getting the nerve pinched off for a time as well as loosing some blood flow. However, this is not a complete loss and so your arm is able to survive because it is still receiving enough oxygen and other nutrients to sustain its existence (as well as having toxins and CO2 pumped away from it).

I had a very difficult time finding any concrete, scientific information on this subject overall.

So, if you would like more information about this, please visit the following links. The first is a WikiPedia link on Limb Infarctions (or an embolism in a limb). The second is from Mental Floss on Why Limbs Fall Asleep. The third is a somewhat random article on someone's personal experience on Sleeping on their arm.

So, in summary: although I could find no solid evidence on how long a limb can live without its blood supply, it appears to be about 2-4 hours (some sources say 5-8); however, I would like to add that your case appears to be a severe case of an asleep limb, you were/are likely in no danger. Also, if your arm indeed did have circulation completely cut off, it would have turned pale, then blue and later a livid red and purple as the blood began to pool; you then would begin to experience the effects of the limb dying i.e. necrosis, gangrene.


Equation for accurate prediction of PCR yield It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 grams of DNA. This is clearly absurd and not the case.

Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an upper bound - but even so, a very uninformative one), and in practice, yields will fall far short of it because:

Every single duplex of DNA does not denature at each cycle
Primers do not bind to every single molecule of DNA at each cycle
Not every DNA strand gets bound by a polymerase at every cycle
Not every polymerase that binds manages to complete the entire product in time in every cycle
The reaction inhibits itself by depleting dNTPs
The heat denatures the reaction by degrading enzyme

In fact, cursory examination of qPCR output often follows saturation kinetics:

Mathematical methods for modeling qPCR are obviously well developed.

My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?

For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).

An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.

Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in terms of copy number or in terms of moles; the number of DNA molecules of interest is what the reaction is operating on, and the mass of product generated is a function of the length of the product (and, to a lesser degree, on the composition of the product).

The following discussion is sourced from this URL: https://www.csun.edu/~hcbio027/biotechnology/lec3/pcr/p.htm

According to Perkin-Elemer, copy-number amplification of 100,000 fold of the targeted sequence of DNA can be expected from a PCR with 0.1 ng of Lambda phage DNA (a well-characterized and standard DNA isolate) in a 100 µL reaction with > 25 cycles of denaturation, annealing, and extension.

In the above 100,000-fold amplification example, if the targeted amplicon were to be 500 bp in length, the estimated molecular-weight of duplex DNA of 500bp is 325,000 g/mol (based an average base-pair having a molecular mass of 650 g/mol).

The Lamdba Phage genome is 42,502 base-pairs in length.
42,502 bp × 650 grams/mol/bp = 2.762×10^7 grams/mol.

0.1 ng Lambda DNA -> 0.1×10^-9 grams.
0.1×10^-9 g ÷ 2.762×10^7 g/mol = 3.619 × 10^-18 moles.
3.619 × 10^-18 moles × NA (Avogradro's Number) = 2.179×10^6 copies, or 2,179,000 copies.

2.179×10^6 copies × 100,000 = 2.179×10^11 copies.
2.179×10^11 copies ÷ NA × 325,000 g/mol = 1.176×10^-7 grams of sequence.
1.176×10^-7 grams is equal to 0.117 µg or 117 ng.

An amplification yield of 100,000x after 25 cycles would mean at each cycle 1 template would yield 1.58 templates for the next round of synthesis.

How was this calculated? If c is the number of copies made per round of synthesis, then:

c^25 = 100,000 = 10^5
so c^5 = 10
and so 5(log c) = log 10 = 1
so log c = 0.2 and c = 1.58 (approximately)

(Or you could calculate the 25th root of 100,000 on a calculator, if you prefer.)

If we obtain 1.58 copies instead of the theoretical maximum of 2 copies, then the efficiency of the reaction could be said to be 79% (because 1.58/2.00 = 0.79).

One reason this calculation is important is that a slight loss of efficiency is magnified through the amplification. A reaction may appear to have not worked if the efficiency drops (in each cycle) by just a few percent. Optimization is critically important in the polymerase chain reaction.


Why does getting certain chemicals in cuts hurt? More specifically, shampoo. What are the mechanics of detecting a noxious chemical stimulus in terms of which receptors recognise what, how do they do it, and how is this information relayed to the nerve cells?

Why is the pain (and so signal, I presume) larger if one is having a hot shower at the time?

Shampoo contains surfactants, chemicals which cause lipids to emulsify. The cell membrane is composed primarily of phospholipids, which are vulnerable to action by surfactants. In fact, sodium dodecyl sulphate (SDS, often labelled SLS on shampoo bottles), an integral component of many shampoos is also used in the lab (albeit at substantially higher concentration) to achieve cell lysis.

The outer layer of skin is composed largely of a very tough type of cells called keratinocytes, which form an impenetrable barrier to potentially harmful chemicals like surfactants. Once the skin is ruptured, the surfactant can act on cells that don't have the protection of keratin, causing damage to cell membranes, and perhaps even cell death. This will obviously lead to an immune response and inflammation, which is likely to be the source of the burning sensation/pain that one feels.

The inflammatory process involves various immune system-related mediators such as bradykinin and prostaglandins, which act to increase the sensitivity of neurons to pain.

With other chemicals that cause a burning sensation, the mechanism of cell injury might be different, but ultimately, the immune mechanisms kick in, causing inflammation and pain.

Kid & Urban (2001) reviews the processes that cause inflammatory pain in great detail (full text is available for free).


Are there any culinary fruits that are not botanically fruits or accessory fruits? Many culinary vegetables are botanically fruits. For example, the tomato, bittergourd and the cucumber are generally considered culinary vegetables, but they are botanically considered fruits.

Does the reverse also hold true, in that are there any plant parts that are considered fruits culinarily, but are botanically not considered fruits or accessory fruits?

I think there aren't any, with two tentative positive results. Of course, it is hard to prove a negative. But here are my arguments:

Logic. there is little reason for this to happen. A culinary fruit is supposed to be sweet, and plants tend to store sugars in their botanical fruits, not in other parts (although by this logic, there should be tuber-fruits too).
Source checking. I went through two books intended as comprehensive reference works in the kitchen, The professional chef and McGee On Food and Cooking. They don't list a (culinary) fruit which I could identify as a botanical non-fruit, with one contentious case. Note that On Food and cooking's chapter on vegetables is structured according to plant part, and it has a subchapter called "fruits used as vegetables" - but it does not have a chapter of "vegetables used as fruit" or similar.
Language. People tend to mix up the two categories of "culinary fruit" and "botanical fruit" until the difference is pointed out to them. While they don't follow the correct botanical definition of fruit, a plant part seems to have to check the "used by the plant for reproduction" check box to be called a fruit, to the point where many words related to "fruit" evoke a harvest-like image such as "to come to fruition", or also words for "barren" in many languages which literally translate to "without fruit", e.g. the German unfruchtbar. So even when a food fulfills the "plant part" and "sweet snack" criteria, it is not called a fruit if it's not (commonly perceived as) a seed container.

The contentious case coming from the books is rhubarb. The professional chef lists it as a fruit, while McGee calls it "a tart stand-in for fruit" in the vegetable chapter, and mentions it again in the fruit chapter, as "a vegetable that often masquerades as a fruit". Kitchen terminology is by no means standardized, so if you were to question random cooks about rhubarb categorization, I guess you'd get a mixture of "a fruit" , "a vegetable" and "I don't know" answers.

An idea I had while writing the answer: maybe you can count ginger. Ginger has many uses in the kitchen, but it is available as a candied snack, which is else only common for fruit. McGee lists it as a spice, although he explicitly speaks of "the dried spice" without giving a category for the fresh rhizome. I think most cooks won't dub ginger "a fruit" but would be willing to include candied ginger in a bowl of mixed candied fruit.

Some petals and leaves are also made into jams, which would support a fruit categorization. Nevertheless, I've never heard of them being referred to as fruits. Prominent examples are rose petals, violet petals and verbena leaves (although one could argue that preserving verbena produces a herb jelly, not a jam).

This answer encompasses Western cooking traditions. It is possible that other cuisines have a different view of what a "fruit" is - for example aloe is frequently used in sweet preparations, maybe the leaf flesh is eaten as fruit somewhere.

So in the end, it comes mostly to your willingness to stretch the definition of a culinary fruit. It is certainly not the case for the most commonly eaten fruits.


Hummingbird cross Bering Strait Hummingbirds travel to Alaska during summer. If global warming continue, allow birds stay longer in Alaska, can hummingbirds cross Bering Strait to Russia, then spread in Asia?

The ruby-throated hummingbird flies 500 miles nonstop across the Gulf of Mexico during both its spring and fall migrations

The Bering Strait is about 82 kilometres (51 mi) wide at its narrowest point, between Cape Dezhnev, Chukchi Peninsula, Russia

Based on the two facts above, it appears possible for a humming bird species to cross the Bering Straits if the weather becomes suitable to survival. Who would have thought?

That said, I am not sure how a humming bird who know which direction to fly in to make a successful crossing.


Why can humans feel electricity? What evolutionary process has provided humans with the ability of feeling electric current? Besides lightning and electric eel, what natural hazards include electricity that poses a threat to humans?

Electrical currents stimulate neurons aspecifically. For example, the BrainPort artificial vision device conveys visual information through electrical stimulation of mechanoreceptors in the tongue. Similarly, cochlear implants and retinal implants convey acoustic and visual information through electrical stimulation of the inner ear and retina, respectively. The list goes on. Bottom line is, none of these organs (tongue, ear or eye) evolved to process electrical stimuli. And in fact, there are no specific current or voltage sensors in man. Electric currents aspecifically stimulate neurons, causing them to fire. When sensory afferents are activated in this way, sensory perceptions are generated.

In case of lightning (electrical shock to the skin) it is mainly pain and heat receptors that mediate the sensation. In the case of the BrainPort, it is the tactile receptors on the tongue that are mainly stimulated (taste perceptions are rare). In case of cochlear implants it is auditory nerve fibers and in retinal implants it is optic nerve fibers that are stimulated. Hence, various, and in fact all, neurons can be stimulated by electric current.

Note that sharks feature Ampullae of Lorenzini. These sensory organs are electroreceptors, which allow sharks to sense the bio-electrical fields of prey under water.


Earliest ancestor of humans who could integrate into modern society Assuming the current model of human evolution to be correct, approximately when did the earliest ancestor of humans live, who was intelligent enough, that if raised from a young enough age, could learn the necessary skills to live in today's society:

learn a modern language
learn to read and write
learn to use most common tools and household items
learn to drive a car, use a telephone, a computer, have an average job.

Interesting question.

The organism would have to be monogamous, that's for sure, otherwise it would be too competitive and it would be a beast - as chimps are. Chimps couldn't integrate into the modern society.

So, monogamy is the prime prerequisite as it's also prerequisite for intelligence. Bipedalism is another obvious prerequisite, as you need an organism with fine motorics of front limbs - and fingers.

For "modern language" you need high intelligence and the ability of abstract thinking. Same goes for reading and writing.

Humans split from great apes between 8 and 4 million years ago. Problem here is that every new piece of fossil of a human ancestor is classified as a new species, so there's very little we're certain of. I'd say the first organism capable of doing the above things existed around 200.000 years ago. Either homo erectus or, more likely, a Neanderthal.


Can you help identify this tree from my garden? The picture is an evergreen tree.

I have seen very similar trees in Northern Italy. I would appreciate any help.

It's a Juniper, genus Juniperus.

If will feel prickly, and if you run your hand along the branch from the out to the inside it will feel very prickly. If you run your hand in to out, it will be marginally less so, but still uncomfortable,

Crushing the leaves in your fingers will release a sharp, tangy, not unpleasant smell.

Juniper Juniperus communis is native to some parts of in England, Scotland and Wales, and north and west of Ireland, and in fact most of the temperate forest regions https://en.wikipedia.org/wiki/Juniperus_communis#/media/File:Juniperus_communis_range_map.png

The berries are used to flavour gin.

However there are many other species of Juniperus that are often planted as ornamental trees, so it could well be one of these. https://en.wikipedia.org/wiki/Juniper

Best way for a positive ID is take a small bit with you to a large garden centre, or arboretum, and head to the juniper section and compare the look, feel and smell of the specimens.


Characteristics of radius of blood vessel Which properties do determine the radius of blood vessel?

I have these thoughts

distension,
elasticity,
contractility and
cross-sectional area of the walls.

Is there any other properties?

The radius of a blood vessel is entirely defined by only two parameters:

1.blood pressure

2.compliance of the vessel walls

Of course, active contraction can decrease the vessel radius. Physically, this is a decrease in compliance, so the above relation always remains true.


What is the mechanism by which quitting smoking causes increased appetite? I guess it has something to do with  sugar regulation.

Does anyone know something more about this?

What is the mechanism by which quitting smoking causes increased appetite?

Research has generally focused on weight gain, rather than increased appetite, since it's a more objective outcome.

Smoking cessation has been clearly and consistently shown to be associated with weight gain, in both retrospective and prospective studies, and nicotine replacement seems to reduce some, but not all of the effect, at least while it's used.

There is an excellent, though now aging review of both the effect and potential mechanisms behind a paywall by Filozof. One of the most cited early articles is free at NEJM.

The mechanism of this weight gain is an active area of research, and, as discussed in Filozof, includes increased appetite with associated increase in calorie intake, decreased resting metabolic rate, and decreased physical activity.

Leptin, a hormone that increases both satiety and energy expenditure, is actually increased in people who stop smoking at the same time they are gaining weight. This finding has been convincingly demonstrated and replicated. Leptin insensitivity is a strong candidate for the primary driver of the increase in appetite (and weight gain) after smoking cessation.

Of course, since cigarette smoking causes profound changes in gene regulation, smoking cessation likely does as well. The full answer is almost certainly multifactorial.


What is this red and white striped wasp? I saw this dead wasp in a park in Hong Kong.

First of all, it isn't a wasp, but a true bug. After a long search in the databases about Hong-Kong's insects, I found that it is a red cotton stainer. Wikipedia says "Dysdercus cingulatus occurs in Sri Lanka, northeastern India, Bangladesh, Thailand, the Philippines, Sumatra, Borneo, Papua New Guinea and northern Australia".  iNaturalist.org has a number of photos, including some that match the one in the question, and confirms that the bug occurs in Hong Kong.

These insects are serious pests of cotton and there are several other species of them, some of which occur in North America:

  The cotton stainer is most common in southern Florida and in Cuba. It has been reported in Jamaica and Puerto Rico, Alabama, Georgia, and South Carolina. In view of its scarcity in north Florida, it must be presumed rare in the other three states mentioned. Dysdercus andreae ranges from southern Florida to most of the Antilles and Surinam. Dysdercus mimulus ranges from southern Florida, Texas, and Mexico into Central America and the West Indies. The fourth, undetermined species is known in the United States from two specimens taken at Key Largo Key and Homestead, Florida.

--University of Florida

Here are some pictures to compare with these one in the question:


There are small parts between Genes in an Operon that does not encode for any amino acids. What is the purpose of these parts? What is the purpose of these parts in the translation process ?
Picture to demonstrate below :

The regions between the genes on a prokaryote operon are transcribed into the messenger RNA  but are not translated into proteins.  Because they are not translated, they are characterized by the general term UnTranslated Regions (UTRs).  A typical operon having two genes is shown in this diagram from Wikipedia:

The UTR which occurs between the protein-coding genes contains the sequence for a ribosomal binding site (RBS) in the transcribed mRNA.  An RBS is a site where a ribosome can attach to the mRNA so that the Start codon of the following gene is in the correct position to begin translation of the protein.  (Of course, the 5' UTR preceding the first gene also has an RBS sequence.)  An RBS contains a particular nucleotide sequence to match up with a complementary sequence of the ribosomal RNA of the ribosome; this sequence is known as the Shine-Dalgarno sequence.

(Note that these inter-gene UTRs are not called introns; introns occur only in eukaryotes and occur within a gene, between the Start and Stop codons.)


Why does my room suddenly look 'reddish'? My eyes seem to adapt to color To get the context of this question clear, I would like you to walk through some parts of my house.

We'll start with one of my rooms as it appears normally -

As evident, this part of my house has a creamish tinge to it, also the balcony door is open which further gives this room a yellow tint. Nothing special. I'll call it "area Y" (for yellow)*. Let's move on.

Here we arrive in another part of my house which has greenish/blue shades acting as a sunlight blocker. This gives this entire place a greenish/blue tint as shown. (Ref. "area G")

So, now let's visit the area Y again. I am always surprised with what my eyes now see. This. {1}

You see, the same room, same lightning, yet the room now looks much more reddish than before! That's what intrigues me, why does it  happen? Why my eyes suddenly become sensitive to red color?

I am not a biology student but I do know that our eyes have cones which specialize in color perception, and that there are different types of cone cells to perceive different types of colors (If I remember my high school biology correctly).

So, I somewhat get a feeling of what's happening inside my eyes (or the brain perhaps?). I suspect that as I go to area G, my eyes 'adapt' to the dominance of bluish/green light, either by decreasing pigment of blue cones or by increasing pigment of red cones, which makes my eyes more sensitive to the other end of visible light spectrum (red-yellow), causing an 'outburst' of red coloration in area 'Y'. Since pigments need time to degrade, by the time the red color pigment of my cones decreases, its activity is less than normal. It may be increased as the blue pigment's activity is less than normal and I see a reddish tinge for few moments.

This was a pure hypothesis from my part, but it seems correct to me. But why do my eyes even adapt to blue color? Why can't my eyes be  unbiased towards colors?

{1} Obviously I photoshopped the red tint in the image how else could I have replicated my vision? Though it's not the most accurate description of what I see it's still a very close approximation.

Short answer
The phenomenon you describe can be explained by the negative afterimage effect, which indeed is elicited by adaptive processes in the retinae.

Background
In the retina there are three types of color photoreceptors, called cones. They are sensitive to red, green and blue, respectively. Colors are processed in the retina through a process explained by the Hering model. This model assumes that there are two sets of opponent colors, namely red - green and blue - yellow (Fig. 1).

This model assumes that in the red-green opponent channel the red cones inhibit the output of green cones and vice versa. In the blue-yellow channel the blue cones inhibit the green/red (= yellow) cone output and vice versa.

Now look at the visual illusion shown in Fig. 2. This illusion nicely illustrates the effect. After looking at the image for half a minute, your cones adapt to the color input. Particularly relevant to your question is that the green cones adapt to the green and become less responsive to green (this happens when you are in your "greenish blue shade acting as a sunlight blocker. This gives this entire place a greenish [blue] tint as shown. (Ref. 'area G')." Now this in turn lowers the green inhibition of the red-half of the red-green opponent channel. In turn, when you enter your "part of [the] house [with] a creamish tinge to it, [] 'area Y' []" the green channel will not inhibit the red-half and everything will have a reddish hue to it, akin to looking at the white half of the illusion after 30 seconds below.

Reference
- Sci Am, October 2013

Fig. 1. Hering model of color vision. Left panel: brightness coding. Right panel: opponent colors code for color, namely the red-green and blue-yellow channels. source: Bio.SE

Fig. 2. Visual afterimage illusion. Look at the fixation dot in the middle of the tripartite circle on the left for 30 seconds. Don't look away. Now look instantly to the white part on the right. If you don't see much, or only vaguely, try again. Blinking may help to shortly enhance the illusion. source: Sci Am


Example of invertebrates that are attracted to heat? I would like to test a device that outputs heat in order to attract schistosome parasites in water. However, I would like to use a substitute, since I cannot find schistosome parasites for sale.

Are there any organisms that are attracted to heat and are easily accessible?

The tendency to be attracted toward heat is called thermotaxis.

Documented cases

Thermotaxis has been documented in

C. elegans

Ploff and Sokut 2010

Slime molds Meloidogyne incognita

Pline et al 1988

Drosophila

Rosenweig et al. 2004

Mosquito Aedes Aegypti

Patterson and Brown 2009

Lake sculpin (Cottus extensus) larvea

Wurtsbaugh and Neverman 1988

Mammalian sperm cells

Bahat et al. 2003

The best documentation is on C.elegans. There are probably many undocumented species that display thermotaxis but above are the only documented cases I could find.

Many of these species are easy to find in biology labs. Mammalian sperm cells are very easy to find if you are a male but it may take complex methodology to observe thermotaxis on cells. Bigger organisms are of greater interest. Drosophila might be the way to go.

Do you really need to test with another species?

Whether the test is a good idea was not part of your question but I thought I would comment on it anyway!

I am wondering whether testing your device on a different species is of much interest to you. Testing that your device creates a thermal gradient is sure of interest but one species may react very differently to a specific gradient than another one and it feels a priori to me that you'd be waisting your time by testing it on a different species.

I think it would be more interesting to just place thermometers (if you have access to good accurate thermometers) along space and measure temperature to ensure that a gradient exists and make sure that the temperatures and steep of gradient are within the range of what schistosome may experience in nature.

I am not involved in this research and you may have good reasons of yours of testing your device on a different species.


Is there a consensus on whether or not race exists on a biological level? The most recent survey I could find was from 1985 which said that 16% of biologist disagreed that "[t]here are biological races in the species Homo sapiens."

I was wondering if there's been a change in this position.

Anatomically modern humans are less than 200K years old, left Africa (or possibly Africa and Arabia) only 60K years ago, and migrate quite a lot (think of the Mongol invasion).  So you would not expect to have clear divisions into subspecies.  And indeed a quick search of google scholar pulls up no claims in the literature for human subspecies of anatomically modern humans (i.e. no subspecies of homo sapiens since Neanderthals and Denisovans).

On the other hand, it's certainly the case that you can work out a rough phylogenetic tree of humans.  Native americans are descended from certain northern and eastern asians, and so in the 1400s were more closely related to them then they were to other humans.  Similarly, Austronesians (of Indonesia and Polynesia, e.g.) are more closely related to Taiwanese aborigines than they are to Australian aborigines.  This tree is complicated by how much more migration there has been in the last 1000 years than there was previous to that, but it's still biologically meaningful.

But here's the striking thing: traditional notions of "race" do not match up well with this tree.  The deepest and most fundamental phylogenetic splits in the human tree are within Africans.  If you were going to try to "scientifically" come up with races, you'd end up with something vaguely like one for Khoisan, one for other Africans, and one for all non-Africans.  Even ignoring modern admixture, traditional races are not monophyletic.  Any clade including all "black" people includes all people, any clade including all "east asians" includes all native americans.  (Also note that traditional notions of "race" are not stable over time, remember that "Irish" used to be a "race" on the US census.)

Modern admixture even more clearly shows the non-genetic nature of traditional "races."  One genetic study of people who identify as African-American, found that African ancestry can be as low as 1% and as high as 99%, with the median African-American having 18.5% European ancestry (with 30% having European y-dna).  Furthermore, relatively ancient admixture (for example, in the Northern Africa, Northeastern Africa, Middle East region or in Madagascar) also complicates the situation significantly.

To summarize, although human genetic diversity is a real biological phenomenon which can be used to figure out the geographical history of people's ancestors, traditional notions of race do not match up well with the biologically meaningful concepts.


Can Coronaviridae mutate into something as dangerous as Flioviridae? Can coronaviruses mutate to an extent to get as dangerous as fliovirusues such as Marburg viruses, Ravn or Ebola Zaire?

Each existing virus can mutate until it becomes ready to affect new species, organisms, cells or whatever.

Coronaviruses too are capable of mutating, so they could become more dangerous.

But can coronaviruses (which cause respiratory tract diseases) mutate into filoviruses (which cause hemorrhagic fevers)?

Of course not.

Filoviridae and coronaviridae are two different families of viruses, like felidae and canidae are two different families of mammals, in the order carnivora.

And you would never ask if cats can mutate in dogs!


Why can't pyruvate be used directly in the Krebs cycle? Why can't pyruvate be used directly in the Krebs cycle? Why does it have to be converted to acetyl before it enters the cycle?

Excluding the reason that the shape of pyruvate is different than acetyl and therefore it would not fit the enzymes involved in the Krebs cycle, what is the advantage of converting pyruvate to acetyl?

Oxidative decarboxylation of pyruvate to acetyl-CoA by pyruvate dehydrogenase is coupled with reduction of NAD+, which can feed into the electron transport chain.
CoASH activates the acetate: hydrolysis of the thioester is thermodynamically favourable and drives the reaction catalyzed by citrate synthase.
Conversion of pyruvate to acetyl-CoA commits it to a subset of possible fates (including the tricarboxylic acid cycle) and is therefore a key regulatory step.

You can read more about this in most introductory biochemistry texts, like this one.

Also note that pyruvate actually can enter the TCA cycle via carboxylation by pyruvate carboxylase to oxaloacetate. This reaction requires energy in the form of ATP and is used to regenerate TCA cycle intermediates as they are siphoned off for anabolic pathways.


Does an annealing temp higher than primer's Tm contribute to primer dimer? I am attempting to reproduce results from a number of journal articles all referring to the same SNP. In doing this I'm using the same primer set outlined in the articles. When I attempted a run the other day I experienced what I can only assume was primer dimer (~40bp product, bands not visible at expected bps.) While the primers and restriction enzyme were the same among numerous articles, the annealing temperatures in the reaction varied a fair amount (52-59C). All were above the individual Tms of the primers which struck me as odd.

Calculating the Tm via primer blast here are the numbers:

Forward Tm: 50.14  [5'-GCTCTACTTCCTGAAGACCT-3']

Reverse Tm: 51.67  [5'-AGTCTCACTCACCTTTGCAG-3']

Other sites gave slightly higher numbers (54-55) but they are still below the 57C that I used in my reaction. I do not have access to a gradient thermocycler otherwise I would have tried a range myself.

If an annealing temperature is chosen above the individual Tms how do the oligos have a chance to anneal with the template and eventually extend? I remember hearing the Tm calculation is more involved and includes finding where the melting curve changes direction. But on the surfance I would think the primers would never have a chance to anneal at such high temperature? What is wrong about my interpretation?

I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.

Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using?

Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).

If you start seeing non-specific products at that Tm, I'd do what we call a "Touchdown" PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it "touches down" to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the "restrictiveness" of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.

Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.


Given an EC50 value, how do I reproduce the sigmoidal curve from which this was calculated? All-trans retinoic acid (atRA) is a potent ligand for a nuclear receptor called retinoic acid receptor alpha (RARa). The concentration of atRA at which RARa is half maximal is 19nM. The dose-response curve is sigmoidal, with concentration (log scale) on the x-axis and percentage of maximal activity on the y.

How would I use this information to reproduce the dose-response curve?

Thanks

Basic sigmoidal curve looks like that: zero at $-\inf$ and one at $+\inf$. All in between should look like an integral of gaussian distribution. Take a look on this wiki page for more information. Now, the question, why sigmoidal curve is integral of gaussian function, I will leave out for now. My understanding is that gaussian distribution tells you how much system response will increase (say, efficiency of treatment) if you increase stimulus by $dx$. E.g., how much response changes when you go from $5$ to $5+dx$ versus from $10$ to $10+dt$.

The problem, as you might realize, that gaussian distribution has two parameters: mean value and width of the function. When you construct your fit, frist one will be 19nM, but second, $\sigma$, is unknown from your question. What you don't know is how rapidly response changes when you increase concentration by little around your EC50. So all your sigmoidal plots will go through same point but with different slope, like that:

Without knowing second parameter, $\sigma$, it makes little sense to plot your sigmoidal curve. However, if you want to, this is MATLAB code. See that cumsum() function effectively integrates gaussian distribution rendering sigmoidal curve.

c = 0:100; % range of concentrations you test
sigma = 1; % unknown parameter
m = 19; % your EC50 19 nM
g = 1/(sigma*sqrt(2*pi))*exp(-((c - m).^2)/(2*sigma^2)); % gaussian
gs = cumsum(g);
plot(c, gs)

If you want, you can plot it with log-scale of X, using semilogx() instead of plot().

NB here I started with Gaussian function and its integral just as a wild guess. You real function might very well be something like $f(x)=\frac{1}{1+e^{-x}}$. "Sigmoid" function is just description of general shape, not mathematical definition.


Is chloride necessary for animals? Of the twelve well-known atomic constituents of our body eleven elements have specific properties obviously relevant to their rôle, making them indispensable. Oxygen (electronegativity and valence), carbon and hydrogen (both elements have virtually unique properties), nitrogen (amino group), calcium (calcium(II) is necessary for bones in vertebrates), phosphorus (use of phosphate in nucleotides and ATP), sulfur (–S–S– bridges), sodium (Na+ is a small cation), potassium (K+ is somewhat larger, together with its companion and presumed substitute Rb+), iron (used in hemoglobin because of properties of a transition metal), magnesium (Mg2+ takes part in the ATP cycle, if not anything else).
What about chlorine? A search resulted in

Chloride is involved in the exchange of oxygen and carbon dioxide in the red cells.
In this, chloride passes into the plasma (chloride shift) and bicarbonate into the cells.

(https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/chloride), certain use by muscle cells and also some mention of ligand-gated chloride ion channels in neurons. Chloride in stomach secretion may be dismissed because is used as a generic acid (that is, to complement H+), not for its own special properties. And no mention of biological chlorine compounds other than ionic (such as, having a C–Cl bound) can be quickly found.
Which cells absolutely need specifically Cl− to function? Is the anion mandatory for animals to live?

My answer may be a little basic, but I think it is comprehensive:
Many elements are special; for instance, many metal ions such as iron or cobalt are required as cofactors or in catalytic sites due to their chemistry. Oxygen is highly electronegative, that also grants it some of its functions. But... without delving too much into things... chloride is the most basic constituent of saline, without which it would not be saline. Here are 3 very, very important and yet

It works well with alkali and alkaline earth metals, hydrogen, and many compounds... it's a natural pairing!
You cannot separate positive and negative charges in a solution at a macroscopic level. It's not a feasible thing to avoid harboring chlorine atoms as part of biochemistry.
It accounts for a large portion of extracellular fluid tonicity.
etc...

Thus, most inter- and extra-cellular fluid is relatively chloride ion rich, across the entire bush of life. To my knowledge there is no life, tissue or cell on this planet that does not contain chloride ions as part of its makeup by necessity. It is simply heavily constrained in evolution as a basic component. It's just not practical to obtain K+ or Na+ or Ca2+ ions without Cl-, it is so common in nature.
If you want specific examples, you can always mention its indispensable roles in neuron firing (transmission of axon potentials) and general cellular homeostasis, which is dependent on electrochemistry and osmolarity and stuff like that which is heavily influenced and dependent on the presence of a regulated concentration of solvated Cl-.


What's the relationship between snail movement and rain? I have a question about the relationship between snail and rain. A few days ago I found snail shells in a moist area and I brought them in for crafts work (I thought they were empty because snail usually come out if you poke them). After a few days it rained, and I found that the snails have moved from the space i put them in (but not far). My question is why did they move after it rained  outside but not when I brought them in a week before?

The movement of organisms towards water is termed hydrotaxis. 'Hydro-' refers to water and '-taxis' refers to movement. Hydrotaxis has been investigated in animals such as the nematode Caenorhabditis
elegans (Wang et al., 2016) and, closer to snails, the gastropod Littorina
littorea (Gendron, 1977). Animals may sense the water content of their surrounding environment and moisture content in the air to move where they are more comfortable.
Animals need specific amounts water in their bodies to allow effective metabolism. We can control our bodily water content by taking a drink but simpler animals aren't afforded that luxury so they need to move towards/away from water. Your snails likely moved because the water levels in their bodies dropped as they 'dried out' over the week. They could then have sensed a gradient in the moisture content of their surroundings and moved towards it. Mechanisms in animals' bodies can give animals responsive behaviour, as seen here. For instance, C. elegans uses its cGMP pathway, neurons and biochemistry to respond to water content with movement (Wang et al., 2016).
References

Wang et al. (2016). cGMP Signalling Mediates Water Sensation (Hydrosensation) and Hydrotaxis in Caenorhabditis elegans.

Gendron, R. P. (1977). Habitat selection and migratory
behavior of the intertidal gastropod Littorina
littorea. J. Anim. Ecol 46 79-92