text:
Light microscope specimen size
I was going through sample questions for Science Olympiad, and one of the questions went like this:

A cell is observed through a light microscope at 4x magnification. The cell takes up about half of the visual field. What is the approximate length of this organism?

I know from prior knowledge that a cell can be anywhere from $10$ to $100$ micrometers, but I don't know how to figure out a cell's size with the information I'm given. Usually when I do problems like this, I am given the size of the field of view. Is that not needed to solve this problem?

http://pob.k12.ny.us/cms/lib/NY01001456/Centricity/Domain/517/Measuring%20%20With%20a%20Microscope%20SB201312_9_13.pdf Have a look his should help..

@Polisetty Those slides just pretty much review what I already know... is there something I missed?

Is this an mcq? since the question says, "approximate", you can assume the fov to be 5mm for 4x. Though it changes also with the magnification of your eyepiece. We were told to remember the fov values for 4x, 10x, 40x, 100x.. approximately - 5mm, 2mm, 0.5mm, 0.2mm These were approximates. This was a long time back.. maybe someone else can answer better.. Here's a full table - http://www.seoenterprises.com/shop/pages.php?pageid=12

@Polisetty thanks for the chart; also what's a mcq?

a 'multiple choice question'. huehuehue.

@Polisetty lol, no

Some cells can be much larger than the range you listed, examples that come to mind are some eggs (the yolk of a normal chicken egg is a favorite example), some algae, and I believe some amoebae too; not a bad rule of thumb for mammalian somatic cells but just a hint to not be overly focused on what is "typical" if the question doesn't define or depend on it.

@BryanKrause Never thought of that...biology textbooks always say cells are between 10 and 100 micrometers

@suomynonA Do you have a source for that? I wouldn't be surprised if there was a "typically" in that sentence, or if the topic was clearly relating to non-gamete animal cells, or something like that, because that certainly isn't true overall.

@BryanKrause The science olympiad rules, I copied it verbatim

@suomynonA I meant for your statement that "biology textbooks always say..." - I'm assuming that isn't written in the science olympiad rules?

@BryanKrause I just checked Campbell biology, it says "most cells" so I guess there are exceptions

The best  "approximate" answer in my opinion is: 2 times the length of the visual field :P


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Does blue light cause stomata to open or close?
In my biology lecture notes, it says that blue light causes stomata to close.
But thinking about it logically, since plants absorb a high percentage of blue light compared to light at other wavelengths, so wouldn't it cause stomata to open?

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Which two organelles absorb acid?

I stain an unknown acid with purple dye. Later, you find the cell in two organelles. What are they?

I am guessing that one of them is lysosomes, because they break down unwanted elements. What would the second one be? Mitochondria?

Take a look at this.

@SanjuktaGhosh So my answer of lysosomes and mitochondria is correct?

I think the acid / base terminology is confusing in histology. In my understanding, this is not about pH, it's about charge. "Acidic" stains are deprotonated, and therefore negatively charged molecules, and so they are attracted to positively charged structures. Most proteins are positively charged, so protein-rich structures tend to be stained, while nucleic acids (which are negatively charged) are not.

It is about pH in the sense that acidic dyes will be deprotonated and negatively charged at neutral pH. If the pH is lowered below the pKa of the dye, it will become neutral.

The principle of staining works in such a way that acidic dyes stain the complementary basic components of the cell hence acidic dye rather than staining lysosome which is acidic will stain the relatively basic components of the cell.

What are complementary basic components? Specifically the complementary aspect.

So it stains the nucleus and ribosomes?

Hi. I am not sure of basicity of some cell organelles. Hence I have provided how staining works because I saw wrong answers; it definitely does not statin nucleus because nucleic acids are acidic in nature.

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Which species of iron-reducing bacteria are hyper-sensitive to copper?
I would like to know which species of iron-reducing bacteria are inhibited in their iron metabolism by a copper concentration of less than 500 nano moles per litre.
Searching the internet, I can only find Klebsiella/Enterobacter/Aerobacter aerogenes, and I'm not even certain that that is an iron-reducing organism.
According to one reference, there are "other" iron-reducers which are similarly allergic to copper, but it doesn't mention which they might be.
I have done cultures in which iron-reduction appeared to be inhibited by a copper concentration of less than 100 nano moles per litre, and I am trying to identify the organism by a process of elimination.

Presumably these are environmental cultures? If so, work on eliminating the common ones first. You might need to do this by culture and test, though you may also be able to do it through next-gen sequencing and looking at abundance changes between with and without copper. Just because you can't find data on the internet doesn't mean that a particular species isn't inhibited, it might just be that it has never been tested.

Thank you for replying bob1.  The cultures were done in rainwater, though unfortunately I no longer have a sample of the organism.  At the time when I was doing this, I didn't know that iron reducing bacteria existed.

I don't have a list, but copper has a pretty strong antifungal and antibacterial action, at least against pathogenic species.

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Why doesn't alum coagulate my cyanobacteria?
My collected rainwater has a pronounced blue-green tint which I believe to be due to the presence of cyanobacteria.
I have been trying to remove the cyanobacteria using aluminium sulphate, but it doesn't seem to work.
Would anyone like to suggest why?

Do you have a good microsocope with which you could confirm the identity of the microscopic organisms?

Thank you for replying.  Unfortunately I didn't see your response for some reason.
I have come to the conclusion that the problem organism is not cyanobacteria.
I will ask another question to clarify the issue.

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Can PCR detect phosphorylated protein?
I'm trying to detect the level transcriptional protein inside cells. However, the cells contained both of this protein that is phosphorylated and not phosphorylated. Can RT-PCR detected the level of both of them? If yes can it detect them separately?

Have you thought at all about what PCR measures? Maybe even from Wikipedia if you've forgotten?

No. PCR (and quantitative PCR, or qPCR) rely on primers. They will amplify DNA flanked by primer regions, and this 'multiplied' DNA will be detected (and quantified).
PCR can be used to detect DNA. Reverse transcription followed by PCR (RT-PCR) can be used to indirectly detect RNA. Neither method is used to detect protein abundance, or post-translational protein modifications such as phosphorylation. This is because the modifications are not inherently encoded* in the nucleic acid sequence. They occur only on the protein level. Also, the abundance of a transcript tells you very little about how much protein will actually be produced from it, and how long this protein will remain in your biological system. A single mRNA can result in two very differently-modified proteins, and PCR would not be able to distinguish between an mRNA producing one kind or another. Also, phosphorylation is often a temporary modification, it's good to remember that.
*unless you have transcript variants (that produce protein isoforms) which omit or gain sequences that are modifiable, in the environment of a specific biological system.

It is up to you whether or not you answer a question, but I do encourage you to read the help section on answering entitled "Answer well-asked questions". @Bryan_Krause wrote a comment encouraging the poster to think about what PCR does. You told him. Which response will most help him develop as a scientist?


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Animal with "advantageous" trait in a environment where the trait is never utilized (high cold tolerance in mild climate) - natural selection occur?
If you were to put an animal with a certain type of seemingly advantageous "trait" into an environment where the trait was not necessarily needed, ex: Putting an animal with a high tolerance for cold into a mild climate, what kind of natural selection occur? Balancing?

It becomes redundant and has no positive selection pressure, so it becomes vestigial, become intermediary performance, changes in quantity to something useful but less adapted to the extreme, and may even disappear, although highly useful genes tend to stay hidden in the chromosomes for many millions of years rather than just disappear.

Recipe for selection
There is selection on a specific phenotypic trait if and only if

There is variance for this trait in the population
This variance is, in part at least, explained by genetic variance
The trait covaries with fitness

The first two points can be reduced to a single point by stating "The trait has some non-zero heritability in the population". For more information about heritability, please have a look at Why is a heritability coefficient not an index of how “genetic” something is?.
This recipe is often called Lewontin recipe.
Applying the recipe to your case
So, in the model you consider, some individuals are cold tolerant and some aren't, so the first point is checked!
We will assume that the difference in cold tolerance is caused by genetic differences. Second point is checked.
Does the trait covary with fitness? As you defined that, in the environment considered, being cold tolerant does not have any impact on fitness, then no, there is no covariance between the trait and fitness. The third point is not checked and therefore, there is no selection happening.
Are you sure there is no cost to being cold tolerant?
Note, btw, that it is not rare to observe (or at least to assume) that some adaptation such as cold tolerance would come at a comparable cost when the environment is warm enough.
For example, increased cold tolerance might be mediated via anti-freeze proteins. The production of such proteins might be costly for the individual. In such case, we would have a covariance between fitness and the trait (cold tolerant individuals would have lower fitness that individuals that are not cold tolerant) and hence selection should act as to reduce the frequency of individuals that are cold tolerant in the population (always assuming an environment that is warm).
What else could cause the frequency of cold tolerance to evolve?
In absence of selection, the frequency of cold tolerance individuals might still evolve in the population. Things like genetic drift, selection at linked site or selection at correlated trait or migration can typically affect this frequency.

What if I were to phrase the question, "after putting them into the mild climate, would you expect positive, purifying, or balancing selection to occur?" Thus making you choose one? Or is there no grounds for any of the three?

Real world example - Primates' ability to synthesize vitamin C (clearly a good thing for most species) held no benefit to species that ate a very fruit-rich diet, and the vitamin C synthesis pathway gradually accumulated mutations and become non-functional.

@iayork - and would that be a kind of "selection" on the gene?

@biostudent4451 it would be the absence of selection, allowing random drift leading to mutational inactivation (possibly also some negative selection reducing metabolic costs but I don't know if that's been demonstrated)

@BioStudent4451 would you expect positive, purifying, or balancing selection to occur? I would expect, no selection. Hence none of the three you mention (assuming mild climate and not fitness trade-off of any kind).


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What ways are there to determine how big genera are?
I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data sets), but I am looking to find more ways to look at 'how big is a genus?' in terms of biodiversity. Any ideas or comments are greatly appreciated!

Or even species delineation techniques that could be used for genera?

If you are you aiming to compare genera widely across families and orders, you should consider that taxonomic levels (such as genus) are used very differently between orders. This means that taxonomists are using quite different criteria to delimitate genera, so the differences you might observe would probably be caused by these different definitions/criteria as much as "actual" differences.

Bearing in mind that the information is bound to be incomplete (as is the list of existing species), you could use the NCBI taxonomy database. For example, checking the page for the Drosophila genus will give you an idea of its size.
For more precise numbers, you can download the taxdump.tar.gz file from NCBI's FTP server (link), extract it and run the script below on the file nodes.dmp (a dump of the database info).
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;
my (%opts,%children,%ranks);
getopts('t:',\%opts) || do { print STDERR "Invalid option"; exit(1); };

my $taxid=$opts{t}||die "Need a taxid: -t\n";

sub getchildren{
    my $p=shift; ## The taxid of interest
        my $found=0; ## will be 0 unless we find a new kid
    ## For each child of this taxid
    foreach my $kid (keys%{$children{$p}}){
     ## Get the kid's kids
     foreach my $gkid (keys%{$children{$kid}}){
         ## If this one hasn't been seen before
         unless (defined($children{$p}{$gkid})) {
      ## Add it to the list of this taxid's children
      $children{$p}{$gkid}++;
      ## We found a new one, we need to test again.
      $found=1;
         }
     }
        }
        ## If we found a new one, run again
        getchildren($p) if $found==1;
    }
    while (<>) {
        ## Remove trailing newlines
        chomp;
        ## Parse the current line
        my ($name,$parent,$rank,$rest)=split(/\s*\|\s*/);
        ## Save the current taxid as a child of its parent
        $children{$parent}{$name}++;
        ## Save its rank (species, genus, order etc)
        $ranks{$name}=$rank;
}

## Recursively get all children of this taxid
getchildren($taxid);

# Count only species as children
my @kids=grep($ranks{$_} eq "species", keys(%{$children{$taxid}}));

# Print out the results
printf "Genus %s has %s members\n", $taxid, scalar(@kids);

Assuming you are on or have access to a *nix environment, save that file as genus.pl and run it on the nodes.dmp, giving the taxid of your genus of interest:
perl genus.pl -t 9257 nodes.dmp

The output of the above example (Ornithorhynchus) is:
$ perl genus.pl -t 9257 nodes.dmp
Genus 9257 has 1 members

If we try on Drosophila, we get:
$ perl genus.pl -t 7215 nodes.dmp
Genus 7215 has 738 members

This is realy not the most efficient way to do it (far better to do this in the script itself but I don't have the time to implement that now), but if you don't mind waiting, this will give you the numbers for all genera:
for i in $(grep -w genus nodes.dmp | awk '{print $1}'); do
        perl genus.pl -t $i nodes.dmp;
done

Genus sizes are usually measured in number of species, since a particular species under a single taxonomic authority shouldn't be found in more than one genus. Check out Strand and Panova, 2014 for some numbers on number of species found in each genus on average across several thousand genera from eight major taxonomic groups.


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What is a 21q21 deletion?
I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement:

We report three patients affected with neurodevelopmental disorders
and harbouring 21q21 deletions involving NCAM2 gene.

I am not sure what a 21q21 deletion is. I have read that 21q refers to long arm of chromosome 21, and that 21q21 refers to position 21 on the long arm of chromosome 21.
However would a 21q21 deletion, refer to this whole section of the chromosome being missing, with this section including the NCAM2 gene? Any insights are appreciated.

Two likely scenarios.
Interstitial deletion. More likely.
Where just a small internal part of the chromosome is missing. This is like pressing "delete" for a while in the middle of a text document.
Deletions from the end of the chromosome to some point.
Chromosome 21 is the smallest, and people survive having the whole p side of the chromosome  missing, even all the way down into band 21 on the q side.
There are more recent articles than the one you saw, look on google scholar for ncam2 deletion and sort by date.
Wikipedia article.
https://en.wikipedia.org/wiki/Chromosome_21
This document below mentions specific cases of (severe) 21q21 deletions (page 15).
https://www.rarechromo.org/media/information/Chromosome%2021/21q%20deletions%20FTNW.pdf

I would suggest looking more into karyotype nomenclature; it is admittedly a bit odd. Here is one related question/answer that puts it in context.
I haven't looked at the paper in detail but generally what it means is that there is some cytologically relevant big chunk of chromosome that is missing that roughly overlaps with the chunk of chromosome that we find at band 21 of chromosome 21 (not position 21). Note that these cytobands/karyotype/G bands visible in a chromosome spread under a microscope, so these are quite large deletions.
Looking at the paper methods, it is clear that in 2/3 cases they confirmed the deletions by looking at karyotype data (FISH/chromosome spreads):

For Case 2, CNV confirmation and parental studies were performed by metaphasic and interphasic FISH on leucocytes using BAC RP11-43A6 (chr21:18,414,905e18,567,253, hg19 build). For Case 3, CNV confirmation was performed by G-banded karyotype. Parental studies were not available.

The terminology is quite outdated now as usually we are looking at sequence data these days, which has much higher resolution, but a lot of the stereotypical chromosomal abnormalities still carry these confusing names. And seeing it on a chromosome under a microscope is still the gold standard for these large chromosomal events.


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What does it mean to "cure" microscope slides?
I am reading a journal paper and I have come across the following statement in the materials and methods section regarding the preparation of microscope slides:

Coverslips were washed once more with PBS, inversely mounted on
microscope slides with ProLongTM Diamond antifade mountant containing
DAPI (Invitrogen). Slides were cured for 24 hours at room temperature
before observation.

I am not sure what exactly is meant by the statement the "slides were cured". I have searched on Google for some answers but I have not found anything useful. Any insights are appreciated.

In this context, "cure" is a chemical term. Definition from Wikipedia :

Curing is a chemical process employed in polymer chemistry and process engineering that produces the toughening or hardening of a polymer material by cross-linking of polymer chains. Even if it is strongly associated with the production of thermosetting polymers, the term curing can be used for all the processes where starting from a liquid solution, a solid product is obtained.

So here it means that the slides were incubated at room temperature for 24 hours to let the mounting media harden. Of note, not all mounting media harden, some may require specific conditions to cure like UV light (example), and the curing step changes the properties of the mounting media like the refraction index. From the ThermoFisher website :

Formulations of mounting media that can add favorable properties such as optimizing the refractive index to match that of glass, preventing photobleaching, or preserving samples for long-term storage are widely available. Keep in mind that some require time to “cure” or harden. For mounting media that need time to cure, it’s important to let the sample fully harden before imaging so that you don’t inadvertently damage or destroy your sample by moving it around on the slide or cause photobleaching of your stained cells. Typically, the refractive index of the mounting medium will not reach its specified value until after it has fully cured, and its photoprotective properties will increase during the curing process. The degree of hardness after the mounting medium has fully cured will also vary; some will set like jelly while others will set like hard plastic


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Is 'constitutive effect' the proper term for explaining a biological effect that occurs due to the constitutive knockout of a gene in a mouse?
I am working on an experiment involving the analysis of expression of a protein X in wild-type (+/+) and knockout mice (-/-). In the knockout mice, the gene of interest has been constitutively knocked out. For both genotypes, I am analysing postnatal day 2 (P2) and postnatal day 10 (P10) mice.
If in the knockout P2 and P10 mice, the levels of protein X are significantly increased compared to the wild-type P2 and P10 mice respectively, one could say that this effect could possibly be due to the gene of interest being knocked out. However, I was wondering, is 'constitutive effect' the proper terminology to explain a biological effect that occurs due to a gene being constitutively knocked out?
Any insights are appreciated.

"...one could say that this effect could possibly be due to the gene of interest being knocked out." Assuming the wildtype and knockout mice share a common genetic background and appropriate controls are performed, you should be able to say this with more confidence than "possibly."

Not necessarily... knockouts are a rather crude and problematic tool for studying regulatory systems. Have you read "Can a biologist fix a radio?"

I have generally seen the term "constitutive" used to refer to a "always on" expression of a gene with no anticipated regulatory interaction. Thus the term "constitutive knockout" seems a little bit oxymoronic to me, and I would tend to prefer a different term, like simply "knockout" or, if you really need to differentiate from conditional knockout, "unconditional knockout."
Likewise, if you wrote "constitutive effect", I would tend to interpret that as an effect of a gene being on, not a gene being knocked out. And even then I would find the terminology unsatisfying, as again it's mixing ideas of regulation (effect) and non-regulation (constitutive).
I would suggest you keep the terminology more direct and simply refer to the knockout itself, e.g., "knockout effect", or "effect seen in knockout mice".


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Did Carl Linnaeus ever name a species he never saw?
According to this post Carl Linnaeus named more than 13,000 species which is definitely quite impressive. If we consider a 50 years career it makes about 5 species per week! It would feel impressive that he could actually take time to find, observe and describe that many species.
Apparently Linnaeus named species from outside Europe such as the Wild Turkey (Meleagris gallopavo, Linnaeus, 1758). This surprised me a little bit as travelling accross the atlantic wasn't all that common in the middle of the eighteenth century. Also, the wiki article on Carl Linneaus says:

Boerhaave offered him a journey to South Africa and America, but Linnaeus declined, stating he would not stand the heat.

It made me realize that there are actually many non European species that have been described by Linnaeus such as the Llama (Lama glama, Linnaeus, 1758).
I heard of Linnaeus trip to Lapland and I always pictured Linnaeus as a field naturalist but now I am wondering

Where did he get his specimens from? Did he have an army of graduate students exploring the world for him?
What fraction of the species he named did he really see in the wild?
What fraction of the species he named did he really see alive? (has he ever seen a Llama and a Narwhal?
Did he name species based on other people description but without ever seeing one dead or alive?

Just to add to Gerardo's great answer, there is a lovely paper that describes a specific instance in which Linnaeus described a bird species, Certhia pinus, on the basis of two illustrations (by Catesby and Edwards) as well as a description by Brisson taken from Catesby, without having seen any specimens. Unfortunately, the two illustrations turned out to be based on two different species, which became known as Dendroica pinus and Vermivora pinus. The authors of this paper, Olson and Reveal, clarified this situation by creating a new name for Vermivora pinus: Vermivora cyanoptera Olson and Reveal, 2009.


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What is meant by "opposing plasma membrane" with respect to cell adhesion molecules?
I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about cell adhesion molecules (CAMs) and I have come across the following:

CAMs are involved in homo‐ or heterophilic interactions with molecules
positioned on opposing plasma membranes, and such interactions are
referred to as trans‐interactions. In addition, CAMs are often
involved in homo‐ or heterophilic interactions with other
membrane‐associated molecules positioned in the same plasma membrane.
Such membrane‐lateral interactions are referred to as
cis‐interactions.

I know that cell adhesion molecules are proteins mediation cell-cell or cell-extracellular matrix interactions. However, in the above excerpt from the book in the following statement: CAMs are involved in homo‐ or heterophilic interactions with molecules positioned on opposing plasma membranes, I am not sure what exactly is meant by "opposing plasma membranes". I think that this refers to the plasma membrane of a neighbouring cell the CAM is interacting with, however I am not fully certain.
Any insights are appreciated.

Opposing means facing each other, so the two outer surfaces can interact. Like two opposing armies.
I found an article:
"Pharmacology of cell adhesion molecules of the nervous system"
at
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644493/
doi: 10.2174/157015907782793658
"...CAM-induced intracellular signalling is triggered via homophilic (CAM-CAM) and heterophilic (CAM - other counter-receptors) interactions..."

Thank you for your reply. Just to clarify, do homophilic interactions between CAMs always join two surfaces of the same cell? In the same book, I have read that the cell adhesion molecule NCAM2 interacts homophilically in trans, and the book states that trans interactions happen when CAMs interact with molecules positioned on opposing plasma membranes. Any insights are appreciated.


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PCR and Semiconservative replication
Why does PCR use heat as opposed to helicase like in semi-conservative replication in order to separate the double DNA strand?

Simply because it is ways more practical and there is no need to use a helicase. Heating is fast and convenient and denaturation is reversible. Also all the DNA is denaturated, so afterwards, primers can bind to their target sites, setting up the start point of the polymerase.
If you want to do this with and helicase, you need to make sure that you have a heat stable polymerase (at least at 72°C), you need to have the right places on the DNA unpackaged and finally, you need two enzymes in the reaction (which is more expensive than just having one).


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Osmosis vs protein-binding in preserving foods through salting
I had assumed that the preservative function of covering foods with NaCl or brine was due to osmosis killing the microorganisms on the food by dehydration.  However, I am now wondering to what extent denaturing of bacterial protein through interaction with salt ions could be responsible for killing the microorganisms.  And what evidence suggests a dominant role for one or the other mechanism.  I hope someone can clarify this matter for me.  Thanks in advance.

In addition to killing microorganisms, the salt may provide a better environment for some 'beneficial' organisms, and a less beneficial environment for other 'problem' organisms. For instance, in production of kimchi and sauerkraut, salt encourages lactofermentation to the detriment of more harmful bacteria and fungi.

This is interesting, and implies that the relative importance of osmosis vs protein-binding when preserving food with salt depends on the type of microorganism targeted.  But I still wonder about the importance of osmosis in food preservation, whether or not lactofermentation is involved.  In the latter case, are harmful microorganisms killed by dehydration?


text:
Confused about definition of bulk flow of water by osmosis
As a teacher of high school and introductory college chemistry, I used textbooks that defined osmosis as a flow of water (only) through a membrane that prevents other substances such as dissolved salts from passing through.  But in more advanced text, discussing osmosis through aquaporins in the plasma-membrane, bulk flow by osmosis implies that the water carries along dissolved substances.  So which is it:  pure water or a solution that moves by osmosis?  (I'm somewhat naive about biology, as my degrees are in physical chemistry and metallurgy.  Biology is way more complicated!)

Can you provide a citation or quote? I'll answer by my guess about what's being talked about, but it would be nice to be able to confirm.

Bulk flow and osmosis are different; I'm guessing your text might be talking about using osmosis to drive bulk flow, but they are occurring at different stages.
For example, if you get your water from a water tower, your house's water pressure is driven by gravity. However, the water tower could be filled by an electric pump. You could say your water pressure is driven by an electric pump, but the pump isn't really pushing water into your house, it's just pushing water up a tall tower so that gravity can act, and if you didn't realize this fact you might be confused about how you can still have water pressure even when the power goes out.
Similarly, you can drive bulk flow by osmosis. If you have a closed space (e.g., a "tube") and pump salt (or anything else water soluble) into it, it can pull water from the surrounding tissues via osmosis. As the pressure of water increases in that closed space, it can now flow in bulk through that tube. Plants can use this mechanism to deliver nutrients up a stem: they pump in ions/molecules inside the stem, which pulls in water from the soil around. Because the space is rigid, instead of expanding the water goes up the stem in "bulk": anything else carried in the water will be pushed up with it. Then, when target tissues pull in solutes, osmosis again causes water to follow, and by only pumping solutes in one place and out another you produce a bulk flow of water.

Bryan, thanks for your answer.  But please clarify the example of plants delivering nutrients up a stem.  Does this mean that the liquid that enters the roots from the soil by osmosis is essentially pure water, but once it has entered the tube-like stem it carries with it nutrients that were in a lower place in the stem?

@S.Fishman The general concept is that cells in the roots pump in any ions, etc, from the soil that the plant needs, and therefore water is pulled in via osmosis. Not totally pure water, but also anything else that can freely cross membranes. The root cells then pump those ions into other cells or cavities and water follows. The whole system is actually pretty complex and plants use a lot of combined forces to move solutes in a couple different systems, so you can read more broadly about xylem and phloem.

I should also add that I simplified a bit by talking about a "tube", because in the context of nutrient transport in plants you can also have living cells that are connected to each other via openings between cells; they aren't really just a tube anymore in that context, but from the perspective of water and stuff dissolved in water the principle is the same.


text:
Transmitted electrons in TEM
When some electrons of the electron beam pass through the specimen, what exactly happens after that in order to produce the black white image? What I understand is that electrons transmitted collide with a film and make that part of it black on the image, and those that don't collide make their part white. But why is it said that electrons that pass readily make the area brighter or more electron lucent and vice versa for scattered electrons?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular I'm not sure this is the appropriate for this question since it appears to be a physics (or maybe engineering question) rather than anything directly related to biology. Thanks!

Thanks for being curious about a biological subject on a site about biology. As a contributor here, I deeply apologize that your curiosity is being stomped upon.

I apologize for asking here but I didn't really focus on the site to ask in since I'm studying it from a histological source.

I'm voting to close this question as off-topic because it is about the physics of TEM rather than biology.

The pixels in a TEM image are whiter or blacker based on the dose of electrons that impact that pixel in the whatever detector is being used to form the image, be that photographic film, a scintillation screen, or a direct detector camera.
As for how the image that reaches the detector is formed by the specimen being imaged, there are two different mechanisms.
Amplitude Contrast is relatively simple - denser parts of the specimen scatter electrons strongly enough that some electrons do not make it to the detector at all, so pixels below these parts of the specimen will receive a lower dose than pixels below less dense parts of the specimen.
Phase Contrast is more complex, and is responsible for most of the contrast in high-resolution cryo-TEM. Briefly, the specimen is illuminated by a parallel beam of electrons and every "pixel" of the specimen scatters some electrons but lets most of them pass straight through without interaction. The scattered electrons go off in a different direction than the main beam but are focused back by the lenses to the same point on the detector as the unscattered electrons. Because the scattered beam took a different path from the unscattered beam, and because electrons are waves as well as particles, there is a phase difference between the two beams which causes them to interfere. Typically, areas of the specimen that scatter electrons more will cause destructive interference, so darker pixels. If there is no scattering, then there is no interference, so brighter pixels. There are many resources explaining the technical details of this mechanism (1, 2, 3), but these tend to focus on crystalline specimens.


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small airborne microorganisms, are in many instances attached to bigger particulate substances?
From https://biology.stackexchange.com/a/90193/56476

very small airborne microorganisms, are in many instances attached to bigger particulate substances in the air, whether liquid micro droplets or solid particles. ... but this may be reason for higher risk of respiratory infectious diseases when PM2.5 air pollution gets high.

Can someone confirm this great logic?
I think it is true, but just need a confirm from the public! :)
Many thanks.

You should surely address your concern about this to the person whose answer you are quoting, asking for evidence to support the statement, rather posting a separate question. If you really must post a separate question, you need to show that you’ve tried to find the answer yourself.

I don't know about air, but that's totally true for water: turbidity is a measure of water particulates, and micro-organisms naturally attach to particulates and feed from them.


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If a gene is missing from an operon that structures a protein, then would that protein not be made properly?
From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein.
I obtained a genome in my study and looked for genes that constitutes part of a metabolic pathway, and ended up finding that one of the genes in an operon was missing.
Does that imply the protein made from those genes in the operon will not be made properly or other genes will compensate for the loss?

From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein.

Genes in an operon can code for protein subunits, but they can also code for separate proteins. Often an operon will have a few genes responsible for one core function, with other accessory genes that may help regulate or enhance that function is some way. Sometime genes are fused, combining multiple subunits into a single gene. In other cases, subunits can have related functions in the absence of other units.
For example, The ArsAB complex uses ATP to pump arsenic from bacterial cells, conferring resistance. But many bacterial Ars operons lack the arsA gene. Minus this subunit, the ArsB transporter still functions to efflux arsenic from the cell, just less efficiently, harnessing the proton motive force instead of burning ATP.

... ended up finding that one of the genes in an operon was missing.
Does that imply the protein made from those genes in the operon will not be made properly or other genes will compensate for the loss?

If the gene is truly missing, it's can't be transcribed, and the subsequent protein can't be made, but the remaining genes will probably still work. I would start by asking what the operon's function is, and then consider whether the missing gene is essential for that function (hint: If it's missing and the rest of the operon is still there, it's probably not essential). If it is essential, then consider whether it's truly missing. Are there other open reading frames in the operon that could encode something with similar function? Could the organism have multiple copies of the same operon (possibly found on a plasmid)?


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Coronavirus origin could be bat, why this happen while people have been eating bats for centuries?
Sorry for my lack of understanding, Why now, when people been eating bats for centuries? If bats are simply a vector, where does that virus come from?

Please see the meta discussion and contribute. I thoroughly disagree that biology.SE doesn't have the expertise to answer questions about biological concepts and disease mechanisms as they relate to virology. They are, in fact, explicitly on topic. This question's problems are related to the lack of prior research. Address that issue and I will vote to re-open.

Bats are reservoirs of many important human pathogens, some are emerging infections (e.g., 2019-NCoV, the coronavirus in the news recently), and some are not (e.g., rabies).
Contact between humans and bats is certainly not a new phenomena, but there is more required for an emerging infection than a reservoir and a new host. There must be some bridge that allows a virus to cross a previously effective species barrier. For SARS, there was an intervening amplifying host, the palm civet.  We've now had long enough to study the molecular biology, so this is now quite well described:

Once SARS-CoV had jumped from bats to civets, it underwent further mutations in civets. The first K479N mutation allowed SARS-CoV to jump from civets to humans and the second S487T mutation allowed SARS-CoV to transmit from human to human, leading to the severe SARS outbreak in 2002–2003.

It may be useful to understand that, as they are RNA viruses, coronaviridae have a high error rate, increasing the rate of mutation. Additionally, making a species jump may allow for novel recombination.

I think you could expand a bit on the lack of stability in viral populations.

@BryanKrause done. Feel free to expand further if you'd like.

The four endemic human coronaviruses are all bat-origin coronaviruses that have jumped into humans in the past 100 years, so the premise of the question is wrong.

@iayork that's fascinating. For some reason I was remembering bovine coronavirus, rather than bat as a source for human coronaviruses.

A more recent study suggests that two of them may have passed through livestock first (https://www.ncbi.nlm.nih.gov/m/pubmed/29551135/) and may or may not have started in rodents


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Flying Insect Identification
What insect is this?

Found in the UK, approximately 10mm-15mm in length.

That is clearly a mayfly (family: Ephemeroptera) — using that may help you find an answer for yourself. It would also be very helpful if you were to [edit] your post to include "as much information as possible on location/habitat, size/characteristics and behavior." (from the species-identification tag description) ——— In particular, what is the local environment is like and can you give more specific location information than "UK"?

if you want to learn more about this group of insects you can take a look here https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ephemeroptera

That insect looks quite like a Mayfly, it's an ancient insect that belongs to the order Ephemeroptera. I'll go a step further and guess that species, that one there is most probably a Green drake, they aren't harmful at all as in they don't sting or bite but if a lot of dead mayflies pile up they can cause respiratory inflamations, asthma, hay fever that sort of stuff.
They're a vital part of the pond ecosystem. Here's a picture of a Green drake and it's quite similar to your picture. Credit to Missoulian Angler
I think some of the major reasons why it is a Mayfly are a s follows:-

The transparent wings are a minor giveaway.
The three tail filaments are a major giveaway.
Very short almost non-existent antennae

Welcome to Biology.SE! You are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. ——— Thank you for taking the [tour], but you may also wish to consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

There friend, added a picture.

Thank you for the update! Please provide a citation/source for the image you are using — images must be credited to their creators just like quotes are to their authors. This is generally considered good practice in scientific communication and will help other users understand by providing context. ——— In addition, it would be very helpful if you could describe the key features that allow you to be certain this is a mayfly and what makes you suspect a Green drake in particular. Thanks again!

There mate edited as you said I should, I think that should put me in the clear. Grateful for your sound advice


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Appropriate model to test if environmental variable is significant between two species?
I want to know if a given environmental variable has an effect on the range of two species/two groups of species. Specifically, I am interested in testing if one species has a "preference" for higher/lower ranges over the other (for example, do blue frogs prefer colder temperatures than red frogs?). I have occurrence data for my species as well as environmental data in a grid over the area. Can anyone point me in the right direction?

Welcome to Biology.SE! This question seems like it might be a better fit for the statistics site. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

Do you want to test of they have different environmental preferences (in relation to a set of environmental variables), or if there is a positive/negative relationship between their ranges? Your Q seems to have bits of both, but they are not the same thing.


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How to calculate percentage of DNA that ancestors contributed?
In David Reich's book "Who we are and how we got here" there is a graph explaining that more we go back in our ancestors generations, the least we have chances to have any DNA inherited from one of these ancestors because the number of ancestors is doubling every generation while the number of stretches of DNA is only increasing by 71.

In the left side of the graph, there is a percentage indicating how many ancestors contributed to our current DNA. For example : 50% of 1024 ancestors after 10 generations.
I don't understand how this percentage is calculated and it is not explained in the book.
Could someone help me understand it please?

The answer I'm going to give is more or less copied from Graham Coop's post, but I'll try and summarise it here.
A single generation ago, we have 2 ancestors. If we go another generation back, we have 4 ancestors (your 4 grandparents). If we assume that there is no inbreeding within the ancestral population, every time we go back a generation, the number of ancestors doubles.
On the other hand, the amount of your DNA you inherit from each relative halves each generation. You get ~50% of your DNA from your mother and ~50% from your father. These are inherited in large blocks which are split up by recombination events. If you go back a generation, you inherit ~25% from each grandparent.
However, because of stochasticity in how recombination occurs, you don't inherit exactly 25% from each grandparent. What you really inherit is a value distributed around 25%. There is a nice discussion of the ins and outs of it here. As an extreme example, if your parents and grandparents transmit entire chromosomes without recombination, then it is possible not to inherit any DNA on that chromosome from the other grandparent.
It's quite unlikely ($p=4$ x $10^{22}$) that you don't inherit anything from a single grandparent. However, as you go back through generations, it's increasingly likely there are some relatives who don't contribute anything to your DNA.
For example, 8 generations back, there's around a 20% chance that any given ancestor didn't contribute anything to your genome. Therefore, we can say that the number of genealogical ancestors a given generation back is one minus the number of ancestors who contributed nothing. This is why, even though 10 generations back we might have 1024 ancestors, perhaps only around 50% of them will have contributed anything to your DNA.
I'm not entirely sure about how the figures in this book were calculated; whether it was from simulation or not. However, the results should be more or less the same as how Graham Coop calculated it in the above post.

Yes that's right, if we look at the Graham Coop's plot, him and David Reich seems to find the same chances to get ancestor's DNA (like 50% for 10 generations ago). But I don't understand how do we get from 1024 ancestors and 757 stretches to a 50% chances when 757/1024 = 74%.


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Was Dr. Livesey's treatment a valid one in the Treasure Islands?
Here is that incident from Treasure Island by Robert Louis Stevenson, where Billy Bones had a 'minor' heart attack or a stroke (according to R.L. Stevenson).
To give a little background about Billy Bones, he was a pirate, a toughened and hardened person who has gone through the deadly and unethical ordeals of life. He was an alcoholic and used to drink rum a lot. Dr. Livesey had previously warned him of taking any rum at all. But its quite a daunting task to let go a life long bad habit. Another thing worthy to be mentioned is that (to me it felt) Billy Bones had a very short temper which is indicative that he is a very likely candidate of high blood pressure.
In one incident, Billy Bones had a fight with an old foe of him. His foe escaped after collecting some major injuries caused by Billy Bones namely known as the Captain in Admiral Benbow inn. As the fugitive left the vicinity, Billy Bones gasping called out for rum and immediately he fainted.

I heard a loud fall in the parlour, and running in, beheld the captain lying full length upon the floor. ...He was breathing very loud and hard, but his eyes were closed and his face a horrible colour.

Jim called in Dr. Livesey downstairs who was treating Jim's father upstairs.

“Oh, doctor,” we cried, “what shall we do? Where is he wounded?”
“Wounded? A fiddle-stick's end!” said Dr. Livesey. “No more wounded
  than you or I. The man has had a stroke, as I warned him... I must do my best to save this fellow's terribly worthless life; Jim, you get me a basin.”
When I got back with the basin, the doctor had already ripped up the captain's sleeve and exposed his great sinewy arm. It was tattooed in several places...
“Prophetic,” said the doctor, touching this picture with his finger.
  “And now, Master Billy Bones, if that be your name, we'll have a look
  at the colour of your blood. Jim,” he said, “are you afraid of blood?”
“No, sir,” said I.
“Well, then,” said he, “you hold the basin”; and with that he took his lancet and opened a vein.

My question is about Dr. Livesey's little surgery. R.L. Stevenson writes after this 'surgery',

A great deal of blood was taken before the captain opened his eyes and looked mistily about him.

It almost had an immediate positive effect on the patient. My question is about Dr. Livesey's little surgery. What did he do here? Was it any form of valid treatment?

Welcome to Biology.SE! Thank you for taking the [tour], but please also go through the help pages starting with [Ask] questions effectively on this site. ——— I think this question is too speculative for this site since answers to it will necessarily be "primarily opinion-based". You might want to investigate whether this is an acceptable question for [medicalsciences.se]. In addition, we encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

@tyersome This question is only primarily opinion based to people who aren't familiar with the topic, which is perhaps more about history than biology.

@DeNovo — Since the question is based on event in a work of fiction, there can be no criteria for declaring an answer "correct". Therefore I can't see how this question (as written) could get an answer that was anything other than opinion based speculation ...

OP, are you interested in whether venesection is currently a valid treatment for stroke, or whether it was when treasure island was written or set?

@tyersome The question is about whether venesection is an appropriate treatment for stroke, which is readily answered. The primarily opinion based close is often an "I'm not familiar with the topic" close. A common mistake. Biological is a broad field. I wouldn't worry about it.

@DeNovo — Your question to the OP could guide them towards making this a valid question, but that doesn't mean that it is answerable in its current form, which is focused on fictitious events.

Let us continue this discussion in chat.

@De Novo, what was that word? 'venesection'? Thanks a lot. I'm only interested about the treatment. That's it. I guess my question phrases it clearly.

@Ahmed yes, venesection, the procedure described by "he took his lancet and opened a vein". Are you interested in whether that is currently a valid treatment for a stroke, or whether it was back when the book was written or set. Those are separate questions.

The procedure described here is called venesection. It is no longer standard of care, but was when Treasure Island was written.
Here is an excerpt from the first edition of Cecil's Textbook of Medicine (1927):

During the acute apoplectic attack the following therapy may be employed: The patient should be put to bed with the head elevated. If he has fallen to the ground the clothing around the neck must be loosened. Difficulty in swallowing contraindicates the administration of nourishment by mouth. An enema may be given. When the face is puffy, the pulse full and strong, and there is reason to suspect hemorrhage, venesection is advisable. It should be employed only for plethoric individuals, not for patients who seem asthenic or arouse suspicion of thrombosis. Usually 250 to 300 cc. of blood are removed.


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Fungi in my Solarium - how do I stop it?
Noticed fungi growing in my solarium in a few spots - probably a few spots where moisture is getting in.  It is really tough, like rubber.  Can cut some of it out with a utility knife, but even that was not an easy process.  Couldn't dig all of it out as it has gotten into some little crevices.  How can I treat this?  Tea tree oil or Oil of Oregano, or ?
The type of flooring is Bamboo.
The spotty things you see on the floor are spider droppings.. how that critter got in there is a mystery - room is always closed, way up on the 3rd floor where I never see any spiders, room is hardly used, and no openings for little flies or anything to get in for its food...?  Anyways, I digress... my real concern is to stop this fungi growth!
Thanks in advance...

Welcome to Biology.SE! Are you sure this fungi and not some sort of overzealously applied sealant? If you are sure it is fungal, does it have any odor? ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

Yes, definitely fungi.  I put the floors in myself, and this area is inside, and does not need sealant - was not there for 4 years, but this time I checked, I was surprised to see this growth.  It is a bit moist, and does smell like mushrooms...!

I'm thinking that this site is probably not the best place for this question — maybe [diy.se] would be a better fit? ——— That being said, fungi are tough, so I doubt any surface treatment is going be much help. Since fungi generally like moisture I'd check for leaks from outside and inside — also make sure the humidity in the room is being kept reasonably low. After that I think you would want to remove what growth you can (replace the affected floor boards if possible).


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Nerve/muscle fibre depolarizaitonand repolarization balance
if continously sodium is pumped in during depolarization and pottasium is pumped out during repolarization, eventually there will more sodium and less sodium inside. How the does the fibre/cell return to the balance?


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Inequality factor for similarity sensitive diversity
In a research article, Lou Jost has introduced the concept of inequality factor. The paper is "The relation between evenness and diversity", published in 2010.  Inequality factor allows an intuitive interpretation of the slope of a diversity profile. It corresponds to "the number of maximally uneven communities" is very intuitive.
I could not find the analogue of inequality factors in context of similarity sensitive diversity, for instance, Leinster-Cobbold diversity. Is there any equivalent notion of inequality factor for the similarity sensitive case? Could anyone suggest me some readings?


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How does fluid pass through the glial limitans into the subarachnoid space?
I have often heard that the cerebrospinal fluid (CSF) and interstitial fluid (ISF) are in free exchange. Because the CSF eventually drains (predominantly) into the dural venous sinuses, ISF's ability to access the subarachnoid space actually allows the brain to eliminate metabolic waste products that would otherwise remain the parenchyma. ISF presumably accesses the subarachnoid space, mixes with the CSF, and eventually, through arachnoid granulations, drains via the dural sinuses.
While that is fine and dandy...there are two layers that the ISF must first pass in order to access the subarachnoid space: the glial limitans and the pia mater.
How does ISF pass through the foot processes of astrocytes, which comprise the glial limitans? Does the H2O remain largely in the parenchyma while waste metabolites are selectively transported across the astrocytes and into the small spaces between the glial limitans and pia mater?

Excellent question. This is an active area of research.
The glia limitans defines the external most layer of brain parenchyma. Previously thought to primarily be a barrier against migration and growth of neural cells out of the brain parenchyma during development, recent work has characterized its involvement in regulating the immune environment of the CNS. A 2017 JCI paper demonstrated that the tight junctions of the glia limitans are inducible in mouse in response to inflammatory cues. You may find the associated editorial helpful. In addition to demonstrating a dynamic role for the barrier function, you can see that tight junctions are not the standard state, and the typical state allows passive diffusion as well as active transport of small molecules between the CSF and brain ISF, but the question is not fully resolved.
Importantly, this is mouse data, and mouse data in particular cannot fully resolve questions about human astrocytes.


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Why are the grey matter structures of the inferior medial frontal lobe not directly (not via white matter) connected?
I have recently been trying to understand the three dimensional nature of the brain for a neuroanatomy class. Part of this strategy has included learning about structures such as the falx cerebri, tentorium cerebelli, anterior dural girdle, etc in order to understand the physical barriers that surround different parts of the brain and therefore separate them from one another. For example, the reason that the cerebellum and floor of the occipital lobe are not directly continuous is because of the tentorium cerebelli.
One issue that I have recently come across is understanding why the inferior medial component of the frontal lobe, in the region just anterior to the pituitary gland and optic chiasm, are not directly continuous (i.e. the left cortical hemisphere at this location is not continuous with the right cortical hemisphere). I have attached some photos to clarify my confusion:

As you can from this image, the falx cerebri's anterior extent leaves a small opening (indicated by the red line) that would, presumably, permit grey matter from the left hemisphere to be directly continuous with grey matter from the right hemisphere. However, no such connection exists. This is readily confirmed using an inferior view, such as that indicated in the following picture, boxed in red:

As you can see from the boxed area, the medial inferior cortical grey masses from the left and right hemisphere (which are likely the subgenual division of the anterior cingulate gyrus) are distinctly separate. This separation is clearly not related to the falx cerebri, as the anterior descent of the falx cerebri occurs further in front of this area (as indicated by picture 1).
Could anyone offer an explanation as to why these structures are distinctly NOT continuous at this point? Further, if anyone could confirm whether any part of the cortex exhibits grey-matter-continuity (i.e. not via white matter tracts) between the left and right hemisphere, that would be greatly appreciated.

Could anyone offer an explanation as to why these structures are distinctly NOT continuous at this point?

The crista galli physically separates the straight gyrus.

Click to zoom

Click to zoom

... that would, presumably, permit grey matter from the left hemisphere to be directly continuous with grey matter from the right hemisphere. However, no such connection exists.

They are not physically touching in that location, elsewhere the two hemispheres are not connected (even though physically touching) by gray matter.

Further, if anyone could confirm whether any part of the cortex exhibits grey-matter-continuity (i.e. not via white matter tracts) between the left and right hemisphere, that would be greatly appreciated.

Except in rare cases, for example agenesis of the corpus callosum (ACC), communication between the hemispheres is via the anterior commissure and the corpus callosum.
The two halves are separated by a deep longitudinal fissure, see this animation:

sorry, but I do not believe the crista galli separates the WHOLE straight gyrus...it only separates the anterior portion, by virtue of the falx cerebri, which is illustrated in the very first picture I posted.

That's OK. I didn't claim that it does nor do my images show that, as explained in my second paragraph it's not the only factor; watch the animation, where it pauses.


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How broad are the conclusions that one can make from a heterologous expression experiment?
I am studying whether a neural protein regulates the activity of the protein GSK3. I am using heterologous expression systems where I am overexpressing the neural protein in CHO cells (via transfection) to see if it affects the levels of GSK3 in transfected cells vs controls. I am interested in seeing whether the neural protein regulates the activity of GSK3, and I have found that the levels of GSK3 are higher in the transfected cells vs control. But as I am using CHO cells as a model system, how broad are the conclusions that I can draw from this experiment? For example, will I be able to generalise what I found to neurons, or hypothesise that the same thing that I observed in this experiment occurs in neurons? Any insights are appreciated.

Hi, @ceno980: I've noticed you asking a number of questions that would be well-suited to the proposed Synthetic Biology SE site. Want to join the proposal?

GSK3 is interesting because as a kinase, it is itself regulated by its phosphorylation status (particularly by Akt in neurons). Therefore, more protein does not necessarily mean more activity. For example from E13.5 to E15.5 GSK3 levels do not change but activity steadily increases. Hence if you increase GSK3 levels in neurons, it may not mean that downstream effects would change substantially, so I think although promising the in vivo effects may be hard to deduce from this experiment. If you see similar effects in in vitro neurons, you can be a bit more confident of potentially seeing similar effects with in utero electroporation in vivo


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Receptor tyrosine kinases: What is meant by basal phosphorylation of the receptor?
I am reading a journal paper about the insulin receptor. The insulin receptor is a receptor tyrosine kinase, and upon ligand binding, undergoes autophosphorylation of intracellular tyrosine residues.
Regarding this paper, the terms "basal phosphorylation" or "phosphorylation in the basal state" of the insulin receptor is frequently used. However, I am unsure what the exact definition of basal phosphorylation is.
Is it the phosphorylation the receptor undergoes under physiological/normal conditions in vivo without the addition of exogenous insulin?
For example in the paper, they treat brain slices from wild-type mice with exogenous insulin, and they report that the phosphorylation of the insulin receptor exceeds the basal state.
Any insights are appreciated.

I think these excerpts are helpful in understanding the authors' use of basal, both in reference to insulin levels and insulin receptor phosphorylation --

As expected, insulin receptors from untreated WT slices are not detectably phosphorylated in the presence of low basal levels of insulin, but become rapidly phosphorylated upon exposure to exogenous insulin. In contrast, insulin receptors from MHCI-deficient $β2m^{-/-}$ $TAP^{-/-}$ hippocampi show significant basal phosphorylation, which is comparable in magnitude to insulin-stimulated phosphorylation in WT slices (Fig. 1A).

By increasing the threshold for insulin
receptor activation, MHCI ensures that dynamic insulin sensitivity is preserved, even on a background of basal circulating insulin.

In this context, I would interpret basal phosphorylation to mean the extent of receptor phosphorylation in tissue in the presence of a stable concentration of circulating insulin concomitant with fasting levels of blood glucose.

Your final definition is circular.  How does “baseline” clarify “basal”? You need to reword that.

@David good point. I've attempted to clarify -- I'm open to suggestions if still unclear.

That fits. “Basal” is not a precise term anyway. It is used to acknowledge that even without experimental manipulation, the molecule or process you are stimulating is not completely absent.


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Can cell adhesion molecules have intrinsic enzymatic activity?
I am learning about cell adhesion molecules (CAMs), and I know that they mediate cell-cell and cell-extracellular matrix adhesion via homophilic and heterophilic interactions. I have read that CAMs can be divided into four families based on their protein sequence and structure, including the immunoglobulin superfamily, integrins, cadherins and selectins.
I know that immunoglobulin superfamily CAMs are defined as having immunoglobulin domains in their extracellular domain.
However, I was wondering if a protein has immunoglobulin domains in the extracellular domain but a protein kinase domain in the intracellular domain (e.g. TYRO3), can it still be classified as a cell adhesion molecule belong to the immunoglobulin superfamily?
I know that the intracellular domains of CAMs can interact with cytoplasmic proteins, thus regulating intracellular signalling cascades. However, I have never read about CAMs themselves having any intrinsic enzymatic activity.
Any insights are appreciated.

Not related to Ig superfamily CAMs but beta-catenin is a good example of a structural protein that also acts as a signal transducer. Many proteins have dual functions (moonlighting).

Ebnet K (2017) Junctional Adhesion Molecules (JAMs): Cell Adhesion Receptors With Pleiotropic Functions in Cell Physiology and Development." maybe just adds info to the comment above which does not answer your question?  I think any cleaving or phosphorylation can be considered an "enzymatic activity". Maybe you should elaborate on "intrinsic" enzymatic activity". Premise is that CAMS like "antibodies" (immunoglobulins)   "transduce" as a middle part, adhering and detaching, without any cleaving or phosphorylation? Can you give some example for: "CAMs can interact with cytoplasmic proteins"?

No, they can't.
You're right, you "...have never read about "CAMs themselves having any intrinsic enzymatic activity"  - because this category does not exist. There is no explicit definition, any search to no avail. However, categorization as shown by Wikipedia, Immunoglobulin_superfamily does not suggest that categories as defined are not mutually exclusive.  Hence, featuring the immunoglobulin domain cannot turn a tyrosine kinase receptor into a "cellular adhesion molecule".
Interestingly, your question seems to come up both with what those mutually exclusive categories might have in common - the immunoglobulin domain - and what - still - sets them apart: the enzymatic activity.
Some "backbone" to your question might be the question if any receptor that does not have enzymatic activity may be considered or even termed CAM, which is illustrated by the B cell receptor's popularily known presentation of antigen to T4 cells: two cells clung together by receptor, still, that is a receptor, it is no CAM. This it what makes me suggest that categorization is more formal than material.
And, what may not easily be understood in your question:
As you ask about "intrinsic" enzymatic activity you do not seem to inquire about the signaling cascade that ensues the binding of cell adhesion molecules (CAMs) to internal proteins  which, themselves, may be enzymatic. In fact,   cell adhesion molecules do not seem, per se, to be involved in cell signaling at all. That makes differentiating even more intricate: if some CAM as a ligand induces enzymatic activity it might be termed "enzymatic"; however, your question is not about the exclusion of receptor-like ligands from the set of CAMs, but, to the contrary, about the inclusion of proteins that - like tyrosine kinase TYR3 - are considered "receptors" into the set of CAMs (trying to be precise: you do not ask about TYR being included into CAMs but about TYR-like, i.e. receptor-like, proteins, being included in CAM). Those categories "receptors" and "CAMs" are mutually exclusive. A receptor - if defined receptor - even with no enzymatic acitivity is not a CAM.
"CAM" implies non-enzymatic activity, and the enzymatic tyrosine kinases you refer to are,  in concept,  opposed. This isn't trivial as you state that tyrosine kinases have the immunoglobulin-like epitope on the extracellular end. To answer your question: that doesn't change the kinase receptors being excluded from the class of CAM membrane proteins.  Untrivially, what CAMS and Tyr3 (e.g.)  share is their being located on or within the cell membrane. Both's function may be considered  cell to cell communication.
Some reference:
Rüdiger Horstkorte et al., Basic Neurochemistry (Eighth Edition), 2012https://www.sciencedirect.com/science/article/pii/B9780123749475000092
"Ig-like domains are frequently found protein domains. For example, in the human genome, there are more than 750 identified proteins with at least one Ig-like domain. Prominent examples are, in addition to the above-mentioned immunoglobulin-related molecules, receptor tyrosine kinases, co-receptors such as CD4 or CD8 and many cell adhesion molecules."
In literature, it seem's there can't be found any material arguments for delimitation.
CAMs may, in my opinion, be opposed to enzymatic proteins of the cell membrane, especially TYRO3 and other tyrosine kinase receptors, by their working principle: CAMs do not cleave as enzymes do, but adhere as specific ligands, and disolve, or do not adhere but choose. They have perfect fit or don't. They succumb to conformational change, but unlike enzymatic membrane proteines do not inflict it, by cleaving or fusing (phosphorylation). Their conformational change may even be mechanic (pulling two cell membranes tight to each other when fusing cells).
For instance
Integrins (which form a category of CAMs, cp [Wikipedia, Cell adhesion molecules]:2
"Integrins are transmembrane receptors that facilitate cell-cell and cell-extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways..." - This may lead to think of CAMs, e.g. integrin as some form of receptor, as they can bind to ligands themselves, and vice versa categorize enzymatic receptors as CAMs, as in a wider sence, CAMs, e.g. Integrin can support enzymatic receptors, TYR-receptor, moreover:
From Wikipedia, Integrin: "Integrins play an important role in cell signaling by modulating the cell signaling pathways of transmembrane protein kinases such as receptor tyrosine kinases (RTK). While the interaction between integrin and receptor tyrosine kinases originally was thought of as uni-directional and supportive, recent studies indicate that integrins have additional, multi-faceted roles in cell signaling. Integrins can regulate the receptor tyrosine kinase signaling by recruiting specific adaptors to the plasma membrane."


text:
What does it mean to "nucleate multi-protein complexes"?
I am reading an article about the mTOR signalling pathway and I have come across the following:

mTOR nucleates at least two distinct multi-protein complexes, mTOR
complex 1 (mTORC1) and mTOR complex 2 (mTORC2).

I am not sure what is meant by "mTOR nucleates 2 multi-protein complexes". From the paper, I understand that mTOR is a component of the mTORC1 and mTORC2 complexes. I have read the definition of 'nucleate' online and it means to either "to form into a cluster" or "to act as a nucleus for". However in the context of this article, I am not clear about what is meant by "nucleates" in the above statement. Any insights are appreciated.

Here nucleation has a rather physical meaning. mTOR acts as the starting assembly point of the complex.


text:
What is the difference between a paralog and an isoform?
I am reading a journal paper about the protein kinase GSK3 and I have come across the following statement:

Although commonly referred to as isoforms, GSK3α and GSK3β are
actually paralogs, homologous proteins derived from different genes.

I am not sure what the difference is between an isoform and a paralog. I have Googled both definitions and paralogs refer to 'genes that derive from the same ancestral genes'.
Whereas isoforms refer to 'any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed'
These definitions seem quite similar to me so I was wondering if there are any significant differences between paralogs and isoforms? Any insights are appreciated.

Maybe it would help to make a bullet point list, with properties of isoforms on one list, and properties of paralogs on another, and compare them?

Please also note that "Google" is not a source, but a search engine — providing references for the definitions you are using would make it easier to evaluate those definitions and also make it clearer that you have done the expected homework before posting! In general, quotes must be referenced — this is considered good practice in scientific communication and will help other users understand the context for your quotes. Thanks!

I think the confusing thing here is that the two terms come from different fields of biology. While describing something similar, they emphasise different aspects.
The term paralog is mostly used in evolutionary biology, when one wants to find out how genes developed. Paralogs are, as you correctly found out, genes that originate from the same ancestral gene which duplicated. Thus, you would use this word when you want to emphasise the evolutionary relationship.
The term isoform on the other hand is not interested in evolutionary origin, and in fact it is not perfectly defined. This word is used when people studying the molecular biology of an organism discover that there are proteins in this organism that have a very similar amino acid sequence. Here, the interesting question is what differences in function these similar, but slightly different proteins might have. The evolutionary origin is not asked for, and thus there are two different definitions of isoforms:

Some people define isoforms only as variants of the same gene that underwent different post-transcriptional modifications (e.g. English Wikipedia), thus, paralogs would not be isoforms.

Other people also allow paralogs in addition (e.g. German Wikipedia).

In your paper, I guess that the author wants to emphasise that the proteins are not the results of different splicing but encoded by two different genes.


text:
Which terminology is better: Heterologous expression system or heterologous cell model?
I am reading a journal paper and I have read that the authors expressed the extracellular domain of the protein NCAM2 which is normally found in the brain in CHO cells. I know that this is an example of heterologous expression.
However, when referring to these CHO cells which are overexpressing NCAM2 I am wondering whether the terminology 'heterologous expression system' is more appropriate compared to 'heterologous cell model'?
Any insights are appreciated.

I would suggest that the preferable term depends on whether you are talking about the cells or talking about the modifications.
In other words, I would refer to the NCAM2 expression package as the "heterologous expression system", which is then integrated into the CHO platform in order to create a "heterologous cell model."
My reason for this suggestion is that the expression package is the core construct without which there is no expression, and that this package might potentially be transferred into other cell lines to construct other cellular models.


text:
What does bregma -4.36mm mean?
I am reading a journal paper. In this paper, they inject adeno-associated viruses into the brains of rats. In the below figure, there is something that I want to clarify:

In Figure A, I am not sure what is meant by "Bregma -4.36mm". I have read that bregma and lambda are two locations on the surface of the skull that allows for stereotactic identification of parts of the brain.

What is meant by the -4.36mm after Bregma? Any advice is appreciated.

4.36 mm anterior to (in front of) Bregma, it's the label for this coronal section of brain
If you look up a rodent brain atlas, the coordinates need some reference point; they typically use skull features, either Bregma or Lambda, for the anterior/posterior direction. They've likely taken their section, compared it to the atlas they have, and labeled it with the atlas page that looks most similar to the section.
The medial reference is usually the midline, so measured in mm left or right of midline. The dorsal ventral reference is typically a flat line between Bregma and Lambda, as well.


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Receptor tyrosine kinases: What does "tonic activation", "tonic inhibition" and "tonic brake" mean?
I am reading a journal paper about the insulin receptor (IR). The insulin receptor is a receptor tyrosine kinase, and upon ligand binding, undergoes autophosphorylation of intracellular tyrosine residues.
In this paper, they have shown that major histocompatibility class I (MHC-I) regulates the phosphorylation of the insulin receptor by inducing conformational changes in the intracellular domains of IR.
One thing that I have seen is that this paper uses the terms "tonic activation",  "tonic inhibition" and "tonic brake". For example, they have the following statements:

Insulin receptor signaling is tonically activated in MHCI-deficient
mice, and inhibiting insulin receptor signaling rescues synapse number
in these transgenic mice, suggesting that loss of MHCI relieves a
tonic brake on insulin receptor signaling to increase synapse density.

And:

Neurons with reduced cell surface MHCI are profoundly insulin
insensitive at the level of the receptor, due to ongoing tonic insulin
receptor activation.

I am not sure, in the context of receptor tyrosine kinases, what the terms tonic activation/inhibition/brake mean. I have searched online, but haven't been able to find a precise definition.
Any insights are appreciated.

Tonic in this context is the opposite of "phasic". Tonic receptor activation is slow or constant or the level of activity at "rest", whereas phasic is fast or in response to some stimulus.
When talking about an insulin receptor, if someone mentions an "increase in tonic activation" they probably mean that receptor activity (in this case, kinase activity or probability of phosphorylation) at a constant, low insulin concentration is higher. You might observe this because of a stronger affinity for insulin, or by a mechanism that allows the receptor to be active even without binding its ligand. The latter seems to be indicated if they are talking about a cell that's insulin insensitive - if the receptors are already active at rest there is nothing for the ligand to do.
A "tonic brake" would be something that inhibits or opposes the tonic activity of something; in the case of phosphorylation that could be something that either prevents phosphorylation or causes dephosphorylation.


text:
Can you use images taken at different exposure times in western blot image analysis?
I am doing Western blot data analysis where I have images from a number of experiments (where the samples in the experiments are biological/technical replicates). For each experiment, I labelled the membrane with antibodies against the same proteins of interest.
I want to combine the data from these experiments so that they are all displayed on the same graph.
I took my images at a variety of exposure times (e.g. 5 sec, 30 sec, 1 min, etc). For one protein X, I have found that the images taken at 30 seconds exposure are the best for analysis, as the bands are saturated at higher exposure times.
However, for one experiment, for the protein X labelling, I cannot use the 30 second exposure image for my analysis as there are ghost bands. I have an image taken at 5 seconds exposure which I can use instead.
I was wondering when combining data from western blot images from different experiments, for a specific protein of interest (e.g. protein X), do all the images have to be taken at the same exposure time? All the protein X images I will be using were taken at 30 seconds exposure except for one which is taken at 5 seconds exposure.
Any insights are appreciated.

Generally no, you can't directly compare them and you can't easily compare across gels. I have done many hundreds of western blots, a large proportion of which were for quantitation, and in general quantitation on western blots is difficult (because of inconsistency run to run) and not highly quantitative - a 2-fold change is detectable and probably real, but a 10% change - unlikely to be real.
If you want a real example of how to compare and observe this (works with the Bio-Rad system or others where the transfer is in the same space) - run exactly the same amount of protein on two identical gels, place them both into the same transfer tank. Compare protein stain on the membranes after transfer. The one closest to the black terminal will have stronger staining = better transfer.
However, what you can do is convert the numbers you get into a relative expression on each of the blots and then use those numbers for comparison.
For example you compare expression of protein X to a normalizer (often B-Actin) and get fold-change data out of that, or you can compare Sample X untreated to treatments A, B, C and get data out that way.

Thank you for your reply. Just to clarify, I can compare the images at different exposures, but only after normalizing the target protein signal to an internal loading control?

Correct. In fact you need to do this for every blot that you run. You cannot pool results from different membranes otherwise, even if all the conditions under which they were run and probed are the same.


text:
Why doesn't treating neurons with a high sodium solution depolarize their membranes?
I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:

We found that the medium from control slices, transduced with
AAV-CMV-LacZ, incubated in high potassium solution (+20 mM) over 24
hours contained statistically significantly higher IGF1 than that in
high sodium solution (+20 mM), consistent with our hypothesis that
IGF1 is released from pyramidal neurons in an activity-dependent
manner.

I know that increasing extracellular KCl concentrations is commonly used to depolarize neurons in experiments. I have read that the resting neuronal membrane is highly permeable to K+, and that the membrane potential is sensitive to changes in extracellular K+ concentration. Increasing extracellular K+ depolarizes membranes.
This is due to the influx of K+ ions through potassium leak channels (though neurons also have voltage-gated K+ channels, I'm assuming that they have more potassium leak channels).
Under resting conditions, there is a higher concentration of Na+ ions in the extracellular fluid compared to the cytosol of the neuron.
At rest, both the electrical and diffusion forces are driving Na+ towards the inside of the neuron (since the inside of the neuron is more negatively charged compared to the extracellular space).
In the paper, they incubated neurons for 24 hours in serum-free medium plus 20 mM NaCl.
However, increasing extracellular Na+ levels did not depolarize the neuronal membrane (unlike increasing extracellular K+ levels).
Why is this the case? I know that the neuronal membrane contains voltage-gated sodium channels and sodium leak channels. Is it because neurons have a higher number of voltage-gated sodium channels in their membranes compared to sodium leak channels?
I.e. to depolarize the membrane, the Na+ leak channels are not enough, you also need the opening of the voltage-gated Na+ channels.
Any advice is appreciated.

I would start with the Goldman equation, plug in some reasonable values and experiment with the results. Your reasoning I think comes from a common misconception that involves counting positive charges and forgetting that any solution with sodium or potassium cations comes with an equal balanced number of anions. You're never adding just sodium or potassium; if you did, you'd have enough energy in a small solution to create lightning and the charges would rebalance themselves. Membrane potentials are based on really tiny charge imbalances.
Potassium is high inside cells and low outside; if a cell is only permeable to potassium, that would mean a bit of potassium leaks out, following that concentration gradient. The result is a cell that's a bit negatively charged inside. If you increase the potassium concentration outside to equal the inside, there's no concentration gradient for those ions to travel down, so no membrane potential. If the potassium concentration outside is greater than inside, potassium ions flowing down their concentration gradient results in a positive charge inside the cell.
If there is little sodium conductance, changes in sodium don't affect the membrane potential. If you add a bunch more sodium outside, it will depolarize the cell a little bit if there's some sodium conductance, but as long as most of the conductance is for potassium it's mainly the potassium concentration gradient that matters.
Also, this experiment is just adding 20 mM additional sodium or potassium extracellularly; for potassium that may be doubling the concentration or more. For sodium it's more likely a 10-20% increase.


text:
Are there any online resources for finding the signaling pathways that two proteins both belong to?
I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these proteins belong to the mTOR signaling pathway. I know on KEGG if you type the name of a gene involved in a signaling pathway (e.g. GSK3B) in the search bar on the page showing a signaling pathway (e.g. the mTOR pathway), you can find more information about that gene. However, I was wondering if there are any resources online where you can type the names of multiple genes and you can find out the signaling pathways that all of the genes are in?
Any insights are appreciated.

I would try "gsk3" AND "AMPK" at WikiPathways .
Here are some pathways where both GSK3 and AMPK are participants, such as:

And


text:
How can you identify recessive mutations in a gene that has been disrupted by a chromosomal translocation?
I am reading a journal paper about a patient who has intellectual disability. The patient was found to have a balanced chromosomal translocation t(11;16)(q24.2;q24).
This chromosomal translocation disrupted two genes: CDH15 and KIRREL3. By using a genomic probe, the authors fine mapped the 16q24 translocation breakpoint to the second intron of CDH15. The chromosome 11 breakpoint junction sequence mapped to intron 1 of KIRREL3. Only one chromosomal copy of CDH15 and KIRREL3 were disrupted.
However, there is something about this paper that I don't fully understand. The authors state in the following:

We began by sequencing both copies of the CDH15 and KIRREL3 genes in
the patient with the translocation. No alterations were identified,
indicating that the t(11;16) translocation does not unmask a recessive
mutation in either gene.

In the above, it seems that the authors are trying to identify whether there are any recessive mutations in the CDH15 and KIRREL3 genes. I have read online that a recessive mutation is one in which both alleles must be mutant in order for the mutant phenotype of be observed.
However, since the chromosomal translocation disrupted one of the alleles for both CDH15 and KIRREL3, wouldn't you need both alleles of the CDH15/KIRREL3 genes to be intact in order to successfully identify a recessive mutation?
Any insights are appreciated.

You're reading too much into the authors statement.
The authors simply claim they have no evidence for any mutations in the working copies of the genes, and therefore not even preliminary evidence for a recessive mutation.
You're right that if they had found mutations in either gene, this wouldn't be sufficient evidence to conclude the translocation unmasks a hidden recessive mutation resulting in the given phenotype. But this is completely  moot in this case anyway.

They actually claim they have some evidence for a lack of mutations in the non-disrupted copies of the genes, which is stronger than no evidence for any mutations.

Yes agreed - I'd missed that subtlety (or really thought about it at all before)

Re:

I have read online that a recessive mutation is one in which both
alleles must be mutant in order for the mutant phenotype of be
observed.

Perhaps it's better to think of it as "all" rather than "both", as sometimes there are 3 or more alleles, and sometimes only one. When the authors write

does not unmask a recessive mutation in either gene

the unmasking refers to effective disruption of the translocation alleles, leaving only ("unmasking") one remaining non-disrupted allele in each of the two genes. If there were an obvious loss-of-function mutation in either of these alleles, that might be an explanation for the observed phenotype. They've checked to rule out this possibility.


text:
What is a gain-of-function assay in neuroscience?
I am reading this paper and I have come across the following statement:

"We sought to test whether exogenous Kirrel3 expression induces synapse formation via a gain-of-function assay... Because most CA1 neurons do not express Kirrel3, we used this in
vitro specificity to our advantage and tested whether exogenous
Kirrel3 expression in CA1 neurons could induce ectopic DG-to-CA1
synapses".

In the above statement, I am trying to figure out what is meant by a "gain-of-function assay".
I have searched online for a definition for gain-of-function, and all the search results talk about it in the context of virology, e.g. this paper states:

"Gain-of-function (GOF) research involves experimentation that aims or
is expected to (and/or, perhaps, actually does) increase the
transmissibility and/or virulence of pathogens"

I was wondering, in the context of neuroscience research, what is a gain-of-function assay? In this context, does it simply refer to the fact that the researchers overexpressed Kirrel3 in CA1 neurons (which normally do not express Kirrel3)?
Any advice is appreciated.

The function in this case is the formation of synapses.

Nothing special is meant here except the standard English meaning of these words.
The second half of the quoted passage explains what they intend to do:

Because most CA1 neurons do not express Kirrel3, we used this in vitro specificity to our advantage and tested whether exogenous Kirrel3 expression in CA1 neurons could induce ectopic DG-to-CA1 synapses

To find out what Kirrel3 does, they're going to add Kirril3 ("exogenous...expression") and see what happens, and use that to infer something about the function of Kirril3. The cells that don't normally have Kirill3 are gaining its function. The opposite approach would be to remove Kirril3 from someplace that it normally is, which you could call "loss of function" - that might be a knockout animal, RNAi, use of an antagonist or other pharmacological manipulation, etc.


text:
How can SNP arrays be used to detect deletions within a gene?
I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where they have family members with the disease-causing mutations.

For the BMC family, they found using a SNP array that a deletion of ~200 kb between intron 5 and 6 of the IL1RAPL1 gene results in an in-frame deletion of exon 6.
I am having trouble interpreting the graph in Figure D, which is the results of the SNP array analysis. Aren't SNP arrays used for detecting single nucleotide polymorphisms? I am confused because in this paper they are using a SNP array to detect a gene deletion.
Any insights are appreciated.

In the materials and methods of the paper, you will observe the following statement regarding the CNV (deletion) analysis:

CNV analysis was performed using CNV-WebStore (38).

That citation points to this paper, a software package designed to infer CNVs such as deletions from array data.
Recall that SNP arrays are essentially asking "how much DNA from the sample is sticking to each of N probes against specific sequences". The SNP is inferred by comparing how much DNA sticks to one allele vs the other allele on the array. If a specific sequence assayed by the array is simply missing, then you will observe a corresponding decrease in signal.
This is signified by panel D of the figure that you include, where signal in the pink region is dramatically lower.

The OP has asked many questions that could have been similarly answered by doing a little work — I think you are encouraging them to ask low quality questions by rewarding their lack of effort.

@tyersome perhaps a different aesthetic preference. OP has linked to a source, clearly stated their confusion, and pointed to specific items that confused them. They didn't know that "CNV" could mean "deletion", which I interpret as simple unfamiliarity with subject domain. They could probably get the answer with a ton of effort, but same could be said for many questions. I'm not a fan of question "quality" evaluation, but I'd still say it's upper 50% at least. I worry more about stifling curiosity than about encouraging low quality questions. Maybe I'm wrong; feel free to downvote.

It is possible that I'm being too strict based on the OPs failure to respond to past suggestions for improvements and frequent posting of questions that show no evidence of prior research. ——— As for downvoting, I only do that for answers that are actually bad (e.g. contain significant factual errors) and usually only if the poster fails to respond constructively to suggestions.


text:
Sister chromatids during meiosis

Sister chromatids
$A)$ Cross over during prophase I of meiosis
$B)$ separate during the first mitotic division
$C)$ are produced during $S$ phase between cell divisions
$D)$ cross over during prophase II of meiosis
$E)$ are also called homologous chromosomes

My thoughts:

$A$ is incorrect because it's nonsister chromatids that cross over
$B$ is incorrect because they separate during the second mitotic division
Don't know about choice $C$
$D$ is incorrect because there is no crossing over during Meiosis II
$E$ is incorrect because well...it's just not true

So is the answer $C$?

It is C. During S-phase the DNA of each chromosome duplicate and the two sister chromatids formed get attached by cohesin proteins. These sister chromatids separate at Anaphase-II of Meiosis.
From wikipedia:

A sister chromatid refers to either of the two identical copies (chromatids) formed by the replication of a single chromosome, with both copies joined together by a common centromere. In other words, a sister chromatid may also be said as 'one-half' of the duplicated chromosome. A full set of sister chromatids is created during the synthesis (S) phase of interphase, when all the chromosomes in a cell are replicated.