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Would the human body somehow get rid of very fine glass particle(s) that have penetrated the skin?
Assuming that a speck of glass dust has adhered to your finger and after a few days, you notice occasional discomfort when gliding your finger over surfaces (but non if you let the finger alone). It has improved somewhat but still persists lightly after approximately 10 days. If we assume that a single particle has penetrated the skin on your finger, possibly beneath the epidermis layer (meaning it can't be shed through the normal skin shedding process), are there any other ways the body can naturally remove it? Glass is inert, inorganic, and lacks direct receptors that the immune system can recognize. If it becomes encapsulated somehow, can that encapsulation eventually grow out (even under the epidermis layer)? Could it enter a blood vessel and migrate if it's very small?
Also many people say, it would be very unlikely that such things go in the blood stream and moves to the heart, but why is that the case? I mean as long as the particle is small enough, what blocks it to move with the blood stream? And if it really moves in the vessels, is there a natural way how the body could naturally eject it with time?
[This study][1] even notes, that glas particles

less than 20 μm disappeared within 1 year by becoming dissolved in animal clinical studies..

but how can the compounds constituting blood in vessels dissolve SiO2?? From laboratory work, what I know is that glas is very resistant, SiO2 is dissolvable with Hydrofluoric acid!!
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703599/#:~:text=Injected%20glass%20particles%20can%20travel,%3B%20Preston%20and%20Hegadoren%202004).

If we assume that a single particle has penetrated the skin on your finger, possibly beneath the epidermis layer (meaning it can't be shed through the normal skin shedding process), are there any other ways the body can naturally remove it? Glass is inert...

The vast majority of glass is inert, yes, but it's not sterile, and, as such, will lead to an inflammatory reaction encapsulating and eventually (if it's not deeply sub-dermal) expelling it with the outward growing epidermis and shedding keratinocytes.

Could it enter a blood vessel and migrate if it's very small?

Not likely. A shard of glass is very good at cutting/penetrating, but not very good at traveling due to its shape; it gets snagged on things. A very small shard of glass might lacerate or puncture a capillary or venule, but its shape and size would prevent most tiny shards of glass from entering the bloodstream and traveling remotely. Keep in mind that the internal diameter of an epidermal capillary is only 4–6 μm, and that of a collecting venule is 10–15 μm. While it's possible to have a shard of glass of 10μm, it would likely just injure the vessel, causing an inflammatory reaction that would wall it off and probably obstruct/close off the vessel. The only way I could think of to have glass shards in circulation would be to inject them directly into a vein, which has a comparatively large lumen.

if it really moves in the vessels, is there a natural way how the body could naturally eject it with time?

Assuming it is injected directly into a vein, it will get stuck somewhere in the circulatory system and will, through injury, cause an inflammatory response. It will get walled off, and walled off objects not directly under the skin or some surface (alveoli, gut) will just stay put, or the inflammation might cause a problem that the body deals with in another fashion.

...but how can the compounds constituting blood in vessels dissolve SiO2??

It doesn't get dissolved in blood; blood is relatively neutral. It gets dissolved over a long time in the inflammatory-induced encapsulation. How, exactly, I can't say, but I highly doubt that the pH in an environment where free radicals are produced is neutral.
I want to add that the danger from glass shards injected IV is mostly hypothetical, and has not to my knowledge been studied in vivo except once in 1947. The abstract in that paper states

This report on the effects of glass particles when injected into animals indicates that massive doses are required to produce damage to the organs examined during the study.

This is no reason not to use caution when aspirating fluids from glass ampules. Though I have never seen a problem from injecting such fluids locally (I wouldn't expect to be able to see what happens when injected into an IV as it would be remote), why not err on the side of caution? (Fyi: Rubber particles from needle insertion into rubber-stopped ampules results in loads more rubber microparticles in the fluid than glass in a single-use ampule.)
The role of macrophages in the resolution of inflammation
An In Vitro and In Vivo Study of Glass Particles in Ampules

Thanks, our body is awesome ^^ (that still sound a little bad "..walled off objects not directly under the skin or some surface (alveoli, gut) will just stay put". Just the idea that, for example, something from your childhood got trapped in your body and still is inside you and it's like a ticking bomb, maybe suddenly it causes damage somewhere out of nowhere  - scary)

@iwab - I'd say they (the walled off objects) are more like grenades with their pins pulled. The vast majority "rust" (get degraded) and are no longer able to hurt us. One of a few exceptions: tuberculosis, which can be reactivated.


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Toxicity of phaeomelanin
I have been reading an article discussing a study by Tiffany Slater and Maria McNamara in which they identified molecular  evidence of phaeomelanin in the fossil record. Slater is quoted as saying "scientists still don’t know how – or why – phaeomelanin evolved because it is toxic to animals".
I am curious what toxicity is being referred to here, since looking into it has only turned up the fact that phaeomelanin is responsible for red haired pigments in humans as well as reddish coloration in other animals, and the only mentions I've seen of toxicity are either phototoxicity that might occur when exposed to certain kinds of light, or increased susceptibility to skin damage from sunlight.
I did find a few studies in the search results whose titles were completely impenetrable to a layman such as myself, so maybe there is more information there that I wasn't able to dig out.
Is there a little more context around this statement that phaeomelanin is toxic that I am missing? I'm especially interested in information in layman's terms as I am not deeply familiar with the field of biology, but I am always curious!

They were probably misquoted in the press release. That is, the person writing the PR heard "toxicity" when they said "phototoxicity", or thought "phototoxicity" was too "jargony" for a press release and figured just "toxicity" would do fine. Unless you find the authors referring to toxicity in their own writing somewhere.

@David given that you have referenced the actual paper I would be happy to accept that as an answer. Seems like just a bad quote then.

Done that now. I could quote more papers, but the only way to get at what the authors actually meant is probably to write to them. Generally people respond.

The paper in which Slater et al. reported preservation of phaeomelanin does not include the word or root ‘toxic’, so it is difficult to know whether the quotation is correct and, if so, what was actually meant.
The Wikipedia entry for melanin states that as well as being responsible for the ‘red hair’ in certain people (who seem to survive this), phaeomelanins are concentrated in the lips, nipples, glans penis and vagina (depending on sex) of the rest of us. This suggests that phaeomelanins cannot be toxic, per se. The article does go on to say:
“Exposure of the skin to ultraviolet light increases pheomelanin content, as it does for eumelanin; but rather than absorbing light, phaeomelanin within the hair and skin reflect yellow to red light, which may increase damage from UV radiation exposure.”
However this is not the same as saying that phaeomelanin is toxic. Furthermore, the work reported was not concerned with human skin, but the colouration of feathers in the fossils of birds and feathered dinosaurs — presumably an advantageous trait, that outweighed any deleterious effects of UV radiation. This all suggests to me that a complex system for producing different variants of melanins arose in animals long before the appearance of mammals, and that there was differentiation in relation to which cells migrated to or were present in which tissues.

source: Stack Exchange

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

sort: votes


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Why did the effects of the Pleistocene extinction not significantly impact African megafauna at the end of the Ice Age?"
It seems that megafauna extinctions did not have a significant impact on African megafauna at the end of the Ice Age. Humans also lived in Africa relatively commonly during the end of the Ice Age, just as they did on other continents.

we are currently at the end of the last ice age,can you please post some links to the research you have done so far as it will help you get better answers.

Most of the large mammals went extinct in North and South America, Europe, and most parts of Asia more than 10,000 years ago, but the number of large animal species extinct  was relatively low in continental Africa
https://www.sciencedirect.com/science/article/abs/pii/S001282521300175X
https://www.researchgate.net/publication/268077616_Late_Pleistocene_of_Africa

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


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Why both with the hypothalamus in the thyroid-hormone secretion pathway?
The release of thyroid hormones into the blood is controlled by the hypothalamic-pituitary-thyroid (HPT) axis. Briefly:

Cell bodies in the paraventricular nucleus of the hypothalamus detect low circulating levels of thyroid hormone and release TRH
TRH acts on nearby anterior pituitary, releasing TSH
TSH acts on the thyroid gland, causing the release of T3 and T4.
An increase in the concentration of T3/T4 suppresses the release of both TRH and TSH.

My question is: what is the functional benefit of having both the hypothalamus and pituitary involved before the thyroid? Why not just have one or the other? It seems like a lot of energy is wasted in synthesising and releasing a second type of hormone that carries the same information as the first. Surely it would be better to just release one hormone (either TRH/TSH) in response to low T3/T4?
People often say an extra level gives you more control/opportunities for fine-tuning: but do we know what the specifics of the fine-tuning are in this case? What is TRH release sensitive to that TSH isn't or vice-versa?

"...a lot of energy is wasted in synthesising and releasing a second type of hormone that carries the same information as the first." But they are not the same. This (multiple actors & hormones) is a very common aspect of feedback loops for maintaining homeostasis. Your misperception is akin to saying, "Why does a car have both a gas pedal and a brake? Wouldn't it be more efficient to have only one pedal that moves the car when you press it, and when you don't press it, it doesn't (cause forward movement)?" It would be terribly inefficient/dangerous to have to coast to a stop all the time.


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Is kranz anatomy not a defining feature of $C_4$ plant?
In NCERT Class 11 chapter 13 it is written that

The particularly large cells around the vascular bundles of the C4 plants are called bundle sheath cells, and the leaves which have such anatomy are said to have ‘Kranz’ anatomy.

In Chapter 6 it is written for dicot leaf that

The vascular bundles are surrounded by a layer of thick walled bundle sheath cells.

So we can infer that every dicot is $C_4$ plant but when I searched on Google I found that it is not.
Where am I missing? Is the kranz anatomy not a defining feature?

Your conclusion doesn't follow logically.
Statement 1: C4 plants have photosynthetic bundle sheath cells arranged in a Kranz anatomy. (I was actually not able to find your quote in the linked chapter, maybe my mistake.)
Statement 2: Dicots have bundle sheath cells.
It does not follow that Kranz anatomy isn't a characteristic of C4, because the presence or absence of bundle sheath is not the same as Kranz anatomy.
Looking at a different educational site (I have no opinion about this site, but it seems fine):

Kranz anatomy is a specialized structure in C4 Plants where the mesophyll cells are clustered around the bundle-sheath cells in a ring-like fashion. The number of chloroplasts in the bundle-sheath cells is more than that in the mesophyll cells. This is found in C4 grasses such as maize and a few dicots.

So Kranz anatomy is not presence of bundle sheath, but rather a specific arrangement of the bundle sheath with regard to the mesophyll.
Note that C3 and C4 aren't nearly as binary or distinct as we might pretend they are- C4 has in fact arisen multiple times from C3 in evolution, so C3/4 are not even taxonomically groups, but rather grouped based on a characteristic metabolism. A few C3 species therefore seem to share some of the anatomical arrangements.
However, the anatomical arrangement is obligate for C4 plants, whereas it is a rarity in C3. See the beginning of this paper:

Kranz anatomy and C(4) vein pattern are required for C(4) biochemical functioning in C(4) plants...

In conclusion:

Don't trust your textbook completely. Seek out other sources of information. Wikipedia is quite good for this, these days.
C4 and C3 are distinguished by relatively subtle features, some of which are convoluted with the features of e.g. grasses, which can be either C3 or C4.
I found your textbook somewhat confusingly written. However, note that at no point did it make strong statements of classification about C3/4 (that I could find). Instead, it simply aimed to describe some anatomical examples. Know when you're doing description, and when you're doing classification! Ideally the book would have a direct comparison of features laid out very clearly, maybe like this, for the task of doing classification.


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What is the enzyme production rate of a single E. Coli bacterium?
Suppose an E.Coli bacterium intakes a plasmid which encodes for an enzyme, if the promoter strength is known, is is possible to predict the rate at which the enzyme is produced? Is there an equation which could model such a process?


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Is this a juvenile Middle Spotted Woodpecker?
Place: Vienna, Austria
Time: October, 8th, 2023; morning
Behaviour: Likely eating from bark

From apps and pictures, I quickly gained confidence in this being a specimen of the Middle Spotted Woodpecker. It might be my ineptitude in perceiving size over distance, but I remember this specimen as smaller than the 20cm minimum size stated by Wikipedia.
Is it perhaps a juvenile?

From a search i looks like the juvenile has weaker coloration. Size is notoriously hard to do without reference to something of known size nearby, so I would guess (and it is nothing more than a guess) adult.


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Is there a comprehensive Taxonomical ID database?
I know there are resources that outline the latest taxa, such as wikispecies or Kew Gardens. However, I have not found any resources which detail the defining features of each taxa. Are there any resources someone like me could consult?

Who are you? (because of Are there any resources someone like me could consult) Do you mean outside paywall? In any case Kew Gardens is the place (directly or indirectly it is involved). E.g. POWO has descriptions. Else you need an university library.

I'm unaffiliated with any academic or research institutions @GiacomoCatenazzi. If there's no resource outside paywall, I'm open to paying

@imrobert The latest taxonomical descriptions are in the scientific literature. There are committees for naming a number of different groups of organisms, such as the International Committee for Nomeclature of Viruses, which have literature around the naming etc. You could try those. Also, you can often enter university libraries just off the street as it were, and some will even let you subscribe to issue books etc. as an outside person.

The NCBI Taxonomy database is probably a good place to start.
You can look at their taxonomy ID resources and their FTP (linked therein) which includes large datasets.
They also link out to a number of other taxonomy resources.


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Could an animal have a developed Broca's area but no Wernicke's area?
Broca's area's function is for speech production, specifically, the control of muscular movement for speech, and Wernicke's area's function is the comprehend language or communication, Communication being the keyword here. Communication includes the physical gestures and movement of an organism such as the Waggle Dance of honey bees.
Would this mean that honeybees (although they have very small brains) wouldn't have Broca's area as they cannot produce speech but have a slightly developed Wernicke's area?

These are terms used for the very particular organization of human cortex. No animal except humans has a Broca's area or a Wernicke's area. I would leave those words out of the question.

Remember that you're asking about a creature that has had a radically different evolutionary pathway from humans. Remember also  the network-wide requirement to show your research when asking a question. Perhaps start by looking at the different structures and their functions in apes melifera, comparing them with the human brain, then take the [tour], read-up in the [help] especially about [ask], then you can [edit]  your question into shape.

Thank you, will do


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Has there ever been a recorded incident of mule deer bucks raising fawns?
I live in Colorado Springs, Colorado. According to Colorado Parks and Wildlife, there are two species of deer in CO, mule deer, and white-tailed deer. According to CPW:

There are two species of deer in Colorado. Mule deer "mulies" have rope-like tails, evenly forked antlers and extravagant ears. White-tails have smaller ears, antlers with a single main beam bearing smaller tines, and, of course, broad white tails. Mule deer bound with stiff-legged gait, the tail held down; white-tails move with a graceful lope, the flag-like tail held erect.

Given this, I am pretty sure that I saw three adult male mule deer, and one baby mule deer. The four were in a parking lot. There were two bucks that were close to, MAYBE appeared to be guarding, the baby, then a third buck came from out behind a wall, sadly limping, to follow the others away. I found a website that gives example antlers based on age. Judging by these antlers, one of the bucks protecting the baby was probably about 1.5 years old; the other buck protecting the fawn was probably about 2.5 years old; and the third, injured buck was probably 4.5 years old.
As for the fawn, I found this WikiHow page on determining a fawn's age. Judging from this, I would guess that the fawn was around 4 months old. Reason being that the fawn still had most of white spots, and I would guess that it weighed probably between 40 and 60 pounds.
As for mule deer behavior, according to the National Parks Service, mule deer:

live in a multi-generational family of related females and their offspring. Bucks older than yearlings often group together or remain solitary. In late summer and fall, mixed family groups form larger groups that stay together for protection throughout the winter. They break into smaller groups again by the next summer.

So, to be clear, it is not surprising that these three bucks were together. What is surprising is that there appeared to be no female in the area, yet there was a baby with the three bucks. Elsewhere, I have found it specifically stated that for white-tailed deer that bucks play no part in raising. I have nothing so direct relating to mule deer. Likewise, I find no direction mention of bucks playing any role in the rearing of offspring.
So, the question is, has this been viewed before? Is it a known phenomenon that male deer, take care of the offspring in the absence of a mother? Obviously this would not be possible if the fawn was still nursing, but according to the National Deer Association, fawns are usually done nursing by 3-4 months.
The other scenario I thought was possible was that one of the bucks was keeping the fawn around as a mate, but since the fawn has not yet reached sexual maturity, which according to the National Wildlife Federation doesn't happen until 18 months of age, I was not sure how likely this was. Any insight anyone could provide would be greatly appreciated.


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Movement of protons during ETC
I don't understand why protons don't move from intermembrane space into the cytoplasm during chemiosmotic synthesis of ATP.
Technically they should because their concentration is also lower in the cytoplasm and the outer mitochondrial membrane is freely permeable.

It would be helpful to provide references for the various claims in your question: protons don't move to the cytoplasm, concentration is lower in the cytoplasm, mitochondrial membrane is freely permeable. This will help to identify where specifically you are having a question.


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Does Lymph Clot?
According to my professor, lymph has the ability to clot because it contains plasma which has dissolved fibrinogen. He says that as long fibrinogen is present in a bodily fluid, it should be able to clot.
I always thought lymph would not be able to clot as it lacks the thrombocytes to initiate the coagulation pathway. Without thrombocytes the Stuart–Prower Factor would never be released into the lymph stream, and hence the coagulation cascade never occurs.
So does lymph have the ability to clot, and what would be the mechanism for the clotting of lymph?

There happens to be a relatively recent (2021) review on just this subject, also known as lymphatic thrombosis. The text is open access. Unfortunately I don't have time to write a full answer now (hence the comment), but if you're having trouble understanding the paper let me know and I'll write an answer covering the areas you have questions about.


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How is the Allee effect modeled in the presence of a highly variable carrying capacity?
Consider a rather standard model of population dynamics in the presence of a strong Allee effect:
$$ \frac{du}{dt}=u\left(1-\frac{u}{K}\right)\left(\frac{u}{A}-1\right),$$
where $u(t)$ is population, $K>0$ is carrying capacity, and $A>0$ is the Allee threshold---the population below which the species, for one reason or another, cannot survive (for example, a social species which relies on being in large groups for survival).
Now suppose that the carrying capacity is also changing in time: $K=K(t)$. Let us suppose that it is varying in a given, predetermined way due to, e.g., climate change. If $K(t)$ remains larger than $A$ for all $t$, then this model remains acceptable to study population dynamics. But if eventually, $K(t)<A$, then for $K(t)<u<A$, we actually have $\frac{du}{dt}>0$, despite $u$ being both above the carrying capacity and below the Allee threshold. Obviously, this model for population dynamics is no longer relevant in this regime.
It seems that a solution to this problem would be to use the model
$$\frac{du}{dt}=\begin{cases} u\left(1-\frac{u}{K}\right)\left(\frac{u}{A}-1\right) & K>A\\  F(u;K,A) & K\leq A,\end{cases}$$
where $F(0)=0$ and $F(u;K,A)<0$ for all $u>0$ whenever $K<A$ is chosen so that the right hand side of the above ODE is smooth or at least continuous in $K$. My questions are:

Has this been studied in the math biology literature?
If so, is a solution similar to mine proposed?
If so, what is the function $F$ that is used?

this maybe of interest https://iopscience.iop.org/article/10.1088/1757-899X/332/1/012051/pdf

@RoniSaiba That is interesting, thanks.


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FH (familial hypercholesterolemia)and LDL Receptors
I'm trying to understand how FH affects LDL receptors. Does FH affect the function of LDL receptors (mutates them) or the number of LDL receptors at the plasma membrane at any given point? Or both?


text:
Do humans produce an immune response to their own antibodies?
As far as I know, T and B cells form a part of the adaptive immune response in humans. In their early stages, these cells undergo genetic recombination to produce a diversity of antigen receptors/antibodies, before maturing in the thymus/bone. As a part of this maturation process, I understand that the body presents the lymphocytes the full set of molecules present in the body, and ones evoking an autoimmune response are eliminated. This maturation process allows lymphocytes to recognise the difference between pathogens and body cells/molecules.
My question is this:

Since the maturing lymphocytes are not exposed to
pathogen-complementary antibodies before the primary response to a
pathogen, does the body recognise the variable regions of these newly
synthesized antibodies as foreign, generating a second wave of
antibodies?

This might cause the body to produce antibodies it doesn't need to, or unnecessarily remove useful antibodies from the blood by agglutination/phagocytosis.

Are you asking about anti-antibody antibodies?

@MattDMo — Seems quite clear to me what the poster is asking. He explained his problem — asking him to put a (your) tag on it is neither required, reasonable nor helpful. If you don’t understand, say what it is you don’t understand.

My naive response it as follows.
The antigen-binding sites on an immunoglobulin are generally concave in shape. Hence I would anticipate that the antigen-binding site on immunoglobulin-1 would have difficulty binding to the antigen-binding site on immunoglobulin-2.
There may be additional considerations, such that the overall difference of the antibody from its un-mutated precursor is too slight to elicit a strong response.


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Why do (some?) flies aggregate on both sides of a window even when there is no passage between the two sides?
I've observed an interesting behavior in flies that often invade old houses. When flies accumulate on the inside of a window, I've noticed that other flies start to accumulate on the outside of the same window. Interestingly, this occurs even when there's no passage for air or pheromones between the inside and outside.
To eliminate some possibilities:

The inside area is dark, and the flies are attracted to the external light, so light attraction for the external flies can be ruled out.
The use of an aerial insecticide affects only the flies on the inside, confirming that there's no passage for air or pheromones between the two sides.

Is there any biological explanation for why flies would behave this way?

Aerosol insecticides are only effective at quite high concentrations. There could easily still be passage of air/scent/pheromones from one side to the other without reaching the concentrations effective to kill on the opposite side. Dilution will play a big role here. Small amounts leaking through will be diluted enough to be ineffective, but something like pheromones or other things insects are sensitive to at very low concentrations might still be detectable.

I think the answer is a compound statistical effect. First, both window sides correlate with the overall density of flies in the area, 2nd, you only notice an accumulation of flies above a certain threshold (total number), which makes it likely that there are flies on both sides.


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AP2 Binding to LDL Receptor
Is Ap2 always bound to the LDL receptor and only binds clathrin when it detects a change in the LDL receptor, i.e. LDL binds?


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What is the known safety data on phenoxyethanol?
I came across this news article stating that a certain skincare product was declared by FDA to be unsafe for infants due to having chlorphenesin and phenoxyethanol. However, I have been unable to find any claim that phenoxyethanol contributed to any concrete harmful effect at the concentration used in that product. In particular:
  1. I could not find any actual account of harm to infants, and FDA did not report any at that time.
  2. Phenoxyethanol is widely used in many other skincare products with no reports of side effects.
I am aware that chlorphenesin affects the central nervous system, and that seems to be sufficient to explain the FDA warning not to use that product. So why did FDA mention phenoxyethanol as well? What scientific evidence were they relying on, or what biological effect does phenoxyethanol have on infants that can contribute to a risk of "respiratory distress or vomiting and diarrhea in infants" as stated by FDA?

Both of your links are to news articles, not to anything directly from the FDA.

@BryanKrause: I couldn't find the FDA statement in a form I could access, so I did the next-best.

The FDA statement on prohibied and restriced ingredients in cosmetics is here, and it makes clear the limited authority this body has in the US. There is a list of prohibited or restricted ingredients that does not include phenoxyethanol, so it seems strange to me that they would have made a statement about this. But I am neither a US citizen or a toxicologist. A Google search revealed that its use in the EU and Japan is restricted, and there are many articles about whether  it is toxic.

@David: Thanks for finding that! I believe that there may have been unpublished reports of adverse effects on infants of mothers using that product, and FDA decided that the most likely culprits were chlorphenesin and phenoxyethanol in combination, but the problem I have is that I can't find any data at all on how phenoxyethanol contributes to this. I too find this reported statement strange. However it's nearly impossible for both NBC and Reuters to make it up, since otherwise FDA would have easily sued them or at least issued a counter-claim.

@user21820 The health numeral of the fire diamond for 2-phenoxyethanol is a 3 (4 being the most dangerous possible categorization). The SDS from Fischer Scientific lists the LD50 (median lethal dose) in rats at 1850 mg/kg. Wikipedia mentions it is used as a preservative in pharmaceutical products, so my guess would be trace amounts of it under acute conditions would not be particularly harmful. Cyanide and Mercury salts for instance are extremely toxic but you'll still find trace amounts of them in many medications....

@user21820 That being said, if the FDA released a statement advising against administering the product to infants then my advice would be to listen to them. If the statement was restricted to infants then it suggests that an adult would need to be less cautious.

@DavidReed: Thanks for that information! My concern is that phenoxyethanol is used in many skincare products, but the FDA statement only concerns one specific product that gets ingested by infants. So I have no idea about its toxicity in other use cases including sunscreens. Where can I find the Fischer Scientific data that you cited? And do you know about toxicity for long-term daily exposure? By the way, I don't think cyanide and mercury are used in scientifically backed medicines.

@user81820 They are used in the manufacturing process as they are important reagents in organic chemistry. For instance, cyanide is used in the synthesis of ambien. It's impossible to achieve a perfect separation of reactants and products. What matters is that they are within the acceptable tolerance limits.

@DavidReed: Ok, but I don't think phenoxyethanol is merely an intermediate in these skincare products, as it is use as an active ingredient. Anyway do you have answers to the two questions I posed in my last comment? Thanks!

https://www.fishersci.com/store/msds?partNumber=AC130242500&productDescription=2-PHENOXYETHANOL%2C+99%25+250ML&vendorId=VN00032119&countryCode=US&language=en and https://pubmed.ncbi.nlm.nih.gov/31588615/

@DavidReed: Thanks for that! I think in my case (skincare products), the relevant data would be LD50 for dermal contact. I surmise that phenoxyethanol is used at less than 1% concentration in skincare products from reputable brands, and the relevant part of the JEADV article you just cited is "the haematological effects reported in the developmental study conducted in rabbits were observed at a dose approximately 200-fold higher than that used by consumers". Correct?


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Method to detect Protein aggregation
I have a specific human protein that was purified from E. coli.

This protein was tagged with MBP and diluted in an elution buffer.
This protein has a tendency to aggregate, and when it does, it can induce the nearest protein to be aggregated too.
We believe that tagging MBP prevents this protein from aggregating, so that when MBP is cut off from the protein, it will easily aggregate.
I want to confirm this. However, I am not sure how to check if the protein is aggregating or not.

I would like to know whether my protein is aggregated, what is the best method to detect protein aggregation?. I would really appreciate if anyone can give me the reference or protocol.

What do you mean by "my protein is aggregated"? In a sample preparation? In cells?

Welcome to SE Biology. We are happy to try to assist people with biological problems, but we can only do that if we know what the problem is. So, first, please finish reading the [Tour] (we know you haven’t) and then read the Help on asking good questions. You are so close to your own problem that you think more experienced scientists must know what it’s all about. We haven’t a clue! What is your protein? Is it pure, in a mixture, in a cell or what? Why do you think it might be aggregated? Tell us what you are doing and what you observe. Only then can we help you

Thank you so much.  Let me provide some background: I have a specific type of human protein that was purified from E. coli. This protein was tagged with MBP and diluted in an elution buffer. This protein has a tendency to aggregate, and when it does, it can induce the nearest protein to be aggregated too. We believe that tagging MBP prevents this protein from aggregating, so that when MBP is cut off from the protein, it will easily aggregate. I want to confirm this. However, I am not sure how to check if the protein is aggregating or not.  If anyone has any suggestions, please let me know.

@Sketsawy you need to tag people with the "@" to let them know that you are talking to them. Also, the information that you've provided in your comment would be very helpful included directly in the question, so I'm going to edit your question to include it there.

I started writing a comment but it got out of hand so I'm just doing an answer.
There are many many papers that describe methods for detecting aggregation. Below is a semi-random sample.
What exactly is the roadblock that you are encountering? Which of these kinds of methods have you tried? Are you working in live cells or only in vitro? Are you open to putting your protein into yeast?

Removing MBP tags from proteins
Methods in pharma for detecting aggregation (older).
Methods in biomanufacturing for detecting/managing aggregation.
Papers with informative methods sections for testing aggregation (mostly in yeast, which is probably the easiest system for studying prions):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980781/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980676/

https://www.sciencedirect.com/science/article/pii/S0076687906120121

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066306/

https://www.sciencedirect.com/science/article/pii/S1046202306000594

Visualizing aggregates in live cells
Microscopy of aggregates in live cells


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Other than lignification how does secondary xylem attain its stiffness then balance that with remaining living processes?
I read in a textbook that the vascular cambium creates secondary xylem to its inside and outside. These cells, formerly conducting water, dry out and harden. Their cell walls get lignified creating wood, particularly in the cylinder between cork cambium and vascular cambium. This is actually three related questions.

Is a force exerted on the secondary xylem by the vascular cambium? A force that compresses these cells?

If "yes" to number one, how can soft tissues that make up the vascular cambium press so hard on the previous layers of harder (dried out) secondary xykem? Are concentric cylinders staggered so hardness increases gradually, with a stiffer already compressed cylinder exerting more force than newer secondary xylem cylinders?

The secondary xylem (cortex) is living. Medullary rays traverse them and it is adjacent to the living cork cambium. As lignin is deposited in its cell walls, what biochemical processes continue to occur? The hard walls would deter intercellular transport but the cells must continue interacting.

No i don't think cells harden because dividing cells apply force on them, if that was true I think it would make more sense for a tree to compress every time more an more as it divides in vascular cambium. What happensn is that it grows in diametar, I think only a few cells of that mass simply can't act on a much more massive body like that. A small ball will hardly move a big wall( given it is not travelling at speed of space shuttle:). Even if that was the case, I still don't see which force would be behing it, there is no gravity in lateral direction. If increasing diametar would provide more an more preassure on the inside than wider trees would have stiffer and stronger middle than tiny ones. And I don't think that is the case.

I am not an expert in botany, this is only my logic.

I couldn't understand how soft tissue would exert such a pressure either.

That leaves the other questions: what hardens the xylem other than lignin? The cortex is considered alive - how do cellular processes continue when the cell wall is stiff (how do molecules pass through)? The cytoplasm region must still be flexible. It's hard to imagine a soft inside of the cell with a hard cell wall - so hard that a human can't budge even a medium size tree.

It is hard to imagine but, cortex is alive. Just like bone tissue, it can be considered alive and yet it is hard as hell. It is like a castle, strong thick walls yet people can live within it just as well


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Why does the axillary nerve have root value of C5 and C6 only and not C5, C6, C7, C8 and T1?
Posterior cord is formed by the posterior division of all the three trunks, so shouldn't the root value be all the spinal nerves of the brachial plexus which is the case for radial nerve?

It would be helpful to provide sources/references that support your question. Why do you think the axillary nerve has fibers from C7, C8, and T1, in addition to C5 and C6?


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Why are my bacterial smears disappearing?
I'm trying to inspect simple stained bacterial smears. But my smear suddenly disappears after a successful inspection with the oil immersion lenses.
The background can become too red (the color of the stain) and the oil residue coming from the oil immersion objective when it's wiped, is red colored.

Red background
Usual background

Also when I try to wipe the oil from the slide, the smear is removed, even with a gentle wipe.
I'm suspecting three possible causes, which may include dependent causes:

The immersion oil I use makes the smear easy to wipe:
I don't have a dropper that releases just a small drop, but I have used another oil with the same type of dropper that releases more than the needed quantity and it didn't wipe my smear.

The back-and-forth movement that eliminates air bubbles: I hear the spring sound, is this correct?

Smear fixation may not be adequate: could it be possible that the smear can be fixed in an incomplete way so that it resists being wiped from the staining procedure, but not from further manipulation?

My specifications

Immersion oil: Non-drying, non-hardening Cedarwood oil

Stain: Carbol fuchsin (20%)

Smear fixation: heat fixation by passing the slide three times through the flame

Anyone else concerned about the fact it says "Ceder wood oil" instead of "Cedar wood oil"? (There doesn't appear to be a "Ceder Grove, N.J.") Also, "Conforms to ISO-8036/1 Specofication (sic)"?   -- I might recommend trying an immersion oil from a reputable supplier, one whose quality control for materials is reflected in the labeling.

@R.M. A quick image search on the internet appears to indicate that the labeling shown here is trying to imitate the general appearance of labels on genuine products of Cargille Laboratories in Cedar Grove, NJ.

@R.M. - That in itself is an answer. Their slides are mucking up because this is a knockoff product that's probably contaminated or simply contains something like cheap vegetable oil.

Bacteriological smears are a one-and-done scenario. Very few of them are intended for repeat use. Basically, all you can expect is that you observe it and then discard the slide. Wiping the oil off will also remove the bacteria as they are not firmly fixed to the slide, despite the "heat fixation" name, as I will explain below.
If you do want to reuse a slide I would recommend that you get a coverslip and cover your slides, sealing the edges with nail-polish or glue will make these more or less permanent. However, this is tricky because you may need to change your high power objective lens (assuming 100x objective) to cope with the thickness of the coverslip. To do this you will need to look for a longer focal-length on the objective lens. Some higher-quality lenses come with an adjuster for focal lengths.
Heat fixation in bacteriological slides is about two things. Primarily, the heating allows drying out of the specimen, which adheres it to the slide enough that it can be further manipulated. For most stains, simply drying the slide without heating will work perfectly well for adherence. Secondarily, it is about killing the bacteria. This is the fixation part and the name is a hang-over from classical biology where chemicals such as formaldehyde or ethanol were used to "fix" the specimen in an unchanging state (fixed state as opposed to changing).
It should be noted that even with passing the slide through the flame 3x, the slide rarely reaches above about 50 C, which isn't really enough to kill most bacterial species with certainty (food safety tells us at least 65 C for 10 min...), and is certainly not enough for tough bacteria like Mycobacterium species - it's the dehydration from the heating that does most of the killing. In addition, most stains have a fixative of some sort in them, usually ethanol, which will work against most of the common bacterial species (though also not Mycobacterium), again by dehydration of the bacterium, but also protein denaturation.

With the colour coming off, I think you have two problems:
First - staining, make sure that you wash the slide with decolourizer until there is no residual red from the Fuchsin. It's a delicate balance, so takes some experience to get it right. Also, make sure your slide is completely dry after your counterstain and wash step.
Second - I think that cedarwood oil is the wrong choice for immersion oil here. The cedrol and cedrene components strike me as chemically similar to phenol, which is one of the major components of Carbol Fuchsin (Ziehl-Neelson) stain (PDF with components). This means it might well solubilize the stain.
Cedar oil also hardens on the lenses and can easily dissolve the glues that hold the lens together, so be very careful using it with modern lenses.

I'm not doing an acid-fast stain but rather a simple stain if that would make a difference.

@FreezingSoul I don't know off the top of my head, but I suspect you won't get proper clearance of the slide without the acid wash, so will always have some residual red that might come off in the immersion oil.


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Is it true to say neurons like to be stimulated?
I believe I have heard people saying "Neurons like to be stimulated". Although I know stimulating the brain promotes more neurons and connections growth, but does stimulating a neuron benefit the neuron itself? Or on the contrary, if a neuron is not stimulated long enough, does that cause any harm to itself? And then if that is true, can I say that limiting oneself to a narrow spectrum of stimuli is not good in general, considering there are other parts of the neural network not stimulated enough equally?

There's some anthropomorphism here, which might be unhelpful to your question, and then there is a huge generalization, which technically does not follow the first question. What's good for the goose here (the neuron) isn't necessarily good for the gander (the brain), as they are not equal.

I think it's necessary to clarify what someone means when they say this before evaluating whether it is true or not. Too many possible meanings to evaluate otherwise.


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Searching for reference regarding the impact of famine on a woman's grandchildren
I was once told that if a woman experiences a famine, her grandchildren will show epigenetic changes because the egg that the intervening mother came from also experienced the famine.
In other words, the grandchild would be more susceptible to obesity, due to the grandmother's nutritional environment, even though the famine might have been 40-50 years distant.
However, I can't remember where I heard this, and could not locate a reference.

Welcome to Biology StackExchange. Take a look at Transgenerational epigenetic inheritance. Plenty of explanations and references.

Here's an article in Science about the phenomenon:
https://www.science.org/content/article/moms-environment-during-pregnancy-can-affect-her-grandchildren
It references a variety of different studies, not sure which you are most familiar with, but they include a population study of Dutch children whose grandmothers were pregnant with their mothers in 1944 and some more mechanistic studies in mice.


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Why can mitochondria make only 34 molecules (rather than 61 molecules) of ATP ？
Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from the oxidation in the electron transfer system of NADH and FADH2 generated by oxidation of glucose in glycolysis and the tricarboxylic acid cycle?
The electron transfer system oxidizes 10 mol of NADH and 2 mol of FADH2 obtained from glycolyses and the tricarboxylic acid cycle, and up to 34 mol of ATP can be obtained by the electron transfer system alone. Complexes I and II take energy from NADH and FADH2, and complexes I, III, and IV are also proton pumps that pump hydrogen ions against a concentration gradient. The reactions carried out by the four enzymes, known as complexes I–IV, and their Gibbs free energies are as follows;

Complex I: (NADH + H+ + CoQ → NAD+ + CoQH2 — ΔG˚′(1) = -71 kJ/mol)×10
Complex Ⅱ： (FADH2 + succinic acid + CoQ → FAD + CoQH2 + Fumaric acid — ΔG˚′(2) =-2.9 kJ/mol)×2
Complex Ⅲ：(CoQH2 + 2 cyt c(Fe3+) → CoQ + 2
cyt c(Fe2+) + 2H+ — ΔG˚′(3) =   -41 kJ/moll)×12
Complex Ⅳ：(4 cyt
c(Fe2+) + O2 + 4H+ → 4 cyt c(Fe3+) + 2H2O — ΔG˚′(4) =  -110 kJ/mol)×6

Therefore, the ‘net’ reaction, from complex I–IV, is as follows:
10 NADH + 2 FADH2 + 6 O2+ 2 Succinic acid → 12 H2O + 10 NAD + 2 FAD + 2 Fumaric acid — ΔG˚′ (total)
Here,
ΔGo' (total)= 10ΔGo'(1) +  2Go'(2) + 12ΔGo'(3) +  6ΔGo'(4)
= 10*(-71) +  2*(-2.9) + 12*(-41) +  6*(-110) kJ/mol
= -1867.8  kJ/mol
The following reactions then occurs in complex V using the above ΔG˚′ (total);
ADP + Pi → ATP , ΔGo'(5)=  -30.5 kJ/mol
Simply considering abovementioned only,  the amount of ATP that can be generated from the energy derived from a single molecule of glucose entering the electron transfer system via NADH or FADH2 is as follows;
-1867.8/-30.5 =61.2 ATPs
So, my question is as folilows;

Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from a single molecule of glucose in the electron transfer system?

I would like to ask this question especially from the perspective of Gibbs energy balance (in terms of energy loss).
Related

https://chemistry.stackexchange.com/questions/72457/why-delta-g-nfe-and-not-f-integraldne/176835#176835
How many molecules of ATP are actually produced in aerobic respiration?

The fundamental flaw in the poster’s logic is the implicit supposition that if a mitochondrial (or other) oxidation reaction has a standard Gibbs Free Energy change of -x kJ/mol, all of that can be used to drive the reaction ADP + Pi → ATP; and that one can just divide x by 30.5 to find how much ATP is produced.
One cannot.
One needs to consider the actual physico-chemical reactions of the oxidations and the subsequent phosphorylations of ADP. When you do this you will find that much of the free energy of the oxidation reactions is not used to drive a chemical reaction, but is converted into (‘lost’, in the terms of the poster) heat energy.
Even if one considers the simplest situation, ‘substrate level’ phosphorylations — reactions in which the oxidation of NAD+ is coupled directly to the synthesis of ATP or GTP — there is no logical reason why the free energy change should be zero. The oxidation reaction may well have a –ΔG˚′ of greater absolute magnitude than the +ΔG˚′ required to synthesize NTP, and the difference will be released as heat. This is indeed the case for the succinyl-CoA synthetase reaction which generates GTP in the tricarboxylic acid cycle.
However the mitochondrial oxidation reactions are not coupled directly to generation of ATP. They are used to pump protons across a membrane, and to generate a membrane potential, which is the basis of the proton-motive force used to drive ATP synthetase and synthesize ATP. There is no reason to expect that all the free energy from the oxidation reactions will be conserved as a proton gradient and membrane potential, and good reason to suppose that it will not.


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How badly will warmer air affect birds' ability to migrate long distances?
I recently read about how warmer air decreases lift for airplanes.
I wondered whether birds would also experience reduced lift, and whether that might make it harder for them to migrate long distances. And might that endanger some bird species that take long, arduous migration routes?

I suppose it is (sometimes) exactly the same for birds as for planes.
[same]
Newton's second law tells us that Force = mass times acceleration, and Newton's 3rd law tells us that for every force there is an equal and opposite reaction. Because both airline and bird wings are fixed size, they interact with a fixed volume of air, meaning if the air is less dense, they will get less force against their wings as they push the air down.  Thus they generate less lift.
[not same]
However, unlike planes, birds don't use jet engines to suck in air (which will be less dense) to generate their forward velocity at takeoff.  Instead they usually run on the ground or jump.  Their ability to run on the ground or jump should not be affected by air density.  I believe for most birds, taking off is the limiting factor, not sustaining flight once airborne.  Thus, birds should be able to continue flying.
But, once airborne, will hotter temperatures affect their migration? Probably not too much as the CNN article you link to says for planes the effect is 1% for 3 degrees celcius, meaning if the earth warms 3 degrees, birds will only have to expend 1% more energy.  Now it could get worse in some areas, but birds can also move, and if a wind pattern changes, they can just fly to a different area where the wind pattern still exists, so hopefully they'll be alright.
But I don't know enough about bird behavior to say for certain.  But from a physics perspective, there's no reason to suspect birds have it worse than planes in terms of what their wings can do with the air, so if planes lose 1% energy for every 3 degrees warming, birds should lose even less than 1% energy.  Hopefully the planet won't warm much more than 3 degrees. :)
As a final note, once the bird is flying high in the sky, the air temperature should no longer be scorching like it is at ground level, so even though the ground might be 20 degrees hotter, the higher up air probably won't be that much hotter, and remember that near the ground at takeoff, birds get their power from their legs, not wings.


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Perform CHIP-qPCR to detect Myc
I use Panobinostat (HDAC inhibitor) to treat the GBM cells. I saw Myc protein level go down but not mRNA level. Panobinostat is known to inhibit HDAC1 and HDAC2. HDAC2 gene belongs to the histone deacetylase class of enzymes responsible for the removal of acetyl groups from lysine residues at the N-terminal region of the core histones.
I performed HDAC2-CHIP-qPCR in GBM cells treated with DMSO or Panobinostat. When I run CHIP-qPCR for Myc promoter region. I didnt observe any changes in Myc expression level.

A person asked me that Panobinostat reduce HDAC2. I immunoprecipitated HDAC2, why I didnt observe a reduction of Myc DNA level.

I answered that the dose for Panobinostat is not sufficient for the dissociation between HDAC2 and Myc promoter region so there is no change in Myc DNA level (I also did not observe a reduction of mRNA level upon Panobinostat treatment).

That person asked why the western blot showed a reduction of HDAC2? If HDAC2 is down the Myc DNA level must be down. It means that the HDAC2 antibody is not specific or I did something wrong.

I answered that the HDAC2 protein could be reduced in the cytoplasm but not in the histon.
Does my answers correct?


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What is this insect looking like a wasp or an ant?
It looks like a black wasp or big ant with wings. It produces no noise. It mostly sits at one place on the wall, does not move. The young (or another gender) form has unproportionally long back legs, making it look like a spider.
It has big head with big eyes.

Please include the size, location and weather details

These look like flies to me, but I'm not going to go any further than that.  Hopefully someone with more knowledge (and some idea of the location of these images..) will be able to get more specific.

To me they look like wasps.

These are two different kind of insects:
First insect
There is one pair of translucent wings (admittedly, the number of wing pairs is not visible from the photo), what tells us it must be some kind of fly (Diptera).
Further, the antenna is rather short, from what we can deduce it must be a brachyceran fly.
Even further, it has three segments, so we can conclude it is a member of the family "soldier flies" (Stratiomyidae).
A friend (a dipterologist), upon seeing the photo, immediately argued it must be a "black soldier fly (Hermetia illucens), a meanwhile cosmopolitan species that has gained economic importance in organic recycling.

Second insect
This one is much trickier, I think.
It does look like a shore bug (Saldidae): the large eyes, slender and long antenna and legs, the flat and oval body - everything fits.
But shore bugs are tightly bound to their habitats (shores of all kinds of waterbodies). And at least in Europe, it is very unlikely (although not impossible) to find one inside a building.
Also, shore bugs are very agile and are fast runners, jumpers and flyers - what contradicts the OP's description ("It mostly sits [...], does not move").

I have also seet a variant of the first insect but much bigger (about 1.5x).

This is a holometabolous insect, meaning with a complete metamorphosis. Therefore the second picture is not a young, a young would be a larva or a nymph, i.e., it would look nothing like a smaller version of an adult.
The insect on the second picture, if it is indeed the same species, is likely the male.


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Color of Tyranosaurus Rex
What is the color of T Rex. popularly in movies like Jurrasic Park, they display the T rex as green, but is that true. Evidence suggests that T Rex was covered by feathers but recent Studies suggest that it is not the case rather like reptiles they were covered with scaly skin. The color, is basically the wavelength not absorbed by the melanin, and reflected off it like our skin, synthesized in special melanosomes. studies suggest ball shaped melanosomes are containing red melanin and sausage shaped contain black. By studying the shapes of these melanosomes scientists estimated the color of the scales being reddish brown, but is that true, if so, why do most herbivores and many carnivores being greenish and T Rex being brownish?
Thanks in advanced and please don't  mind if my question is silly


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What type of joint is sternoclavicular joint?
I know it is synovial and saddle shaped
It is complex as it involves a articular disc
But I want to know whether it is simple joint ( 2 bones ) or complex joint (more than 2 bones ) as it involves costoclavicular ligament which attaches to the costal cartilage of first rib?


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What is the exact definition of the term 'trait'?
A trait is a characteristic shown by an organism.
For example a Tt plant would show the 'tallness' trait.
It seems to me that, by analogy, sickle cell anaemia (SCA) carriers should show the 'normal' trait, but I have found on various sites that SCA carriers are described as having the sickle cell trait because as carriers they can pass the mutated gene to their children.
This doesn't make sense to me, as showing a trait and passing it to the next generation are two different things. We do not say a Tt plant has the dwarfness trait just because it can pass it to the next generation.
So what is the exact definition of the term 'trait'?

Trait is used to mean alleles  multiple times, no?

I think you are interested in the difference between phenotype and genotype.

@David is there any official book for biological definitions just like we have IUPAC goldbook for definitions of chemistry?

@HarjotDhillon — In a word, no. Biochemists and Molecular Biologists have a joint Nomenclature Commission with IUPAC, which is available on a 20th century website the design of which is unbelievably awful. There are various specialist bodies for taxonomical nomenclature in various fields, but you won't find terms like 'trait' defined anywhere but textbooks. At least not to my knowledge. It's a bit of a moving target anyway, and convention emerges from the usage of the 'leaders' in the fields, without anyone trying to codify it.

I think the confusion stems from the word "trait" being used differently on the website you link, from how we use it in genetics.  From the website:

A trait is something unique about you, like your hair or eye color. Traits are passed down (inherited) from your parents. Genes carry information that makes a trait. People with sickle cell trait (SCT) have 1 sickle cell gene and 1 normal gene.
Having sickle cell trait is not the same as having sickle cell disease (SCD).
Sickle cell trait means you could pass sickle cell trait or disease to your children.

Thus, we see SCT, Sickle Cell Trait, is a specific condition someone can have, just like they could have SCD, sickle cell disease, or nothing at all.
I don't think the use of the word "trait" has much to do with how we use it in biology.  You are right that in biology, we usually use the word "trait" interchangeably with the word "phenotype" whereas in the website you link, it explains "Sickle Cell Trait" is the name of a heterozygous genotype for sickle cell.


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Ames Assay Confusion: Aren't the odds of spontaneous revertants too low to be able to accurately test the mutagenicity of certain compounds?
I am a student conducting a test with the Ames Assay.   This assay uses a strain of bacteria that has a mutation in an amino acid synthesizing operon, which doesn't allow it to synthesize its protein.  The idea of the assay states that if an exposed chemical has mutagenic properties, the bacteria will revert back to the wild type.
If I have a test chemical, what are the odds that, if the    chemical is actually mutagenic, the bacteria will actually revert back to the wild type, instead of having something else be mutated?  Aren't there so many other base pairs of DNA to be mutated, that the odds of the mutation be reversed  are little to none?  Is there something about the specific gene that makes that  area more prone  to a mutation?
As a related question, are there some  chemicals that have a  higher likelihood of mutating certain genes over others, or do all of the genes in a genome have the same probability of being mutated?


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How does one determine what sequencing coverage/depth to use?
In the context of rare diseases, what sequencing coverage will be sufficient to detect the mutated loci (for eg. SMN1, SMN2 CNVs, gene SNPS, INDELs etc) ? How does this relate to statistics and how one is confident of the results? Most commercial sequencing services are marketed as promising 95-99% at 20-30X. My question would be, how we arrive at these values. For example, why is 99% at 20X ideal and how are values derived mathematically?

"20-30x" sounds like depth rather than coverage...

OK, looks better. So, what do you think the % and X values mean in terms of sequencing?

% means the total coverage across all bases, while X is how much each base is sequenced.

Almost there. X is depth - number of times a base was covered by a sequence. So, what might those values mean in terms of sequence reliability?

Of course, I know that the higher the depth, the more reliable the sequence. I'm asking how the value itself is determined, whether 20X, 30X... 100X etc. How is it derived mathematically/statistically? Is it by calculating the power of the assay, confidence levels, binomial probability of errors, or...?

It's literally a count of the number of aligned sequences that cover that spot in the sequence. If you have 1 sequence that covers a base it is 1X, 10 = 10X etc. See: Wikipedia on sequence coverage

My question is, so why do some labs set the metric as 99% coverage at 20X? why would a benchmark of 20X be preferable over 10X for example? I'm not asking what 20X ,30X...vs 100X means, but the thought process behind setting this as a sequencing QC metric, and how it this is determined through statistics. Hope you get my question.

I don't know for sure as it will depend on the individual lab and their purpose, but 99% is about all you can achieve reasonably without repeating sequencing ($$$) and 20X coverage is enough to have reasonable certainty on a base - it's 5% error after all, which is the usual p value of 0.05 in statistics.


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After interphase,there are 2 chromatids in each chromosome so how many total chromosomes are there in a cell
Before interphase each chromosome now has 1 chromatid. After interphase  each chromosome replicates and has 2 chromatids so how many chromosomes are there totally.


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Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests?
Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests (e.g. catalase, oxidase & gram stain)?

"Slide Test Method
Obtain a pure culture of the organism to be tested. Using an inoculating needle or applicator stick, pick a well-isolated colony
and transfer to a glass slide. add 1 or 2 drops of the Catalase
Reagent to the smear." Manual of Liofilchem® - Catalase Reagent

"Test isolates should be in pure culture and 18-24  hours old" Manual
of Oxichrome Reagent, Thermo Fisher Scientific

"A pure culture is required for identification tests. However, the
tests can be applied directly to colonies removed from isolation
plates if there are many suspect colonies that have been correctly
isolated. In the latter case, the test must be repeated after
reinoculation of the colonies tested, to obtain a pure culture.
Identification tests are as follows: appearance and motility, if
living: Gram staining, oxidase test and catalase test." Manual of Standards for Diagnostic Tests and Vaccines: Lists A and B Diseases of Mammals, Birds and Bees, Chapter 2.3.2 Bovine genital campylobacteriosis [Campylobacter fetus]

Is it a concidence that the author stated the usability of these tests with non pure cultures when the concerned organism, Campylobacter fetus, has a positive result in all of  them?
What i mean, the author could be indirectly implying that these tests in such condition are useful only for pre-screening purposes (i.e an experimental positive result with an expected positive result should be interpreted that at least one organism from the tested growth is positive, where an experimental positive result with an expected negative result doesn't necessarily mean that our subject organism is not there)?
I want to understand correctly why a non-pure culture with discrete subject colonies can be bad for atleast some diagnostic procedures. Is it because "Where there is one rat, there are more"? In other words, a fast-growing thus apparent type of contaminant means that there could be more slow-growing thus inapparent types of contaminants, which can be within discrete colonies of the subject organism.
If this is the correct reason, then it sounds to be a problem for highly sensitive molecular methods (e.g. PCR) and culture-based tests (e.g. OF-glucose test & simmon's citrate test) where the number of contaminating cells will be magnified, but not for rapid phenotypic tests as those mentioned, which are relatively insensitive and on-spot.
If this wasn't just a theoretical concern that was commonly exaggerated, then this leaves Gram-negative selective media as MacConkey, not usable for such tests even in pure culture, as:

In obtaining a pure culture, it is important to realize that the
selection of a single colony from a plate does not necessarily assure
purity. This is especially true if selective media are used; live but
non-growing contaminants may often be present in or near a colony and
can be subcultured along with the chosen organism. Krieg, N.R. (2005). Identification of Procaryotes. In: Brenner, D.J., Krieg, N.R., Staley, J.T., Garrity, G.M. (eds) Bergey’s Manual® of Systematic Bacteriology. Springer, Boston, MA. https://doi.org/10.1007/0-387-28021-9_5

A quick comment - the tests in the title are not definitive tests. Definitive tests are the ones that make your presumptive test(s) certain.

I'm not speaking about presumptive or definitive identification, anyway it's still not the best way to reflect what I mean, it's going to be "reliable".

Isn't the answer in the quote you provided from Manual of Standards for Diagnostic Tests and Vaccines? The results won't be reliable.
Having pure cultures by re-streaking the ones you suspect and only using single, isolated colonies for subsequent tests is the very foundation of diagnostic microbiology.
The same quote is specifically talking about campylobateriosis, so mentions those tests because those are the ones to perform on that organism. It is also talking about abundance - if you see lots of colonies of one organism, then that could well be the problem, and should be treated as a presumptive diagnosis. 1 rat = more rats in your analogy.
Of course you can perform (as in, you can physically do them) the tests on non-pure cultures, but they should be repeated on a pure culture to be certain of any result obtained. The risk you run is that an impure culture might give you a result that is not the correct one for the organism you expect, or is misleading. This is especially so if there is more than one organism or strain in the colony being tested. An example of this might be if you have Streptococcus agalactiae and Streptococcus pyogenes in the same culture (both B-hemolytic) - these two will be indistinguishable by Gram stain, but not by further biochemical testing, where a mixed colony would give you both group A and group B Lancefield typing.
Your quote from Bergey's Manual is talking about selection from impure colonies on an early plate or on a selective plate. Of course you can sub-culture contaminants along with your target organism, but the selection of isolated, single colonies lowers this chance, and dilution applies; the more times you streak out, the more likely you are to have a pure culture. The risk of carrying over contaminants by culturing from selective media is that you can't see the contaminant when you select your colony because the contaminant hasn't grown, but is there in a non-replicative state, whereas you are more likely to visually see this contaminant on a non-selective plate as it will grow happily alongside your target organism.
PCR, depending on the primer target(s), is highly specific and usually very sensitive for identification, so shouldn't give an ambiguous or incorrect result, even on a contaminated culture. However, this is dependent on exactly which PCR test used and how the results are presented. For example you might have a multiplex test that detects Pathogen A and Non-pathogen B. Both are common on the body, grow on your medium, and are similar in appearance. You select a colony, which just so happens has more B than A, so the PCR might show up as B present and background A, when A is actually the one causing the problem. Pure culture would give you the correct result.
For any test used in the medical field (including veterinary) will be required to adhere to some form of standardization (ISO etc.) and accreditation for its purpose, and, as a result, should perform reliably when used correctly according to the standard and with appropriate controls. If you start doing things outside the standard, then you are treading in dangerous waters. Follow the procedures correctly, if this means using a test on pure culture, then that is what you should do!

"The results won't be reliable."  why is that? why do you think the results might not be consistent? The first two quotes from the reagents' manuals don't strike me as the quote from the book, because it should be more concerned with the practical matter. Theoretically, there could be an organism with a very strong catalase/oxidase activity that would give a positive result even with an inapparent growth/microcolony hidden under a discrete subject colony. But if such organisms are found in the present, then these manuals should add that this pure culture should be in a non selective media.

"It is also talking about abundance" I think they mean an abundance of discrete subject colonies because, unlike confluent growth, these discrete colonies can't hide something. That makes sense until they tell you to go back and reperform the tests once in pure culture.

@FreezingSoul not reliable because you can't tell if the cultures are pure or not; thus you need to repeat them on pure culture. Yes, you can get the right result with a contaminated culture, but how can you be sure that your result isn't because of a contaminant. Pure culture is always done on non-selective media, so the assumption is that this is how you are doing it, not the converse. though some tests don't apply to certain media types. e.g. catalase can't be done off blood agar because of catalases in blood.

@FreezingSoul ... Remember that lives/health might be at risk here - which is better: do it right and get a result you can be certain of, or do a quick job and get an uncertain result that you then have to repeat and takes longer because you have to go back to the plate, re-sub and do it correctly? If you are doing med lab science, you MUST follow the standard procedures or your regulatory body will be very very unhappy with you when a mistake catches up with you.

@FreezingSoul Yes, discrete colonies was implied in the text. Just because you have a discrete colony from a sample, doesn't mean you have a pure colony; you can get contaminated single colonies, and re-streaking for pure culture will show these to you as the contaminant(s) should show up as abnormal colonies on your sub-plate.  You are overthinking it (again)...

"A. baumannii isolates were obtained from clinical specimens by standard methods, followed by isolation in pure culture on MacConkey agar plates" https://journals.asm.org/doi/10.1128/jcm.02263-09
What I want to say is that if we are going to consider theoretical concerns one time, why don't we do it all the way? If non-pure cultures could mean that our subject discrete colonies might not be as pure as they seem, then it renders selective media not usable for obtaining pure cultures, as Bergey mentions.

@FreezingSoul the risk of impure cultures is orders of magnitude reduced each time you sub it. Remember that a sample might have dozens of species of bacteria in it, but when you pick from a colony you take a very small amount (still millions of cfu) from a colony that might have 1-2 species, streak that out and you should see any contaminating organisms, and then pick a single colony from that. Discrete colonies from a sample might (made up numbers) have a 1:100 chance of contamination, but a colony on a sub-plate might have 1:10,000 or more...

@FreezingSoul ...The I read your quote as meaning they maintained pure culture on MAC. Also note that it is for a study looking specifically at that species, not clinical/diagnostic microbiology, so what they do there is up to them. Likely they got plates of already identified A baumanii and sub-cultured them - that's how I would do it, rather than taking random samples  and having to do all the culturing again.

Does that mean that colonies can have invisible growth that passes their margins and maybe theoretically extend to every side of the plate like radiation?

@FreezingSoul sometimes, motile bacteria can do this. You might not see it easily on a plate depending on the transparency of the medium and effects of the bacterium on the medium.

Let us continue this discussion in chat.


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Can introns be removed when designing protein expressing episomal plasmids?
If your goal is to cause a specific protein to be expressed transiently via an episomally maintained gene, could you just exclude all introns and the exons not associated with that transcript variant when choosing what DNA to package into your plasmid for that gene? So far as I know, the role of introns is usually in allowing alternative splicing and in modifying gene expression. But if you're only interested in one transcript variant, you wouldn't need alternative splicing to occur on the episome, and gene expression is handled in plasmid design by the selected promoters and enhancers.
For those reasons, could the introns (and exons not used for that transcript variant) be excluded? And would that affect the protein produced?

Why don't you use a mRNA transcript for expression cloning?

@Chris Sorry, could you elaborate a bit more? When you say mRNA transcript, would you just put the DNA complement of that mRNA into the expression vector?

Exactly. I can write you a more complete answer about this tomorrow. Basically you "use" the mRNA which has the exact sequence of the expressed gene. Avoids you doing a ton of edits and possible mistakes.

@Chris I would appreciate that! Your comments give me some threads to pull at with reading on my own too in the meantime, thank you!

@Chris If you pulled the transcript variant's mRNA from NCBI or similar, would you just form the complement from the sequence listed there? Or is it already "complemented" where that sequence is what you'd want going in the same direction as your other plasmid components? And could you just use the CDS with a custom promoter like EF1a? Or would you typically use the wholesale sequence from NCBI?

Use the coding sequence from the mRNA form available on sites such as NCBI
The sequences on NCBI etc are already in the DNA form; note the absence of any Uracils, indicating that this isn't actually mRNA as such, but rather a DNA copy of the RNA.
These sequences often contain 5' and 3' UTRs, so to be usable for you, you need to find the coding sequence in the sequence supplied. To do this manually, you can look for the start site ATG and stop sites to find the coding sequence. However, there is an easier way, and this is often useful if you have more than one coding sequence from the same transcript (these might be listed as separate entries in the database): find the label "CDS" (coding sequence) under the "Features" section and click on it. It should highlight a portion of the sequence corresponding to the ORF for this coding sequence.
You can then copy this sequence directly into a the MCS of a suitable plasmid.


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Can Nikon biological microscope model SE be converted to a digital microscope?
I am looking to buy a second hand microscope but I'd like to replace its eyepiece with a digital sensor. I am specifically looking at this Nikon stereo microscope Model SE. I asked the seller but they simply said they're not sure if we can remove one of the eyepiece lens or not.
I'd like to use a sensor like this: https://www.opticscentral.com.au/celestron-5mp-microscope-digital-imager.html

Seems like a good question for the camera seller.

I don't know about every Nikon stereoscope, but I know that the Nikon SMZ-U which I have, supports both replacing eyepieces with cameras, and a dual camera port accessory. But you would need to check the manual for the one you are looking at.
Even if it doesn't directly support using a camera with it, you can use afocal/eyepiece projection, to use it with a camera, though this often comes with reduced image quality.

@BryanKrause As I mentioned, the seller didn't know the answer. Either he is not familiar with microscopes or he didn't bother to check :(

@Topcode So that's like an adapter that sits on top of eyepiece and project to camera? That's good point... I did a search and I found many for telescopes but not sure if it works with microscopes too... I don't see why not tho. Thanks!

@xbmono The ones for telescopes should work, as long as you can get one the correct size for whatever eyepiece is on the microscope

Short answer is yes, with a few caveats.
In general you can use a camera of any sort with a microscope if you have the right adapters and mounts. You can even manually hold a camera and take photos with the eyepeice in place, though it is difficult and hard to get good images due to you moving and the narrow window of focus with a microscope eyepiece. So, basically all you need is that the camera is held steadily at the optical focus point or has a lens mounted on it that will compensate for the eyepiece if removed. You can even get mounts that are designed to hold a cellphone for taking photos. These often have a lens in a tube similar to the eyepiece and support your cellphone via fitting into the eyepiece tube.
The camera you mention has this to say in it's advertising blurb:

The Imager will replace any standard 23mm or 30mm eyepiece on your microscope

The camera is made by Celestron, which is a good, reliable brand for telescopes and cheaper microscopes, so I think it will be a reasonable camera, though probably no better than your cellphone camera.
It looks to me like it comes with an adapter designed to centre the camera down the eyepiece tube and to fit it into the eyepiece tube (images 2, 4, 5 on the page; small black ring with 3 brass screws coming out of it). Whether this adapter will fit into your microscope will depend on the dimensions of your eyepiece.
I note that their images have it mounted on a monocular microscope, but this also shouldn't be a problem; eyepiece lens mounts are fairly standard for a given brand.
One thing to be aware of is that if you have a binocular microscope, you will need to remove the camera if you want to use the eyepieces, unless you can cope with looking down the microscope with the wrong one eye (e.g. camera in left eyepiece will mean you need to look down the right one with your left eye so your head doesn't bang into the camera). You should be able to remove the camera and place it carefully on a bench to use both eyepieces, but you should be careful to not bump it too much (knocks it out of alignment) and aim to not get dirt (fingerprints etc.) or dust on the sensor/lens end - storing in a box/case will be fine though.
I also can't tell if there is some method of preventing dust from getting down the adapter tube for the camera and into the microscope (you definitely want to avoid this!), though this should be minimal anyway. Given that it is Celestron, there's a good chance they have thought of this and have something in place.

Thanks for the complete response. Do you know if the eyepiece of Model SE can be removed or it's fixed? I'm worried, I buy it and the eyepiece is fixed in place or is it standard for all microscopes to have removable eyepiece? Unfortunately the seller didn't know the answer, either he wasn't sure or he didn't bother to check

@xbmono I've not used that particular microscope model, and would need a more complete model number to be able to tell you for sure. However, in my experience, Nikon makes high-end microscopes, which means you get things like functionality to change eyepieces as you like. You may have to unscrew a holder screw, or maybe even unscrew the eyepiece lens (rare, typically microscopes from 50's-60's), but generally these are held in by friction and being angled above horizontal.

I finally bought it and as you said, the eyepiece can be removed, easy! I also tested it with my DSLR camera and a adapter tube I had for my telescope and handheld it because the tube it's a bit large.. but it works fine. I just need another tube with smaller diameter for this microscope.


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Would Adipose Derived Stem Cells Reinjected into Fat Tissue Reorganize into their typical structure?
I've read papers saying that mesenchymal stem cells (and in some cases stem cells in general) retain a degree of tropism for their sites of origin based on epigenetic memory. Is that mechanism strong enough to suggest that adipose derived stem cells purified from lipoaspirate would reorganize into their typical structure within fat tissues if they were reinjected subcutaneously into fat tissue? When I say "typical structure", I'm referring to the uniformly distributed pattern observed here. Also, would cells injected in this way tend to spread out uniformly, or clump around the injection site? Or would that depend on how they were administered?


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Temperature-dependence of circadian rythms
A circadian rhythm is a chemical clock. In the absence of light or other stimuli to entrain it, its speed depends on reaction rates.
As a rule of thumb reaction rates double every 10C as long as the enzymes don't denature. The "rule of thumb" predicts that a mild 0.5C temperature change would alter the 24 hour cycle by almost an hour/day, which is quite noticeable. Does (non-hazardous) heat/cold exposure advance/delay the circadian rhythm? If so, is it in line with the "rule of thumb"?

What do you mean by “entrain”? And presumably the verb, whatever it is supposed to mean, has on object. And circadian rhythms are generally referred to as “biological” clocks. In any case, the idea that  the length of circadian rhythms are limited by the rate (speed) of a chemical reaction or reactions seems to me absurd, given their length. Before twiddling your rules of thumb you need to identify the reactions that you think are limiting in a specific instance.

this question is fully answered in the wikipedia article.


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Competitive inhibition - Similarity between substrate and inhibitor
I have this question -
Q. Competitive inhibitor which binds to the enzyme (a) has structural similarity with the product (b) is chemically similar to the substrate (c) has physical structure similar to the substrate (d) both option (b) and (c)
I'm confused between options (c) and (d). I looked up the answer and it said option (c). But say, for example, malonate [inhibitor] and succinate [substrate] for the enzyme succinic
dehydrogenase, inhibitor and substrate are chemically similar as well :

Image source - https://www.toppr.com/ask/en-bh/question/the-activity-of-succinate-dehydrogenase-is-inhibited-by/
Kindly explain the answer to this question.

You've found an example where they are chemically similar; that doesn't mean this holds for all cases. A lemon is a sour fruit, that doesn't mean all fruit is sour.

MCQs are educational poison, as this example illustrates. Option (a) refers to “structural similarity with the product“, whereas (c) refers to “a physical structure similar to the substrate”. What is the difference between “structural similarity with” and “a physical structure similar to”? None that is apparent to me. So the question is designed to trick the student, not to see if he understands what a competitive inhibitor is. This is completely unforgivable. If I want to know if a student knows how a competitive inhibitor works, I ask him. If I’m employed to teach him I mark his answer.

@BryanKrause I've just been introduced to this topic so I guess my knowledge is pretty limited, I looked up the internet too but couldn't find anything. It would be a great help if you could give me an example where the substrate and competitive inhibitor are NOT chemically similar. Thanks:)

@ApogeePoint Tubocurarine at nicotinic acetylcholine receptors? Bicuculline for GABA receptors? Though at some point it depends on what you mean by "chemically similar" since this is a very non-specific, qualitative description. I'd very much agree with David on this that it's better to understand what competitive inhibition is than to learn answers to MCQs like this one.

I also think the MCQ is simply wrong/misleading, as it's only necessary for competitive inhibitors to interfere directly with binding; it need not fit in exactly the same way as the normal substrate. But, for the concept it's trying to teach, it's only really important to recognize that concept. If you continue in biology education you'll learn that almost everything you learn has an exception.

@BryanKrause Okay, now I've learnt that substrate and inhibitor need not necessarily be chemically similar. But my textbook has this - When the inhibitor closely resembles the substrate in its molecular structure and inhibits the activity of the enzyme, it is known as a competitive inhibitor. By molecular structure isn't it referring to chemical similarity?
Textbook link - https://ncert.nic.in/textbook.php?kebo1=9-19 (Page 117, 1st paragraph)

@ApogeePoint Looks to me like just a bad textbook. Yeah, usually when an inhibitor has those characteristics (closely resembles the substrate in it's molecular structure) it's a competitive inhibitor. But that's not the definition of competitive inhibition. Unfortunately, and this is the worst part, it also doesn't actually help you understand what competitive inhibition is to describe it that way. Competitive inhibition describes a relationship between the inhibitor and the substrate, where it's possible to overcome the antagonism by increasing the concentration of substrate...

...that's the competitive part: competition between the antagonist and the substrate/ligand. Physically, that occurs because they're binding in the same place on the target molecule, so if you have more substrate then the inhibitor can't bind, and vice-versa. Binding in the same place means they have to "fit" in the same place, so often that means the antagonist is similar to the ligand, but it doesn't have to be.

But, your textbook doesn't really make that connection, because it tells the story backwards and mixes up the logic in the process.

@BryanKrause I finally got your point! Certain molecules can act as competitive inhibitors, competing for the active site of an enzyme even if they do NOT possess a similar chemical structure as the substrate.
I read this article - https://www.sciencedirect.com/topics/medicine-and-dentistry/competitive-inhibition
And the textbook…yes some parts are messed up! Still thanks a lot for clearing my concepts.

@BryanKrause One last question please, if the target site of the competitive inhibitor and substrate is the same then, they should have similar chemical interactions with the active site to bind and that would mean chemical similarity. So how do these competitive inhibitors manage to compete and bind at the same active site if they are different from the substrate chemically? Is there any mechanism for that?

State of the art is a "transition state mimicry". Make the MCQ even more ridiculous.

Like others commenting, I am not impressed with this question's answers even as multiple-choice questions go. Depending on how the question is interpreted, all 4 could be argued to be correct.
But only C is always true for a competitive inhibitor.  The others are true for some competitive inhibitors, but not all.
What characterizes competitive inhibition (rather than non-competitive and uncompetitive inhibition) is binding at the active site of the enzyme.  Nothing else need be true. An inhibitor that binds the active site regardless of how or why it binds there is considered a competitive inhibitor.  The other two types of inhibition rely on binding to allosteric sites (binding sites other than the active site) that affect catalysis typically by altering the tertiary or quaternary structure of the enzyme.
An enzyme's active site is characterized by its shape (the space it occupies and does not occupy), and which amino acid functional groups project into that site in order to chemically interact with substrates as a part of the mechanism by which catalysis occurs.
In order to bind to the active site, the inhibitor may but does not have to interact with the amino acid site chains involved in catalysis.  But they all must be capable of fitting into the site well enough to stick there, typically through multiple low strength interactions such as Van der Waals forces.  Which means the molecule must have a shape that resembles the substrate enough to fit in its place. It must have "physical structure similar to the substrate" enough to do so. Occupancy of the site prevents the substrate from fitting into the site at all and/or interacting with mechanistically important amino acid side chains. Simple capacity to interact with mechanistically important amino acid side chains is not enough if it doesn't fit into the pocket of the active site as well.
And since the core definition of a competitive inhibitor is binding to the active site and nothing else, similar physical structure is the critical factor that must always be present.  Thus, C is the answer.
But there are issues that can confuse making other answers seem correct even to someone who has a reasonably good understanding of competitive inhibition. First, for enzymes catalysing reactions reversibly (such as carbonic anhydrase which can either take CO2 and water and produce bicarbonate and hydrogen ions or take bicarbonate and hydrogen ions and produce CO2 and water), the products can be substrates so one could argue A is also correct.  They probably discount it because the product of the forward reaction is the substrate of the reverse.  Statement A about competitive inhibitors could only be considered true for reversible reactions, whereas statement C is always true for both reversible and nonreversible catalysts.
Second, as you observed, the primary way an inhibitor has "physical structure similar to the substrate" is because it is chemically similar to the substrate.  But this is not the only way.  In your example consider the case where one carboxyl group (COOH) of the succinate is replaced by a nitro group (NO2). The geometry and size of the nitro group is quite similar to the carboxyl group.  Thus the physical structure is also quite similar despite the chemistry being dissimilar.  3-nitropropanoate inhibits this enzyme by binding at the active site and thus would be a competitive inhibitor of the enzyme.

So the reason C is the best answer is because it is the only statement that must always be true for an inhibitor to bind at an enzyme's active site.

In point of fact, option "C" is not always true for a competitive inhibitor.  A competitive inhibitor does not need to resemble the substrate at all in any respect, nor does an inhibitor need to bind to the active site for (reversible) inhibition to display a competitive pattern: an allosteric inhibitor (one that binds to a site other than the active site) can display competitive kinetics.  This point is very well discussed in Segel (Model 5).

Segel's famous diagram (Segel, (not Segal), p102) is also reproduced here (where Model 5 of Segel is labelled Model e). As a corollary to the above comment: binding of an inhibitor at the active site does not necessarily mean that the kinetics are competitive.  The binding of I to the active site may not prevent but only impair the binding of S to the active site: an inhibitory ESI complex may form with both E and I bound at the active site.

Model 5 was initially proposed by Changeux.  See here: "Models proposed by myself
in 1961 for the feedback inh of L‑Thr deaminase by L‑Ile. Model 1,
named ‘overlapping’, describes the classic model of competitive inhib
by mutual exclusion through steric hindrance of a common site. ...
the substrate and inhibitor compete for the same site on the protein. In
model 2, named ‘no-overlapping’, the binding-sites for the substrate and
inhibitor are topographically distinct and the interaction between them is
indirect or ‘allosteric’."

In addition, an Uncompetitive (or anti-competitive) inhibitor may bind at the active site.  One model for UC inhibition is where I binds to the ES complex. For a two-substrate enzyme (where UC inhibition is common) this could  be at the active site for the second substrate, in which case the inhibition pattern might be UC with respect to substrate 1 but competitive with respect to substrate 2, assuming (in the simplest case) an ordered addition of substrates to form a ternary complex

user338907, who I suspect to be a physical biochemist, further illustrates the original multiple choice problem's poor quality.  His comments also illustrate the difference between understanding something on an intro to biology level and an expert in the field level.  I freely admit that I am not at the field expert level, my undergrad degree is in biochem, but my graduate degree is in molecular biology... meaning I am neither a particularly good biochemist nor a particularly good geneticist (as the joke goes). The more one knows, the more one knows the exceptions from classical cases.

Enzyme inhibition at its base is about kinetics not chemical and physcial similarities. The different types of enzyme inhibitors produce different patterns on a Lineweaver-Burke plots, graphs of the reciprocal of the substrate concentration on the x-axis and is the reciprocal of the reaction velocity on the y-axis. This is how the types were defined. Increase in slope, decrease in x-intercept, no change in y-intercept = competitive inhibition. But that doesn't answer the question asked, why are they saying C is the answer re: chemical vs physical similarity with no kinetics discussed at all.

At the intro level, competive inhibition is described from the "classic model" as Segal calls in in the referenced figure.  And the question as asked references only it: substrate and inhibitor competing for the same site.  So that is how I answered it.  I was aware mechanisms 2, 3, and 4 in the referenced figure were also possible.  But it doesn't help with the answer, nor do the difference between binding at exactly the same site and very close adjacent ones.  I was not aware of #5, which is a major deviation from classic models which is probably why it was not covered in my classwork.

Likewise, I mentioned other inhibition types in their classic cases and in a cursory manner just as contrast to competitive inhibition.  So going into detail about examples of uncompetitive inhibition limited to enzymes with 2 substrates with independent active sites, while more strtictly accurate, would not have been very helpful.  And to get ahead of one other issue. 3-nitropropianoate is not actually a competitive inhibitor because it is not reversible.  It is a 'suicide inhibitor' that binds irrevocably to the active site.  Competitive inhibition, kinetically must be reversible.  But in

ways pertinent to the question, it acts like a competitive inhibitor and would be one is its binding to the enzyme was reversible.  Like other parts of my answer, I simplified.  And while there are those who would argue that such simplification is always wrong, I suspect most of them have not tried to explain something to people at varying levels of experience.  Especially when constrained by trying to answer why one of 4 poorly written answers to a poorly written question written by someone else is best.  And in such as way so as not to confuse and make things even more complicated.


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Can I column purify instead of gel extract?
I'm digesting a plasmid for assembly. In my experience, I always have low yields when gel extracting and purifying. Since I am only making one cut in my vector, could I just purify with a column? Any advice would be greatly appreciated, thanks!.

Yes, this is perfectly possible. There are a few small caveats though:

do not overload the column with too much DNA, as this will result in lower yields
also do not load an amount of DNA which is too small, this may result in loss of your sample. In my experience it worked better cleaning small samples from a gel.
also carryover of salts or Ethanol can cause problems
look up the exclusion size of the column from the manual. They can typically on purify DNA above a certain size and sometimes only work efficiently up to a certain DNA size
they are quick and convenient, but more expensive than a gel