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DNA dependent RNA polymerase
How does a RNAP locate a specific gene? For instance, growth hormone has to be produced and the RNAP has to locate the gene. But the promoter (TATA box) will also be present infront of all cistrons. So how does the RNAP choose the specific gene? Are the promoters specific for specific gene?

Yes, promoters are specific to genes and there is much more to them than the TATA box. There is also a requirement for specific transcription factors. And there are regulatory regions independent of the promoter.

How exactly RNAP find a gene quickly that it is like finding a needle in the haystack

Diffusion. There are thousands of RNAPs in a single cell. Furthermore, it is thought that these polymerases are localized to discrete sites of high transcriptional activity within the nucleus. Also keep in mind that transcribing genes quickly isn't necessarily the objective of the cell. Rather, a cell seeks to transcribe genes at a specific rate (which could be slow or fast).

This question is actually quite relevant. There are many mechanisms that increase the rate of TF-DNA binding- molecular crowding and nuclear organization are some factors. I'll address this in a while. Have a presentation to make.

It could be difficult for RNApol to access genes inactivated because inactivated genes are often tightly packed by chromatin. Many genes have enhancer elements(specific DNA sequences) as well as TATA, and transcriptional enhancers, which are proteins, would recognize enhancer elements in a sequence dependent manner and loosen chromatin structure to make RNApol access TATA sequences easily. Transcriptional enhancers also bind to the General Transcriptional Factor complex (GTF), which contains RNApol, therefore enhancers could bring RNApol to TATA sequences.
Many tissue specific and/or developmentally-regulated transcriptional enhancers are identified. You could say transcriptional enhancers regulate RNApol which to bind.
You can check this link and this.


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Peculiarity of chemo senses
We can easily recall our visual stimulus and auditory stimulus but why can't we recall chemical stimulus like smell and pain?
We can recall a song or picture but we can't exactly recall smell and pain. Why is that so?

This appears, at least to me, a very subjective question that would have to be discussed philosophically rather than with empirical evidence. An interesting topic nonetheless!

Olfactory memories are among the most powerful known. They are so strong that copious salivation occurs when people are directed to think of biting into a lemon or a sourball. What is the basis for your question?

I mean can you imagine a smell of jasmine as visualizing it?

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Catenation and decatenation by DNA Gyrase
Decatenation is done for the replication of DNA and why is Catenation done and is it related to Crossing over

Both DNA Catenation & Decatenation are crucial to the equal distribution of DNA to the daughter cells during the mitotic crossing over. While catenation plays structural role in chromosomal architecture , decatenation facilitates the separation of sister chromatids.

Hi Jank. Can you add some details with some references?

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How long does it take a leech to attach?
How long does it take a hematophagous leech to attach?
Specifically, how dangerous is drinking water which might be infested with leeches?
Presumably, once the leach enters the stomach, it will be quickly dissolved, so the only danger is that it might attach in the mouth or esophagus. Can this actually happen?
(should I ask this elsewhere?)

Apparently, the leech won't wait for you to swallow it, but it'll attach in your aerodigestive tract as soon as it's in it. This case study of children who drank leech-infested water explains pretty well (and in a rather graphical way, in my opinion) what happened to them. I'll copy here just an excerpt (emphasis mine):

A seven year old girl was brought from a remote village (Kamardin Karaiz) with four days history of cough with blood stained sputum after drinking water from a pond. She also developed pain in her throat and was unable to swallow except for liquids. [...]
  Her coagulation profile was with in normal limits however her hemoglobin level was 9 g/dl. [...]
  On direct laryngoscopy a leech was found attached to the right pyriform fossa with its one end in the glottis which was removed immediately. The patient made a smooth postoperative recovery. On recovery the patient had no dyspnea, stridor or dysphagia and was discharged the next day on oral antibiotics.

This article also reports a historical case of a leech attached into the throat of a Pashtun man in India. The leech was removed with no consequences.
In short, leech ingestion will probably result in having a leech sucking your blood from inside your throat. Although removing it will probably grant a full recovery, it doesn't seem a pleasant experience.


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Why do buffalos not leave the lion alone?
In the Buffalo Kill Lion - The Stronger is The Winner video the buffalos seem to be attacking an incapacitated lion.
Why would they do that?
They seem to risk injury for no gain (they don't eat lions).

The gain is one less lion to worry about.

@JAB: I have serious doubts about math capabilities of buffalos ;-)


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Is it "easier" for researchers to detect evolutionary ancestry than distance in the evolutionary tree?
I'm a researcher in another field who has wandered into a problem with applications to biology.  I hope to sell my results by making the following statement:

Given two species X and Y, it is "easier" for biologists to decide whether or not X is an evolutionary ancestor of Y, than it is for them to determine the distance between X and Y in the (unknown) evolutionary tree.

Question 1: Is this statement true in any meaningful sense?  Is it cheaper, less time-consuming, or more accurate to measure ancestry than to measure distance?  Or are the two tasks roughly the same?
Question 2: A reference request - what papers/textbooks could I read/cite to back up this statement?
Thank you!

In short, extant species are not ancestors of one another because, even if they are sister taxa, each has its own separate evolutionary history since they diverged. So, no to question 1.

Do you consider both X and Y to be extant species, or could X be a fossil? It might not make a difference theoretically (see the comment from @kmm), but in practice fossil species are sometimes viewed as representatives of ancestor species to extant species (or to more recent fossil species).

If you take two modern species (let's denote them with A and B) you can't really say that A is an ancestor of B or vice-versa, but you can say that they are related to some extent, that is they have a common ancestor that lived X years ago. But then all eukaryotes are believed to have a common ancestor that lived an eon ago. Hence the notion of phylogenetic relatedness  is relative by definition. That means that all species are related, but when you take a bunch of them you can try to reconstruct the order of speciation. This can be achieved by calculating distances (e.g. genetic sequence distances, morphological distances) and applying an evolutionary model. A brief summary is that you NEED to have a sort of distance to investigate ancestry in the first place and then you clearly NEED more than 2 species for your phylogenetic constructs to make any sense.
Since I find that your statement makes little sense, obviously I can't find a reference to bake your words. But I can give you an exhaustive list of good phylogenetics textbooks for your erudition.
EDIT
I believe that one thing is worth a remark. In fact it is easier to correctly reconstruct the order of speciation events than it is to precisely estimate any sort of evolutionary distance, because the distances we have are models. Simply put they approximate the number of evolutionary events that have happened since the last common ancestor of some species (or better to say the last common set of genomic and/or phenotypic traits, because speciation is a lot more than simple trait-wise divergence). From this point of view you might say that it's easier to estimate ancestry than it is to estimate distance, but then you will be over-simplifying things to such an extent, that you will drop the fact that there is no way you can speak about ancestry without having some distance estimations in the first place. The precision of distance estimations is a separate topic. So your statement will make a lot more sense if you modify it accordingly.

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How does promoter sequence affect initiation?
I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear"
I'm wondering if anyone can suggest sources for more information, or perhaps has seen recent research papers highlighting the properties that cause such variation between strong promoters and the weakest?
I've tried researching but the older research is descriptive rather than mechanistic and the search terms involved are quite ubiquitous so it's hard to actually find more on this specific point.

I agree that it is hard to search for papers but from graduate level classes this is some of the additional insight I have gained. Sequence context of promoters is important. Specific DNA sequences (motifs) can act as binding sites for specific transcription factors and combinations of these transcription factors help recruit RNA pol II to the promoter. These combinations of proteins are spatially and temporally regulated and will help decide if gene that is next to promoter will be activated. A luciferase reporter assay is often used to determine the strength of a promoter.
An example is as follows: A strong promoter might have certain histone marks that would recruit proteins to remodel the chromatin to be more accessible exposing binding sites of transcription factors that help recruit RNA Pol II. A weaker promoter might have less transcription factor binding sites or less chromatin accessibility and thus it is harder for RNA Pol II to be recruited. There are also some kinetics aspects you must keep in mind.

Echoing what was already mentioned: the DNA sequence directly affects the ability to bind sigma factors (http://en.wikipedia.org/wiki/Sigma_factor). Sequence --> bonding --> how often sigmas bind and for how long they bind --> initiation of transcription


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Which of Perutz et al's protein structures other than 3₁₀ helix were correct?
In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, in the paper that documented the alpha and gamma helices, "Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain" (also OA)
I'm reading about this (as reviewed here for example) where the idea is that Bragg et al were disproved - in the words of the Pauling paper:

None of these authors propose either our 3.7-residue [α] helix or our 5.1- residue [γ] helix. On the other hand, we would eliminate by our basic postulates all of the structures proposed by them. The reason for the difference in results obtained by other investigators and by us through essentially similar arguments is that both Bragg and his collaborators . . . discussed in detail only helical structures with an integral number of residues per turn, and moreover assume only a rough approximation to the requirements about interatomic distances bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances. We contend that these stereochemical features must be very closely retained in stable configurations of polypeptide chains in proteins, and that there is no special stability associated with an integral number of residues per turn in the helical molecule.

There was one however, the 310 helix which was correctly identified by Perutz's group in 1950. I don't have any access to library facilities at present and online resources aren't quite the same as a solid textbook. I'm wondering if any of the other forms described were in fact correct?
To list, these were:

27a
27b
28
213
214
38
( 310 )
411
413
213

I'll continue looking in the meantime but it's hard to search when there are subscripts in names, and I would think more experienced protein scientists could give me a quicker answer (or just direct me to where I should be reading)

I'm pretty sure you have it right because Pauling made a big splash with his alpha helix and both beta sheet models years later.

ok i had the time to expand into an answer....

nice reference! I've not read Perutz' book yet - I really need to! Note how Astbury's data had not been correctly evaluated; giving the wrong pitch for the alpha helix, misleading Kendrew and Perutz.  One of the reasons for so many of those crazy helix numbers.

I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper.  And the 310 helix was not really right either - it did turn out to show up occasionally in protein structures though.
At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal structures. Examples being collagen from hair and spider silk fiber diffraction patterns. Fiber diffraction of hair, whose ordered structure consists mainly of alpha helices somewhat aligned to the fiber axis (along the length of the hair) or the mainly beta sheets which constitute silk.
Because it was known that these substances contain mainly protein, building models which would show how regular peptide polymers would produce these patterns.  This happened in chemistry and physics departments worldwide.  The paper you cite is representative to the field.
Pauling caused a splash in the spring of 1951 by publishing descriptions of the alpha helix and the beta sheet (both parallel and antiparallel).  The main advantage that Pauling had was that he had studied the structure of simple di-amino acid structures (notably glycyl-glycine) and understood that the peptide bond had some double bond like properties which prevented it from rotating freely.  As the discoverer of valence bond theory, which united quantum mechanics and chemistry and established the basis for at least most organic/biological chemical structures Pauling must have been practically alone in this insight at the time.
This next set the stage for the dramatic race to discover the structure of DNA. If you read Watsons' memoir, he describes how the MRC in Cambridge was still feeling the heat,  competing with CalTech and Pauling.  He and the young lab there was holding their own against the MRC Cambridge with its multiple nobel laureates; a lab which had established the relationship of x-ray diffraction and chemical structure (the notes on chapter 7 are interesting - follow the link).
Looking back on it, Pauling's main advantage was that he understood the peptide bond better than the rest of the world. By the time DNA was being resolved, the conformations of organic molecules were understood by many and the playing field should have been more level.  I'm not sure I buy the arguments that Pauling would have got the structure without seeing the diffraction patterns and even then maybe not. I might not give such strong credence to the idea that Pauling would have gotten the DNA structure so quickly if he had been able to travel.
Of course Perutz and Kendrew verified the peptide alpha helix themselves when they solved the first crystal structures of hemoglobin and myoglobin, having the final say.  The structures contain a small amount of 310 helix but are otherwise full of alpha helices.  I'm not sure that the secondary structure was entirely confirmed until the 1958 when myoglobin was resolved.

Wow nice essay haha! I thought Coulson proposed valence bond theory, thanks for the historical input though mate, v nice :-)

its a story I've enjoyed learning.  If you're reading that paper you are pretty deep into it yourself!

BTW Chemical valence was a term around before Pauling, but he formulated the quantum mechanical rationale for chemical bonding, which was adjusted by molecular orbital theory, but which we still use today.


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Can men with Klinefelter syndrome produce chromosomally normal sperm?
Individuals with Klinefelter syndrome are XXY. Even though sperm counts are low some individuals can generate enough to be used in IVF and have offspring.
Does this mean that when sperm are formed, the process works correctly to separate all 3 of them and only sperm with a single sex chromosome are formed?
(Excluding same genetic issues happening again of course)

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Seems like there are some hypotheses about this mechanism. This might be interesting: https://www.fertstert.org/article/S0015-0282(12)00654-1/pdf

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What subspecies of Iberian Ibex and what subspecies Golden Eagle are in this video?
In the nature documentary El Hombre y la Tierra, there is a scene featuring golden eagles and apparently some kind of Iberian ibex. The scene should be in some part of Iberia. This is the video which features the animals and location: https://www.youtube.com/watch?v=Yz7FFlFy8eM
Goats:

Eagle and Goats: 1: https://i.sstatic.net/3RHSs.jpg 2: https://i.sstatic.net/eBh2d.jpg Several other images: https://i.sstatic.net/Wpare.jpg
However, these Ibex have small horns and there are none with large horns. I'm not used to seeing this with ibex. Surely it can't be a flock made entirely of females and juveniles? So I would like to ask what subspecies of Iberian Ibex these are.
I would also like to ask, if I might, what subspecies of golden eagle is shown in the clip. I suspect the one which carries off the goat will be the female of a larger subspecies.
If it is not acceptable to ask about both species, please edit the part about the eagle out of my answer. Know that I would be happy with an answer to either question. Thank you very much.

The golden eagle is just one species:  (Aquila chrysaetos) is the most widely distributed species of eagle, it's on all the northern hemisphere.

@com.prehensible My mistake, meant to say subspecies. Do you know what subspecies of aquila chrysaetos is common to Iberia, and which might be present in the video?

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@tyersome Thanks tyersome. I tried to add some images, but it wouldn't let me upload them from imgur.

The upload links must be to files rather than webpages — if you open the imgur images in a new tab (or window) you get a file with ".jpg" extension. I've uploaded the goat images for you, but you should probably put the eagles into a separate question.

Aquila chrysaetos homeyeri: Iberian Peninsula; nw Africa to Arabia and Iran ... don't know about the ibex, it has small deer horns?

@com.prehensible Thanks! The ibex is pretty confusing. I was wondering if it might be a different kind of goat, like some wild breed of a Spanish goat. They have horns more like that.

The eagle is Aquila chrysaetos homeyeri or chrysaetos. Homeyeri comes from the Iberian Peninsula; nw Africa to Arabia and Iran. Chrysaetos chrysaetos comes from the Alps to Sibera and the Iberian Peninsula.
They weight up to 7kg and they can carry a bit less than 3 kilos, big prey includes baby bears, coyotes, foxes, ibex, seals, badgers, dogs, cats, they can attack anything up to 1 meter in width, generally on the neck and the back:

It can defeat anything that can't withstand the powerful talon gripping and slashing, the hullux talon is 4-6.5 cm:
The Ibex subspecies is difficult to tell from the pictures,  although the ibex males and females always live in different herds and congregate once a year, all subspecies adults have horns 40-70cm in length,. The horns grow 8cm per year for 15-20 years after the first year, with females having slightly smaller horns, about 40-50cm.
The group of iberian ibex there are all 2-3 years old.
Groups of ibex entirely with small horns can be found, with other herds of ibex with 55 cm horns living elsewhere, although normally it's a bit more mixed with 4-5 year old individuals mixed in. At the time that the video was made, hunting laws were less strict than today, so it's possible that the bigger individuals of the herd had been shot.


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What happens to the molecules of the pathogens after phagocytosis?
For example, what happens when a bacterium gets digested by a macrophage? I suppose that the macrophage produces the presented antigen from leftovers from the digested bacterial particles. What happens to the rest of the bacterium? Can the molecules from bacteria be used as a source of nutrients for the body? Or will they accumulate/get transported as waste products?

The ingestion of a bacterium by a macrophage involves phagosome lysosome fusion, which you can read about in Abbas Basic Immunology, Ch 2. As you suspected, in addition to bacterial killing and antigen processing, the phagolysosome breaks down bacterial macromolecules, as any lysosome does, using a variety of lysosomal hydrolases. There are export pathways for the end products, including lipids, carbohydrates, and amino acids, as discussed in this review, which does allow for re-use by anabolic pathways. As discussed in the linked review, the process of digestion and catabolite export is regulated, as should be expected. In culture models, nutrient availability appears to be important.


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What species is this interestingly colored brown moth
This fella fluttered into a kitchen at night, maybe from the vegetation in the yard, and I got lucky to trap it in a transparent plastic bag for a while (with enough room to move, which it started doing at about the same pace it had been flying before but sometimes sitting still) so I got a couple of close-up pictures.
I think the coloring and some other features are too far off the familiar plodia interpunctella to be the same species, also a number of other features seem different in appearance and behavior. (Wings not folded straight back and much wider, doesn't like sitting still on wall for extended period of time.)
Length is about 12-13 mm (wings included and folded). It also sat down wings spread out very wide where I first found it (no picture of that posture included).
Location: Southern part of Germany, city landscape with river/lake within half a mile
What species is this and what would it live and feed on (if the adult feeds at all in this species) ?
As it was examined bottom up, I noticed a contracting and expanding movement of the abdominal segments (roughly last 2 images). What is that movement?

It could be Pyralis farinalis, the meal moth. It is a cosmopolitan moth of the family Pyralidae. Its larvae are pests of certain stored foods, namely milled plant products. I don't think it's adults feed as they do not live long after mating.
Here is a link to its Wikipedia article:Pyralis farinalis


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Could anyone kindly identify this bug for me? Is it harmless?
Details:

Found by a wall/window in Brooklyn, NY in a house not too far from the beach
Rooms walls/windows are dusty and spots of mold growing on wall/windows
size of bug: 2 milimeters

Keywords I've tried in my web search and image search:

True bugs, ticks, types of house bugs, sowbug, stink bugs, insects that live/grow near mold, flat bugs, dust bugs

Any suggestions or ideas would be greatly appreciated.

That particular one is dead, so I guess it's completely harmless, a closer picture with different angles would help a lot to identify it  :)


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What factors affect the rate of siderophore production by microbes?
Microbes produce siderophores which are chelators and bind to iron. This is how microbes absorb iron from soil or rock. What causes microbes to increase or decrease the rate of production of siderophores?

Hi Zoe, welcome to Stack Exchange! Despite the biological context of your question, I wonder if this question might fit better on https://chemistry.stackexchange.com/

@Galen, as the question was about microbial mechanisms for siderophore regulation I think that the question is a good fit for Biology. This is likely a gene regulation question.

It might help if you gave a more specific example related to your interest in the question. The answer to your question is going to depend on what type of microbes your are interested in, their specific metabolism, and in what kinds of ecosystems they are found. For example, a gut pathogen might have very different modes of iron acquisition than a chemo-autotroph in a hot spring.

I think that you are interested in how bacteria regulate the expression of genes that produce siderophores. For a technical reference you can see this paper studying Vibrio, or this paper studying Pseudomonas. For a more general review see here.
Note that this is a diverse piece of metabolism and therefore there are likely to be a diversity of mechanisms by which siderophore production occurs, though superficially it appears that there are some general principles you can draw. I recommend looking at those papers and trying to understand the commonalities.


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What is the cause of a protuberant belly in kwashiorkor?
Kwashiorkor is a PEM (Protein–energy malnutrition) usually characterised by a pot belly. Why is there a pot belly in the case of a malnutrition? I have found contradictory reasons. This paper says that it is due to a fatty liver. This website says it is due to excess fluid accumulation in the tissues.
I noticed that these children have very skinny limbs. When I pointed that out to my teacher a few years back, she told me that the subcutaneous fat from the thighs accumulates under the belly. I can find no source confirming that, though.
So, what is the cause of the pot belly?

The Gastroenterology paper you cite doesn't mention distended bellies at all.  There is no dispute that fatty liver is a symptom of kwashiorkor.  But the Wikipedia article makes it quite clear that the cause of the distended belly is edema.

The extreme lack of protein causes an osmotic imbalance in the gastro-intestinal system causing swelling of the gut diagnosed as an edema or retention of water.[4]

And:

Compromised fluid recovery results in the characteristic belly distension observed in highly malnourished children.[14]

Here's another source:

To understand the reasoning for this, it is important to know that in malnourishment, the rounded abdomen is not due to fat accumulation. Instead, the water retention and fluid buildup in the body cause the abdomen to expand. This results in a bloated, distended stomach or abdominal area.

The rest of the article goes into more detail on the phenomenon and mechanism of action.
This source seems less authoritative, but also suggests that weakened abdominal muscles (due to protein deficiency) also play a role:

The swollen belly is the result of not only that enlarged liver, but also the loss of muscle mass, which leads to weak abdominal muscles. Together with a weakened lymphatic system that is unable to keep up with the body’s liquid wastes, when those wastes accumulate in the abdomen, the belly becomes distended.

So the author suggests that fatty liver contributes to belly distension, but is not a sole cause.  None of the sources I looked at mentioned fat accumulation as a contributor, but rather eliminated it.

Abdominal distension is common in kwashiorkor, and many reasons have been proposed for it [1,2]:

Dilated bowel loops (because of gas produced by bacterial overgrowth),
An enlarged liver (because of steatosis, i.e. fat accumulation),
Ascites, i.e. excess fluid in the peritoneal cavity (as part of the
generalised oedema of kwashiorkor), and
Weakness of the abdominal wall muscles.

But these are merely guesses. It is difficult to pinpoint one particular cause, since no studies have been done on this. Possibly, each of them contributes to some extent.
Now it is true that children with kwashiorkor have skinny limbs, but it would not be correct to say that their fat has 'moved' to their bellies. They are skinny because they are not getting enough nutrition to make up for their fat and muscle breakdown. The liver fat accumulation, on the other hand, is because the liver too is diseased. It is unable to metabolise lipids as it normally does [3].
References

Klein S. Protein-energy malnutrition. In: Goldman L, Schafer AI, editors. Goldman's Cecil medicine. 24th ed. Philadelphia: Elsevier Saunders; c2012. p 1388–90.
Ashworth A. Nutrition, food security and health. In: Kleigman RM, Stanton BF, St Geme JW, Schor NF, editors. Nelson textbook of pediatrics. 20th ed. Philadelphia: Elsevier; c2016. p 295–306.
van Zutphen T, Ciapaite J, Bloks VW, et al. Malnutrition-associated liver steatosis and ATP depletion is caused by peroxisomal and mitochondrial dysfunction. J Hepatol. 2016;65(6):1198–1208. https://doi.org/10.1016/j.jhep.2016.05.046


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Can hunting of large specimens of a species make the size and weight of the species tend to be smaller?
Siberian tigers in the wild don't grow as much as they used to be in past (in the 1900s).
Their average weight was measured 176 kg in 2005 study. But it was also said that those tigers observed in study were sick and in conflict to humans.
I think their smaller size is because of low prey density because at that time, hunting of animals that come as tigers' prey was high.
Could it also be because all the large specimens were shot?

Welcome to Biology.SE! Please add a reference for the study you are citing — this is both expected practice in science (and on this site) and helpful for providing context for your question. Thanks!

I don't know of any research about this on tigers or any other terrestrial predators, but this is a well-known phenomenon in "trophy" animals1 (i.e. big game hunted for sport) and wild-caught fish1-4.
1: Allendorf, F. W., & Hard, J. J. (2009). Human-induced evolution caused by unnatural selection through harvest of wild animals. Proceedings of the National Academy of Sciences, 106(Supplement 1), 9987-9994.
2: Heino, M., Pauli, B. D., & Dieckmann, U. (2015). Fisheries-induced evolution. Annual review of ecology, evolution, and systematics, 46.
3: Monk, C. T., Bekkevold, D., Klefoth, T., Pagel, T., Palmer, M., & Arlinghaus, R. (2021). The battle between harvest and natural selection creates small and shy fish. Proceedings of the National Academy of Sciences, 118(9).
4: Bowles, E., Marin, K., Mogensen, S., MacLeod, P., & Fraser, D. J. (2020). Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?. Evolutionary applications, 13(6), 1128-1144.


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What is this bug living on the plaster in my home?
It's a small larva looking creature that pops out of a volcanoe-esque hole in the bathroom. SE United States.

Sort of looks like a barnacle... but could be the start of a wasp nest if it is on a ceiling. Can you comment on whether it is submerged in water or what sort of surface it is adhered to?

It's on typical drywall on the wall in my home.

Opening is about a mm big.

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Bird identification - hawk
These fledglings are learning to fly in Salt Lake City, UT. What species are they?

Welcome to Biology.SE. Please include an estimate of the size of these birds and if possible pictures of the adults that are likely to still be feeding them. To me these look like fledgling Red-tails, but the eye looks bluish rather than yellowish. However, that might be due to the lighting in your picture and this is a notoriously variable species. At any rate I think these are a buteo of some sort ...

Based on your location and the unique coloration/arrangement of the feathers near the ear area, I would say these are Northern Harrier (Circus hudsonius) chicks.


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Can anyone identify this chrysalis?
What kind of chrysalis or pupa is this? It’s about an inch and 3/4 long and is hanging off the brick siding of a house in Piedmont North Carolina. It wiggles when it is touched. It has been hanging there for at least two or three weeks.


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How do fish persist in the upper parts of mountainous rivers with waterfalls?
I was recently traveling in a remote mountain region and hiking alongside a very small river.
What caught my attention was the fish in the small ponds under the waterfalls.
These ponds were just a couple of square meters in size and each one housed between 5 and 10 fish.
The course (do you mean flow?) of the river combined with the waterfalls mean it was basically out of question that they could swim / jump upstream.
In such small mountainous rivers, how do fish remain in the upper parts over the course of hundreds of years.
I mean the size of the ponds and the amount of fish did not look to me like it could be sustainable for a population. And there should be the occasional one going down.
Are there examples or situations where the upstream population becomes extinct?

Welcome to Biology.SE! I edited your post, but please check to make sure I haven't changed your meaning. In your third paragraph you say that "... course of the river combined with ..." — did you mean flow. If not, can you clarify what it is about the river that makes you think it was impossible for fish to migrate upstream? Thanks!

@tyersome "Course of a river" is a common term. It refers to the path the river takes, including the path traveled across the surface of the earth, elevation changes, flow changes as a river goes through shallow/wide or narrow/deep sections, rapids, etc.

things to consider 1. some fish are very good at getting upstream and some can even climb the rock behind a waterfall 2 a rivers course now is not what it has always been, just because there is a waterfall now does not mean there was always one.

@BryanKrause — I am familiar with that usage, but in the context of that sentence (using "combined with") it appeared to me that the OP might mean something different, which is why I requested clarification ...

Sorry, my bad, I'm not a native English speaker :) @Bryan Krause is right


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Which varieties of Aurelia aurita do not have a polyp phase?
According to this "In some Aurelia aurita, the polyp stage does not exist.", but they don't cite anything. Is there a resource detailing life cycles of various jellyfish or do I have to find their list and search articles one by one?

I've edited your post to correct some formatting and improve the tags (please avoid creating new tags unless they fit many questions). I also replaced species with varieties in your title, since it doesn't make sense to talk about species within a species. ———  Also note that questions are better received here if they demonstrate that you have a done a significant amount of prior research — for example you could [edit] your question to tell us where you've looked for answers (other than the original website), what you do know about the topic, and where exactly you still have questions.


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

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

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

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

This is a false wolf spider called Zoropsis spinimana:

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

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

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

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

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

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

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

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


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Identity of a spider found on Cyprus
I'm trying to identify a little friendly spider seen in Cyprus. She is brown, around 0.7 inches (2cm) long with white-striped legs, and a small dotted back. This seems like a pumpkin spider, but the head is way too big.

Welcome to Biology.SE. Did you observe any behavior that could be added to your question — for example it looks like your spider might be raising its rear legs.  In addition, it would be helpful if you could add a clear photo from the front that shows the pattern of the eyes — this is an important diagnostic feature for many spiders. (Also, note I edited to (I hope) make your post clearer and correct your tag. Spiders are not insects, but instead in a separate group of arthropods that includes scorpions.)

Following the recommendations from tyersome about eye pattern and behavior I was able to identify this little spider as a Male Araneus Diadematus. They are common garden spiders and harmless, their bite is similar to a bee sting and pose no threat to human life.


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What insect is this? Found in a dying tree
I recently found this insect near where I live, where my childs play always! Is it dangerous ??. What insect is this ?
Is it poisonous?
Its about 3cm
Picture:

I live in Montreal, Quebec, Canada

Welcome to Biology.SE. Can you [edit] what the 3 cm is measuring into your post? (e.g.s: head to tip of abdomen vs. tips of antennae to tip of the ovipositor, which is the "drill" sticking into the wood). If you can specify the type of tree that you found it on that could also help. ——— This wasp is likely only dangerous to the wood boring larvae she is trying to lay eggs in, but we can't give health advice on this site. At any rate if you (and your children) don't harass her, she'll most likely pay you no attention at all.

Looks like some kind of https://en.wikipedia.org/wiki/Parasitoid_wasp Maybe even the species in the first example picture

Yes that's exactly what I saw ! Thanks for the response!

Does this answer your question? Is this a hornet?

From Gil Wizen's page, it's a wasp.

Giant ichneumon wasps (genus Megarhyssa) are some of the biggest North American wasps thanks to the females’ long (10cm) ovipositor, which is longer than the wasp’s own body. These wasps might look fierce but they are actually shy and harmless insects. They are parasitoids: their larvae develop as parasites living inside the body of other insects. The female’s ovipositor is therefore not a stinger, but an organ used to inject eggs into the larva’s host. (emphasis mine)

Here is one of his amazing photographs or the wasp laying eggs (into a dead tree).


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Can you identify these ants?
I think they could be carpenter ants, but not sure.

Welcome to Biology.SE! Identifications questions should also include: 1) the location (e.g. country and region — the more specific the better) where you observed this organism; and 2) an estimate of the size of the organism. Please [edit] your post to include this essential information. ——— In addition, we don't provide advice about pest treatment (especially regarding safety), so I've deleted that part of your question. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!


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What is this black and white worm in a white case?
The case is very small and it's an off white color.
The thing living inside can come out of either end. It's a black and white looking worm. It will poke its head out and move everywhere!

They are all over my back porch and some are even coming in my house!

Could you link more (and clearer) pictures please?

Related: https://biology.stackexchange.com/questions/15845/what-insect-is-this-india/15856#15856

Related Question.

Related: Identifying a creature that appears to be a worm wrapped in a cocoon, What is this black and white worm in a white case?,  Help in identifying an unknown arthropod, What insect is this? (India), Identify this smooth-cocoon worm from Southern India, Small worm living in some kind of cocoon......

Related:  What is this animal that hides in dustlike structure?, What in the world is this critter?, What is this hard shelled insect in my house?, What is this insect found commonly in coastal India?, Insect identification - pantry moth vs clothes moth

Does this answer your question? Identifying a creature that appears to be a worm wrapped in a cocoon


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What kind of deciduous tree is this?
This image was captured on October 10th, 2020 in Haliburton, Ontario, Canada. Any help identifying the tree species is greatly appreciated. Rob.

I think it's a poplar tree, very fast growing, light wood, often used for matches, very often has a white saprophytic tea color mushroom growing on the tree stumps. https://en.wikipedia.org/wiki/Cyclocybe_aegerita
The description is missing bark photos and leaf anatomy photos. It can also be a birch or a willow, very difficult to ID from just that photo.

Are you sure it isn't quaking aspen (Populus tremuloides), which is in the Poplar family, but called aspens in North America.

He can tell by comparing the bark which is a lot whiter on tremuloides.


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What kind of purple flower is this?
Shot in a garden in Haliburton, Ontario, Canada on June 18th, 2020. Flowerhead size approx. 1 1/4" diameter across.

Identifications questions should also include: 1) habitat information — e.g. was this growing in a marsh? were there any other plants nearby that you could identify?; and 2) an estimate of the size of the organism. Please [edit] your post to include this essential information. ——— Also note that such questions should be given the species-identification tag and that thanks/signatures etc. should not be included in SE posts.

fyi, Google Lens is pretty good at identifying plants.

How nice it would be if all images of flowers were stereographic like this (from here). =)

That looks like it could be a cultivar of Geranium sanguineum (Bloody crane's-bill or Bloody geranium) or something closely related.

Image source: Keith Weller, USDA Agricultural Research Service, Bugwood.org — CCA3.0.
Some features that are consistent with this id are: the five identical bilobed petals, flower size and shape, hairy stems, and leaf form (palmate with five lobes each with three large 'teeth'). The flower features I can distinguish rule out related genera such as Pelargonium and Erodium, which have flowers that are not radially symmetrical. If this is a Geranium, then there should be 10 free stamens and the stigma should have a style with 5 branches.
This species is cultivated and typically blooms from June to August, which fits your described location and time.


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What kind of tree has leaves like this?
Shot taken in Spring, on May 22, 2020 in a forest in Haliburton, Ontario.

Your other question also shows a Beech.

Please see the guidance at https://biology.stackexchange.com/tags/species-identification/info for species ID questions and use that tag when you ask for ID.

This is a beech tree. From the leaves only it is hard to say which species it is exactly, but given your location it is probably the North America Beech, Fagus Grandifolia.
See this leave from the second Wikipedia article for comparision:


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Is that a sundew?

I have bought the seeds for a sundew/drosera (growbro.nl) but I have pretty serious doubt if that is really the plant I wanted :-)
If not, what kind of plant is that I have grown?

This is not a sundew. A simple Google search can confirm that.

Thanks. I still hoped that it is maybe just a transition phase and it will look as the actual sundew.

That looks a bit like a member of the genus Impatiens some members of which are invasive.
Some images can be seen here.
Flower pictures would be helpful for identification ...


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Is "cell proper" considered a biology term / well defined concept?
I am asking this question after writing an answer on English Language & Usage sent me on an expedition through the internet. The originating question asked about the meaning of the word proper after the word cell.
At first I was certain that it was a biology term, describing some sort of cell. I am not a biologist. After some pushback, I researched a bit and found what seems to be the original definition in a book from 1853.

It is a mistake to apply the word cell sometimes to the cell with a membrane, sometimes to the cell without a membrane, and sometimes to the membrane without the cell. Since the contents of the cell constitute the essential part of it (see p. 155), since it forms, before the secretion of the (cellulose-) membrane (pp. 156-167), a separate entity, possessing its own, essentially proper, membranous boundary (the primordial utricle, pp. 169-173), we must call this internal body the cell proper, unless we restrict the term cell to the enclosing wall or chamber, and give the internal body another name. If the name is restricted to the internal body, we cannot, in the great majority of cases, say that new cells are formed in the old, but merely that they are formed out of the old, for even the primordial utricle shares in the division, in the propagation of cells by division. Therefore when daughter-cells are said to be formed in the mother-cells, or to slip out from the mother-cells, or mother-cells are said to be dissolved and absorbed, these phrases must be admitted only as conveniently abbreviated expressions, "mother-cell" being here used instead of maternal cell-membrane.
(bold emphasis added)

My question is: Is cell proper considered a biology term or concept that would be understood by an expert of cellular structures?

I have never heard this term - so it most likely never catched.

this sounds like an old term that, to my knowledge, is no longer used - not surprising given how much more we know about cellular physiology/structure and functions

This isn't a special biology term, it's just an English usage thing. "The X proper" just means "the X, strictly speaking". As well as the question you quote, see also this question on ELU.SE. I would expect this use to be understood by many biologists who speak English as a first language, but there are certainly clearer ways of saying it.
Regarding this particular example, the author appears to be proposing a way of defining a vacuolated plant cell. It sounds like he is proposing a definition that excludes the cell wall, but he confusingly calls the cell wall the "(cellulose-)membrane" (the 'primordial utricle' is the cytoplasm, I think). However, I am afraid I am not an expert in the history of plant cell biology and can't really comment on whether it is a useful contribution to, or synthesis of, the state of knowledge at the time.

I agree with the suggestion that this is mostly just a standard usage of "proper."  However I would caution that most scientists would probably not understand "the cell proper" to exclude the cell membrane! If I ever wrote that, it would be in a sentence like, "The extracellular matrix, while not part of the cell proper, is an essential aspect of a cell's behavior."

@AJK absolutely. Although I would probably need to read more of the original text to work out exactly what the author is describing - it seems he's talking about something to do with the membranes of vacuolated plant cells, and I haven't studied plant cell biology since first-year undergrad. That said, I can think of very few biological definitions from 1853 that remain helpful today!

@AJK have read a bit more around it and added what I understand of his proposed definition, with caveats. Please do feel free to elaborate on it.


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Flies without wings
some time ago I spotted a wingless fly in my small garden. I thought to myself that it's rather weird and most likely just a random thing. But after some time I spotted more wingless flies and just a minute ago I took a photo of one specimen:
You can see that it also lacks a leg. The sightings were separated with at least few days each (I wasn't paying too much attention at first), so I think it's very unlikely it's a same fly, because spiders and ants would probably hunt it down long time ago. Unfortunately it's the only documentation I currently have although I'll try to get more. Does anyone know what could be the cause?

I just saw two today! It's strange honestly, I just thought it was some weird wingless flies. First time I saw them and I laughed  I think they're called Wingless Solider Flies.

louse flies are known to drop their wings after they find an animal to lay their eggs on,i am not saying that it is a louse flie as they have a very flat body.

Please [edit] your post to include as much of the following essential information as possible to improve your chances of getting a good answer: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible)); 2) the location (e.g. country and region — the more specific the better) where you observed this organism; 3) habitat information; and 4) an estimate of the size of the organism. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.

It would help a lot if we knew where you are, many islands have wingless flies for instance.


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What are these small, indoor bugs?
I live in Switzerland and have noticed these small bugs appear in my bedroom, either slowly crawling on the parquet flooring, lazily buzzing around or dead on my windowsill (as pictured):

I'm not sure if these bugs are currently appearing more often – or if I just notice them more because of the fact that I'm spending a lot of time in my bedroom due to Corona lockdown.
The only hint I've got is a friend saying that they live in wooden floors. No idea if that's correct.
Thanks for any help or hints!

I doubt you'll get a positive ID from that photo. It might be some woodboring beetle, maybe genus Anobium or Hedobia. FTR, if they are chewing on your wooden floors, you might be able to hear them if you listen carefully.
I suggest you collect some, maybe even living, in a small tube and ask a specialist. My first idea would be someone at a nearby university or natural history museum working in entomology, and specifically on Coleoptera if possible.

I think this is a species of Varied Carpet Beetles. The varied carpet beetle (Anthrenus verbasci) is a 3 mm-long beetle belonging to the family Dermestidae. They are a common species, often considered a pest of domestic houses and, particularly, natural history museums, where the larvae may damage natural fibers and can damage carpets, furniture, clothing, and insect collections.
Source: Varied Carpet Beetle

This is incorrect

This is what I could find closest to those shown in the image. I might be wrong.


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Can plants break down cellulose for energy?
I know humans and other animals start using their own proteins as food when starving. This made me wonder if a plant that is deprived of sunlight, after using up its sugar reserves and other carbs, could break down parts of its own woody structure in order to feed the rest of itself.
Googling yielded no useful results, which leads me to think the answer is no. I've never heard of plants themselves possessing cellulase, only certain animals.
Additionally, I would imagine that cellulose is not easy to transport, so it would have to be decomposed by the region of tissue surrounding it - which obviously couldn't last for long before that region died due to cannibalizing itself.

Then deciduous trees would absorb back their leaves rather than losing them in autumn. I think that plants can take back most things from leaves except cellulose.

breaking down cellulose is very different than breaking it down FOR energy, which are you looking for> it would not surprise me if there are plants that can break down cellulose but do so at a net loss.

Plants do not produce extra cellulase to break down cellulose for an energy boost when they are grown in dark conditions (that I know of). But remember, cell walls are the structures maintaining turgor pressure in the cells, so breaking them down would be very costly to plant survival. A couple notes: plant cell walls have more components than just cellulose, and they ARE dynamic. In dark-grown conditions, plants elongate (etiolation) during which time, enzymes (expansions) break down cell wall bonds to allow the cells to elongate the stems of the plants. Elongation is an evolutionary advantage to find light when things get shady.
To read more about what the cell wall is made of, and the function it provides to the cell, try watching the Khan Acadamy video about cell walls. Light signaling is an entire field in Plant Biology (example). Read more, if you are interested in how immobile plants handle shading from other plants or periods of darkness. Plants do break down proteins for reuse! Read more about plant vacuoles if you're interested in how they recycle and break down some molecules and proteins when needed (related to your question's parallel to animal cells; although, not cellulose breakdown to replace photosynthetic sugar output).

This is a good answer, but it is much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, the most directly relevant part of your answer is indistinguishable from opinion and someone with no plant biology background will be unable to judge your assertions. ——— Note that links often break, so we prefer that you also include citation information. This is a good example of how to format references. Thank you!


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Can different proteins be produced during translation of a single mRNA in eukaryotes?
Is there a translational mechanism that eukaryotes can use to produce different proteins from a single transcribed mRNA?

Yes; you may like to look up post-translational modifications. (https://en.wikipedia.org/wiki/Post-translational_modification)

I have suggested an edit to the title — if that is not correctly summarizing your question can you please clarify what you want to know.  Please also edit your question to specify whether you are interested in the phenomenon of polycistronic mRNAs as suggested by @user1136, which is also a reasonable interpretation of your question as it is currently written.

@tyersome — You are being too restrictive In asking if the poster is referring to polycistronic mRNAs. The question is ok as it is, except it may well have been asked before. I’m not in a position to check.

@David — I'm sorry, would you mind explaining what you mean by "too restrictive"?  I was trying to ask for clarification about the poster's intent, but I'm gathering it reads differently ...

@tyersome — There’s no reason to restrict an answer to one type or mechanism, especially as the poster doesn’t know the answer, and an answer would be more generally useful that covered polycistronic viral RNAs, alternative initiation, read-through, frameshift and post-translational proteolysis. I’m travelling at the moment, but if nobody finds the duplicate I feel exists, I’ll answer it comprehensively myself next week.

thanks for the input! I wanted to know if there is a way to get two or more proteins from one mRNA. I did not know of any eukaryotic polycistronic mRNA, and was looking to see if there is such a case. If not, if there is any way to alter translation to obtain multiple proteins

Possible duplicate of Can a single strand of mRNA form different polypeptide chains?

There are multiple mechanisms that are known to lead to translation of substantially (or entirely) different proteins from a single mRNA. While these mechanisms are more typically seen in viruses, I'm focusing on examples documented within the endogenous transcriptome of eukaryotes.
Alternative translation initiation
One process that can lead to different proteins being translated from the same mRNA in eukaryotes is the use of alternative translation initiation sites.1,2 Translation typically starts with a [pre-initiation complex](https://en.wikipedia.org/wiki/43S_preinitiation_complex) recognizing the 5' cap and loading onto the mRNA. This complex scans until it finds an appropriate start site. The choice of start site depends on the how well the ribonucleotide sequence matches the [Kozak consensus sequence](https://en.wikipedia.org/wiki/Kozak_consensus_sequence).3 If the region around the first AUG is not a good match for that consensus then a process known as [leaky scanning](https://en.wikipedia.org/wiki/Leaky_scanning) occurs and the pre-initiation complex can continue along the mRNA until a "good" start site is found.
While this can result in proteins with different functions, they will typically still have large regions of amino acid sequence in common. One example of this is in a kinase known as MK2, which is "a key regulator of transcription, migration, death signaling and post-transcriptional gene regulation".4
Polycistronic mRNAs
While more common in prokaryotes, in some cases eukaryotes also have polycistronic transcripts5,6.  These transcripts encode multiple separate proteins (i.e. from independent open reading frames). The examples that I have found for mammals are all bicistronic (operons with two genes): LASS1-GDF1, SNRPN-SNURF, MTPN-LUZP6 and MFRP-C1QTNF5. You can search for those gene pairs, but there doesn't seem to be a huge amount of information available and in many cases one of the genes is almost completely uncharacterized. Eukaryotic operons (aka polycistronic mRNAs) are ubiquitous in trypanosomes, appear to be very common in nematodes (round worms), and are also frequently seen in Drosophila (a fly).6
Translational read-through
[Translational readthrough](https://en.wikipedia.org/wiki/Stop_codon#Translational_readthrough) aka. stop codon suppression occurs when an in frame stop codon is ignored either stochastically or under specific conditions and translation continues beyond that point. This leads to a C-terminal extension of the protein which in some cases has been shown to have functional implications7,8. An example of this is the [PSI+] prion in yeast, which promotes translational readthrough throughout the yeast transcriptome by inactivating a factor involved in translation termination.7
Translational frameshifts
This is well covered in the answer by @acvill.
References:
1: Kochetov, A. V. (2008). Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays, 30(7), 683-691.
2: Wan, J., & Qian, S. B. (2013). TISdb: a database for alternative translation initiation in mammalian cells. Nucleic acids research, 42(D1), D845-D850.
3: Acevedo, J. M., Hoermann, B., Schlimbach, T., & Teleman, A. A. (2018). Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Scientific reports, 8(1), 4018.
4: Trulley, P., Snieckute, G., Bekker-Jensen, D., Menon, M. B., Freund, R., Kotlyarov, A., ... & Gaestel, M. (2019). Alternative Translation Initiation Generates a Functionally Distinct Isoform of the Stress-Activated Protein Kinase MK2. Cell reports, 27(10), 2859-2870.
5: Tautz, D. (2008). Polycistronic peptide coding genes in eukaryotes—how widespread are they?. Briefings in Functional Genomics and Proteomics, 8(1), 68-74.
6: Blumenthal, T. (2004). Operons in eukaryotes. Briefings in Functional Genomics, 3(3), 199-211.
7: Schueren, F., & Thoms, S. (2016). Functional translational readthrough: a systems biology perspective. PLoS genetics, 12(8), e1006196.
8: Loughran, G., Jungreis, I., Tzani, I., Power, M., Dmitriev, R. I., Ivanov, I. P., ... & Atkins, J. F. (2018). Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. Journal of Biological Chemistry, 293(12), 4434-4444.

I have found the question that this is a duplicate of. May I suggest about how your answer could have been improved. Its strong point is the references it gives, but as most readers will not follow them up or may not have access to all the papers, you could — in my opinion — improve the explanation in your commentary. Just saying "alternative translation" does not make it clear to the uninformed what you mean. The answer to the original by @WYSWYG is not perfect (IMHO), but he gets it right by referring to alternative initiation and mentioning sites. And he also mentions read-through.

@David — Thank you very much for all your valuable feedback and tireless work on maintaining standards on this site.  Do you think it would be better to close this question as a duplicate?  If you think is worthwhile to keep this question I'm happy to work on implementing your suggestions in my answer ...

I had voted this as a duplicate (the text of my comment is autogenerated when one does that) but nobody else has seconded that — perhaps because the original is not specific to eukaryotes. My advice is to go ahead and improve your answer, explaining the basic Kozak mechanism in eukaryotes and how it has emerged that this is a simplification in many cases. If the question is ever closed as a duplicate I don't think you will loose your points, and you could always delete your answer and repost it on the original.

@David — Thank you for your encouragement! I finally found the time to put some more effort into this and while I'm not really satisfied I'm done for today. I welcome any further feedback you are willing to provide.

That's fine. I do have a list of all the di- and tri-cistronic transcripts in Drosophila in supplementary material to a paper I published, but that would be a bit OTT.

Separate from the alternative translation start site mechanism that tyersome describes is programmed translational frameshifting.  This is independent of alternative splicing or post-translational modifications, and happens when a ribosome switches reading frames while a protein is already being translated.  Typically, this phenomenon is associated with viral translation, and allows viruses to encode many proteins on relatively short genomes.  Take HIV as an example: the polyprotein gag-pol requires efficient −1 frameshifting for expression of the individual gag and pol gene products.
In eukaryotes, examples are more sparse.  Check out this review from 2012 --

... examples of mammalian genes that utilize −1 frameshifting are the mouse embryonic carcinoma differentiation regulated (EDR) gene and its human ortholog PEG10. A slippery sequence of G GGA AAC, in combination with a pseudoknot, mediates highly efficient −1 frameshifting, similar to viral frameshifting motifs (Clark et al., 2007). Recently, a programmed ribosomal −1 frameshift has been identified in the adenomatous polyposis coli (APC) mRNA in Caenorhabditis elegans that is mediated by a slippery sequence A AAA AAA or A AAA AAC (Baranov et al., 2011). The functional relevance of this frameshift is uncertain.

Frameshifting events are often mediated by conserved RNA secondary structures, like pseudoknots and stem-loops.  For some specific examples of the types of structures involved in frameshifting, see the following publications:
Identification of a New Antizyme mRNA +1 Frameshifting Stimulatory Pseudoknot in a Subset of Diverse Invertebrates and its Apparent Absence in Intermediate Species
Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%
−1 Frameshifting at a CGA AAG Hexanucleotide Site Is Required for Transposition of Insertion Sequence IS1222

Some more recent examples of (potential) programmed translational frameshifts in eukaryotes:
Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes
Preprint: Extensive programmed ribosomal frameshifting in human as revealed by a massively parallel reporter assay

+1: This is a helpful addition, but your last two links are eubacterial rather than eukaryotic  examples.  Did you find any non-viral examples that have been shown to have functional significance in eukaryotes?

Updated my answer to include more recent examples of programmed frameshifts in eukaryotes.  Thanks, tyresome


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Why can't H3O+ ions pass through aquaporins?
Aquaporins are proteins that facilitate the movement of water (and related molecules) through cell membranes. (Also, these transport proteins are very specific about what they transport.) Interestingly, aquaporins can facilitate the passage of glycerol but not H3O+ ions. This is difficult to comprehend as the structure of glycerol is quite dissimilar to H2O while H3O+ is quite similar to H2O.
What is the reason behind this?

This question has been directly addressed by the paper The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel. I think it's a pretty good one too! I paste the abstract below:

Aquaporins are efficient, yet strictly selective water channels.
Remarkably, proton permeation is fully blocked, in contrast to most
other water-filled pores which are known to conduct protons well.
Blocking of protons by aquaporins is essential to maintain the
electrochemical gradient across cellular and subcellular membranes. We
studied the mechanism of proton exclusion in aquaporin-1 by multiple
non-equilibrium molecular dynamics simulations that also allow proton
transfer reactions. From the simulations, an effective free energy
profile for the proton motion along the channel was determined with a
maximum-likelihood approach. The results indicate that the main
barrier is not, as had previously been speculated, caused by the
interruption of the hydrogen-bonded water chain, but rather by an
electrostatic field centered around the fingerprint Asn-Pro-Ala (NPA)
motif. Hydrogen bond interruption only forms a secondary barrier
located at the ar/R constriction region. The calculated main barrier
height of 25-30 kJ mol(-1) matches the barrier height for the passage
of protons across pure lipid bilayers and, therefore, suffices to
prevent major leakage of protons through aquaporins. Conventional
molecular dynamics simulations additionally showed that negatively
charged hydroxide ions are prevented from being trapped within the NPA
region by two adjacent electrostatic barriers of opposite polarity.

The difference between glycerol and and a protonated ion such as H3O+ is charge, and many ion channels are selective based on charge too. Of course, other properties play a role, such as size and steric shape, but charge is a very important one and this applies to a great many channels beyond aquaporin!


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Is this a hornet?
I live on the 2nd floor of an old apartment building in Vancouver BC (Canada). A couple of years ago we had an issue with a hornets nest that was difficult to remove because of its location. They managed to find a way into the actual apartment despite window screens etc. We thought the issue had been resolved, but today I saw this flying around outside my window:

The main body was maybe 2-3 inches, but it had a very long "tail" or I guess what might be stinger. Never seen anything that large before. This insect was much larger than the hornets from previous years (which were at most 1 inch in length)
What type of insect is this, and should I be concerned?

This is not a hornet, this is an Ichneumonidea wasp, which is a superfamily of parasitoid wasps with about 100,000 species. I would go so far as to think it is within the Ichneumonidae family and think that it is probably Rhyssa lineolata, though I am certainly no entomologist of any sort. Note that because there are so many species, it might be quite hard to identify, though this is a large one, and has the very long ovipositor so that should narrow it down for someone more skilled at ID than me. Most Ichneumonid wasps are much smaller and lack the long ovipositor.
All parasitoid wasps lay eggs on or inside another species of insect or arachnid, where the egg hatches and uses the host species as food for its larval development. These sorts of wasps usually parasitise larvae of wood-burrowing species, so they use the long ovipositor to drill into the wood and deposit their egg(s). There's some footage and images of this for a Rhyssa species on Wikipedia
I don't think this species will sting as the ovipositor is too fragile and long to be easily manipulated to sting someone. These sorts of ichneumonids usually are looking for dead wood with grubs in it, so it could potentially indicate that you have some grubs in wood in/around your house, but it is much more likely that there is a tree with a dead branch nearby.  Apparently they are also attracted to fresh sawdust (thanks to comment from @polypipewrangler)
As far as I know, these are solitary wasps - they don't build nests, so you won't see more than 1 or 2 at a time.

They are also attracted to the smell of fresh sawdust.

That makes a lot of sense given 1) right outside my window is a whole bunch of trees and 2) theres been some construction outside as well. Thanks!

@PolypipeWrangler I didn't know that. I will edit it in. I wonder if this is because the burrowing larvae are putting out "sawdust" as they burrow.


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What is this bug? (Northern Italy)
I found two of these going around my room, looks like they entered from the window. Size is about 8-10 mm. Colour a very light translucent brown.
Any ideas of what it could be and if it's dangerous? The image is blurry as it was startled by the light and started running around :)
I live in Northern Italy and weather is humid heat (32° C, 62% RH) if that helps.

That looks like a sow bug, but white. The ones in my area are brown.

Welcome to Biology.SE. Identifications questions should include: 1) one or more clear closeup photos of the organism (photos from multiple angles if possible); 2) the species-identification tag; and 3) habitat information. Please [edit] your post to include as much of this essential information as possible. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.


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How to decipher references in natural history works of the late Renaissance and early Modernity?
Old botany books from the 17th, 18th and 19th centuries (and maybe also some later ones) enumerating lists of species used to give references to their sources as abbreviations consisting of one or few truncated words and sometime numbers.
For example : C.B.Pin.316. or H.Mal.6.79 or Prod.Par.Bat. (see highlighted parts in the following screenshot extract).

Source : https://www.biodiversitylibrary.org/page/502858
The meaning of these abbreviations may have been clear to the scholar of those times, but are quite enigmatic to non-initiated people. And I couldn't find within the books any intelligible list of these references.
I would like to know if there is a somewhat comprehensive list of such abbreviations giving the full wording of the references so that it could be possible to look up for them. Browsing the internet with just the abbreviation mostly gives meaningless results from popular websites (many in social networks ...).
I did find out the meaning of some of these abbreviations:
for instance: C.B.Pin. means Caspari Bauhini Pinax Theatri Botanici, which is this book: https://www.biodiversitylibrary.org/bibliography/713 and the number (here 316) gives the page where the plant was listed in this book.
However, there is a huge number of these enigmatic references, so some help would be really welcome.
I looked at the International Plant Name Index (IPNI), but it does not seem to have results for these abbreviations.
I searched the web for:

"prelinnean book abbreviations", which returned one result of some interest but did not give anything near my desired list.

"prelinnean references", which lead me to this article: C.E. Hutchings, 1903. A supplementary catalogue of the Sturtevant prelinnean library. Miss. Bot. Gard. An. Rep. 1903, pp 233-316. but these are the complete book titles, without the abbreviated forms so that it's quite impossible (or very difficult) to use such material.

I also tried combinations involving such words as "old botany books" "old references in botany books" but could find nothing suitable.

I have found what may be the holy grail. It is a book known as "A Botanical Materia Medica" by Jonathan Stokes. This has several volumes, but the one you want is volume 1, which has no appended "volume X" in the title.
A list of abbreviations can be found on page XIII (or 13 for those not familiar with Latin numerals), just after the introductory letters and dedication.
You can read the volume for free on Google books (let me know if the link doesn't work; I made it into a .com link from my country one...)
I found this by search for "cam hort botany"; "cam hort" being one of the abbreviations in your supplied picture. This lead me directly to one of the Botanical Materia Medica volumes by Stokes, which lead me to think it may well have a list of references somewhere, so I then searched for "botanical materia medica stokes" and working from there.

Thank you so much ! That was exactly the kind of list I was desperately looking for !
I'll keep an "open ear" to possible other lists like this one, maybe of more recent and/or more comprehensive compilation, but as a first result, that's a brilliant one ! Thanks again !

@botaflo no problem. I have come across a similar question before on another site. I'm a former botanist myself (now virologist), so I know the frustration. I also like old texts of this sort, so if you have access to the originals, know that I am deeply envious.

;-) no need for envy : I only access such texts from behind my screen. Yes old texts are cool. It's such a great chance to at least have access to them through internet !

I have found a database which lists some abbreviations, it's on Tropicos.
But it seems quite limited in the search possibilities, for instance: looking for "Hort. ups." does not find the "Decas plantarum rariorum horti upsaliensis" which is abbreviated in this database as "Dec. Prima Pl. Rar. Hort. Upsal.", neither does the search for "Hort ups", nor "hort" nor "ups".
So if you don't give it exactly the correct abbreviated form, it might not succeed. You might have better luck if you have the right beginning and there are not too many options.
Still, it might be of interest for someone, and it does give something like what I was looking for, so I'll leave that link here.
Oh, and there is also this one here.
And the IPNI does provide some search for publications, but no index of abbreviations (but it may be worth to try searching for bits of abbreviations).

I was not so happy with all of these so I made my own list. It's on my Wikipedia sandcast.

[Edition, June 5, 2022] I just found "An Explanation of the AUTHORS Names" in the Gardeners Dictionnary by Philipp Miller (1768), which looks quite close to what I was looking for.


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Grasshopper vs Tarantula?
This past weekend (October 2021) while hiking west of the VLA in New Mexico (near Datil, NM, ~2200m elevation) my wife and I came across a strange sight. A small (5cm long), likely immature, Aphonopelma peloncillo walking near the trail. That was not particularly unusual this time of year. However, as it moved we noticed that it was being followed by a grasshopper, which was roughly as long as the small tarantula. While the tarantula was still, the grasshopper would walk (not hop) up behind it, the tarantula would notice and skitter forward 10-15 cm, and the process repeated itself over a distance of a meter or so. Several times it appeared that the grasshopper made to attack the rear end of the tarantula. Eventually the tarantula said enough is enough and skittered out of sight rapidly. The scene was mesmerizing enough that neither of us got out our phones to take pictures (sigh).
Based on pictures at insectidentification.org and Wikipedia and going by memory (stupid - no pictures), the grasshopper was likely a Differential grasshopper, Melanoplus differentialis. The size (females up to 5 cm) and territory fit. Sources given indicate they eats plants. Given the season it seems unlikely to me that, were they female, they would still be laying eggs - one of the few reasons I can think of they would try to drive off a tarantula.
Is this a known behavior for a grasshopper? Was it protecting territory (do grasshoppers even have territory)? It is hard to imagine that the grasshopper was attempting to prey on the tarantula. Any information (journal articles welcome - I've searched on Web of Science with no success) available?

Welcome to Biology.SE. Interesting question — is there any chance you could provide more details about the grasshopper? Knowing what species it was could help with you getting a better answer. I do know that some species of grasshopper are omnivorous, but I don't know whether they've ever been reported to attack spiders (let alone a tarantula).

What an interesting observation! Perhaps it was a kind of carnivorous orthopteran? I would suggest using BugGuide's Browse tab to narrow down candidates, and check the Data tab for any likely taxon to make sure it is found in New Mexico.


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What is this bird species in the Pacific NW?
I don’t think it’s a Black Phoebe, as they have black beaks not white. Is it a Grosbeak? This was taken in the Pacific NW.. . Sorry for the pic quality.
If this isn’t the right place to post this, please tell me where.

That is a Dark-eyed Junco, Junco hyemalis.  This one is a member of the "Oregon" subspecies, J. h. oreganus, which used to be considered a species, Junco oreganus, before a number of species were combined because they are capable of interbreeding.  The are small, ground-feeding birds, primarily consuming seeds and insects. There are two white outer tail feathers which are prominent when they are flying.
 (image: Andy Reago & Chrissy McClarren via Wikipedia Commons)

Thank you! That’s what it is. I have an app, Merlin Bird ID, that lists birds in the pac nw (or anywhere in the world actually), but the first pic didn’t look like it at all. Which is why I missed it. But as I went in and looked at all the pics the exact bird was there.


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What species is this larva?
I'm trying to identify the species of what I think may be some kind of Lappet Moth larva? (wild guess based on some internet sleuthing)  But the markings don't really match nicely with any photos I can find.
It's light grey/blue-ish, with sparse tufts.  Horn-like hairs at the head and not much going on at the tail.  It's about 75 mm long (not quite 3 inches).
It was found in a bag of grass clippings after mowing the lawn.  Geographic location is the Bruce Peninsula in Ontario, Canada.  Did not find any others like it on the property.  It's unfamiliar to me (first time I've seen one like it).
Can anyone more positively identify?

Might be American Lappet Moth (Phyllodesma americana), check the trees above for more. If convenient, stretch it out a little, or make it angry to see possible orange bands.


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What is the normal flora in Respiratory Tract (Upper and Lower)?
I opened my notes and it stated :

pharynx, trachea, bronchi : << flora normal
bronchioli & alveoli : steril

which I doubt because many papers I read stated that the lower-respiratory tract is not as sterile as we thought. However, the normal flora in the respiratory tract in all of these papers have different kind of bacteria. For example: one paper stated that the upper respiratory tract has Corynebacterium spp., Dolosigranulum spp., where other papers stated that viridans group streptococci, Staphylococcus epidermidis, etc. were found.

Welcome to Biology.SE. Can you please [edit] your question to add more detail including: 1) references & links to the papers you've consulted (example of how to format references; and 2) the organism is question (I'm guessing you probably mean for humans, but this is [Biology.SE] not [MedicalSciences.SE]). As written this may not be a great fit for this site since it seems to be asking for a list of microorganism names, so please also tell us why you want to know this. That may influence what kind of answer is appropriate.

I've done some copy editing on your post, but please make sure I've not altered your intended meaning. In addition, note that the abbreviation of genus names (e.g. you originally wrote S. epidermidis) should only be done after the full name has been written out. In the future please check your posts for spelling and readability before posting. Finally, please clarify what your question is — are you asking whether the lower respiratory tract is normally sterile or are you interested in the composition of the normal flora — each post should only have a single question.


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circular pattern of mold on quince
Could someone explain why mold on my quinces grows in well separated circles around a center? To make clear, what I mean I post the picture

Somewhat related to fairy rings?

Looks like you may have Monilinia fructigena, brown rot, or at something similar (possibly also called brown rot, but from a different species). This pattern isn't special to quince, but to this fungus.
The formation of these rings is called "zonation", and the concentric rings are from areas of growth that are primarily spore-forming versus not.
Hall (1933) gives an extensive description of the different factors necessary for observing this growth pattern, but ultimately the key factor is light. Patterns of light-and-dark conditions while the fungus spreads causes alternating phases of growth, with one phase comprised of more sporulation.
Another source: https://www.cabi.org/isc/datasheet/34747

Byrde, R. J. W., & Willetts, H. J. (2013). The brown rot fungi of fruit: their biology and control. Elsevier.
Hall, M. P. (1933). An analysis of the factors controlling the growth form of certain fungi, with especial reference to Sclerotinia (Monilia) fructigena. Annals of Botany, 47(187), 543-578.

Thank you for your answer, I have no access to the publications, which are not online. Is it possible that the factor light means just day and night?

@trula Yes, day and night.

thank you again


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Phytophagous worm identification
These worms appear soon after the rain lilies flower and slowly nibble on the leaves growing big and chubby. They are about 5cm long, have many small red legs underneath, have no spines or spikes, and are soft-bodied.
They leave tiny green balls of excreta. I have never seen them metamorphose.  I live in Andhra Pradesh in India. Can anyone tell what species they are? Are they dangerous?

I think it's a caterpillar (an insect), not a worm.

I think you have an Indian Lily Moth (of the genus Polytela). It is considered a minor pest. Their habitat seems to only be around India and its surrounding area.

Their worm matches yours ... smooth, dark, but red patches and white spots:

If you dig in your garden, you may encounter these pupae:

And they eventually grow into these beautifully-multicoloured moths:

Here is a video showing their movements and their life cycle:
https://www.youtube.com/watch?v=2l0oxZM_6XY

But it's quite curious that I have never seen the moths [they look absolutely stunning]perhaps the birds eat the larvae before they turn into pupae?


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Why do mosquitoes appear to be repelled by magnets?
A few days ago, I was playing with magnets and thought of placing one near a live mosquito (I had it held between my two fingers so it had no chance of escaping). When near the magnet, it twitched and flew away! I tried the same with semi-alive mosquitoes, but nothing really happened.
I googled about this and learnt that mosquitoes have got to do something with magnets, but I'm still confused. Could anyone tell me why mosquitoes get repelled by magnetic fields?
PS. I'm no biology student, so please go easy on me, thank you ahead of time!
Source (PDF)
EDIT: Strickman et. al. (2000) says:

we found that some specimens had a significant magnetic remanence
Could this possibly be the reason why mosquitoes may get repelled by magnetic fields?

That paper also states:

the mosquitoes were able to detect the magnetic fields but sensed a magnetic pattern that was impossible in nature.

Reference:
Strickman, D., Timberlake, B., Estrada-Franco, J., Weissman, M., Fenimore, P. W., & Novak, R. J. (2000). Effects of magnetic fields on mosquitoes. Journal of the American Mosquito Control Association-Mosquito News, 16(2), 131-137.


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What is 'refractile' cell morphology?
I can't find a definition for 'refractile' (not 'refractory', and not explicitly in an optical context).
As in:

A tumour cell phenotype features increased proliferation, anchorage- and growth factor-independenth growth and ‘refractile’ cell morphology

It's not in any of the dictionaries I can access online, nor in the Oxford Dictionary of Biochemistry and Molecular Biology. Any help would be appreciated, thanks.

I'm not sure, but i think it refers to an actually refracting activity of those cells in phase contrast microscopy. For example, (as you can see here ) the nerve cell bodies are refractile.

Yeah, that's specifically of the 'lateral periphery'. This just says 'cell morphology', Actually I think it means they grow to a higher density

From the Biology Online Dictionary, refractile refers to:

... the ability of cellular granules to refract or scatter light.

Tumor cells can be more "dense", as they are usually rapidly dividing, and so need extra ribosomes to maintain protein production, may have a higher DNA/RNA content reflecting increased transcription and duplication, more mitochondria to power the cells, etc. This can alter the refractive index of a suspension of tumor cells as compared to organ-matched normal cells, for example.

Essentially, yes. Refractile would be of the cell itself rather than describing the solution, and they've overridden existing limits on growth (growth factor dependence etc.) It's just a term in physics, not a biological one related to granules.

Please note that this explanation may not be the actual physics definition, but it will help you to understand the concept of ‘refractile’ cell morphology.....
From the statement below by www.brittanica.com it appears that light is both partially reflected by & partially refracted or "transmitted" (think absorbed) into the object it is hitting. (Technically transmission is NOT absorption, but for this purpose it's easier to think of it as being absorbed by the cell/cell parts).
So when light hits the cells/cellular parts in a scan, some of the light is reflected back and some of the light is "absorbed" by the cell/cell parts. The amount of light "absorbed" is variable for each cellular component, and therefore, the amount of light reflected back is also variable.
In the scan or microscope, we actually "see" the reflected light. Not the refracted (absorbed) light and because the light reflected is variable, we are able to "see" the different components of the cell (i.e the different amounts of light reflected by the various parts).
So the statement ‘refractile’ cell morphology means that the cell has components which absorbs light at variable amounts and therefore, also reflects light at different amounts. Essentially, you are able to "see" the cell morphology & its differences because it refracts (absorbs) some light and reflects the rest.
Hope this helps get the concept. =)
"When a ray of light is incident upon a plane surface separating two mediums (e.g., air and glass), it is partly reflected (thrown back into the original medium) and partly refracted (transmitted into the other medium)."
https://www.britannica.com/science/radiation/The-structure-and-properties-of-matter#ref398785


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Why can sodium oligomannate (GV-971) improve cognition in people with Alzheimer's Disease?
There is a Phase 3 placebo-controlled clinical trial to evaluate the efficacy of sodium oligomannate (GV-971) in the treatment of mild to moderate Alzheimer's disease (AD).
A Study of Sodium Oligomannate (GV-971) in Participants With Mild to Moderate Alzheimer's Disease (GREEN MEMORY)
Why can sodium oligomannate (GV-971) improve cognition in people with Alzheimer's disease? What is the mechanism of this drug in AD?

Are you asking us to judge the outcome of a trial in advance? Could you [edit] to tell us what the actual question is, add relevant detail, at the moment it's not clear how the trial you've linked might relate to the mechanism of action (if there is one).

I am just curious about the mechanism of this drug.

From Wikipedia, albeit not the best source for this sort of thing:

The mechanism by which sodium oligomannate may function is unclear and several possibilities have been proposed,[6] including amyloid beta disaggregation,[7] mediation of inflammatory responses to amyloid plaques,[8] protein binding inside neurons,[9] and alteration of intestinal bacteria.[10]

The page also mentions:

It was conditionally approved in China by the National Medical Products Administration in 2019 for mild to moderate AD to improve cognitive function.[1] However, the clinical data supporting its potential benefits have been received skeptically elsewhere[2][3][4] and are considered insufficient for approval in other countries.

Importantly, it's not necessary to know a drug's mechanism to get it approved, only to show that it is safe and effective. The mechanism for antidepressants, for example, is still not known, for any of them, we just know that they work better than a placebo. We also know what receptors in the brain they affect and the local mechanisms there, but without a better scientific understanding of depression it's not currently possible to understand which combination of those molecular effects give the behavioral effects.
Similarly, Alzheimer's disease is not understood mechanistically, so it's very plausible to develop drugs for it without knowing the mechanism. For this drug, it seems like both the mechanism and efficacy are not known to the standards expected by regulators in the US and EU for approval.
The proposed list of mechanisms mentioned on the Wikipedia page sound a bit to me like a collection of all the different theories of mechanisms for Alzheimers' disease itself, which is still poorly understood.