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Do we know all the possible human hair colors?
I occasionally see people with blue hair and I always assume it is dyed. I wonder how justified is that assumption. Have biologists determined all the possible human hair colors? Or is it possible that if an embryo was exposed to the right amount of radiation in the right place it could get green hair or some other hitherto unseen color?
NCBI lists some alleles of MC1R together with their effects on the phenotype but I don't know how exhaustive their data is (and also other genes might be at play).

Have you checked Wikipedia? https://en.wikipedia.org/wiki/Human_hair_color

Do you mean natural? I spent a lot o time in a cancer hospital with my wife and I have seen, for example, pinkish hair that I could bet was not dyed. I've also seen bluish and greenish, but can't begin to guess if it grew like that or was coloured artificially.

Melanin is the only biologically coded for pigment amongst mammals and most animals broadly speaking. Some birds are exceptional in this case where reds and greens can be seen (in which case often some dietary component is required for the synthesis of these abnormal pigments).
In humans, the entire variation in skin, hair, and eye color is a consequence of varying treatments of melanin. Melanin traditionally comes in two forms, namely eumelanin and phaeomelanin. The former can come in a brown or black variety while the latter is responsible for the reds and oranges seen in human pigmentation (e.g., localized to the lips, nipples, and nether regions).
Red pheomelanin serves as an accent and does very little as far as protection from UV radiation is concerned; the brown-black melanin serves that purpose. The cells in your body that produce melanin are known as melanocytes, and the MC1R gene you mentioned codes for a receptor that localizes to the membrane of these cells. This receptor acts as a light switch that indicates whether the melanocyte ought to be producing red pheomelanin or brown-black eumelanin. An agonist that binds to this receptor is coded for by the ASIP gene and is also partially responsible for pigmentation differences throughout the animal kingdom.
In most people this receptor functions as intended, and melanocytes in the skin produce varying degrees of brown-black eumelanin (the extent of which depending on one's ethnic background) while pheomelanin is switched on in the few key areas listed above. When both copies of the MC1R gene inherited from each of your parents are disfunctional, this switching mechanism no longer works and your melanocytes will produce primarily pheomelanin ubiquitously across your body. This is what we know as 'redheads'.
What isn't immediately obvious is that red-haired individuals are not unique in just the aspect of their hair. Their whole body presents with a deficiency in eumelanin and as such they also carry a pale/rosy complexion as well as an inability to tan and a propensity to sunburn easily. This is a consequences of the fact that eumelanin is our primary defense against UV radiation.
While melanocytes in the skin and eyes are responsible for the production of melanin, the melanin in one's hair gets there as a result of a handoff between melanocytes and the keratin producing keratinocytes. Melanin within melanocytes is produced and stored within organelles known as melanosomes and, through a complex formed by the 3 genes MYO5A, RAB27A, and MLPH, the transfer of these melanosomes through the tendrils of the melanocytes to the keratinocytes is facilitated. Defects in any of these 3 genes can result in a condition known as Griscelli syndrome (types 1, 2, and 3, respectively) where the transfer of melanin from melanocytes to keratinocytes is impaired.

As a consequence the hair of one of these individuals appears silver, and when looked at under a microscope you can see the inconsistent nature of the melanin being transferred to the hair during its development:

To summarize, the only pigment that appears in hair is melanin, and thus the only possible hair colors are: the entire spectrum between blond and black; red in the case of MC1R defects; silver in the case of the Griscelli syndromes; and of course white in the case of albinism (which I needn't cover).

You mentioned blue hair color but I think this might be due to a misconception about how blue eyes came to be. Blue eyes are not due to a blue pigment (rarely is blue ever found in nature), but rather due to a physical manipulation of the light being reflected due to the microscopic structure of the eye. So in the same way that the sky and  water can appear blue due to manipulation of light, so can the human eye. The blue of human eyes is typically covered up by melanin, except in the case of those carrying a specific one-letter mutation within the HERC2 gene that results in the absence of melanin in the eye.
Not just black and white: pigment pattern development and evolution in vertebrates
Signaling Pathways in Melanogenesis
Rab27a and MyoVa are the primary Mlph interactors regulating melanosome transport in melanocytes

Comments are not for extended discussion; this conversation has been moved to chat.

Bright bird coloring, like butterflies, is usually not the result of pigmentation but microfibers forming a texture that refracts and reflects light almost the same way as a holograph - which explains why the same bird can appear different colors based on the angle they're viewed from.  Viewed up close, those feathers are not actually blue or whatever color they appear to be from a distance.

Is it conceivable that human hair could develop (via some mutation) with the microscopic structure needed exhibit other colors via reflection & refraction?

@R..GitHubSTOPHELPINGICE funny you should ask, theres a mutation that causes a condition know as "pili annulati" where the hair follicle has air bubbles in it and they create reflective bands in the hair. I always have my eyes peeled for any new papers about this because the genetic origin of this is not known

In that case, it seems plausible that there may be more colors (depending on your definition of color).

Time to break out the CRISPR set and get my follicles to produce some turacoverdin.

Technically, isn't the silver of Griscelli Syndrome the same thing that causes blue-haired cats (most famously the Russian Blue and British Shorthair), when it occurs in someone with what would have been black hair? Looking at wikipedia, I think it's the same gene, too, at least for the non-lethal variant of the syndrome.

@nick012000 But blue cats aren't really BLUE, at best they're just a sorta-kinda cool toned grey. Another option would be mixed hair like a bluetick hound or a blue roan horse, but this also isn't BLUE, just kinda-sorta-maybe-blueish. You get this with some people who have black hair and are greying from age, but the light conditions have to be very favorable to describe it as blue.


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Following mRNA vaccination, do proteins mostly exit "naked" from transfected cells or by some more indirect route (EVs etc.)?
Related to someone's elses disbeliefs in how proteins produced from a mRNA vaccine end up in B cells; in theory the process could be more complicated than "naked" egress (which arguably does have simplicity in its favor). There's at least one paper that discussed spike proteins observed egressing in extracellular vesicles (following mRNA vaccination) but it doesn't really say whether this is the common route. And from the general gist of that paper, EVs seem to interfere with detection, so I'm guessing that's not the usual route. For yet another alternative, I could imagine that transfected cells first get killed by CD8 T cells and it's mostly this debris that gets picked up by B cells.
Interestingly, on the last angle, one review mentioned that

Comparative studies performed by
our research group and others demonstrated that nucleoside-modified mRNA LNPs
outperformed unmodified mRNA LNPs in translation capacity, but failed to elicit successful
CTL [cytotoxic T cell] responses due to the drastically reduced production of type I IFNs [119, 157].

So it seems that the mRNA vaccines currently in clinical use for infectious diseases like Covid-19 (which do use nucleoside-modified mRNA) are pretty unsuccessful at killing cells, which makes the 3rd pathway I was considering above somewhat unlikely as a major contributor. (The research group which wrote that review seems focused on cancer immunotherapeutics, and the two cited studies definitely are about that. The lack of CTL activation is a big deal for cancer therapy.)
So, what direct evidence is there for how proteins most often come out cells following mRNA vaccination, particularly in nucleoside-modified vaccines?

During (mRNA) vaccination the spikes mostly don't exit the cells, they get anchored onto the surface membrane. It means that -something nobody talks about- they are likely taken by (dendritic) cells after the cell dies, because the cell is detected by the immune system as "infected". Klling (+phatocytize+presenting on MHC-II the non-self parts) the infected cells is something else almost nobody talks about, whereas it is a very important part of the immune system.

At the 2nd dose things are obvious: the spikes on the surface of the cell are detected by the antibodies produced after the 1st dose which triggers antibody-dependent cell cytotoxicity (NK,..) and phagocytosis (macrophage,dendritic cells,..)

This paper did a serious study of the trafficking of the spike, adding a "HA-tag" (in S1) to detect the spike with labeled antibodies.

@reuns: Thanks for the link. Somewhat inconclusive though. Regarding your other comments, I doubt cell death is the major pathway because the vaccine is administered IM and muscle cells don't regenerate if they completely die (they have complex repair procedures if they're only damaged), but there have been no reports of people losing deltoid muscle strength following vaccination. If killer T-cells persistently target muscle cells it results in major pathologies like IBM (Inclusion Body Myositis), which is very hard to treat.

S.Seneff, G.Nigh suggested that B cells are activated in spleen, not in the muscle. "... the migration of immune cells carrying a cargo of mRNA nanoparticles via the lymph system into the spleen. These immune cells would produce spike protein... and the spike protein would induce B cell generation of IgG antibodies... neutrophils in the marginal zone of the spleen... interact with B cells, inducing antibody production (Puga et al., 2011). This is likely crucial for successful vaccination outcome." https://dpbh.nv.gov/uploadedFiles/dpbhnvgov/content/Boards/BOH/Meetings/2021/SENEFF~1.PDF

I linked to this this paper in a comment on the other question. They detect spike protein on the cell surface using labelled ACE2 or an anti-spike antibody.  They don’t talk about it at all in the paper; just the method and results in supplementary information.

" are pretty unsuccessful at killing cells" - are those vaccines successful  at inducing  B cell production?

@Fizz "but failed to elicit successful CTL [...] responses due to the drastically reduced production of type I IFNs" - This is of high interest. Thanks. I miss some follow up text explaining your  inference that comes next: ("So it seems...): What is the effect of Inteferon block on dendritic and regular host cells? If there is no interferon dendritic cells do not survive their uptake of virus (interesting!!), and, inversely, presenting regular host cells (muscle etc.)  are not apoptotically killed by T cells (not induced) but collapse to "debris"? B cells not induces in lack of T4 induction?

@Roman Riabenko Please set up an anwer based on that reference and the like.

@reuns "... something nobody talks about- they are likely taken by (dendritic) cells after the cell dies, because the cell is detected by the immune system as "infected"... That idiom "Nobody talks about" should wake up the dogs... If anything isn't explicitely mentioned in textbook it should be evident. I do not believe what you say is the following: if infection of target body cell (muscle, epithelium) happens faster than uptake by APC, dendritic cells - "sth. no one thinks of as a possibility" - there should be no apoptotic killing, and that should give a mess - for uptake by PAMP etc./APCs

@reun Your "first comment" seems more and more valuable.  Please set up a question  if it's right or wrong what you are "trying to say". You mention MHC1 and 2 - if dendritic or macrophages clean up debris by non-apoptotically passed away cells  that would be no uptake of "live virus". Similar to  m-RNA-nano-vaccines  debris may contain  some intact mRNA that is still "workable, presentabl" on MHC1. Even more surprising: Not necessary! Regular dendritic MHC1 uptake just has  to catch up, interconnection to B by T4-Helpers. Then, there is both MHC1 and 2 presentation. Textbook doesn't say so!

@PeterBernhard Thank you for challenging me to post an answer. I found the article that I referenced relevant, but I do not know the answer. I just tried to make a hopefully useful comment.

re "picking up debris", Buchrieser et al. e.g., Syncytia formation by SARS-CoV-2-infected cells might be of interest. CoV-infected host cells seem to express spike protein outside the MHC, thus not attracting t-cytotoxic cells -  maybe just falling apart to "debris".

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Why such strange enzyme kinetics?
I measured some enzyme kinetics in a practical course using a substrate-based FRET assay. Unfortunately some of my plots show weird effects. There was always a decrease in signal after 35 minutes. But the curve always regained.
During the whole measurement the plate was placed in the reader, and was heated to 37°C.

My question is: Does someone know how/why this effect occurs?
Thanks for your help!

Those points are within the error bars of the previous measurements, so perhaps they aren't statistically significant. How many replicates did you do?

Worth considering whether it is an effect of the instrument or the system. What would happen if you preincubated your plate for 10 minutes? Would you have the "dip" after 25 minutes or again 35 minutes?
I know our plate reader will want to calibrate its detector at some intervals, perhaps that coincidences with 35 minutes for your combination of variables?

In addition to these suggestions, running the samples on a different instrument could be informative.

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How do viruses attacking the outside of the body invade if the upper strata of the epithelial layer is metabolically inactive?
The top two layers of the epithelia, the layer of skin on the outside of the body, are the stratum corneum and the stratum lucidum. Both of these layers are metabolically inactive, in other words they are dead cells that do not manufacture anything. Since viruses rely on the manufacturing apparatus of their host cell to proliferate, how do viruses infect and penetrate these two layers?
This question pertains only to viruses that infect the body of the host through the epidermis. So, that would include viruses that cause warts, herpes viruses and viruses that infect the respiratory epithelia like cold viruses. If these different kinds of viruses penetrate epidermal defenses in different ways then that would be relevant to the answer.

This article might provide you some answers.

Viruses generally can't penetrate the stratum corneum and stratum lucidum - that's (partially) why we evolved tough skin. I could hold some virus in my hand and wouldn't get infected unless I had some sort of break in my skin like a scratch. Our skin is extraordinarily good at protecting us from the huge numbers of potentially pathogenic microbes we encounter on a daily basis.

The viruses cited are typically transmitted directly to blood, e.g., via microcracks during sexual intercourse. In general, viruses cannot infect through the skin, but rather through the mucous membranes in respiratory tract, digestive system or sexual organs.

Since viruses rely on the manufacturing apparatus of their host cell to proliferate, how do viruses infect and penetrate these two layers  [stratum corneum and the stratum lucidum] ?

Who says they do penetrate them?

So, that would include viruses that cause warts, herpes viruses and viruses that infect the respiratory epithelia like cold viruses.

The respiratory epithelium doesn't have a stratum corneum nor a stratum lucidum. There are no "dead cells on top" of that epithelium.
If you're curious how the respiratory epithelium is protected (to some extent) on its outer surface, there are antibodies "lurking" in the mucus that covers the ciliated cells. These antibodies bind their target pathogens sometimes to each other in larger clusters, which in turn enables them to be trapped in the mucus mesh network. (https://erj.ersjournals.com/content/49/1/1601709)


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Allometry of vision, can mice see their own fingers?
Looking around, I've found a lot of research on the allometry of visual acuity and vision at a distance, but not so much on vision close-up. As I understand it, the "near point" of vision is largely determined by the optical/focusing power (diopters) of the lens, which is itself determined by the refractive index and lens curvature (lensmaker's equation). Assuming the refractive index is constant, this implies smaller animals should have the more powerful vision (assuming smaller eyes) necessary to resolve something as close to their eyes as their own claws. Does measurement agree with this hypothesis? What is the scaling relationship? Is there a single one, or is it sensitive to eye type like acuity is?

Exciting question, and anticipations are largely met for mice (featured in title). Mice have a closer focal point than humans. As less than 2 cm they can likely see their fingers. Assumption on constant refractive index would require to further assume that viewing angles are different as numerical aperture changes. Mice having a more powerful vision system could be considered true.
Recent publication with measurements underlying above: https://doi.org/10.1364/BOE.3.000715
Generalization beyond mice would be interesting, but likely require control for other things such as habitats and whether predatory animals, ....


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Why do veterinary vaccines have shorter effect?
In humans activated T-lymphocytes persist until end of life, and activated B-lymphocytes persist many years, so most vaccines don't need to be reapplied and the few that do are reapplied after 10 to 15 years (recommendation varies slightly by country).
However cats (and dogs) are vaccinated every year, with individual vaccines reapplied after one, two or three years.
Does the immune system of cats differ so that it loses the activated lymphocytes faster? Or why are the vaccines (recommended to be) reapplied so often?

Can you give an example of the same vaccine that is recommended every year for dogs/cats but only every 10-15 years for humans?

I get an influenza vaccine every year, and now expect to get a COVID booster after 6 months.  Tetanus is 10 years, or if you have a wound that might result in an infection.  (I'm human, BTW :-))  Perhaps one reason canine vaccines are given more often is that your dog can't really tell you when s/he's sick, until it's too late.  Some are for things that are invariably fatal and/or easily transmitted, like rabies.  So perhaps one factor is "better safe than sorry".

@jamesqf, Influenza is a different vaccine every year. Tetanus is bacterial, so 10 (but it's 15 here) years make sense as it relies on B-lymphocytes only. What's going on with the covid one is not yet understood, so I'd leave it out for now.

Unfortunately rabies vaccines decline in effectiveness over time.
The first key study was by HN Johnson in 1954. He tested 25 dogs 1 and 2 years after receiving a vaccine. The dogs in the control group all died. The dogs inoculated at 1 year had a 100% survival rate. The dogs challenged with rabies at 2 years had an 88% survival rate. So, apparently there was some degredation in the vaccine effectiveness after a year.
Rabies vaccine duration effectiveness was also studied in the following experiment:
Dodds WJ, Larson LJ, Christine KL, Schultz RD. Duration of immunity after rabies vaccination in dogs: The Rabies Challenge Fund research study. Can J Vet Res. 2020;84(2):153-158.
In this study the effectiveness of the vaccine declined over time. All of the beagles in the control group died. In the 6 year group, survival was 80%, but it dropped to 50% in the 7 year group and only 20% in the 8 year group.
So, given these kinds of numbers the tendency has been to try to do an annual vaccination to maximize the level of protection.

But is there any idea of the underlying mechanism why that happens?

@JanHudec According to current knowledge, the only long-lived immunological cells are long-lived bone marrow plasma cells which can drip out serum antibodies for years unlike other immunological cells which are mostly dead after a month or two. So, if a vaccine loses effectiveness over the course of years, the only apparent cause would be a gradual decline in bone marrow plasma cells which are producing rabies antibodies.

And memory T cells, no? Those should be even longer lived given thymus shrinks with age. And the question than basically boils down to how long do the two kinds of memory cells live in carnivores.


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How many of each structural component of SARS-CoV-2 are there?
I'm interested in the composition of SARS-CoV-2, including how many copies of each protein are present in an assembled virus, as well as the overall mass and density.  There are a few recent papers such as Klein 2020 and Yao 2020 which provide a lot of useful info on the structure of the virus, but they do not completely answer that question.  For example Klein estimates 48 (range from 25 to 127) copies of S, but doesn't say anything about how many copies of M, N or E there are.  I have not been able to find a full answer even after a pretty thorough literature search.  Considering how good molecular biology (and imaging) tools are nowadays, and the importance of the subject, this seems like a pretty astonishing gap in knowledge.
Question: What is the exact composition (stochiometry) of SARS-CoV-2, in terms of how many copies of each building block are present in each virus particle?

Spikes are somewhat easy to see and count on an electron microscope image. Not sure why you think the other ones are just as easy to see/count.

And I'm rather doubtful you'll find a firm answer. Seven years after SARS discovery, there was still disagreement as to its M-assembled structure. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486061/

Even shotgun mass spec should be able to quantify everything using the quantity of RNA as a reference.  Tools today are way better than in 2011 when the Neuman article was published.  Could you please link any articles that show people trying to do this kind of quantification and running into problems?

@Fizz I agree that it would be hard to get this type of data from SEM.  There may be other options that allow proteins to be counted, for example TIRF or STORM single molecule imaging, or TEM with antibodies conjugated with gold nanoparticles as contrast agent

Probably there are some data of this kind, surely not as exact as in stochiometry. There must be a basis for this picture https://commons.wikimedia.org/wiki/File:Coronavirus._SARS-CoV-2.png?uselang=de . Ah, note that the virus membrane itself is stolen from the host cell and not made by the virus.

@jk-ReinstateMonica Yes, although the virus membrane is budded off from cell internal (organelle) membranes of the ERGIC, not the external cell membrane.  For that wikipedia picture, it originally comes from https://nplus1.ru/, there is a nice article about how it was made (with a bibliography even).  But it doesn't seem like there is an accurate count of M or N in any of the bibliography sources either :)


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Why do neurons turn black in Golgi staining?
I am learning about the Golgi staining of neurons. I know that to this day it is unknown why some but not all neurons in a tissue get stained. I have read online that to harden the neural tissue, Golgi submersed samples for up to 45 days in a 2.5% potassium dichromate solution. He then soaked the samples in a 0.5-1% silver nitrate solution for different amounts of time to dye some of the cells black.
I have read a number of online sources about Golgi staining but none of them explain why neurons turn black. Is it a chemical reaction between potassium dichromate and silver nitrate that turns the neurons black?
Any insights are appreciated.

First result on google for these reactants: when a colorless solution of silver nitrate is mixed with a yellow-orange solution of potassium dichromate, a reddish precipitate of silver dichromate is produced. AgNO3(aq)+K2Cr2O7(aq)→Ag2Cr2O7(s)+KNO3(aq) The black is result of contrast between brightfield backlight and opaque precipitate.

The black/brown color is because silver chromate is in the cells.
As you say, the precise mechanism is unknown but this is more about why exactly silver preferentially precipitates within neurons by this procedure, and not other cell types, and also importantly why it does so so sparingly - the key to the Golgi method is that only a minority of all neurons actually get labeled, and get labeled very strongly. If all neurons and processes would be labeled, you would not be able to see any of the details in a single cell.
Pasternak, J. F., & Woolsey, T. A. (1975). On the “selectivity” of the Golgi‐Cox method. Journal of Comparative Neurology, 160(3), 307-312.
Scheibel, M. E., & Scheibel, A. B. (1978). The methods of Golgi. Neuroanatomical research techniques, 89-114.
Špaček, J. (1992). Dynamics of Golgi impregnation in neurons. Microscopy research and technique, 23(4), 264-274.

Out of curiosity, I spent a while trying to find a counterexample of this stain being used in non-nervous tissue. I cannot find anything. It seems to be so widely used for neurons/glia and for nothing else. Curious whether and why the chemistry has been restricted in utility to nervous tissue only...

Yes, according to Spacek (1992)

the Golgi deposit has been identified as silver chromate by Fregerslev et al. (1971) and Chan-Palay (1973).

I don't know why it's black when in neurons and not dark brown though...
Actually Spacek (p. 265) describes the crystals as dark brown.

It's more of a dark brown, it's not that easy to tell the difference in a microscope, especially looking against a brightfield - any dark color is going to throw a substantial shadow.


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How do tall trees transport water at night?
I was studying transportation in plants and I came across two ways in which plants transport water.
The first one is root pressure. In this method, epiblema cells of root hairs actively absorb minerals from the soil. This creates a concentration gradient of water inside the roots and outside the roots and hence leading to a formation of a column of water. But this method can only be used to transport water for short heights.
In tall trees, the method of transpiration is seen. The evaporation of water molecules from the aerial parts of a plant leads to a phenomenon like a suction pull therefore transporting water.
But in the night, the stomata are closed which means that transpiration can't take place. And root pressure also cannot satisfy the needs of the tree because it is a tall tree.
Then how tall trees transport water in night?

Welcome Xavier, were expected to show our researches here on biology. Please take the [tour] and refer to the [help] for info as to how we work. Why would the stomata being open during the day enable water to reach heights above that possible by that created by the osmotic gradient at the roots? Ie. what do the stomata have to do with it? Perhaps researching capillary action might give you an idea about what it is you want to ask, then you can [edit] to clarify a bit.

Transpiration isnt an yes or no phenomena. The stomata can be opened at various degrees. And transpiration rate depends upon windflow, humidity, sunlight and many other factors. And even if stomata are closed, the cohesion tension bridge will not be lost.


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What is the difference between 4th generation sequencing and NGS?
The generation of sequencing technologies has come on leaps and bounds and there are stark differences between the types of technology used. There is a great Q&A here What is the difference between second and third generation sequencing?
NGS refers to high throughput massively parallel sequencing technology (See illumina's marketing page). 4th generation sequencing has been used to describe single molcule nanopore based technology (Nanopore-based Fourth-generation DNA Sequencing Technology).
So is NGS just a massively parallel version of 4th gen, or is there a more fundemental difference?

Older related question: https://biology.stackexchange.com/questions/21080/what-is-the-difference-between-second-and-third-generation-sequencing

I think that all of this is pure marketing and can be safely ignored. There is no basis for the generations of sequencing in chemistry or instrumentation, except possibly that second-generation (Illumina) was a massive parallelization of first-generation sequencing (Sanger)  through clever chemistry and instrument modifications. It is merely "I want to argue that this technology occupies a particular niche right now".
All of these terms are obviously very imprecise. I had not heard "4th-generation" before; having analyzed all of these data types, I personally would lump nanopore into the third-generation sequencing box with PacBio: they are long, relatively noisy reads that grew popular around the same time for roughly the same applications and are currently under very active research and development.
I would allow that these two technologies (PacBio and nanopore) are definitely distinct from Sanger (much older, now fairly restricted to specific applications like confirming plasmid sequences) and Illumina (older, mature tech with deep market penetration, making tons of money and trying to hold onto market share).
"NGS" itself is a rather silly term for similar reasons, as it is now clearly a technology that is fighting for relevance in certain applications where it was once dominant (e.g. genome assembly). If we must apply generational terminology to Illumina, it is clearly second-generation. This is one of Joe Felsenstein's oft-repeated rants.
Nanopore itself is as far as I know established in 1996, whereas the first publication I am aware of that forms the basis for PacBio is 2003. For comparison, the Solexa sequencing that became the basis of Illumina instruments from thence was introduced in 2005. So any meaningful chronology also does not support these generations.

Illumina sequencing is not massively parallell Sanger sequencing.  Sanger generates different length sequences each with a single labeled base.  Illumina labels all the bases, takes an image, the strips the label off, and adds the next labeled base to image.

@swbarnes2 that is a good point- I would still label the chemistry as derivative (sequencing-by-synthesis, but a lot, and with optics and fluorophores and non-terminal chain extension), but I will correct my answer.

Nanopore took longer to commercialize though (by ONT, 2015) compared to SMRT (by PacBio, 2011). This adds massive confusion to any attempt to order these two. Some authors use LRS (long-read sequencing) to group them. There was also pyrosequencing, which has now been commercially discontinued, as another "generation" perhaps.

There was a slightly more clear Q here about those (commercially speaking) pre-2010 "NGSes" https://biology.stackexchange.com/questions/7075/what-is-the-difference-between-solid-454-and-illumina-next-gen-sequencing


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Examples of physiological differences between isolated & non-isolated individuals
I'm looking for examples of organisms (or biological units at some other scale, like cells) whose physical and/or behavioral properties develop differently depending on whether the individual is in close contact with others. In particular, I'm interested in cases where individuals are specialized for fairly narrow functions as part of their usual collective existence (e.g. as animals in a society or cells in a tissue) but develop facilities for more autonomous/self-sufficient operation (possibly including significant anatomical changes) when isolated.
The example that originally came to mind (which isn't really even what I'm looking for) is heart cells that beat together when touching. A slightly better one might be colonial organisms like pyrosomes. I hope there are even better examples in which the "solitary" form exhibits distinct differences from the "grouped" one. Are there animals or plants that do this? Microscopic organisms (maybe other zooids)? Thanks in advance.
(Sorry if this question is too vague/abstract. For more context: I'm helping a friend with some nonfiction writing, and we're looking for a metaphor from nature to introduce a passage about how pandemic-related isolation has spurred some people to "blossom" artistically/intellectually/etc.; it'd be really cool if there were an organism that similarly "grows into a new version of itself" when separated from its neighbors.)

I think it would be helpful to explain your goal; otherwise it's a pretty broad question that could possibly be answered any number of ways, which isn't a good format for a SE question.

Thanks for the feedback! Edited to explain my goal.

Just for info, we have a [worldbuilding.se] site as well as a [writing.se] site -  this question might have easily fit on the former, more-or-less as is.

Thanks! A fictional example of what I'm describing wouldn't be as compelling as a real one from biology, so I'll leave my question here unless it's deemed not appropriate.

You can ask for a "finite list" of real-life examples, but you'd need to specify environment and such. Worldbuilding uses real science to create fictional worlds (and, to be fair, there's quite a few magic related ones too). Not an answer to this, as it's late for me to start writing answers, but what leapt to mind immediately on reading it was slime molds, worth a read.

Welcome to Biology.SE. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] or delete your question accordingly. I have voted to close this as needing focus — this is a question that would require a textbook to answer, which is both impractical and expressly off-topic for this site. In addition, as currently written the cells in any multicellular organism would seem to fit your criteria, as would any social organism. Plants also grow differently when crowded vs. isolated — e.g. compare tree farms to isolated trees ...


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What species of insect is this, spotted south-east of Berlin? Habitat: forest near lake shore, Size: body 40mm, w/o antennas and ovipositor
This insect has been spotted south-east of Berlin (2021-10-31).

Please [edit] your post to include as much of the following essential information to improve your chances of getting a good answer: 1) habitat information; and 2) an estimate of the size of the organism. ——— Please see the [tour] and the [help] pages starting with [Ask] questions effectively on this site for details.

does this answer your question?

For starters, looks like in the family ichneumonidae

I found a picture on the internet with a resembling insect that was specified as Rhyssa persuasoria. But when I looked this species up it shows a much darker color (black). This is puzzling me. Also bob1's response points to a species of the same shape but different color.

@VolkerOtto there will be some natural variation in colour within the species. At best you could probably say Rhyssa genus or perhaps the closely related Megarhyssa, but I think those have some brown/red in them rather than just black and yellow/white.

There's a nice PDF guide to the british species of wasps etc. here I'd expect similar species in most of Western Europe, though maybe not the exact species.

@bob1 thank you very much for sharing this guide and your profound answers - very helpful.

You can try uploading the image to iNaturalist.org . Very good site for getting help on species id.


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Why are there so few full-length antibody structures?
I’m a student in the Biochemical Engineering field and the professor at the department just told us in a lecture that if we want to use a full-antibody structure for simulation purposes there aren’t very many of them. He suggested that we start with 1hzh.pdb.
So I wondered whether he was correct and, if so, why there wasn’t anyone using crystallisation or NMR to look into the structures of the antibody drugs that have come onto the market. Perhaps it costs too much and it’s very time-consuming? But, even so, I imagine that it would still be worthwhile.

You have received three answers to your question and have had enough time to consider whether you find any one of them helpful and convincing. If so, you should accept that question. If not, you might at least thank those who took the time and trouble to answer.

Apologize for the delay. Thanks for your time answering the question and providing all the comments. Really appreciate all of your opinions.

The more flexible a molecule, the more difficult it is to get a crystallization that actually tells you something about the molecule's free-phase arrangement/behavior. Basically (the best) crystallography requires you get a molecule to grow (crystals) in the same conformation.
The hinge in IgG1 for instance appears to be able to rotate from 0 to 180 degrees (although range may be more limited in actual molecules, depending on the "bulk" of what's attached to the hinge). If you somehow manage to grow a crystal of a full IgG you'll just get a snapshot of that at one angle. (That 2011 paper says there was still a single such image for a full-length [human] IgG1 for instance--the one binding HIV (IgG1 b12) found in your 1HZH file.)
According to a 2018 review only 4 full structures of IgG antibodies had been determined; by PDB entry with year of paper publication:

1IGT [1997] -- "a mouse IgG2 with 3 hinge disulfide (SS) bonds, while human IgG2 has 4 SS bonds"
1IGY [1998] -- a mouse IgG1 with 2 SS bonds
1HZH [2001] -- a human IgG1 with 2 SS bonds
5DK3 [2015] -- a human IgG4; "the hinge SS was more stabilized due to the conformational alteration of S228P mutation"

Of these, only the last one, pembrolizumab, is used therapeutically, as far as I know, but the first one, was (interstingly) a [proposed] veterinary product at one point (Mab231--against canine lymphoma); the USDA suspended its license after it failed in larger trials. The 2nd one is an antibody against phentobarbital. The 3rd/HIV one (1HZH = IgG1 b12) is not the one that's been (recently) approved for treatment  as Ibalizumab.
The first of these papers (1997) notes some earlier attempts at full structure crystallography; mostly successful in special cases where there was reduced hinge mobility:

Other intact antibody structures have been studied by X-ray
crystallography (Silverton et al., 1977; Guddat et al., 1993;
Marquart et al., 1980). In two myeloma proteins, the flexible
hinge regions connecting Fab and Fc segments were deleted
(Silverton et al., 1977; Guddat et al., 1993). The molecules
were structurally restrained and, perhaps for this reason,
appeared as compact T-shapes, the angle between Fabs close
to 180°. A third antibody, Kol, had an intact hinge, but the
Fc was so disordered that it was not possible to orient it
with respect to the Fabs (Marquart et al., 1980). The two
Fabs and a portion of the hinge (upper and core) were,
however, visualized.

The first two [fully successful] papers (1997-1998) came from the same lab/group. As I'm not expert in this area (or even in biochemsitry) it's hard for me say what was the breakthrough that enabled the full structures IgG crystal analysis in the late 1990s; the papers aren't incredibly explicit on that. There was certainly a heavy amount of computation involved on the X-ray diffraction data, conducted on a Cray C-90 supercomputer at that time; mentioned in these late 1990s papers. And the diffraction experiments were not conducted in the university where the authors were employed but at the Stanford Synchrotron Radiation
Laboratory (SSRL) and Brookhaven National Synchrotron Laboratory, respectively; almost certainly because they used the large synchrotrons available at these labs, as opposed to smaller X-ray sources. There are entire papers on the subtelties of cryportection needed in order to leverage high-energy X-ray sources.
The 2001 short paper in Science on IgG1 b12 is actually devoid of much method details, but the same (Scripps) group has published a longer paper in 2002 in JMB; there they say they (also) ran their diffraction at SSRL (beamline 7-1). No details on computational resources though.
The 2015 paper on IgG4 acknowledges the Canadian Light Source where the diffraction was conducted
on beamline 08ID-1 with synchrotron radiation. Interestingly, this paper also used TROSY (NMR) to confirm packing details and 1D NMR to compare hinge behavior in solution of a serine-to-proline replacement in the hinge (more on NMR below).
The 1997 and (to a lesser extent) the 2015 paper have most details on the computations involved (well, in this group of 4 papers). Basically prior Fc and Fab crystal diffraction "signatures" (ideally for the same antibody) are highly desirable and the software basically does a search trying to locate them in the larger "picture". But this can fail and manual hints based on parts of Fc/Fab (e.g. from similar but not the same antibody) may have to be entered to guide the search etc.
The 2002 paper has some hints why the automated search can fail (beyond the hinge problem) even when the Fab's structure has been previously analyzed separately; when the whole antibody is crystallized asymmetries are observed:

Importantly, all three of these intact antibodies
crystallize with one whole IgG molecule per asymmetric
unit, even though their respective space
groups and crystallization conditions vary. Thus,
although the two halves of the antibody are identical
in sequence, they are not identical in structure.

A (single) crystal structure will not--in itself--let you experimentally verify how much hinge freedom there is. Tomography techniques such as IPET are more sensible for the latter. Resolution is (much) lower, but if just want to capture the angles available in the hinge with something attached, it's far less time consuming. Feed the results into a targeted molecular dynamics (TMD) package together with the crystal structure of Fab & Fc, and you get something like this

As for [3D] NMR (which you also suggested), it cannot be easily used because of the too greater size of full-length antibodies (IgG: 145-160 kDa) vs 40 kDa typical limit for NMR. Basically with 3D NMR, the bigger the molecule, the "blurrier" the image your're going to get. While Wikipedia mentions a couple of proposals/experiments for larger molecules, it seems those didn't really take off in everyday practice.
There are actually some papers that have done spectroscopy NMR on full-length antibodies, but present the results with caveats like:

It should be noted that mAb2 used in this study [...] is an example of an intrinsically stable and soluble antibody. Despite this, at a very high mAb2 concentration the measurable NMR parameters registered quite significant differences as solvent conditions were varied, highlighting the inherent sensitivity of this NMR technique. It can be anticipated that other, less stable mAbs, which require more careful formulation to achieve satisfactory solubility and stability profile, would show even greater variation in NMR measurables.

There are also several papers e.g. Marino et al. (2017),
Brinson et al. (2019) on 2D NMR on MAb, but again for the purpose of determining the higher-order structure (in solution); although the resolution may be a bit better than IPET (but still below crystallography), it requires more complex math.

The methodology for the Science paper is in the Acta Cryst. D paper I discuss in my answer, and which you might have cross-referenced. I have upvoted your answer because it deals predominantly with the fact that the hinge region is flexible and thus there are a number of structures, and also because it reviews the 21st century literature. But without my own answer, the way you start would be incomprehensible to most and especially the poster. An initial statement that there are only a few full length structures and this is because of the flexibility would improve your answer no end.

There IS a problem!
In a previous version of this answer I focussed on various historical, technical, goal-related and commercial reasons for the predominance of structures of antibody fragments (Fab and Fc) rather than complete immunoglobulins (two copies of heavy and light chains) — the “full-antibody structures” of the question. I retain this as an appendix as I think it still of interest, however I had missed the main reason.
The main reason can be found in the two papers on 1HZH — the anti-HIV antibody mentioned by the poster. In a nutshell it is:

Full length antibodies have regions that convey functional flexibility, resulting in a variety of conformational forms in the same pure protein.

To quote from the paper describing the crystallization:

The Fab and Fc domains are connected by hinge regions of exceptional flexibility that facilitate changes in shape for bivalent attachment to antigen and for effector interaction. Electron microscopy of rabbit and mouse IgG has provided evidence for flexibility and arm rotation at the Fc–Fab and Fab–Fab interfaces, most of which is associated with the central hinge region.
The inherent molecular flexibility has complicated crystallization of intact antibodies.

And lest there be any doubt about the relative numbers:

While well over 200 structures of antibody fragments, mainly Fab and Fab0, have been determined [in the year 2000], crystals of intact antibodies have only been reported eight times… Only Dob, Mcg, Kol, Mab231 and Mab61.1.3 have yielded structures or partial structures.

And the paper points out the limitations of even these structures:

These early results suggested that for antibodies with normal hinges the relative placement of the Fc with respect to the Fab arms is not fixed and is free to assume a wide range of configurations.

Solving the problem
The general approach adopted by the authors is summarized in their statement:

Nevertheless, a well ordered antibody crystal can be obtained if a single conformer is incorporated into the crystal lattice owing to stabilization by crystal contacts. In this manner, a single ‘snapshot’ of an antibody structure can be obtained from the plethora of possible conformers.

Achieving this was far from simple — as far as a non-expert can judge from reading their full account, and the fact that the details of their achievement was regarded as justifying publication in the top journal, Science the following year. I reproduce below an image showing what they refer to as

a “snapshot” of the broad range of conformations available in solution.

where the hinge regions are marked.

Reflection: Utility of full-length high-resolution structures
Obtaining a high-resolution full-length immunoglobulin structure is obviously important in itself, but as the answer from @Fizz documents, there had been only one other subsequent structure of this type by the time of a review in 2018. Why is this? Granted it is intrinsically difficult, but one the basis of the difficulty — the range of different structures caused by the hinge flexibility — is also the answer. No one specific structure can be regarded as definitive, so that, as the other answer illustrates, lower resolution images of a range of structures became of greater interest, and these can be related to the high-resolution full-length structures.
Appendix: Minor reasons (from my original answer)
Historically, a fragment containing the constant domain of immunoglobulins could be crystallized from polyclonal antibodies because it was identical for antibodies of different specificities (within a class such as IgG), whereas the different variable regions prevented crystalization. One had a mixture of molecules. It was for this reason the abbreviation Fc arose — it stands for fragment crystallizable. region.
Polyclonal antibodies were available from tumours before artificial means of generating them arose, but the point of interest was the antibody-binding site, so that the Fab fragment — which was easy to generate — would serve the purpose. It is much easier to crystallize and analyse such fragments than the whole immunoglobulin, so that is why they were (and are used).
Finally, one studies the areas of immunoglobulins that are the focus of your scientific interest (and for which you can convince grant authorities are worth funding). For example, if you are interested in interaction with antigen, you solve the structure of the Fab region; if you are interested in the interaction of the constant region with other molecules (or the difference between different classes) you solve the structure of  the Fc region; and only if you are interested in a problem like the relative orientation of the different regions under particular situations do  you make the effort required to solve the structure of whole antibody.

There are thousands of structures in the PDB of neutralizing antibodies against all sorts of viruses using all sorts of methods (NMR,x-ray,electron microscopy) as complex or stand alone. I guess your professor has certain requirements that are rarely met, e.g. specifically anti-HIV-1 IGG of certain quality; then he/she only found one structure that suffices.

What search on PDB do you use that enables you to say with certainty there are thousands of compelete Ab structures?

I didn't say that.

You said there are thousands of structures. Either justify the statement or edit it. But even if you edit it to, say, “quite a few”, I would expect you to supply some examples. The principle for answers on this list is that they should be supported by evidence.

I suspect now that you may have skimmed the question and not realized the emphasis was on the structure of the whole antibody, which is quite clear if you read the papers describing the motivation for the work on 2HZH. If this is the case you may wish to consider whether to withdraw your answer.

The OP wondered "why there wasn't anyone using crystallisation or NMR to look into the structures of the antibody drugs coming into market so far". It is most important to clarify this misconception; ABs are heavily studied (source: PDB). I checked the mentioned AB and saw that it was an anti-HIV full IGG, but the actual question does NOT state that it has to be a full AB! You edited the OPs question to put emphasis on this aspect just so that it fits your answer. Most simulations are done on protein fragments anyways. It IS the Professors choice to take "full" AB!

The title of the original question started "Why are there so few full-length antibody…" That is quite clear and I did not at any time alter that. I put the emphasis in the actual question because many new posters do not realize that it is best to repeat the key points in the body of the question — it should stand alone. It is also easy when answering to miss something in the title — I've done it myself — especially if one is answering on a phone, but there is no doubt that was what the question was about, and looking up the literature on 1hzh makes that clear.


text:
Measuring innate caring about offspring and long term surivavability
I am not a biologist, and don't have much technical knowledge of biology.
That being said, having observed the real world, it seems that, at least for mammals, human beings seem to "care" more about their offspring than other mammals might. One reason, of course, is the fact that human babies/children require more assistance than other mammal babies.
Imagine, however, that at any given point in time, we can summarize the resources that a mammal needs as $X$. A fraction of that $X$, call it $x=F/X$ goes towards the children. This could be for human beings, the fraction of income devoted each period to the child, for lions the fraction of meat given to cubs etc.  If a species gives $x=0$, then trivially, the species dies out. If a species gives out $x=1$, the species might still die out because it can only donate resources for one period, and the infant may not be able to fend for itself next period.
If one were to plot this $x$ over time across species, it would necessarily decrease, as the infants become autonomous eventually.
Is there any empirical work that correlates such a measure of "devotion of resources" to long-term survival of the species? In other words, are those species that survive long term best able to calibrate this $x$ to an optimal one to maximize survivability?

Arguably, 100% of any animal's resources go to offspring or are intended to go to offspring (sometimes you get eaten too soon), it's just a matter of how exactly those resources are allocated to different phases of the offspring's life. A female mammal is going to give a lot more post-birth resources than most other animals, but it doesn't seem quite fair to discount the effort put into eggs by other females, even if no post-natal care is given. Many species give every ounce of energy they have left to make as many eggs as possible and die immediately after.

And, certainly, animals spend some of their own resources running, climbing, or flying about, so that doesn't go directly to offspring, but it's still an indirect cost of preparing to reproduce. Even males that don't seem to put as much direct resources into offspring put resources into competition with other males, locating mates, etc, which are all resources dedicated to ensuring their next generation.

Yes you are right @BryanKrause . I thought of this after watching videos of say, lions eating before their cubs, when both were hungry. But this makes sense according to what you say, as the lion's survival is more crucial to the propagation of the next generation than say, any particular cub's.

@BryanKrause - The first thing I thought of when I read this was a male (mountain goat/whatever antelope) headbutting so many other males that it dies before they do (more energy expenditure and less time for nutrition), but gets to sire more offspring. It's not just about food allocation.


text:
What is an example of a benign or beneficial de novo copy number variation?
Duplication events in particular. In any species. Have enough genomes been sequenced and studied to identify any? It is rather easy to find studies which identify them with diseases but have they ever looked for benign or beneficial instances?

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. This will also allow you to clarify and focus your question — as written it sounds like you haven't read this relevant wikipedia page. Please take the [tour] and consult the [help] starting with [ask] for details.

I've provided an answer, but I'm not sure whether it actually addresses the question, given "de novo" in the title. I assume you're looking for examples of nonpathogenic CNV mosaicism in somatic tissues? Clarifying edits would be appreciated.

Copy number of the human salivary amylase gene (AMY1) varies across populations and is positively correlated with the starch content of traditional diets.1,2 Amylase gene copy number expansions are common in the evolutionary histories of several mammals.3

References

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007 Oct;39(10):1256-60.
Carpenter D, Mitchell LM, Armour JA. Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity. Hum Genomics. 2017 Feb 20;11(1):2.
Pajic P, Pavlidis P, Dean K, Neznanova L, Romano RA, Garneau D, Daugherity E, Globig A, Ruhl S, Gokcumen O. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife. 2019 May 14;8:e44628.


text:
Kansas Spider Identification, found in Pasta Package
I live in Kansas. I found a spider inside my macaroni pasta package after dinner (6pm), and I really want to figure out its species.
Since I have consumed food from that package, I'm especially concerned if itself or its eggs and/or whatnot could be poisonous to human. I think the spider didn't bite me, unless it has painless and asymptomatic bites.
The spider is brownish in its color, and approximately as large as a penny (~2 cm diameter). I have taken pictures of the spider (currently alive, in the sink) attached below. I really appreciate your help!!

It is a crab spider, likely of genus Xysticus but possibly genus Ozyptila. If you needed to get down to genus, bugguide (https://bugguide.net/node/view/63082) says that we can differentiate these genera by counting the macrosetae (the thick hairs) on the front legs. You would need some high-quality zoomed photos to check those.
In general, eating spiders is not toxic for people or animals. Many animals (birds, fish, cats, etc) eat spiders without having the spider venom affect them in any detrimental way. The venom in crab spiders is not much different from the majority of other spider families in North America. (Black widow and Brown recluse venom are exceptions when it comes to bites from the spider, and I don't know how bad it is to eat those... but these crab spiders are not related to those dangerous ones).

Venoms (basically by definition) need to enter the body through a wound to be effective, as they involve larger compounds that can't be absorbed through the skin or digestive tract. As long as your digestive tract is free from ulcers, there shouldn't be any danger to swallowing something venomous.

Thank you so much for the information!


text:
Trouble in understanding graph of pressure time in different chambers of heart

In the book, it is written that from 0 s to 0.125 s-Atrial Systole; 0.125 s to 0.325 s-Ventricular Systole; 0.325 s to 0.6 s-Ventricular Diastole
Why a bump is there from 0.125 s to about 0.175 s in the pressure-time graph of left atrial pressure and why is the pressure in the left auricle increasing during the ventricular systole and ventricular diastole stage (from 0.175 s to 0.45 s)?

A previous Biology.SE question has a diagram with a bit more information on it...

When the ventricles starts to contract, the AV valves close as the pressure rises very quickly in the ventricle and exceeds that of the atria; the blood in the atrium is going to be squeezed a bit at that point between the atrial wall and AV valve, that's the little uptick "0.125 s to 0.325 s".
From 0.175 s to 0.45 s the AV valves are still closed but blood is trickling into the atria and they're getting passively distended. You can see the pressure drops again when the AV valves open and the ventricles begin to fill from the atria.


text:
Is tumor necrosing factor alpha now properly referred to as "tumor necrosing factor"?
"Because LTα is no longer referred to as TNFβ,[64] TNFα, as the previous gene symbol, is now simply called TNF, as shown in HGNC (HUGO Gene Nomenclature Committee) database." says https://en.wikipedia.org/wiki/Tumor_necrosis_factor#Nomenclature.
Is this correct? What, if anything, does it say about someone if he calls it "tumor necrosing factor factor alpha" ?
So my question is: Is tumor necrosing factor alpha now properly referred to as "tumor necrosing factor"?

This is an old problem when nomenclature changes: People will still use the old nomenclature and it will only cease with time.

@Chris Are there some that refuse to call it by the new name, like those who insist on saying "degrees centigrade", even though they know the new name, but just don't want to be told what to say? Are there people who think the old name is better? Is the old name better?

I think it is simply a habit. I noticed the same with cMyc (old name) and Myc in another field. It took a while, eventually it came through.

@Chris When you say "a while", do you mean years or decades?

I observed this for a few years. But this is only anecdotal evidence.

In papers I've participated in recently we've called it TNFα. No reviewer has corrected us as far as I can recall.
Near as I can tell, we've done this because we do not read the HUGO Gene Nomenclature Committee database any more often than we read the dictionary cover-to-cover. Instead, we read and cite papers in the literature, and since many of those are older than this apparent change, and even more recent ones are in turn citing older papers, TNFα is the only nomenclature I knew of until your question posted here.
I could have guessed that a "TNFβ" or something similar exists/existed at some point, but I really have no knowledge or familiarity with it, certainly far less than with TNFα, so a renaming there is not really of any interest or relevance to me.
Biology is a massive field and every niche has its own set of terminology that is more or less familiar.
If people in the field decide over time to start using the new name, then that will propagate the new usage. I don't see a strong motivating factor to rename in the meantime: the old name isn't misleading or easily confused with something else, it's not derogatory or offensive, the new name doesn't provide additional context or function. If anything, there's a temporary motivation to not change, in that use of the old term far outnumbers use of the new.
I suppose you can think of me however you'd like based on my explanation here - I don't have much control over that.

I just realized that the Wikipedia article didn't explain why a change in the name of the gene means the name of the protein should be changed. Do I understand it correctly: tumor necrosing factor alpha is a protein? And not a gene?

Tumor necrosis factor alpha is the protein product of the gene TNF in humans, which is also known as TNFA.


text:
Why do veins contain lower concentration of proteins as compared to arteries?

In Q 9.b, it is said that the blood in Y has lower concentration of proteins/amino acids as compared to the blood in X.
But why is it so?
The blood in Y should have more protein as the tissues may secrete some proteins into the blood as they flow like they would in case of lymph going through lymphatic vessels.

Well, that's sort of the issue, the tissue in the image isn't specified - is it gut, lung, liver, kidney? It's impossible to generalize a conclusion as we're not homogeneous colony organisms. Can you add detail at all about the specifics of the question?

The tissue isn't specified in the question

Well, I guess that's the answer then, "They don't, unless they do."

"In this image it is said that the blood in Y has lower concentration of proteins/amino acids as compared to the blood in X." - the image doesn't say this to me at all, is this a quote from someplace? What's the actual statement? I don't see how anyone can begin to approach a "why" without first clarifying what's being explained. Where did you encounter this image? Who is telling you about X and Y and what precisely do they say? Is it even intended to be true or just a prelude to asking some other question?

lower concentration of proteins/amino acids/fatty acids/other named nutrient

This answer key wants to allow an answer that the blood at Y has fewer nutrients than the blood at X because you should assume that some respiring tissue is taking up nutrients from the blood supply.
In my view, "proteins" does not fit on this list. Protein is not a "nutrient" at the cellular level. For some reason, the person who made this answer key included protein in the allowable list. Your question should not be "Why do veins contain lower concentration of proteins" but rather "Why does this answer key allow for 'protein' as a possible answer". Maybe they don't want to make a distinction between protein and amino acids for some reason; I disagree with them, but that's okay. Maybe some student made a good argument for protein in some specific tissue and they simply decided to include it in the answer key as close enough.
I would very very strongly advise against using an answer key as a way to study a topic, only to judge your potential answers to that question. Read the text that goes along with it, where the author has made a more intentional approach to the content. Reading the answer key is not a good shortcut.


text:
Does the ribosome have protein kinase activity?
The ribosome synthesizes proteins by translating the mRNA. The nascent peptide needs to go through the nascent polypeptide exit tunnel in the large ribosomal sub-unit before it reaches the cytosol where it becomes exposed to possibe modification.
Is there a ribosomal protein capable of phosphorylating the amino acids of nascent polypeptides before they exit the ribosome?

No — there is no ribosomal protein with protein kinase activity.
It is difficult to provide conclusive evidence for a negative statement, but the two objective points I can make in support of my view are:

All eukaryotic (and prokaryotic) ribosomal proteins have been sequenced in a wide range of organisms. None shares the characteristic motifs of protein kinases.

There are hundreds of different protein kinases in eukaryotic cells, and these show a wide range of specificities towards different proteins. Many proteins are not phosphorylated at all. Hence, it is difficult to imagine what purpose a ribosomal protein with protein kinase activity could serve.

However…
The protein RACK1 (Receptor for Activated C-Kinase 1) is closely associated with the small subunit of many eukaryotic ribosomes, even though it is not designated a ribosomal protein under the standard Sx numbering system. The substrates of the activated C-kinase for which it is the receptor are not the proteins being synthesized on the ribosomes, but apparently cellular proteins involved in signalling pathways.


text:
Why can't humans digest dietary fiber when we can digest starch?
So, I can see that there's a couple of questions touching on this subject already, but none of them answer the aspect that I'm curious about:
Dietary fiber is a polymer composed of multiple starch molecules chained together, and starch molecules are polymers composed of multiple sugar molecules chained together, right?
So, why are our bodies are able to digest starches and not dietary fiber, when the process for digesting starches involves breaking up the starch polymers into sugar molecules? Why can't the same enzymes used to break down starches break dietary fiber down into its component starch molecules, or break individual sugar molecules off of the ends of them?
Is it simply a matter of time, and we simply pass put the partially-digested remains of the dietary fiber because it doesn't remain in our gut long enough to properly digest? I know that cows have multiple stomachs to facilitate the digestion of grass, but I also know that they've got symbiotic bacteria helping them out as well.

You are mistaken about dietary fiber — please read the linked wikipedia page and [edit] or delete your post according to whether you still have a question.

@tyersome Huh, it looks like there's more than one kind of dietary fiber. TIL. I think I'm asking about cellulose specifically, then.

Then I suggest you read up on what cellulose is — it is not starch (the bonds between glucose units are different).

@tyersome If the correct answer is something like "starches are held together with A bonds, dietary fibers are held together with B bonds, and the enzymes only work to break A bonds for X reason", I'd be happy to accept that answer.

How much organic chemistry do you know? This is ultimately a question about glycosidic bonds ... and since dietary fiber isn't one thing so there is no general answer, which means you need to focus your question.

@tyersome "How much organic chemistry do you know?" I've watched some cooking videos on Youtube by people like Ann Reardon and Adam Ragusea, and I know the general sort of high-school stuff about cells.

Did the nice answer from @MattDMo help you? If so please accept it — if not, please leave a comment explaining why. In addition, your post needs to be edited to fit this answer. ——— I suspect you will need to learn the basics of organic chemistry to really appreciate his answer. If so, there are many resources available online, but I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy can be very helpful.

@tyersome I was waiting 24 hours so that people in other time zones could post their answers, then I forgot. Answer accepted.

"starches are held together with A bonds, dietary fibers are held together with B bonds, and the enzymes only work to break A bonds for X reason"

What you wrote here is correct. A is primarily an α(1,4)-glycosidic bond and B in cellulose is primarily a β(1,4)-glycosidic bond.

From Chemistry of Life at abpischools.org.uk
Maltose is one of the disaccharides produced when starches are broken down, while cellobiose is a disaccharide from cellulose.
Alpha bonds are broken during digestion of starches by the enzyme known as α-amylase, in particular one that specializes in breaking α-(1,4) bonds (there are other alpha bonds, like α-(1,2), as well). Humans express a number of α-amylases. However, β-(1,4)-amylase is only expressed in bacteria, fungi, and plants. Even cows and other grass-eating animals can't digest cellulose on their own – they have massive colonies of bacteria in their digestive systems to do it for them.
The reason α-amylases can't break β bonds is that the two different molecules have rather different chemical "shapes", even though the structures look very similar in the flat drawing above. You may have heard that enzymes work by a sort of "lock and key" model. The substrate (the thing being chemically altered by the enzyme) fits into a specifically-shaped binding pocket surrounding the active site on the enzyme, just like a key fitting into a lock. If the key is the wrong shape, sometimes even by just a little bit, it won't fit properly and won't open the lock. In the same way, if a potential substrate doesn't have the correct chemical "shape", it won't fit into the binding pocket of the enzyme and be acted upon.


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Do spiders learn how to build webs?
Concerning spiders, is there any research on whether web-building is an inherited behavior, or if it must be observed and learned?
e.g. Has anyone hatched spider eggs in isolation and observed whether the descendants still know how to build a web?

Spiders’ ability to weave webs is a classic example of an innate or instinctual behavior. They do not learn to make webs.
The earliest English-language scientific publication that I can find to back this claim is Porter 1906 1, which focuses on variation in the webs of Orb-weaving spiders:

The web of the Orb-weaving Spiders has long been one of the classical examples of animal instinct. It is so definite and complex, and yet so frail a structure and must be rebuilt so often under varying conditions that, a priori, we should expect it to furnish one of the best of fields for the study of the variation of instinct. If the cell of the Honey-bee varies so that, according to Prof. Wilder (73, pp. 654,655), who quotes Prof. Wyman in this connection, there may be a gain or loss of one cell in ten, then from a knowledge of the differing conditions under which the spider works, together with the frailty of the web as compared with the cell, we have as much, and even more, ground for thinking that even greater variation will be found here.

In his review of the literature, Porter directs readers to Menge's 1843 work About the way of life of the arachnids 2 for an overview of spider physiology and behavior, as well as works by Wagner 3,4 as specific references for spider instinct and its variation. Unfortunately, these works are not written in English, so I cannot verify their claims.

References

Porter, J. P. 1906. The habits, instincts, and mental powers of Spiders, Genera, Argiope and Epeira. The American Journal of Psychology, 17(3), 306–357.
Menge, A. 1843. Über die Lebensweise der Arachniden. Neuste Schr. Naturf. Gessell. IV, Danzig.
Wagner, W. 1897. L'Industrie des Araneina. Mem. de l'acad. Imp. des Sci. de St. Petersburg. Tome, XLII, No. II, pp. 269.
Wagner, W. 1900. L'arraignde aquatique (argyroneta aquatica Cl.) son
industrie et sa vie. Materia de psychologie comparde. Bull. Soc. Moscou, pp. 61-169.

Could you add a bit more detail please? For instance, does that paper have evidence that the very first web a spider makes is no worse than their last one?

@terdon It seems to me like (though I know absolutely nothing about this topic) being able to recognize issues with their web and improve upon it next time would require a lot more intelligence than just copying the way another spider makes their web, since it'd involve connecting the problem with its solution.

It may be off-topic, but (regarding the first reference) why was such a zoological paper published in a psychological journal?

Spiders have been sent to the ISS to see if they can weave a web in zero gravity.  The interesting thing is that their first attempts were a mess, then after 2 days they mastered it.  It shows at least some level of learning.  But it is learning from experience, not from imitating others.

For many species the mother abandons the eggs after laying them and there is no maternal care (sometimes the mother dies after laying eggs, so really no possibility of maternal care). Paternal care is generally completely lacking as well (and sometimes the father is expected to die before hatching). And many of those species are solitary, so not learning from other unrelated spiders. So for those spiders web weaving is obviously innate.
As a bonus, this includes some species of the most dramatic web weavers, orb weaving spiders.
(Note that other spider species are fantastic mothers with a prolonged period of child-rearing, so I guess it's possible that it's learned in those species, but Occam's razor suggests that it's innate in all spiders.)

Welcome to Biology.SE! This looks like the start of a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion and provides no guide to further leaning. This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site.

This isn't necessarily true though. I learnt many things from my own parents, but I certainly didn't learn how solve an equation, speak French, or make armpit farts. All those came from other people. Proving that web building is innate would need not only removing the parents from the scene, but also all other spiders - and I think that's the experiment the OP is looking for.

@Graham "[M]any of those species are solitary, so not learning from other unrelated spiders."

@Graham and further, how do you rule out self-learning?  How would you prove the spiders inherently knew how to build webs rather than learned to do it on their own?

@CharlesStaats Thanks - I missed that little bit.

@RyanL You'd expect there to be a progression of complexity/competence in the designs, if they're learning. Birds' flying ability is a great example - they see their parents and practise in the nest whilst their wings develop, and chicks raised without a "role model" bird may not ever learn.

@Ryan_L Some of the spiders in question have very distinctive webs. https://en.wikipedia.org/wiki/Web_decoration So that seems to rule out learning from other species. In terms of learning from their own species, some of them tend to only live a year or less (they can live longer if the winter is mild, but the expected life cycle is that eggs survive the winter but adults do not). -- It's also possible that something is innate but still improves over time, e.g. crawling in humans. A newborn doesn't have the muscle control to crawl but will start crawling even without observing others crawling.


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Why do animals with more mass tend to have brains with so much more mass when it seems like a similar mass brain should be able to do the job?
Why does a wolf have a brain so much bigger than that of a poodle, when a poodle's brain is big enough to do the job, I would have thought. Likewise, if tigers are not smarter than house cats, why do they have brains that are so much bigger? Brain tissue is metabolically expensive, and so you'd think there would be a strong selection pressure to have the smallest brain that could do the job.
I'm familiar with the idea that a large body needs a large brain to control it, but I've never understood why that should be the case. And since poodles are modified wolves, it should be easy for wolves to quickly evolve poodle brains in nature. Has anyone tried to create a large breed of dog with a small brain, to see whether it's possible, and what problems if any the animal has in controlling it's body, for example?
So my question is: Why do animals with more mass tend to have brains with so much more mass when it seems like a similar mass brain should be able to do the job?

"Why are animal brains so often so big and therefore metabolically expensive?" I don't think you have the best wording here. I think what you are asking is why do animals with more mass tend to have brains with more mass when it seems like a smaller brain should be able to do the job. Because typically when people say "large brains" they are referring to brain-body mass ratio and in this sense, animal brains are often not very big.

@DKNguyen I agree with your comment and have edited the question accordingly. Thanks.

I have to challenge you here on size of wolf and poodle brains. How well do you think a pack of poodles would do at hunting and tracking elk? Communication (social skills), working together, solving puzzles, self-sacrifice (a wolf female will nurse an alpha female's pups when the alpha needs to hunt - like during very lean times - to the point of her own starvation), these survival-of-the-pack tasks require brainpower! Poodles are smart, but they need people to solve their problems. That, and doggie eyebrows so they can beg effectively.

@anongoodnurse: But this raises a question.  Is the OP comparing wolf brains to toy poodle brains, or to standard poodle brains?  Per Google, a grey wolf brain weighs about 119.5 g, that of a standard poodle 92.5, and a toy poodle 59.1 g.  So there's a greater percentage difference between the two poodles, than between the standard poodle and the wolf.  The wolf typically weighs a good bit more than the standard poodle, too, so the ratio of brain mass to body mass is about the same, or maybe ever higher, for the standard poodle.

@jamesqf - Those are good questions, but the OP doesn't really elaborate. I'm only pointing out that you can't expect a wolf to operate with the brain of a poodle; they are not equal in nature. My guess would be that brain tissue samples of wolves and poodles would show some interesting differences.

The search term for these studies is "brain body size scaling" if you type in "brain body size" you end up with ratio studies. https://pubmed.ncbi.nlm.nih.gov/14673198/ https://www.frontiersin.org/articles/10.3389/fnana.2014.00077/full#B23

@DKNguyen The pubmed article you linked to makes sense to me. Just because energy is plentiful, that doesn't mean you should waste it. There's less selection pressure for a small brain that can do the same job just as well, but there is still pressure. Depressing that it says, "Brain size scales with body size across large groups of animals, but exactly why this should be the case has not been resolved." It's amazing the things that are still mysterious in biology. I think both sexual reproduction and sleep are still unexplained. Also homosexuality in humans.

@anongoodnurse Do you have any evidence that wolves are smarter than poodles?

Poodles are smart animals; so are wolves. They are different, and you seem to think that a poodle's brain is adequate for a wolf. It's not. Surviving in the wild takes a certain kind of intelligence that domesticated dogs don't possess; they lost it through domestication (and picked up eyebrows, curly tails, floppy ears, etc.) The majority of dogs on their own die quickly (yes, some wild dog packs do well for a while.) Release 20 poodles into the wild; they will not hunt and bring down an elk.

@anongoodnurse Is that a fair comparison though? What if the poodles were raised by wolves? Poodles were bred as hunting dogs after all.

@DKNguyen - I don't know that anyone has been unkind enough to try that. First, the wolves would eat the dogs. Second, domestication for over 30K years has taken the aggression needed to hunt out of dogs, and given them appealing eyes and eyebrows so they can enchant us. Third, poodles' jaws can't crack bones as well as wolves' jaws. Fourth, if poodle pups were substituted for wolf pups and accepted by a female grieving the loss of her pups, wolf cubs mature more quickly, which matters for survival. Etc., etc. Personally, I believe they could not learn to be wolf-like.

I think that you can find a good answer to your question in a more careful evaluation of the hypothetical that you pose:

since poodles are modified wolves, it should be easy for wolves to quickly evolve poodle brains in nature.

How easy is it, actually, for a wolf to evolve into a poodle vs. evolving only the wolf's brain into a poodle's brain?
The answer can be found in the science of evolutionary developmental biology (evo-devo), a good popular introduction to which can be found in the book Endless Forms Most Beautiful.
In general, evolution of scale and morphology operates by controlling the differentiation of tissues in the early development of a body-plan via Hox genes and other related regulatory elements. When understanding their effects on an organism as a whole, in many cases, each such gene can be thought of as a variable that shifts or distorts a body coordinate system. The more fundamental such a gene is to the body plan, the more widespread its effects will be and with a greater degree of side effects. This means that sometimes it's actually much easier to select for a large complex of linked changes than for a single specific change.
In fact, it turns out that for many animals the overall scale is one of the easiest variables to control! Consider, after all, how much you yourself changed in scale during your own growth from birth to adulthood, while maintaining viability and system integration the whole time. Many animals can thus readily become bigger by running the growth program more or smaller by running it less, and these scale changes are often also associated with neoteny. It is, in fact, pretty easy to turn a wolf into a chihuahua, and a chihuahua is pretty close to a wolf pup.
To change only the brain of the mature animal, however, is actually harder, requiring a more specific selection signal. Brains appear to have gotten bigger with respect to body under selection pressure that led to novel architectural features giving specific highly-competitive capabilities. Selection pressure for a small brain, however, would likely be about metabolic burden instead, and there are a lot of potential strategies for reducing metabolic burden, at the same time that many of the variables affecting brain size are likely to be entangled with other critical features as well, such as the jaw.
Bottom line: it's evolutionarily a lot harder to shrink just the brain than to shrink the whole animal.

'Evolutionarily harder' would be an explanation if small-bodied-small-brained wolves had the same ecologic niche as big-bodied-small-brained wolves. Then the 'hardness' would come into play. But that is not the case

@bukwyrm The point is about the ability to follow moving constraints with regards to a niche.

https://www.frontiersin.org/articles/10.3389/fnana.2014.00077/full#B23

@bukwyrm: While I don't know their brain sizes, coyotes are basically smaller wolves - close enough that they interbreed to create the coywolf.  Then there's the even smaller fox.

@DKNguyen Was that link posted in support or in opposition to my answer? From my read, it is consistent.

@jakebeal Indeed.

@DKNguyen That paper  you linked to ( https://www.frontiersin.org/articles/10.3389/fnana.2014.00077/full#B23 ) seems to use way more jargon than necessary. I find it very hard to understand, not because the concepts are hard, but just because of the way it is written. Even with instant look up of words with Google, I can't read it, which I suspect the authors are glad about.

@MatthewChristopherBartsh Yeah, I did a lot of filtering when reading it.

What is it that this paper says, that you think supports your evo-devo-inspired answer? They go into the nitty gritty of neurons/g in different clades of mammal, but it is neurons/g brain matter (of different locations in the brain) not /g animal mass. Additionally they explicitly say that there is much more going on than simple whole-brain scaling - so what gives?

@bukwyrm I do not claim it as a direct support (note that it is not in my citatations), only that its findings (high consistency across scale within a clade, differences linked to anatomical differences between clades) are consistent with the same evo-devo model that leads to my answer.

Well, it's worth noting that the number of neurons doesn't scale linearly with the brain size; in particular for two dogs analyzed by Herculano-Houzel et al. (2017), the number of neurons in the cortex scaled the least:

Both dog individuals examined (a 7.45 kg mixed-breed and a 32 kg golden retriever) had larger brains than the cat (brain mass in dogs, 58.4 and 114.5 g, respectively; cat, 34.8 g), and also more brain neurons than the cat (dogs, 1.8 and 2.6 billion neurons, respectively; cat, 1.2 billion neurons). The same applies to the cerebral cortex of the dogs, at 46.2 g with 429 million neurons and 84.8 g with 623 million neurons, against 24.2 g with 250 million neurons in the cat. Strikingly, although the cerebral cortex of the golden retriever was almost twice as large as the cortex of the smaller dog, it only had 46% more neurons than the smaller dog cortex (as expected from the non-linear scaling of cortical mass with number of cortical neurons [of carnivora in general]);

And the authors of this paper also write that this unsurprising because cortex neurons are apparently the most expensive to scale up in numbers:

We have previously shown that the metabolic cost of the brain is proportional to its number of neurons, regardless of brain size, and that neurons in the cerebral cortex cost on average 10 times as much energy as neurons in the cerebellum (Herculano-Houzel, 2011). Thus, cerebral cortical neurons are expected to be both more vulnerable to caloric shortage than other brain neurons, and to also contribute more to decreasing total metabolic cost when their numbers are reduced than the loss of other neuronal populations would.

And seemingly being a bigger carnivore with somewhat more cortex neurons might actually make one a little bit smarter. The paper notes in support of that that:

Cognitive performance in carnivorans was recently addressed specifically by Benson-Amram et al. (2015). Across these species, even though brain size relative to body mass is a significant predictor of success in opening a puzzle box, species with larger absolute brain volumes also tended to be better than others at opening the puzzle box (Benson-Amram et al., 2015).

(This paper might have been somewhat sensitive to the method used for testing, like the scaling of the box. It actually found that [unsurprisingly to me] bears were champions at opening boxes... but Herculano-Houzel's paper actually found that bears don't have that many cortex neurons... "the brown bear has [...] 251 million [cortex] neurons, which is only about as many as the house cat, even though the brown bear cortex had a nearly 10-fold larger mass". So something doesn't quite click here.)
Anyway, your hypothesis that a cat and a lion (or actually a bear) have the exact same cognitive abilities might not be correct, when generalized. (Lions have as many cortex neurons as dogs, on average, 500 million, according to Herculano-Houzel.)
There is also a 2019 paper by Horschler et al. on dogs specifically that finds something similar based on more data on dogs:

Using citizen science data on more than 7000 purebred dogs from 74 breeds, and controlling for genetic relatedness between breeds, we identify strong relationships between estimated absolute brain weight and breed differences in cognition. Specifically, larger-brained breeds performed significantly better on measures of short-term memory and self-control. However, the relationships between estimated brain weight and other cognitive measures varied widely, supporting domain-specific accounts of cognitive evolution.

I haven't looked at their methods section yet.

"We have previously shown that the metabolic cost of the brain is proportional to its number of neurons, regardless of brain size" - That is a salient first half of an answer- it is not about size, it is about number of neurons, - but the other half, showing why big dogs need so many more neurons (even if it does not scale liearly with mass), is missing


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For animals with separate hermaphrodite and non-hermaphrodite populations which is more common, female + herm or male + herm?
I think the question already says it all.  I know there exist animals that have both herm and female populations and other's with herm and male populations, I'm not personally aware of any animal that has herms, males and females but I suspect that also exists somewhere.  I'm just curious which of these sex combinations is most common, ie which is most likely to evolve.
If you could also speak to why one sex combination may be more prone to evolve over another I'd be very interested in that, but I'd settle just for knowing which combination is more common.
I'm asking specifically about simultaneous hermaphrodites here, I know sequential hermaphrodites exist but that would just complicate the question.

Androdioecy (the coexistence of males and hermaphrodites) is very rare in animals, and vanishingly rare in vertebrates (just three species of fish). Coexistence of males and parthenogenetic females is considerably more common, at least in insects (often in different generations).
Gynodioecy (the coexistence of females and hermaphrodites) in animals is thought to be rarer by an order of magnitude. In fact, before 1975 no examples were known. Gynodioecy is, however, much more common and widespread than androdioecy in plants (though still <1% of angiosperms).
You can find details of different sexual systems and the number of species they occur in from the Tree of Sex.
Sources:

Mongue et al, International Journal of Organic Evolution, 2021
Weeks, International Journal of Organic Evolution, 2012
Fautin, Nature, 1975

The resource you list doesn't include nematodes (or many other major groups of invertebrates) — Caenorhabditis elegans is a famous example of an androdioecious animal. Can you provide one or more references that directly address the OPs question — whether androdioecy or gynodioecy is more common in animals? Both seem to regarded as rare, but a cursory search only turned up one example of the latter in animals (Epiactis prolifera), which would suggest that the former is fact relatively more common ...


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How do the maximum rates of calcium pumping compare between the calcium ATPases SERCA and PMCA
Two important Calcium ATPases found within cells are the Sarcoplasmic reticulum Ca2+ ATPase (SERCA) and the Plasma membrane Ca2+ ATPase (PMCA). Both use ATP to help maintain resting calcium concentrations within cells as well as play important roles in calcium signaling.
How similar are these two calcium pumps? More specifically, how do their maximum pumping capacities compare to each other? I would assume that just because they are both calcium ATPases it does not mean they are similar in all properties. For example, the Wikipedia page linked above even mentions how

The endoplasmic reticulum calcium pump...[is] inhibited by the tumor-promoting agent thapsigargin, which does not affect the plasma membrane calcium pumps.

Have any studies been done that compares the pumping capacities of these calcium ATPases? Or maybe is there a way to determine it based on their structure, roles, etc.?

I am not sure why this is being voted to be closed as a homework question. Can the close voter give pointers?

I didn't vote to close, but the rationale is likely as follows. Posters are expected to show that they have thoroughly researched a question before posting — "Tell us what you found and why it didn’t meet your needs". This is not my field, but faced with this problem I would search for reviews of calcium ATPases — general and specific — using, say Google Scholar. Just restricting yourself to a very short Wikipedia article is hardly enough.

Thanks @David, will do!


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Could a tree grow in a low pressure environment?
Could a tree grow in a low pressure environment? If you had a pressure say, 10% of that of Sea level could a tree grow if it was in the proper soil and watered regularly?

related https://biology.stackexchange.com/questions/1242/what-is-the-lowest-pressure-at-which-plants-can-survive

Does this answer your question? What is the lowest pressure at which plants can survive?


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Nastic movements in Insectivorous plants
Questions:

What type of plant movement is shown by each of Sundew, Venus Flytrap and Pitcher Plant? What is the mechanism of the movement?
Can a movement be both Chemonastic and Thigmonastic? If yes, so any plant in Question 1 show both?
Give example(s) of exclusively chemonastic and exclusively thigmonastic movement.

Description:
Sundew (Drosera sp.), Venus Flytrap (Dionaea sp.), Pitcher Plant (Nepenthes sp.) are 3 examples of Carnivorous Plants.
These plants use rapid movements to capture their prey and then digest them to fulfill their Nitrogen requirement as they grow in Nitrogen deficient soil.
My Attempts:
I have found different answers according to different sources.

According to one source, tentacles of both Sundew and Venus flytrap curve in response to soluble proteins placed in the centre of the leaf. So, both of them are Chemonastic.
According to another, Chemonasty is exhibited by long peripheral tentacles of sundew. Closing/Bending of glandular hairs of sundew in response to nitrogenous compounds.
According to Wikipedia, Sundew and Venus Flytrap shows thigmonasty.
Interestingly, none of the above sources mention Pitcher Plant. According to a friend, Pitcher Plant shows free movement (moves its leaves at its own will). Is that true?
Finally, according to me, all three should be thigmonastic. Because all three trap the insect once the insect touches it. So, it is influenced by touch, thus, thigmonastic. Maybe some of them are chemonastic as well (I don't know which ones).

Hi everyone! Sorry for making the question too big. For a smaller version, just read the Question: part.

Also, in our school, a T/F question was: Chemonastic movement is noticed in Pitcher Plant. This is a reason that I am asking this question.

So, I studied abo them a little more, and came to a conclusion, which I am adding as answer.

Answers:

Sundew and Venus Flytrap show both Chemonastic and Thigmonastic movements. Pitcher plant doesn't move at all. Reasons in Description.
Yes, Sundew and Venus Flytrap show both Chemonastic and Thigmonastic movements.
Mimosa pudica, bunchberry and mulberry plants show exclusively thigmonastic movement. Still didn't find any plant that shows exclusive chemonastic movement.

Description:

In Sundew and Venus Flytrap, trigger hairs contain some proteins that sense touch. Although the in response to nitrogenous compounds part is hoax (since even if you put a stone in the trap and move it a little, then it will shut. After a day, it will spit that stone out.)

In a Pitcher Plant, no movement occurs. Rather, a slippery substance on its opening lid makes the prey slip in. Watch this video.

I still didn't find any exclusively chemonastic movement, and also still don't know for sure if the mechanism in venus flytrap and sundew invokve something chemical (not exclusively thigmonastic) since according to Wikipedia, Venus flytrap shuts its leaves even if a non-living thing falls in.


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Is there a database of plants chemical contents?
A database where given the name of plants, one can know the molecules it contains.

Let me know if this helps you. http://bidd.group/CMAUP/

The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are request for resources (these end up being opinion based). Please [edit] your question to ask as specific focused biological question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please see the [tour] and consult the [help] starting with [ask] for details.


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What insect eggs are these?
There are only 3 eggs. A pink colour with stripes on it. Is it possible to identify the species? Found right below a window, on the wood.
I'm in Bangalore,
India.

These are caterpillar/butterfly eggs belonging to the Rounded Palm-Redeye (Erionota torus).
Here is an example of the eggs of a leaf:

The larvae / caterpillar form looks like this:

And fully formed butterfly looks like this:

All these pictures can be found on the iNaturalist page for this taxon:
https://inaturalist.ca/taxa/219475-Erionota-torus/browse_photos?quality_grade=any&photo_license=any&place_id=32239
And the geographical range of observations of this species includes your area:

Nice answer! +1. (Never thought I'd think, "Ugly butterfly...")

@anongoodnurse it used up all the pretty on its eggs.

@anongoodnurse Yes, I my first impression of the adult was that it was a moth

Wow! Thank you so much for the answer! I've seen these around the house!