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Blood serum transfusions - could vaccines against the anti-A/anti-B etc. antibodies be derived, at least in theory?
People with the AB-positive blood type have all three of the A, B and RhD antigens present on their red blood cells, and no antibodies to these in their blood serum (aka blood plasma.)
This means that they cannot receive blood serum transfusions from people of other blood types, as their serum does contain these antibodies. In general, a person's blood serum contains antibodies for whichever of the A/B/RhD antigens are not on their blood cells, and no others.
Otherwise, an acute haemolytic reaction would occur.
The most-upvoted answer to another question on Biology.SE used a quote from Dean's "Blood groups and red cell antigens", chapter 5 to explain why these antibodies were present:

ABO antibodies in the serum are formed naturally. Their production is stimulated when the immune system encounters the "missing" ABO blood group antigens in foods or in micro-organisms. This happens at an early age because sugars that are identical to, or very similar to, the ABO blood group antigens are found throughout nature.

In a hypthetical future situation where the demand for blood serum transfusions was high, would it be possible to vaccinate young AB+ children against these antibodies? I'm thinking of injecting proteins similar to the antibodies, to train the immune system to produce "anti-antibodies". The memory-B cells would hopefully produce these fast enough and in large enough quantities to destroy the original antibodies and prevent ill-effects when a transfusion was given.
Would such a vaccine be feasible?
If not, would an immunisation relying on very small quantities of the actual antibodies (not enough to damage/agglutinate significant numbers of red cells) be viable?
I'm aware that if/when such antibodies pass through the placenta, they can lead to haemolytic disease of the newborn, so a newly-born child might be too young to receive such a vaccine. I'm imagining a situation where the number of such antibodies would not be high enough to cause these complications, or where the fake antibodies would not bond to the red cell antigens.
Source:
Dean, L. (2005). Blood groups and red cell antigens. 1st ed. Bethesda, Md.: NCBI.


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How do injected purified anti-D antibodies prevent the natural production of antibodies in order to prevent Hemolytic Disease of the Newborn?
Treatments involving Anti-D antibodies are given to pregnant women carrying Rh+ fetuses when the mother has an Rh- blood type in order to prevent Hemolytic Disease of the Newborn during the 2nd pregnancy. The anti-D antibodies are injected during later stages of pregnancy and right after birth in order to eliminate any Rh+ blood cells in the mother before D-antigen antibodies are produced naturally by the mother. If antibodies do not attack cells directly, what stops the mother's macrophages from engulfing the antibody bound Rh+ blood cells, becoming an antigen presenting cell and hence initiating the process of producing antibodies and saving the antigen in memory cells? Are the Fc receptors on the macrophages not compatible with the injected anti-D antibodies?

I think you've misunderstood some of this. The treatment doesn't involve giving someone anti-D antibodies to destroy Rh+ cells - indeed, those antibodies would cross through the placenta and potentially cause the disease in the newborn. An antibody treatment based on Rho(D) immune globulin does exist, but this functions by preventing the immune response which would otherwise cause the production of anti-D antibodies.

Hmm, it seems even I was wrong in part - the treatment involves "a solution of gamma globulin containing anti-D" according to Rudmann's textbook (p439)

@Astrid_Redfern Thank you very much for your input. Still, if the gamma globulin contains anti-D, then my question is still relevant right?

I think your question is indeed relevant. I'm doing a bit of research to see if the antibodies really are intended to destroy the Rh+ red cells, as I'm not sure if that's their purpose.

Related: https://biology.stackexchange.com/questions/35531/why-is-the-administration-of-exogenous-anti-d-not-harmful-to-the-foetus

Made a bit of progress by learning that antibodies can either be of a neutralizing or non-neutralizing nature: https://en.wikipedia.org/wiki/Neutralizing_antibody
"Neutralizing antibodies on the other hand can neutralize the biological effects of the antigen without a need for immune cells"
The anti-D antibodies in Rh Immune Globulin are of a neutralizing nature: https://www.sciencedirect.com/science/article/pii/B978012374432600035X  Could it be that sensitization is avoided because the Rh Immune Globulin does not tag the Rh+ blood cell for phagocytosis by macrophages?

source: Stack Exchange

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

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Sextuplet corn (Zea mays with branched ear)
In 2019 I planted some sweet corn next to some Hopi blue flint type corn. Of course my mistake was apparent once I started to see the ears. The closer the two types were to each other, the more they were mixed. So this year, not realizing what might happen, I planted the solid blue seeds that I had saved. I don't know much about corn, clearly, and assumed that if I planted blue seeds, I'd get all blue corn. Not the case. Most was all kinds of different colors, shapes, including some kernels that were clearly sweet corn, with most being a field corn, some with a dent, most without. Then some plants had some nice large ears of large blue kernels.
Okay, so that is just the backstory in case it will help. I ended up with this one 'cob' that is actually 6 small cobs all on one stem. Very bizarre, and I can find nothing like this online. I am curious if anyone can tell me how this happened, and perhaps if planting those same seeds would result in more of this. I took a video to get the best look of this oddity. https://youtu.be/xIAYaRwgQ-k

Welcome to Biology.SE! This sounds very interesting, but please [edit] one or more clear photos of the unusual cob into your post — the standard for questions (and answers) on this site is that they must provide enough information without requiring users to go to external sites. For example you could upload stills captured from your video. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Thanks!

Thank you, I was unable to upload before due to your size restriction and I didn't have an easy way to resize.

This looks a lot like a ramosa mutant (for example see the ears in panels A,G,H - taken from Figure 2 from Gallavotti et. al. 20101).

Ramosa mutations affect the branching pattern of the inflorescence (i.e. the ear and tassel in maize - aka. corn in the US) and are typically highly variable.  These are thought to be partial reversions to the phenotype of teosinte, which is the putative ancestor of maize2,3.
The unusual ear you collected may have resulted from a spontaneous mutation (possibly transposon driven), but also could be due to infection by a fungus (these sometimes secrete hormones that create developmental effects), or even insect damage to the developing ear.
If this phenotype was due to a heritable mutation you may notice an effect on the tassel (more densely branched), but IIRC this can be quite subtle. The best evidence for this being genetic would be seeing this phenotype recurring in subsequent generations. If possible plant kernels from the strange ear in an isolated area. It is also possible to do controlled crossing in maize — if you go this route I would suggest that you try to self pollinate (i.e. take pollen from each plant's tassel and put it on that same plant's ear).
You also might find this short video to be of interest.
If you get plants with similar phenotypes in this or a subsequent generation I can put you in touch with someone working on ramosa genes who might be interested in having some of the seed if you're willing to share ...
References:
1: Gallavotti, A., Long, J. A., Stanfield, S., Yang, X., Jackson, D., Vollbrecht, E., & Schmidt, R. J. (2010). The control of axillary meristem fate in the maize ramosa pathway. Development, 137(17), 2849-2856.
2: Iltis, H. H. (1983). From teosinte to maize: the catastrophic sexual transmutation. Science, 222(4626), 886-894.
3: Bennetzen, J., Buckler, E., Chandler, V., Doebley, J., Dorweiler, J., Gaut, B., ... & Walbot, V. (2001). Genetic evidence and the origin of maize. Latin American Antiquity, 84-86.

Thank you very much! I do hope to try some hand pollinating the next time I have an opportunity to garden. I would certainly be willing to share seed if it seems that they would pass this phenomena along to their progeny! I'd love to see what a capable person could do with this, if it is genetic. Being in the Pacific Northwest, it would not surprise me if fungus played a role. ha

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Have cruciferous vegetables been genetically altered to reduce cooking odors?
As a young girl my mother always kept a bottle of "Air Wick" under the kitchen sink. When she cooked cabbage, cauliflower, broccoli, etc., she would open the bottle, pull out a green sponge that was on a wire, and place the opened bottle on the counter. It absorbed the strong odors of those foods that would normally penetrate other rooms. Today when I cook those same vegetables I don't notice those strong odors of my youth. Have those vegetables been genetically altered to reduce their strong, lingering odors?

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, it is important to define what you mean by "genetically altered" — almost every food we eat has been under selection by humans for many generations. Is that what you are trying to ask about? ——— We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

perhaps she cooked it for longer and used difference of oil/salt/vinegar.

Perhaps your sense of smell is not as good as it was when you were young?  I'd also be more than a little skeptical about the "absorbing odors" claim.


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What type of creature makes those mounds?
Location: South Ireland,
Appeared: 2020
Nearest river: 500 meter down hill south
Water is running down the hill also but there’s drainage to not flood the grass
Seen before: potted plant
I  used earth like this from a different location to plant a potted plant into a plant pot and those type of mounds happened afterwards in there also. Just on a smaller scale.
Never seen anything move though. Probably night active.

What size are the mounds? How close are you to a body of water (river, lake, etc)?

Added measurements and water proximity

do you know what worm mounds are like? if it's in a lawn then it's probably a worm cast, worms dig by passing soil through them and travel to the surface to place blobs there like black spagettis, when it rains they can lose their spagetti shape, so you only have 20% of your ones, the most recent that are still spagetti shaped.


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How do I stimulate a neuron extracellularly, specifically the sphenopalatine ganglion
Apologies if this is too basic of a question, but I am an electrical engineer, just getting into neuromodulation/neurostimulation.
For my senior project, I am trying to make a device that stimulates the sphenopalatine ganglion. I have read as much as I can online, but some basic questions seem to not be answered. Answers to any of these would be really really helpful, as well as any resources to continue my research:

When I'm trying to 'stimulate' a neuron, I am really trying to trigger an action potential, correct?
Can I just send current across the exterior of the membrane to trigger an action potential?
Is is possible to stimulate a neuron without piercing the membrane? I know an action potential is the voltage across the membrane, so how can I change that voltage without piercing the membrane?
I believe I need to record the action potentials of the neuron, to make sure that my device is targeting the correct location and working properly, is this possible without piercing the neuron?
From the literature, I found that a 10 Hz electrical pulse works best for the sphenopalatine ganglion stimulation, but I am not sure how frequency plays a role in this.

Sorry again if that is a lot, but I am new to the field and have a lot of questions. Thanks in advance for any help!

I'd highly recommend collaborating with an electrophysiologist. You wouldn't want a neuroscientist without other training to wire up the electrical in your house (frankly, probably not even an electrical engineer, either, this is an electrician's job). Doubly, triply, 100X, 1000X more important to collaborate with someone with human electrophysiology expertise if you plan to get anywhere near a human with this. Not something that can be covered in a SE Q&A.

Hey thanks for the quick response. So I am kind of working with some neuroscientists/electrophysiologists in the field, but they are very busy and my manager says we should get some prototype finished before we meet with them.
So I need to do my background research (which now includes a SE Q&A) before I can get the help for my specific project and bring it to an actual human. It's an inefficient system, but it is what it is.

The simple answers to your 5 questions are: not necessarily, yes, yes (you're an electrical engineer; membranes are capacitors), yes but this is complicated, it's complicated - I doubt any of those really get you closer in your project, though.

As @BryanKrause mentioned, these are expert level questions. You cannot build a prototype without some knowledge of electrophysiology. There are entire books and experimental manuals written on this topic. Perhaps you can build a computer based model just to present the idea but it would not be wise to build a prototype without getting the neuroscientists on board.

Thanks to both of you for your answers. I'm wondering what books you are referring to about these specific topics. Even if I cant get a working prototype, I need to at least have a basic understanding of electrophysiology before I meet with them, just so I could have a better conversation. Any help would be great!

@Brian The two undergraduate neuroscience books I usually recommend are Purves or Kandel. The electrophysiology sections should have a lot of concepts familiar to you from the electrical part of your physics courses, but they probably focus on patch clamp electrophysiology from a technique standpoint. You have a very specialized target so from there you're probably headed to the literature. Google scholar tends to give me the most thorough results; medical indices like PubMed might miss some articles in journals with more of an engineering focus.


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What is the name of this bird from Tanzania?

I took this picture in late 2018 in Tanzania. The Birds of East Africa book does not include it and I've been unable to identify it looking on the web. Can someone help me identify it, please. Thank you!

That looks like a knob-billed duck.
Their range includes Sub-Saharan Africa, India, and Southeast Asia.

Picture source


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Why don't weak detergents lyse the nuclear membrane?
A low concentration of a non-ionic detergent lyses the cell membrane, but leaves the nuclear membrane intact. Both are phospholipid bilayers, so why is only the cell membrane lysed?
Under these conditions, are the membranes of other organelles lysed?

Great question. It seems only zwitterionic detergents are talked about when lysing organelle membranes. I don't see why lots of 'weak' detergent wouldn't get the job done if the only goal was to lyse the organelle membranes.

First, an important fact   about non ionic detergents- {1}They have a hydrophilic head group that is uncharged and are preferred for their ability to break lipid-lipid and lipid-protein interactions. They have limited ability to break protein-protein interactions and are often referred to as non-denaturing detergents and are used to isolate biologically active membrane proteins.
Generally, moderate concentrations of mild (i.e., nonionic) detergents compromise the integrity of cell membranes, thereby facilitating lysis of cells and extraction of soluble protein, often in native form.
An example would be Triton X-100. {2} Non-denaturing detergents such as Triton X-100 have rigid and bulky nonpolar heads that do not penetrate into water-soluble proteins; consequently, they generally do not disrupt native interactions and structures of water-soluble proteins and do not have cooperative binding properties. The main effect of non-denaturing detergents is to associate with hydrophobic parts of membrane proteins, thereby conferring miscibility to them.
The following article is about the same protein insolubility that I have written above, but in the nuclear membrane of chicken RBC’s. {3}

Protein has been selectively extracted from isolated chicken erythrocyte nuclear envelope by (1) dilute MgCl2/Triton X-100 followed by (2) concentrated MgCl2/Triton X-100 solutions. Certain proteins appear to be selectively dissolved in the first solvent and may occur in the nuclear envelope primarily as lipoproteins. Among the proteins insoluble in the low MgCl2/Triton X-100 wash, as well as in 500 mM MgCl2 without Triton previously used in the preparation of the envelope fraction, the quantitatively major polypeptides dissolve in a combination of high MgCl2 and Triton X-100. Further, much of this dissolved protein precipitates when the MgCl2 concentration is lowered by dialysis. The insolubility of these proteins appears to result from a combination of ionic and hydrophobic interactions and may explain the resistance of nuclei to various manipulative procedures including nonionic detergent washes.

The conclusion is that the protein insolubility of these detergents is what makes the nucleus resistant. You know that the phospholipid bi-layer is common for both- the cell membrane and the nuclear membrane. But underlying the inner nuclear membrane is the nuclear lamina, a fibrous meshwork that provides structural support to the nucleus. The nuclear lamina is composed of one or more related proteins called lamins.
Coming to your last question, using the example of Triton X-100 and leukocyte cells, a paper says: {4}

Leukocyte membranes except the nuclear envelope were solubilized in a buffer that contained 1% Triton X-100.

Which means that all membranes- including mitochondrial, dissolve in the detergent because they do not have an additional protein layer in them, like the nucleus does.
1-http://www.genotech.com/protein-research/detergent-accessories.html
2-https://www.thermofisher.com/in/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/detergents-cell-lysis-protein-extraction.html
3-https://pubmed.ncbi.nlm.nih.gov/999948/
4-https://link.springer.com/article/10.1007/BF00554425


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How exactly does chemotherapy cause anemia?
I’ve been trying to figure this out for the past few hours but I still can’t find something as in depth as I’m looking for. So far all I’ve found is that chemo drugs kill bone marrow cells and some other drugs can damage the kidney which decreases red blood cell production, but I’m looking for something a bit more in depth.
From my understanding, there are multiple “groups” of chemo drugs (such as alkylating agents, antimetabolites, etc), so I assume there isn’t one answer which covers every group (unless, hopefully, I am wrong). I’ve read explicitly that some groups, like alkylating agents, are known to cause death in bone marrow cells. This also made me question if anemia/bone marrow cell death is a side effect from every chemo drug. If not, is it known which groups of chemo drugs are most likely to cause anemia and how exactly they do cause anemia (as in anything more in depth than “they kill red bone marrow cells”)? I’ve also read that some chemo drugs containing platinum can damage the kidney, but I wasn’t able to find how exactly it damages the kidney in a way that red blood cell production is decreased. I’m assuming this is due to a decrease in EPO production/secretion? If anyone has any relevant information/sources I would greatly appreciate it! Sorry if this is really specific and if this happens to be the wrong place to post such a question.

https://medicalsciences.stackexchange.com/questions/tagged/chemotherapy


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Measuring the protein content using UV Vis
The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ethanol. Since ethanol precipitates the protein can I still determine the protein content of my sample using UV Vis at 260nm absorbance? or the protein content can be measured by its precipitate using a different method?

How do you want to measure the concentration of a solution when part of the dissolved content is not in the solution anymore?

ohh.... Even if the pure ethanol is at low temperature, still it cannot measure the protein content of the solution?

How do you know how much precipitated?

From what I know protein binds with ethanol forming a precipitate but I don't know if the temperature affects the precipitation because I also don't know if I can still read the protein content of the sample solution at 260nm using the UV Vis spectrophotometer. Some are saying that it can still be read when cold ethanol is used but I don't know if its true because most of the solutions that are subjected to UV vis are usually clear solution or clear colored solutions. that's why I'm asking.

How would precipitating (some of) the protein with ethanol or any other method help you to measure the A280 of a protein solution? The Bradford or Coomassie dye is to measure absorbance around 600 nm.


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What is the representation for Sulfur in organic matter?
We often represent organic matter with the following equation:
$$
(CH_2O)_x(NH_3)_y(H_3PO_4)_z \tag{0}
$$
For example, the organic matter with the Redfield ratio has the form of $(CH_2O)_{106}(NH_3)_{16}(H_3PO_4)_1$.
But if we want to put inside the element Sulfur ($S$), which form below should we use?
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(H_2S)_m \tag{1}$
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(S)_m \tag{2}$
$(CH_2O)_x(NH_3)_y(H_3PO_4)_z(SO_4)_m \tag{3}$.
These different forms assume the different covalency of sulphur (-2, 0, or +6). Which form above should we take to describe the composition of organic matter with S?
I guess maybe Eq.(2) $(CH_2O)_x(NH_3)_y(H_3PO_4)_z(S)_m$? Because in this way, sulfur has the covalency of zero, which is the same as carbon (0).
I asked this question because I found many papers use the Eq.0 to build the mineralization of organic matter (e.g., O2 oxidation, [R1] in Table 2 here. See Fig.1 below). The amount of O2 depends on the assumption that carbon in OM has the covelency of zero (then, 1 mole of C corresponds to 1 mole of O2).
Since I didn't find a paper that put S into the OM compositon to balance the similar equation like [R1] in Fig.1, I am curious about which covalency value is "more common" for such an equation (because Sulfur's covalency can affect the amount of O2 needed).

Welcome to Biology.SE! Please provide a more focused question. Those chemical formulae are gross simplifications of the species that exist in biological compounds. For example, carbon and nitrogen commonly participate in both single and double bonds with themselves and other elements (also in aromatic contexts), and can also form triple bonds in biological molecules. Similarly sulfur can occur in several oxidation states. This makes your question in its current form impossible to answer in any way that I can see as meaningful and so I'm going to vote to close as "Needs details or clarity". ...

(cont) Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. Thanks!

I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

@tyersome Thanks for your advice! I have edited my question to make it more clear. Yes for example carbon in the organic matter has several oxidation states, but when modelling it, we often assume its oxidation state is 0. Under this assumption, we can balance the equation. So I'm curious about if there is a common "assumption" for sulfur.


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Is there something amounting to "check sums" in genetic code?
Humans use checksums for many different applications in informational processes.
Genetic code is used as a "program" to synthesize proteins, so it could (I'm a layman when it comes to biology!) make sense that its integrity is protected in some way. And since there are just so many cells in a human body a few "retries" could be attempted when encountering bad strands in one source during DNA replication or protein biosynthesis.
Because minute mutations can have a big effect, I was wondering if there is any mechanism that amounts to check sums in genetic code? And if (no) such thing has been discovered as of yet, is there any theory as to why (not)?

I would suggest reading more about error correction in DNA replication, homology-directed repair (https://en.wikipedia.org/wiki/Homology_directed_repair), polymerase proof-reading (https://en.wikipedia.org/wiki/Proofreading_(biology)#:~:text=In%20bacteria%2C%20all%20three%20DNA,and%20excises%20the%20mismatched%20base.), translational proofreading (https://www.pnas.org/content/113/48/13744). I doubt that there is any mechanism that amounts to checksums. I think that there are many cases in which an error-checking/correction procedure has something kind of like checksums.

You should also consider the balance between costs and benefits from such a system. Would evolution be possible with such a system? Biological check sums could only be maintained if preventing all change is beneficial over evolutionary timescales ...

@tyersome yeah, actually it should be. Because if the same "check" fails on the same segment of RNA/DNA the "error correction" could give up.

@MaximilianPress thanks for those links. It'll take some time for me to read through all of that. Feel free to write up an answer around those. Again, as a layman I know too little so perhaps my analogy was "off" and so even if these mechanisms may strictly not amount to being check sums, these links appear to be in line with my question (from my perspective).


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Do mRNA vaccines cause transfected cells to be killed by cytotoxic T cells?
Based on my research on how mRNA vaccines (specifically for COVID-19) work:
An mRNA sequence, that contains the sequence of the coronavirus spike protein, is absorbed by some cells. These cells now produce foreign coronavirus spike protein. These cells then present some of the produced foreign spike protein on their surface via MHC I complexes so that they can activate a cytotoxic T cell and cause it to produce lots of copies of itself (cell-mediated immune response). Some of the foreign spike proteins are also released from the transfected cells which allow for B cells to activate a humoral immune response and for professional antigen-presenting cells to present the foreign spike protein on MHC II complexes to activate helper T cells.
My Question:
As far as I understand it, once a cytotoxic T cell encounters a cell that has a foreign protein presented on an MHC I complex, the T cell kills the cell that has presented the foreign protein before it leaves. This means the cells transfected with mRNA through the COVID-19 vaccine (even though a coronavirus hasn't actually hijacked them) will eventually be killed by cytotoxic T cells that encounter them since they are presenting foreign spike proteins on their surface. Is this not toxic for the body since it is killing your own cells? Or does the fact that the mRNA sequences are not self-replicating contain these cell deaths to only the transfected cells and only a few cells die in this process so that the vaccine is not toxic overall?

There is a question on stackexchange that is not only related
Why cytotoxic T cells don't kill dendritic cells when they present antigen?
Your question refers to "some cells" (explanatory text) and "transfected cells". Thus, any cell that takes up the m-RNA-vaccine is referred to. However, any answer must be based on the different types of cells involved in immunization, vaccination and - in killing infected cells, in the end. There are the immune cells which present antigen, there are, as well, the body cells which present.
The explanatory text of your question speaks of "presentation".  The very first paragraph of Wikipedia on "Antigen presentation https://en.wikipedia.org/wiki/Antigen_presentation seems to even limit the term  "presentation" to presentation by immune cells, which would exclude any body cells, like muscle cells transfected with vaccine antigen.  This might illustrate that immune cells are different from body cells in respect of presentation of antigen that becomes target of cytotoxic t-cells.
Both immune and body cells  take up antigene, however the immune cells, by presenting prime naive T-cells, i.e. activate the T-cells. The related question  cited asks about the fate of the immune cells.
As for  the fate of body cells like muscle cells you refer to  in  the last paragraph of your question the video message you link to in your own answer seems to refer to those body cells: transfected cells will simply be killed, but not enough of them to cause harm.
Here are additional remarks, enjoy: I think  it is an open question if the transfection as such would lead to cell death (assuming some failure of cytotoxic T-cells, not doing their job). Think of vaccination that transfects with "attenuated", if not live virus: even if the virus is incapable of - natural - replication  it is unlikely that the host cell whose ribosome machinery has been usurped can keep up its metabolism. I would like to be allowed to mark the following as a new thought of mine: the fact that the antigen is being presented speaks in favour of the cell not being able to survive - which is counterintuitively (how can a cell infected by virus still be able to digest, process, transport and present antigen on its MHCs, at all? Looks like it will stay alive.)
From the very fact of antigen presentation it is possible to infere, in my opinion, that the cell will not survive transfection. Host cells may  have their  own, inner defence mechanisms which are able to beat infection without any presentation of antigen - think of "interferon", but also, nowadays, of double stranded RNA, dsRNA.  A cell that is successful in defeating the virus without engaging the adaptive immune response would cancel out its survival by presenting and attracting cytotoxic t-cells. So it is a possibility that cells in spite of being transfected by mRnA vaccine do not die.  However, that would be considered a vaccine failure.
So with effective vaccination transfected body cells will die.
Caveat: from my reading of textbooks it is a possibility that vaccination might be effective even if body cells are not transfected, but that is beyond your question. Premise of your question is that a cell is being transfected (then what happens?).
A reference on the  possibility  that a "transfected cell" might survive by self defence  would be  "RNA interference",
https://en.wikipedia.org/wiki/RNA_interference
Last not least - see  the video you linked to - there is "B cell immunity".
To my mind it is a possibility that B-cells become transfected by mRNA vaccine - if so, they should present the antigen as an endogenous on to cytotoxic T-cells which makes your question very relevant in respect to B-cells, in my opinion. However, B-cells produce antibodies, considered most important in vaccination. This speaks in favour of B-cells taking up antigen via their B-Cell receptor that should be among cell debris of transfected cells that died - for instance few muscle cells transfected by vaccine. What you need here, in respect of B-cells is authority on either cross-presentation of endogenous antigen by B-cells (if mRNA is being uptaken through membrane, if B cells are transfected) or, authority on B-cells "only cleaning" up dead cell's antigen as part of dead cells, killed by virus or immune cells.
My answer is in line with the answer you already gave -  elaborating on what is in fact causing the cell's death:
"Do mRNA vaccines cause transfected cells to be killed by cytotoxic T cells?"
Yes,  mRNA vaccines cause transfected cells to die.

"So it is a possibility that cells in spite of being transfected by mRnA vaccine do not die. However, that would be considered a vaccine failure."  Absolutely wrong. Further mRNA doesn't last forever in cells, so it's entirely plausible the intra-cell infection clears without the cell dying. It's not at all a given the cell will be killed before the exogenous mRNA inside it "runs out". https://medicalsciences.stackexchange.com/questions/25522/is-the-code-from-the-mrna-vaccine-executed-by-the-cells-as-a-one-off

Interesting you say "absolutely wrong" - as I cling to "would be considered" (a failure). Literally: to consider that way would be absolutely wrong? The faster, better the vaccine works the sooner T-cytotoxic cells will kill the transfected cells presenting. Conversely, any no showing up of killer cells might be termed a failure. Still, I will try to amend my answer. Thank you!

@Fizz re "It's not at all a given the cell will be killed before the exogenous mRNA inside it "runs out". -  Any reference I'd consider valuable. What happens to antigen once expressed on MHC? Your premise: antigen on MHC vanishes mRNA "inside runs out", correct?
Did you know that antigen presented on MHC is returned and recycled to the cytoplasm? Is it being "re-presented" then, again? Alternatively, "to recycle" includes hiding away from? P.S. Remove to chat is all right with me.

“Is this not toxic for the body since it is killing your own cells? ”

Yes, cytotoxic T cells do kill mRNA vaccine-transfected cells, but not to the extent of harming your body. This is because the mRNA vaccine cannot be not integrated into the host genome, mRNA then will be degraded after translation within hours, preventing spike proteins variants to be continuously produced. Meanwhile, these locally produced antigens will mark the cells as "transfected", and induce immune response against the virus, including the activation of cytotoxic T cells, which directly kill the infected cells without damaging healthy tissues [1]. In some people, this process might cause some degrees of inflammatory responses, including pain, redness, swelling, fever, etc [2].

Individual vaccine antigens induce innate immune responses that may differ qualitatively or quantitatively according to the vaccine composition, but that induce a good adaptive immune response.

Once all transfected cells are eliminated and the antigens are no longer present, the level of antigen specific cytotoxic T cells will return to baseline [3].
Resources

Wadhwa A, Aljabbari A, Lokras A, Foged C, Thakur A. Opportunities and Challenges in the Delivery of mRNA-Based Vaccines. Pharmaceutics. 2020; 12(2):102. https://doi.org/10.3390/pharmaceutics12020102

Hervé, C., Laupèze, B., Del Giudice, G. et al. The how’s and what’s of vaccine reactogenicity. npj Vaccines 4, 39 (2019). https://doi.org/10.1038/s41541-019-0132-6

DiPiazza AT, Graham BS, Ruckwardt TJ. T cell immunity to SARS-CoV-2 following natural infection and vaccination. Biochem Biophys Res Commun. 2021;538:211-217. doi:10.1016/j.bbrc.2020.10.060

Additionally: This happens as well to virus infected cells, but to a much greater extent.

cells transfected with mRNA through the COVID-19 vaccine (even though a coronavirus hasn't actually hijacked them) will eventually be killed by cytotoxic T cells that encounter them since they are presenting foreign spike proteins on their surface.

It's not a given that happens before the exogenous mRNA inside the cell runs out. There's a decay process for mRNA of any kind, and exogenous mRNA is particularly targeted by intracell innate responses like TLR7 (although mRNA vaccines try to counter this with nucleoside modification, which delays the process).
Further, MHC-I isn't a flag that goes up an stays like that forever until the cell is killed. MHC-I is subject to recycling.... and it's a darn complicated process whose duration depends whether the MHC-I is fully or sub-optimally loaded, but it happens regardless of whether any killer T cell shows up to answer the "suicide-by-cop 911 call" or not.
Both the question and the 3 existing answers to it apply the "deterministic computer model" to biology, taking processes that in reality happen with some probability (which may be pretty low) as being 100%.
And it turns out that nucleoside modification has a somewhat surprising side effect: it reduces killer T-cells leaving helper T-cell activations intact (which help with the production of antibodies). 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].

The research group which wrote that review seems focused on cancer immunotherapeutics, and the two cited studies definitely are about that. The lackluster CTL activation is a big deal for cancer therapy, but not really a problem for priming your immune system against an infectious disease you haven't yet encountered "for real".
In the 1st of those two papers cited there's an interesting [pair of] graph[s], showing the point I mentioned previous about killer vs helper T-cells.

And since mRNA vaccines are normally injected in skeletal muscle, it's also worth knowing that

Muscle fibers do not normally express major histocompatibility complex class I (MHC-I) molecules, and their reexpression is a hallmark of inflammatory myopathies.

Last paragraph - so interesting! Let us know what did you Google to find that reference, please.
Isn't it common textbook knowledge that any i.e. all nucleated cells express MHCI?
So "overexpression" in that paper to be understood as "expression at all", as basic expression is zero?
And, this is in favour of any regular, non-immune-system host cell needs not be targeted for immuization, which is by dendritic, APC, cells and lymphocytes alone, to successfully occur?

Quote: "MHC-I is subject to recycling...." - I think you are right that recycling does not imply any "restauration" i.e. any "come back" of what has been "recycled". When watching  recycling of a motorcyle do no await any new"1", smile.  Quoting your quote at "darned":  "...removed from the surface followed by intracellular degradation or recycling to the cell surface, in a process likely involving ..." - Surprise: there is "no interdiction of reconstitution": is spike antigen presented on MHC recycled to surface or not? Again, what did you google, I'm out for even more reference, thanks!

Maybe of interest to you:  B Cao, "Muscle stem cells can act as antigen-presenting cells..." in case you do further research on muscle cells not expressing MHC.  There is more reference, stating muscle cells, under normal circumstances, do express "some" MHC, which wouldn't be zero. Of general interest, why not eleborate? Muscle cells are fused cells, multinucleated (textbook wisdom: "all nucleated cells feature MHC").

@PeterBernhard: thanks; the abstract doesn't say anything about MHC though. I'll have to look into the paper to see what mechanism (if any) is being suggested. The paper simply uses an Ad vector.... speaking of which there's a Q about those here (being effective vectors for expressing genes in muscles):  https://biology.stackexchange.com/questions/97523/how-do-adenoviruses-interact-with-muscle-tissue-that-it-makes-them-acceptable-as/

According to the person who made this video's response to my comment asking this question, the transfected cells are killed by cytotoxic T cells, but the amount of transfected cells dying is not enough to cause irreparable harm since the cells regenerate themselves fairly quickly through division. Plus, the acquired cell-mediated in addition to humoral immunity is well worth the risk of an mRNA vaccine over a standard protein vaccine (which only leads to humoral immunity). If anyone has a better answer than this please let me know.

muscle cells do no regenerate, and covid vaccine is done to muscle cells

@ManudeHanoi: true, which is why this can't be the major pathway by which mRNA vaccine eject their proteins. Killer T cells merely targeting (let alone killing) muscle cells is the hallmark of serious pathologies like inclusion body myositis, which is very hard to treat. With hundreds of millions of doses of mRNA vaccines administered, you'd expect significant reporting of long-term deltoid muscle strength loss, but nothing like that has been reported among the vaccine side effects.

@ManudeHanoi: also "Muscle fibers do not normally express major histocompatibility complex class I (MHC-I) molecules, and their reexpression is a hallmark of inflammatory myopathies" https://pubmed.ncbi.nlm.nih.gov/23850081/ Basically skeletal muscle cells are unkillable by killer T cells under most conditions.


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

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

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

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

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

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

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

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

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


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Why do large, aromatic residues prefer beta-pleated sheets?
I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning behind this finding. I have made an educated guess based on my findings on alpha helix propensities:
In alpha helices, branched and aromatic R-groups are not favored as the g+ and g- isomers can extend into the helix and interfere with the hydrogen bonding. In beta pleated sheets, however, the R-groups are pointed perpendicular to the hydrogen bonds, and even large R-groups like that of phenylalanine or tryptophan will not able to reach the site of hydrogen bonding. Coupled with the fact that smaller amino acids will rather be more tightly bound to each other (so they prefer helices, e.g. collagen helix, alpha helix, save space, amide hydrogens and carbonyl oxygens closer together), larger amino acids therefore favor formation of beta pleated sheets.
I need a few key pieces of info to really accept my own explanation (if it is correct) as factual. First, I will need proof that beta pleated sheets are more structurally rigid than alpha helices (or else, smaller R-groups like that of alanine and cysteine will also prefer beta pleated sheets). I also kinda want to see the structure of beta pleated sheets with large R-groups to further ground the thought in my head, as I can't really see how R-groups like valine (heavily branched) will not affect hydrogen bonding. As an example, I attach one that I found for alpha helices.

are you familiar with visualization software such as Pymol or VMD?

I have found this image on Biology LibreTexts, and they have answered my question. Like I suspected, the large residues will mainly project out of the beta pleated sheet and will not interfere much with the backbone hydrogen bonds. In alpha helices, however, the branched and aromatic residues are still able to project into the helix (as they are not pointing completely outwards) and disrupt the bonds.
To better visualize it, imagine a foam cylinder and toothpicks poking out of it at an angle. Now imagine the toothpick branches out in all directions (to simulate rotamers). It will poke the cylinder again. Now imagine a flat foam board with toothpicks sticking out of it up and down at an angle. Even if it branches out, it will not ever poke the board again unless it branches backwards (impossible for residues, I reckon).
In beta pleated sheets, aromatic interactions between two aromatic rings might further stabilize the structure. In alpha helices, the residues are pointing away from the helix and therefore not that close to each other; but in beta pleated sheets, they are close enough to interact.
I have also found a viable reason to why beta pleated sheets are supposedly more "rigid" than most other secondary structures. Alpha pleated sheets are really compact and only involve one peptide chain, whereas beta pleated sheets are less compact and include two or more peptide chains, limiting the movement and decreasing the overall entropy.
If you still have trouble visualizing, visit the Biology LibreTexts page and look at their splendid diagrams modelling the secondary structures. They really helped me in understanding it. It is quite elusive, so I'll link it here

This table is from the Wikipedia page for α-helix:

As you can see aromatics are not the worst offenders. In fact, barring proline (whose backbone torsion angles are unsuited to helices), Gly is the worst offender. A likely reason for this is Gly being too flexible i.e. its small side chain H allows it to adopt backbone torsion angles unsuited for α-helix.
As another example let's look at silk, an extended anti parallel β-sheet structure, from libretexts.

As you can see, the small side chains of Ala and Gly in fact allows the β-strands to come close enough to form backbone hydrogen bonds. In fact, from the same reference I quote - "Unlike the α helix, though, the side chains are squeezed rather close together in a pleated-sheet arrangement. In consequence very bulky side chains make the structure unstable."
So it is not entirely true that aromatic amino acids prefer pleated β-sheets.
So what are we missing? We are missing the chemical environment in which the the amino acid residues are placed. Remember, most of the propensity charts we look at are average propensities across known protein structures. In a specific protein, its specific chemical context can radically change the secondary structure propensities.

I am aware of the effects of proline and glycine on secondary protein structures, but didn't find it relevant to the question, but thanks for further clarifying it anyways. Your example of silk is really insightful as well. However, I am still wondering why the aromatic residues have a higher average propensity (through various chemical contexts,  like you mentioned); at least, relatively higher than smaller residues like on alanine, glutamate etc.

Also, I am confused when you say that alanine and glycine allow the beta-pleated sheets to come close enough to form backbone hydrogen bonds. Aren't backbone hydrogen bonds formed despite the residues (excluding proline)? Do you mean the hydrogen bonds will be stronger as they are closer together? In antiparallel beta sheets the amide hydrogen and carbonyl oxygen are pointing directly at each other, so I doubt they will not form bonds even if there is more space in between.

@chematwork The strength of a hydrogen bond depends on the distance between the bond donor and acceptor, electronegativities of the atoms and the angle donor--H--acceptor. So if you have bulky side chain residues in beta sheets (e.g. a benzene ring is around 4 A in length) you can see that they will weaken  hydrogen bonds as the distances between the bond donor and acceptor will increase.

@chematwork — This answer is far better than yours because it exposes the fundamental fallacy of “the average beta sheet” of your question. The average human being has one ovary and one testicle. Alpha helices do allow certain general principles, but the variety of conformations of beta-sheets in proteins, and the variety of their environments preclude all but the most superficial statements. When few structures were known, this sort of thing was all one could say. Fifty years have passed since then.

@David I checked the beta sheet propensities of aromatic side chains and while they have high average  propensities, I seriously doubt a polypeptide of only aromatic side chains will show a tendency to form a beta sheet. Sadly I don't have enough expertise to run MD simulations to check this.

@chematwork  “A polypeptide of only aromatic residues”.  What relevance does that have to real proteins?


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SARS-COV-2 detectability versus viability
This week (#47 of 2020) two meta-reviews were published in the Lancet.
Ct values and infectivity of SARS-CoV-2 on surfaces, a brief review published on 19 November in The Lancet Infectious Diseases, observed that culturable virus samples are correlated with Ct values of 29·3 (steel surface) or 29·5 (plastic surface), whereas Ct values of 32·5 (steel surface) or 32·7 (plastic surface) correlate with the detection of non-culturable virus.
SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis, published on 19 November in The Lancet Microbe, furthers this observation and concludes that by such metrics individuals infected with SARS-CoV-2 are not infectious after day 9.
Does this suggest an upper bound of nine days for viable virus in a standard environment (22°C, 40-60% RH) or may surface conditions be more hospitable than living cells?


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Why does sequencing virus proteins take time?
According to the below paper, the coronavirus spike protein sequence was available to scientists by end of february 2020 - the begin of march 2020 timeline. I had this question that why does sequencing of a virus protein take so much time (I am a software engineer, currently studying molecular biology to better understand the pandemic, hence I am seriously unaware!) ? The reason of asking is because, in case of another epidemic, we might need to spend again a lot of time to sequence the protein. This might be a real concern!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151553/#:~:text=At%20the%20time%20of%20the,remain%20identical%20or%20almost%20so.

Note that the protein sequence is inferred from a DNA sequencing experiment, not sequenced separately.

@MaximilianPress Yes, that is an important point, and one that I neglected to state explicitly in my answer.  Thank you for clarifying in yours -- Protein sequences are inferred from the DNA sequence using gene/ORF calling software.

You really can’t expect us to read through this paper to discover what exactly is the time period between what events you feel is “so much time”. Sequencing the genome of a virus in itself can be done very quickly. I suspect that you may be confusing stalking  the deer with cooking the venison. If you don’t know where the meat got to before it got to the supermarket, perhaps you need to do some reading. Biology perhaps?

Sequencing a viral genome requires isolation of the virus, propagation in cell culture, extraction of nucleic acids, and preparation of a sequencing library.  Once sequences are obtained, a genome can be assembled de novo using (untargeted) shotgun reads, and gaps in the genome can be spanned with (targeted) Sanger sequencing.  This process can take weeks to months depending on the availability of resources and the growth characteristics of the virus.
For details on how the 2019-nCoV genome was sequenced, see Zhu et al., published January 2020:
A Novel Coronavirus from Patients with Pneumonia in China, 2019

Thanks @acvill, that answers my question. So, "the availability of resources and the growth characteristics of the virus" are the reasons. Thanks again!!!

Note that mine is a very general answer and is indeed pessimistic about processing times.  Your question would be much improved if you walked us through your logic in deducing what you describe as "so much time", per David's comment.

Sequencing DNA (which is what was done for the COVID virus, post reverse transcription as it is an RNA virus) does not take very long. A NextSeq instrument can provide results in <24 hours. Protein sequences are inferred from the DNA sequence using gene/ORF calling software.
SOme of this is suggested by @acvill, though I think that they are pessimistic about time estimates. Viral genomes are pretty easy to assemble (matter of hours). In principle you can dispense with the isolation step too, though that makes the analysis more complex.
It is all the medical and bioinformatic stuff around the sequencing, e.g. isolation and analysis and ethical paperwork (necessary!), which takes time.

Thanks @Maximilian Press, that was very informative! "A NextSeq instrument can provide results in <24 hours" was useful information to know. Thanks again!!!


text:
Help identifying a bug which looks like a housefly and mosquito hybrid
I'm from Kochi, India (southern part of India). I found this bug inside my house , it was about a centimeter long . But how can such an hybrid be possible. (It was raining before I found it).
1: https://i.stack.imgur.com/Dlyio.jpg

Welcome to Biology.SE! Do you have some reason to assume this is a hybrid? If not, that is an extremely naïve assumption to make and I encourage you to remove it from your question. Please also [edit] additional information such as local ecological factors including the dominant types of plants and if possible clear close-up pictures from multiple angles. This may enable someone to narrow down the identification of this insect.  ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. Thanks!

This is a long-legged fly (Condylostylus spp).  Unfortunately your image is not sharp enough to give a specific species.  See this post of another Indian fly that is virtually identical to yours:
https://www.jungledragon.com/image/13762/long-legged_fly_-_condylostylus_spp.html

Thanks for your answer. However, Your post does not provide enough evidence /support for you to definitively claim the genus of the OP's specimen. Please consider explaining why you think this is the correct genus.

The OP and many other visitors will likely see your post and consider it fact. This is insincere given that it appears (based on what evidence you provide here) that you simply did a Google image search. The picture you link to is from a photography website with no evidence of taxonomic expertise. (It seems to just be amateur photographers tagging their own photos). Much more convincing and reputable sources exist and should be used as support if you truly feel confident in your answer. Again, please consider updating to strengthen your answer. Thank you


text:
How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?
Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA:

Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-links. However, they are not all of the same kind; there are four kinds, called adenine, thymine, cytosine, and guanine, but let us call them A, B, C, and D.
...
Next comes the question, precisely how does the order of the A, B, C, D units determine the arrangement of the amino acids in the protein? This is the central unsolved problem in biology today.

Feynman taught his lectures during 1961-1963. Do we now know how does the order of adenine, thymine, cytosine and guanine affect the order of the amino acids in the DNA?

I have found that starting with a relatively accessible and reliable source like Khan Academy is very helpful to learn about an unfamiliar area. Wikipedia is also generally a good starting point and you can then check their references. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

Yes, it was solved in the early 1960s, starting about 1961.  See Wikipedia's Genetic Code - History, and perhaps "Establishing the Triplet Nature of the Genetic Code".


text:
Do the posterior legs of mosquito plays the role of antenna?
I have had this question for years and this stems from the observation that when I bring my hand close to a mosquito lying on some surface (e.g : wall) I see its posterior legs - which are in a strange posture then (going upwards - moving slightly toward my hand...
I wonder whether these legs have another role than standing ? Correct me if I'm wrong but in my humble knowledge some arachnids have the front pair of legs endowed with sensory function ,so is it a similar case with mosquitoes ?


text:
Creating a phylogenetic tree from my selected publicly-available sequences (WGS) in NCBI
I'm currently writing a paper on the comparison of virulence genes for a group of bacteria. I got my data from publicly-available whole genome sequences in NCBI. Now, I want to create a phylogenetic tree for these species but since I'm working from home, I'm using my old laptop that makes it hard for me to process data. Can you recommend any software/ site/ tutorial/ paper that I can use to generate a phylogenetic tree easily? This is also the first time that I will create a phylogenetic tree and I'm not sure how to proceed without downloading and processing too much data that my current laptop can't handle.
Thank you!

What file format(s) is your data? standard phylo tree format is i.e. Newick or New Hampshire format... So you can just go on google and search "freeware Newick tree display program" or something.

My data is actually the WGS in NCBI for 55 bacterial strains. Is there a way to create a tree out of these without downloading and processing a large size of data?

what about their tree viewer? genetics informatics forum is called BioStars.

@aliential The OP wants to create a tree, not just to visualize a tree. Rimuru show us a few of your bacterias, everything is about the size and the alignement step. If it is your first time then use blast to extract a well-aligned 2000 nucleotides region, then use online tools such as http://www.trex.uqam.ca/index.php

Will you be comparing each one of the virulence genes to each other? If the WGS sequence is annotated for your gene you can take those sequences and use software like MEGA to create a phylogenetic tree. But you have good internet and your laptop does not have enough processing power (you haven't provided laptop specs) use an online tool like @reuns mentioned.


text:
The Fish-Tetrapod Transition, evolution of the "elbow" in Stem Tetrapods
The Acanthostega and Tulerpeton limbs seem to form "elbows" in an axis perpendicular to the flexor and extensor plane of the fin. They seem to "flex" their "elbow" forwards, pre-axially. And, I assume, keep it permanently "flexed", a bit as if their humerus, ulna, and radius has been one single "V-shaped" bone. This adaptation positions the primordial hand forwards. Is this pretty much correct? Why I wonder, I always understood elbows as bending in the flexor/extensor plane, but in the first terrestrial life it seems to be in the pre-axial/post-axial plane. That probably has implications for how limbs continued to evolve, and for the embryogenesis of limbs in mammals like humans. I found that interesting.

keep in mind the orientation of limbs has changes between early terrestrial life and yourself. A salamanders forelimb bends very differently than yours. Consider you are looking at a 2D representation of a 3D structure. Also what makes you think those early limbs could not flex in the flexor/extensor plane?

Link to get you started. https://www.geol.umd.edu/~jmerck/geol431/lectures/d05limbs.html

Try reddit/ask paleontology or something. That question confused me. Simply put "it looks like these species had limbs at a fixed angle, is that correct?" Not really! You'd have to find cartilage wear marks and round joint zones on the bone to figure that out, and the litterature barely gives much info on the biomechanics of the forelimbs.

The current research doesn't venture many details on the elbows/radius/ulna and locomotion biomechanics.
For the moment they just say the elbow was "slightly flexible" and that the bones were transitioning towards a round shape.
You can research deep into the resources and will perhaps find more.
Here are a resource which give context, found via "locomotor performance in stem tetrapods"
https://www.researchgate.net/publication/236460049_Historical_Perspectives_on_the_Evolution_of_Tetrapodomorph_Movement
There's also a 3D study of the legs here: https://www.researchgate.net/publication/227857349_Three-dimensional_limb_joint_mobility_in_the_early_tetrapod_Ichthyostega
https://sandykawano.weebly.com/locomotor-biomechanics-for-moving-onto-land.html


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Tree identification
I went to Araku few days ago and saw this tree in a garden .

Here are the leaves

I know the pic of fruits is a bit hazy and out of focus,but it's the best I have.

These trees were in a cluster ,behind a patch of Nerium shrubs beside the pavement of the garden.

Please provide as much detail as possible for the most accurate ID. If you have additional photos showing the leaves in detail, the bark, the general shape/size of the tree, etc. please include them. Please also comment on the relative sizes of the flowers/leaves/tree in your images and include any pertinent info about the ecology/environment of the tree (e.g., was it in a forested part of the garden, along a sidewalk, part of landscaping, etc. etc.) Thanks

Last picture is flower buds

This appears to be a flower of a tree in the Syzygium genus.
Because there are many species (1200+) -- many which are intentionally planted as ornamentals outside of their native range or have the propensity to become invasive -- I cannot confidently provide a more specific species given the garden location in which you found your specimen (and lack of further details).
I include, as an example, an image from the University of Connecticut of Syzygium jambos, which is not native to India, but is known to grow in nearby regions.

Notice the similar floral architecture to your specimen: dominant androecium (literally hundreds of stamens), whitish color, 4-lobed calyx, prominent hypanthium, etc. Multiple flowers also similarly cluster at the end of branches as in your photo.

Read more about S. jambos's floral description  here.

Sometimes-similar Eugenia cannot be totally ruled out based on your limited photos/details, of which 25 species occur in India. However, Syzygium still seems much more likely.
Overall, I can update my answer with more details once you've updated your post.


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Definition of synaptic strength
The canonical definition of action potentials found in textbooks states that action potentials are all alike in shape.
From techniques such as spike sorting which are used to attribute electrophysiological recordings to individual cells, we know, however, that shapes and amplitudes of action potentials vary.
Synaptic strength is defined as the average amplitude of postsynaptic potential evoked following a presynaptic action potential.
Given that the incoming action potentials might differ for different synapses (and for instance lead to more or less vesicles being released), how can we hence have a uniform definition of synaptic strength?

What do you mean by uniform definition of synaptic strength? Synaptic strength has nothing to do with shape or amplitude of action potentials so why do you think that is relevant?

Why not? Say the amplitude of an AP is larger, then could it not be that the number of vesicles being released at the axon terminal is larger as well, hence leading to a larger PSP by a stronger depolarization at the axon terminal?

"action potentials might differ for different synapses" and synaptic strength can be different at different synapses. The latter says nothing about the cause. It remains unclear where your confusion lies, maybe setting up a specific scenario where you think the synaptic strength has a different definition than the one you gave ("average amplitude of postsynaptic potential").

I see - I think the confusion was that synaptic strength could be distilled to structural properties of the synapse (such as area of the postsynaptic density). But as you mention the definition is independent of the cause (e.g. effect of APs of different amplitudes), right? Thank you for the clarification

Ok, if that's your confusion I understand now, I'll move my comments into a short answer. Let me know if this covers it.

Although action potentials do vary from neuron to neuron between different classes of neurons and neurons from different areas, the differences that appear in extracellular recordings are due to recording conditions, such as the distance of the electrode from the neuron and the part of the neuron that is being recorded. Hence, the different action potential shapes observed in extracellular recordings are not inherent to the neurons. Spike sorting takes advantage of the different conditions that each neuron is recorded in an attempt to separate them into different units, i.e. candidate neurons.

Thank you @vkehayas this distinction is extremely helpful

@vkehayas Some of those AP characteristics can also be measured extracellularly, in particular the spike width differences between cortical pyramidal cells and fast spiking interneurons.

Do spike width differences correspond to different ion channel kinetics?@BryanKrause

Synaptic strength is defined as the average amplitude of postsynaptic potential evoked following a presynaptic action potential.

This is a correct definition. Synaptic strength is a fairly abstracted measure. It can be influenced by both presynaptic (for example: number of vesicles/concentration of neurotransmitter per vesicle) and postsynaptic effects (for example: receptor number and composition). So yes, changes presynaptically such as the character of an action potential can influence synaptic strength, but that isn't a problem: we still represent this as part of the synaptic strength if it affects the average postsynaptic potential.
Biologically, action potential amplitude in the axon does not really matter much for synaptic release, but local conditions in the presynaptic terminal that influence calcium influx do. The section on presynaptic inhibition in the answer here may help a bit.


text:
Red flowering climber ID
Here's another climber from the same garden in Araku Valley

So what is this climber?
Does it have any economical uses?

It's an Ipomea also known as a Morning Glory. There are 600 species of Ipomea including the sweet potato. There are many colors of mixed Ipomea, your one is probably a fairly random hybrid. It is perhaps most similar to Ipomoea Rubriflora and Ipomea Coccinea:


text:
When telomere length is measured, is the method performed on a collection of cells yielding an average?
What are the methods used in measuring telomeres in human or animal subjects?
Can it be done on an individual cell?
Has the following concern been raised and addressed before:
What if there exists a natural variance in telomere length on a cell by cell basis and various methods exist (strenuous exercise etc) that exert selection pressure on telomere length, then if the measurement method in some way involves multiple cells you have the effect of the average length increasing while something else actually occurred. Resulting in all these studies concluding that telomere length increased.

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A telomere can be measured using a flow-fish test. Basically fluorescent markers that bind DNA are introduced to the nucleus of a cell, and then those markers can be counted using a method call flow cytometry.
It can be done on one cell
I'm not sure I understand the last part of the question, but I can say that if the average telemore size increases in a particular sample size, then scientists will not conclude anything based on that data.
If there is a scientific conclusion on telomere size with relation to external selective pressures, there would be statistically significant data that properly accounts for the variations observed in different cells.


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How many giant kelp are there per square meter?
In a high-density giant kelp (Macrocystis pyrifera) bed how many "holdfasts" or roots would there be per square meter of seafloor on average?

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, we expect you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). For example, please add in the species of "giant kelp" for which you want a density. Have you done any research to try to answer this yourself? Please summarize what you found (and where) and what  you still wish to know. Thanks!

The density of Macrocystis pyrifera is pretty variable. According to Dayton et al. 1984 off of the Southern California coast it can range from less than 0.1 to to 1.0 $individuals/m^2$. The variation depends on the location, where there are different exposure levels to high energy waves, upwellings containing nutrients, and predation by sea urchin.
Dayton, P. K., Currie, V., Gerrodette, T., Keller, B. D., Rosenthal, R., & Tresca, D. V. (1984). Patch dynamics and stability of some California kelp communities. Ecological monographs, 54(3), 253-289. https://doi.org/10.2307/1942498


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What is meant by 'genes overlapping inherited structural variants'?
I am reading a journal paper about genes that are related to autism, and I have come across the following statement:

To assess commonality of biological function among rare risk alleles,
we compared functional knowledge of genes overlapping inherited
structural variants in idiopathic ASD subjects relative to healthy
controls

I am not sure what is meant by 'genes overlapping inherited structural variants'. I searched the definition for structural variants and according to Wikipedia, structural variation refers to the variation in structure of an organism's chromosome, such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
However I am not sure what is meant by genes overlapping the inherited structural variants. Does this mean for structural variants that are common between ASD subjects, there are some common genes that are found in these regions (the inherited structural variants)? Any insights are appreciated.

If I understand correctly, what this paper is looking at is rare copy-number variation in ASD cases relative to controls. So in the context of the paper, the passage you quoted is basically saying we found genes that had copy-number variation between cases and controls, i.e. the cases had a pattern of more/fewer copies of a stretch of the genome that includes a gene than the controls. Then they look at the functions of the genes they found in a gene ontology database to see if they seem like they might relate to ASD.


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Sequence structure of antibodies
It is said that

"When a virus or a pathogen enters the body, the immune-response produces Y-shaped proteins called antibodies to bind to the pathogen or virus".
"Also it is possible to extract antibodies from the blood."
Since antibodies are proteins, is it possible to sequence their structure ?
If the answer to point-3 is Yes, then can't coronavirus antibodies be sequenced, more antibodies be produced from this sequence on a large scale, and then these are administered to the infected people ?

I would like to know any challenges to the above mechanism like "difficulty in figuring out the correct antibody or so" ? Thanks!

Looks like you have re-invented monoclonal antibodies. https://en.wikipedia.org/wiki/Monoclonal_antibody

@PolypipeWrangler Yeah, in a way. But this is not done via sequencing of the protein but isolating and identifying the right plasma cell.

Thank you all for the information!

@Chris does this mean that the above mechanism has not been "exactly" applied till date ? I am asking this since you said "not done via sequencing of the protein but isolating and identifying the right plasma cell".

@harrypotter having the protein sequence doesn't help you making the functional protein. Having the relevant plasma cell does.

Giving a simple answer is difficult as the field of humoral immunology is quite extensive. Here is an abbreviated overview.
Our body produces myriads of different antibodies during an immune response, not just one. It is impractical to isolate and sequence one antibody protein as their sequence differs in very subtle ways. N-terminal sequencing like Edman degradation is not practical as it covers only a few dozen residues at most. Perhaps proteolytic digest of an antibody and peptide sequencing is possible, but again this requires a large amount of a pure antibody. Protein sequencing is not practical.
Instead, people sequence the DNA corresponding to a given antibody instead of sequencing the antibody protein itself. As a given B cell expresses one antibody in large amounts, Milstein and Kohler (Nobel laureates) devised a technique to fuse B cells with tumor cells, creating hybridomas. Each hybridoma thus produces a single antibody. Such hybridomas may be cultured – monocultured in fact - in the lab to large amounts, leading to the production of a uniform, single antibody, termed monoclonal antibody. The corresponding DNA sequence of such monoclonal antibody may be readily sequenced.
I would think it feasible to create a library of individual hybridoma monocultures using a patient’s B cells, and then select the hybridoma producing the best monoclonal antibody from the library, and sequence that DNA. Epitope binning [https://en.wikipedia.org/wiki/Epitope_binning] is one example of a technique to identify the best antibody. The successful hybridoma may then be culture to large scale to produce lots of that exact antibody.
Administering such purified antibodies to a patient is not straightforward as this foreign protein will be itself recognized by the patient's immune system and cleared. There are techniques to reduce the immunogenicity of a given antibody, but that will be a lengthy discussion in itself.

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Thanks for the answer. It was useful!

It is possible to sequence these antibodies.
It is likely that these antibodies are already produced, but injecting antibodies into people does not build immunity. At best, it can temporarily mitigate the spread of the virus. It does not build immunity because it would not teach your body to make its own antibodies, which is the purpose of a vaccine.

Thanks @JMorrissette, if I give sequenced antibodies over a period of time, is it possible that these antibodies bind to all the existing virus proteins. Partly we will have destroyed cells but partly the uninfected cells can be saved. Isn't it true ?


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How does HIV know to attack specific immune system cells?
I'm no biologist, but curious of the answer to which I could not find online.
How are Human Immunodeficiency viruses able to detect and distinguish immune system cells with a CD4 receptor on the surface from other cells in the body, in particular other immune system cells without the receptor?
If I have asked the question on the wrong platform, please inform me otherwise.
Thanks

It's not really a matter of "knowing", it's simply a complex chemical reaction.

@jamesqf could you recommend me some reading in this topic?

This paper, specifically the sections titled "HIV Entry Fundamentals" and "Discovery of the HIV Receptors", is a good resource.

@acvill Thankyou very much!

The CD4 receptor is a protein complex that harbors very specific chemistry. A virus is able to bind with the receptor if it harbors a particular protein/set of proteins that are able to interact with the receptor. The virus is basically disguised as something the CD4 receptor recognizes, and from there it is internalized within the cell via a process called endocytosis. You can google viral endocytosis to learn more.


text:
Is the cell cycle applicable to meiosis as well, or just mitosis?
All the diagrams I can find, show the cell cycle as having G1 phase (growth 1), S phase (DNA replication), G2 (growth 2) before the Mitotic phase (mitosis + cytokinesis).
Is there an equivalent "cell cycle" for meiosis, since the chromosomes in parent cell in meiosis also having "double" the genetic material prior to cell division (presumably from DNA replication too)?
Is it simply the same cell cycle as mitosis but with a Meiotic phase instead of Mitotic?
If so, would appreciate if anyone had a diagram :) Thanks!

the problem is meiosis is not a cycle, but you can look up the steps of meiosis easily enough. this borders on a homework question.

The cell cycle is only associated with mitosis. The cell cycle is the normal process of cell division with which cells can indefinitely increase their number by cyclically repeating the process.  When a cell goes through the cycle, the result is two cells that are genetically identical.
Meiosis is a special type of cell division (which can occur only in eukaryotes) that produces cells that are not genetically identical to the initiating cell.  The number of chromosomes in each of the resulting cells is half the number that were in the initial cell.  (These haploid cells can later participate in fertilization, producing a cell with the original number of chromosomes.)  Many of the steps of meiosis are similar to the steps involved in mitosis, but overall the process is more complex. Since meiosis reduces the number of chromosomes, it cannot be repeated and so does not take part in a cell division cycle.


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Is Pars intermedia functional in humans?
My textbook says, "Pars intermedia secretes only one hormone called melanocyte stimulating hormone (MSH)."
My teacher says that in humans MSH is secreted by the anterior lobe because the Pars intermedia is poorly developed and almost merged with the Pars distalis. I am confused as to what is correct. I find nothing wrong in both the arguments. So, is the Pars intermedia in humans functional or not?

Both- the textbook and your teacher are right.

The most obvious function of the pars intermedia in lower vertebrates is the secretion of melanocyte-stimulating hormone (MSH) for the purpose of pigmentary control.
In human fetal life as well, this area produces MSH which causes the release of melanin pigment in skin melanocytes.
In adults,

The human pituitary has no distinct pars intermedia (PI). Instead, the proopiomelanocortin (POMC) producing, adrenocorticotropin (ACTH)- and β-endorphin-immunoreactive PI cells are incorporated within the pars anterior, thereby participating in the formation of the pars distalis.

Edit:

POMC is cut (cleaved) to give rise to multiple peptide hormones. Each of these peptides is packaged in large dense-core vesicles that are released from the cells by exocytosis in response to appropriate stimulation:
α-MSH produced by neurons in the ventromedial nucleus has important roles in the regulation of appetite (POMC neuron stimulation results in satiety) and sexual behavior, while α-MSH secreted from the intermediate lobe of the pituitary regulates the movement of melanin produced from melanocytes in skin.

Sources:

https://link.springer.com/article/10.1007/BF02738816
https://pubmed.ncbi.nlm.nih.gov/6912095/#:~:text=Abstract,the%20purpose%20of%20pigmentary%20control.
https://en.wikipedia.org/wiki/Pars_intermedia

So according to you in human adults Pars intermedia is merged with the Anterior Lobe and therefore cannot be assumed functional?

@NeeravSingla PI is merged with pars anterior, but secretes its own MSH. Hope the edit makes it clearer.


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What does vaccine efficacy mean?
In the last few weeks, Pfizer/BionTech, Moderna and AstraZeneca have each released preliminary estimates of the efficacy of their SARS-COV-2 vaccines.
But what do their respective efficacy percentages actually mean? Is the Pfizer/BioNTech vaccine 95% effective in any person? Or is the success of provoking the desired immune response limited to 95% of the population?
Put very simply: is it 100% effective in 95% of the population, or 95% effective in 100% of the population?

Summarizing, it means 95% fewer infections than the placebo group. How is not yet explained. Whether 95% become immune, or everyone becomes 95% tougher to infect. More importantly, the main purpose of corona vaccines is the old herd immunity. Like extinguishing a fire by hosing down all of the surrounding wood. See below for excellent detail and further reading.

Vaccine efficacy
Pfizer's target measures for efficacy (see the study on clinicaltrials.gov) seem to be:

Confirmed COVID-19 in Phase 2/3 participants without evidence of infection before vaccination

Confirmed COVID-19 in Phase 2/3 participants with and without evidence of infection before vaccination

From Pfizer's study plan (VE = vaccine efficacy):

VE will be estimated by 100 × (1 – IRR), where IRR is the calculated
ratio of confirmed COVID-19 illness per 1000 person-years follow-up
in the active vaccine group to the corresponding illness rate in the
placebo group from 7 days after the second dose. VE will be analyzed
using a beta-binomial model.

(note: they also have other time windows and checkpoints in their analysis plan; which one is reported will shift from press release to press release as they get more data. If you are interested in the details the study plan also describes the planned interim analyses, and some of the press releases discuss deviations they've made from their original interim plans in consultation with regulatory agencies)
This measure is called relative risk, and can be written like this:
%InfectedPerTimeplacebo = NInfectedplacebo / (NStudiedplacebo * AverageFollowUpTime)
%InfectedPerTimevaccine = NInfectedvaccine / (NStudiedvaccine * AverageFollowUpTime)
Efficacy aka VE = %Infectedvaccine / %Infectedplacebo
If you assume risks are the same in the placebo and vaccine groups (they "should" be, but might vary if, for example, people who experience vaccine side effects change their behavior) and the average follow-up time is the same (they should be approximately the same, because they are giving the vaccine and placebo to patients enrolled at the same time), this ratio would tell you that a vaccine efficacy of 95% means that if you took 20 people who would have had a positive test after the placebo, you would only expect 1 of them to test positive if they instead got the vaccine.
Population vs. individual statistics

Put very simply: is it 100% effective in 95% of the population, or 95% effective in 100% of the population?

These are population-based measures. They can't say anything about efficacy in particular individuals by these outcome measures. For example, there is no way to know from a study like this whether the vaccine is 100% effective in 95% of the population, or if it raises the infective dose in everyone by some amount which causes the number of people exposed to this critical viral dose in their environment to decrease by 95% (or some other effect with the same end result).
Other approaches like challenge studies, where vaccinated individuals (or animal models) are intentionally exposed to a certain dose of the virus, can help understand the individual effects of vaccination, as can indirect measures of immune response like antibody titers. These approaches have other drawbacks, however (safety, translating animal results to humans, translating a given immune response to an infection chance, etc).
Beyond just 'vaccine efficacy': disease severity, real-world efficacy
These particular outcomes also say nothing about disease severity. It could be that the people who do test positive despite getting the vaccine get just as sick as the sickest people who don't (interpretation would be that the vaccine protects mostly against mild illness). It could also be the reverse, and that people who get the vaccine and still test positive have a milder illness than they would have otherwise. Efficacy defined by this relative risk ratio does not say anything about this, it only compares positive vs negative rates.
An additional note: these numbers report efficacy in the trial environment. "Real-world" effectiveness (the same measure of effect, but in real world use rather than under trial conditions) might depend on other factors such as differences in the people enrolling in trials vs the general population (both in terms of things like age and preexisting conditions as well as behavior and exposure risks), failure to administer the vaccine properly (including improper storage), failure to complete both doses in timely fashion, etc. This measure of effectiveness also refers only to "primary" effectiveness. One would expect that if enough people were vaccinated, the effect on the population could far exceed the primary effectiveness, because not only do vaccinated individuals have a lower chance of infection, but everyone else in the population also has a lower risk if there are fewer people available to transmit the infection.

Should also note that (as with flu vaccines, which are only around 40-60% effective for the individual) a major purpose of the vaccine is not to provide 100% protection to the person that receives it.  It's to reduce the transmission rate so that the virus doesn't spread.

@jamesqf Meant to include that in my final paragraph but it slipped my mind; included now.

"Efficacy aka VE = %Infected_vaccine / %Infected_placebo" -- did you mean IRR here?

AFAIK the Pfizer vaccine showed that the disease severity was also lowered in the group that did catch Corona despite being vaccinated; none of those developed a severe form. The control group apparently had a few people hospitalized.

It means protection against the virus brought to you by the vaccination.
Around 45.000 people participate in the trial; 50% of these are vaccinated with the trial vaccine and 50% receive a placebo. Additionally, you exclude people from the trial who had had COVID-19 before. Because infecting people with a potentially deadly disease is not possible ethically, you watch both groups for occurrence of the disease.
I have numbers only for the Biontech/Pfizer vaccine, but the principle is the same for the others as well. In this trial 170 cases of COVID-19 were seen: 162 in the placebo group and only 8 in the vaccine group. If the vaccine were to do nothing at all, then you would expect to see similar numbers in both groups, which means that these 8 cases from the vaccine group represent a reduction (or efficacy) of about 95%.
With the vaccine, only 5% will catch the disease, while there is no protection for unvaccinated persons. For the numbers, see the press release from Pfizer and the database entry on clinical trials for this trial.

To further clarify the statement that "with the vaccine, only 5% will catch the disease", this means that 5% of vaccinated people who would have otherwise caught the disease will become infected, not that 5% of all vaccinated individuals will catch the disease (only about 0.01% of vaccinated people did).

@NuclearHoagie Exactly. Without the vaccine you would expect similar numbers of infections in both groups, which is reduced by 95%.

How do you get .05 out of this though? 166/168 is about .988.

@Timkinsella You are right, I somehow added two wrong numbers, which are corrected now. It should be 8 people for the vaccinated group vs. 162 in the control group. See the original publication. Thanks for pointing out.

@Chris There is one more “2” to change to “8” in the third paragraph.  I tried to change it but it’s below the character limit for edits at my rep level, apparently.

@Timkinsella Right, missed that one, too. Now it should be correct. Thanks again.

Saying that a vaccine is $95\%$ efficacious is neither claiming that it has a $95\%$ probability of blocking infection nor that it works $95\%$ of the time nor that it protects $95\%$ of its recipients.†
Rather, a $95\%$ efficacy means that—during the clinical trial in which half the subjects had been vaccinated and half hadn't—among those who eventually developed the disease, the ratio of those who had been vaccinated to those who hadn't is $5 : 100.$

efficacy
among those who contracted the disease,the ratio ofvaccinated to unvaccinated participants
(if effectiveness=efficacy)in any given situation,one is ___ times as likely to contract the diseasewith the vaccine than without

$100\%$
$0 : 100$
$0$

$95\%$
$5 : 100$
$0.05$

$60\%$
$40 : 100$
$0.4$

$50\%$
$50 : 100$
$0.5$

$0\%$
$100 : 100$
$1$  (the vaccine has no effect)

$-20\%$
$120 : 100$
$1.2$  (the vaccine makes you more susceptible to the disease)

Think of vaccine efficacy as a measure of the increase in protection conferred by the vaccine during the clinical trial҂—not as an indication of how frequently the vaccine prevents disease development (whether across time, or among the vaccinated population). To be clear: vaccine efficacy is not a probability.
If the clinical trial was short (as was the case with the Pfizer-BioNTech vaccine), then the published vaccine efficacy could not have taken immunity durationҗ. into account. Therefore the figure may vary—perhaps significantly—as the subjects continue to be monitored over the coming months/years.
† And certainly, 95% efficacy is not the recipient's chance of not contracting the disease, as that depends on their health and exposure, the disease evolution, and other factors.
҂ Technically, vaccine efficacy is the proportionate reduction in disease occurrence conferred by the vaccine during the clinical trial.
җFollow-up data since this Answer was written indicates what the Pfizer-BioNTech vaccine's real-world effectiveness wanes by $10-35$ percentage points six months following vaccination. These figures are complicated by the predominance of a more infectious variant (Delta) which wasn't around during the clinical trial.
P.S. Mathematically, $$\text{vaccine efficacy}=\frac{U-V}U=1-R,$$

where $U$ and $V$ are the respective numbers of unvaccinated and vaccinated subjects who contracted the disease (exactly half the subjects had gotten the vaccination), and
$R=\frac VU$ is the relative risk (the right-side column in the above table).

P.P.S. For the Pfizer-BioNTech trial (in which $43661$ subjects were split evenly between the placebo and vaccine groups), $U=162$ and $V=8,$ so \begin{align}\text{vaccine efficacy}&=\frac{162-8}{162}\\&=95.1\%.\end{align}
P.P.P.S. Note that the Pfizer-BioNTech trial checked only for symptomatic disease, i.e., the $U=162$ and $V=8$ do not include asymptomatic cases of COVID-19 among the study subjects.

Vaccine efficacy is the percent change in the percent of individuals who test positive in the vaccinated group versus the placebo group in a trial. The CDC website explains it here
So a 95% efficacy means the vaccinated group had 95% less percentage of people test positive than in the placebo group. So if the placebo group had a 20% positive rate, the vaccinated group had a 1% positive rate (5% of 20%). If this 95% efficacy is deemed to be statistically significant, it likely means that the positive rate in the vaccinated portion of the population will be 5% of the positive rate in the unvaccinated population.
Normally, if 100% of the population takes a vaccine, a 60% vaccine efficacy is considered enough to cause enough decrease in positivity rate to stop the spread of COVID-19 so 95% is really good. This paper goes into what the vaccine efficacy needs to be if less than 100% of the population takes the vaccine.

I'm sure you'll have seen the recent results of the Oxford vaccine by now! The headlines stated 70% efficacy at first, with the intended regimen of two full doses two week(?) apart, but found (by accident, apparently) that if the first dose was a half dose, the efficacy rose to 90%.

More intriguingly, Professor Jonathan Van-Tam, Deputy Chief Medical Officer for England, said today that of the 24,000 (I think) trial participants who were given the vaccine in either regimen, none of them needed to be admitted to hospital. Does this, I wonder, mean that although the efficacy in terms of not contracting the virus at all was 70% or 90%, the people that did get the virus had milder symptoms than usual, and thus the efficacy in terms of preventing hospitalisation and death is closer to 100%? What would the name for that be?


text:
Why is the "mango fly" called a "mango fly"?

Cordylobia anthropophaga, the mango fly, tumbu fly, tumba fly, putzi
fly, or skin maggot fly, is a species of blow-fly common in East and
Central Africa. Wiki page

Why is Cordylobia anthropophaga among other names called the mango fly? I can't seem to find anything online about why they gave it this name, and I figure they don't eat mangos.


text:
Does Krebs cycle occur in fast glycolytic muscle fibres?
They have mitochondria. So they can have aerobic respiration. (?)
Does Krebs cycle occur in their mitochondria?

Could you please clarify. What do you mean by an “effective” enzyme, and inhibited under what circumstances. The enzymes of the Krebs Tricarboxylic Acid cycle are located in the mitochondria, so their total activity in a cell will obviously depend on the number of mitochondria. But surely that isn’t your question.

@David Our examiner used this term "effective" just the way I put it in the quesion. So effective, how? I don't know either.
But I think we should consider all enzymes that somehow take part in Krebs cycle.
So as you said I think we should consider the enzymes that are located in the mitochondria.
Does aerobic respiration and Krebs cycle occur in white muscle cells?
If they do, then these enzymes are active in mitochondria of white muscles as well as red muscles, but the number of these effective enzymes are fewer in white muscle cells.

The point of mitochondria is aerobic respiration using the TCA cycle, the electron transport chain, and generation of ATP by oxidative phosphorylation. Different muscles types in different species vary in the extent their action can be sustained by a supply of oxygen, so they vary in their content of mitochondria. Although for teaching purposes it is useful to contrast extreme fast-twitch and slow-twitch muscles, there is no requirement for a muscle to be completely anaerobic. Those mitochondria that are present can use that oxygen (and substrates) that are available.