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Molecular Docking Enzyme Inhibitor Biosensor?
I had some task to study Molecular Docking relations with Biosensor and I am really new with this discipline (beginner). I am docking C60 with Glucose Oxidase and my question is: what would happen if C60 inhibited the active site of enzyme? Can the protein still be used by the biosensor or would it be broken because of the active site used by C60?

(1) What is C60?; (2) If C60 is an inhibitor of glucose oxidase, the enzyme can be used as a biosensor of glucose in the absence of C60 and, depending on the mechanism and strength of the inhibition, possibly in the presence of C60 (whose concentration must be determined).

(1)C60 is fullerene nanomaterial; (2)Actually c60 is "mediator" to glucose oxidase in real application biosensor. So in simple ways when glucose oxidase meet the substrate. It will made product which can be detected by c60 and c60 will transfer electron to electrode and convert from chemical to electrical energy. What i confused is how interaction happen between glucose oxidase and c60. If c60 inhibit in competitive then the enzyme cannot be used. Or inhibit in non competitive still enzyme cannot be used.

The biosensor can be calibrated to account for the inhibition. The sensitivity of the biosensor will be lower due to the inhibition, but how much---that depends on the strength of the inhibition.

So if i docking with AutoDock Vina and get energy binding (Gibbs's free energy) -12.0 and -8.0. It's mean -8.0 better than -12.0? Because -8.0 have smaller energy binding which made weak inhibition than -12.0?

Molecular docking energy (score) is not free energy. Free energy can be obtained from molecular dynamics simulations of the enzyme-inhibitor complex, and of the inhibitor alone, in solution (water)---and it's not easy. Yes, the lower the binding free energy, the stronger the binding. But if C60 must bind to glucose oxidase for the biosensor to function there needs to be a proper balance: too weak or too high affinity and the biosensor might be inefficient or insensitive. Complementing the calculations with experimental data is a must.

Okay thats soo helpful logic, i also read about enzyme immobilization before the enzyme attached to biosensor. Is enzyme immobilization make the enzyme rigid? Which mean non-competitive cannot change its structure?

It depends on the site of immobilization and the mechanism of the inhibition. For example, the immobilization can be done via a linker with little, if any, effect on the dynamics of the enzyme. In fact, most intracellular enzymes don't float freely in the cytoplasm but are attached to other macromolecules.


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Why reaginic antibodies are absent in these types of syphilis?
According to Textbook of Microbiology and Immunology
2e, Subhash Chandra Parija, pg.no; 375

These(reaginic) antibodies do not appear in early primary syphilis, latent acquired syphilis of long duration, and late congenital syphilis. Therefore, Venereal Disease Research Laboratory (VDRL) and other tests may show false negative reactions during these conditions.

Isn't latent syphilis detected by presence of reaginic antibodies? Then why is it said that it does not appear in long duration?
Why antibodies are not produced in late congenital syphilis?

To make the diagnosis of syphilis, the most common tests fall in two categories :

Non-specific tests like VDRL test & Rapid Plasma Reagin (RPR) test : those detect antibodies against cardiolipin, present in the treponema but also in our cells.
Specific/treponemal tests like TPPA/TPHA & FTA-ABS : antibodies titers against antigen specific to T. pallidum are  measured.

Non-specific titers decrease when antigenic stimulation ceases : either when syphilis is cured (no more treponema), or in the late stage where the number of bacteria present in non-immune-privileged zone is low (treponema is almost eliminated except in the central nervous system, eyes, testis where it is protected from immune response).
Specific titers fall very slowly if at all, once they are acquired.
Thus in late stage syphilis we get the following : VDRL- TPHA+, a source of confusion since this can also indicate old/cured syphilis.

source: Stack Exchange

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

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Identify this bug (which looks like a cross between a beetle and a bed bug)
I am located in a large Eastern European city. During this summer, a new kind of bug has started appearing in my house (or more specifically, coming into my house from the garden). It's about 1.5-2 cm long, doesn't appear to have any wings, and a relatively strong exoskeleton (makes an audible crack when the bug is squished). Its favorite activities seem to be either sitting in the middle of the floor, waiting for someone to step on it, or sitting on the ceiling and then falling onto somebody's head. Whenever I see one of them, it's almost completely stationary, regardless of the time of day.
Here are pictures of it (sadly, they're very grainy due to my phone's camera's low quality).

looks kind of like a stink bug but the color is off and the image is so grainy that I cant quite make out its geometry.  Definitely some kind of beetle though. Did it stink when you stepped on it ?

I don't recall smelling anything. Most images of stink bugs I found on the internet had a different color on the end of their abdomens, and this is not the case here.

right, but again I can barely see the bug because the image resolution is so grainy.

It looks like your camera's smudged.. have you tried wiping it off?

That is a weevil. Coleoptera, Curculionidae. Weevils have distinctive snouts, and elbowed antennae. They can be crop pests, and eat seeds, but do not spread diseases to humans. I suspect these have just found their way into your home by mistake. https://bugguide.net/node/view/1126677

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


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Snake Identification - St. Louis, MO
We found this tiny snake in the finished part of our basement today. We live in the St. Louis, Missouri area.

The snake is dark greenish-grayish and has very faint lines running the length of its body.  Any idea if it is dangerous/what we should do with it?

It might be a juvenile lined snake (Tropidoclonion lineatum). The What Snake Is That page for Missouri says they are native. In your photo, I see very faint black stripes with a central tan line, which matches a lined snake. Photos of juveniles seem to be rare though.
Lined snakes grow to about 2 feet long and are non-venomous. According to this natural history page, the only venomous snakes in Missouri are pit vipers (of which 5 are native).


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What is the mechanism behind the F-Wave?
Can someone explain the actual mechanism behind the F-wave? Is it really different from a H-reflex response or does it just have another name for historical reasons?
The H-reflex (Hoffmann's reflex) is a reflex motor response triggered by a afferent sensory nerve signals.
As far as I could find, the literature describes the F-Wave as a motor response elicited by "backfiring" motor fibres that were antidromically activated by stimulation. It is unclear to me how such backfiring is coherent with the concepts of refractory periods and normal axonal signal transmission.

This is a great question, and I've had trouble finding any authoritative study; since F-waves are mostly used as a diagnostic tool it doesn't seem like they've been studied much at the mechanistic level. The only non-clinical usages seem to be in pharmacology experiments in intact organisms (in particular people) where people aren't going to be going in and doing whole-cell patch clamp in the spinal cord.
This paper:
Balbi, P., Martinoia, S., & Massobrio, P. (2015). Axon-somatic back-propagation in detailed models of spinal alpha motoneurons. Frontiers in computational neuroscience, 9, 15.
has some relevant simulations, though they don't entire answer your question. However, I think their results are sufficient to make some good guesses. Without developing my own simulations, though, I'll have to mostly hand-wave after establishing some key facts.

Axons are small, so it doesn't take that many ions to depolarize a stretch of axon to threshold. The axon hillock has a lot of sodium channels to sort of 'jump-start' the action potential down the axon, but that's in a context where the rest of the soma is already depolarized.
In a back-propagating action potential, the ions flowing into small compartments eventually meet the soma: the soma is big, and so the number of ions needed to depolarize the soma to threshold is large (lots of capacitance in the membrane to charge): the axon hillock may not immediately bring the soma to threshold. This is called "impedance mismatch" and is also important at synapses (where axon terminals are bigger than the axons).

And so now for the hand-waving component... I can't say for certain which channels are involved, but it's possible that the antidromic action potential depolarizes the soma just a little bit, enough to open some voltage-gated channels but few enough that it takes some time for the rising phase to occur. Could involve other ions that aren't sodium, like calcium; could involve the proximal dendrites as well. Because of the different voltage sensitivities of different channels in different compartments, by the time the whole soma depolarizes sufficiently, the proximal part of the axon has had time to recover enough that it can spike again.
One other piece of evidence in support of this mechanism is that the number of cells that fire an orthodromic spike in the F-wave after the antidromic spike is few and variable - that is, it's a small fraction and that fraction varies from pulse to pulse. That seems to suggest that the specific conditions of the soma and nearby processes matters, so there must be a fairly narrow range of parameters that allows an orthodromic spike to follow.

Thanks for this answer @BryanKrause. That's definitely better handwaving than I could come up with!

H-reflex is a reflectory reaction of muscles triggered by stimulation of sensory (afferent) nerve fibres type Ia. Stimulation should have short duration and small amplitude.
When stimulation is supra-maximal, we can observe antidromic action potential through the motor (efferent) nerve fibres ($\alpha$). This is F-wave.
See: H-reflex Wikipedia and F-wave chapter.

Sure I read the Wikipedia articles and some journal papers before asking. What I want to know is how it is possible for the motor efferents to fire antidromically, and that signal get “reflected back” to elicit a small f wave response. This seems contradictory with the concept of refractory period

@Moppentapper You're right, it is counterintuitive (but possible). I recommend this article.


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Are cloned spieces significantly more vulnereble to deseases than sexually reproducing species?
I would like to be able to compare the risk for species to go extinct implied by their reproduction mechanism in the very short term. Imagine we choose some species A that can reproduce both sexually and asexually and then we make three clones of earth and in one clone we spread 1 million specimen of A that are all reproduced sexually. In another one 1 million that are all asexually reproduced (not in one generation but in like a 100 generations) and in another one 1 million of cloned specimen of A. now I want to compare the probability of each of these three going extinct in 10 years assuming the next generations would also be reproduced like their parents of course.
At the end I would be happy to know if the reason I get for this question depends on how sophisticated the immune system of that specie is.
So if I can fill in the following table with normalized numbers from 1 to 100 I would be so happy.
╔═════════════════════════════╦═════════════════════════════╦═══════════════════════════════════════════════════════════════╦═════════════════════════════════════════════════════╗
║ disease toleration score    ║ clones of a single specimen ║ asexual reproduction of the same specimen through generations ║ sexual reproduction of a couple through generations ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ sophisticated immune system ║                             ║                                                               ║                                                     ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ casual immune system        ║                             ║                                                               ║                                                     ║
╠═════════════════════════════╬═════════════════════════════╬═══════════════════════════════════════════════════════════════╬═════════════════════════════════════════════════════╣
║ simple immune system        ║                             ║                                                               ║                                                     ║
╚═════════════════════════════╩═════════════════════════════╩═══════════════════════════════════════════════════════════════╩═════════════════════════════════════════════════════╝

Right now my intuition tells me it should be something like this:
80 85 100
40 50 70
1  15 30

But I know I can be so wrong.
Please note that I don't want the single "Correct" answer to this question. I would be happy enough with the best "wrong" answer from a biologist. I mean if you know some things and you have some ideas about it that are not so bad but you are not so sure and you think maybe in future science will prove you were wrong. Just tell me that incomplete answer. I just want to learn something more than what I know now. I don't want an ultimate answer.


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What is titratable acid? Why is ammonium not titratable acid?
What exactly do we mean when we use term titratable acid in renal physiology? Why is ammonium not considered a titratable acid?

Ammonium is an ion. Ammonia is a base, not an acid. As far as I am aware this is true even in the kidney.

@David check this out: https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Equilibria/Acid-Base_Equilibria/1._Theories_of_Acids_and_Bases

Titratable acidity is a total amount of acid in the solution as determined by the titration using a standard solution of sodium hydroxide (titrant). In other words, it is the maximal capacity of the solution to "neutralise" base solution.
H$^+$ produced from CO$_2$ and H$_2$O is actively transported into the distal tubular lumen.
Titratable acidity is the amount of the H+ which is buffered by bases present in the tubular lumen. Mostly by phosphate (the highest concentration).
When the urinary pH change other molecules can gain the ability to buffer H$^+$.  For example creatinine (pKa about 5.0) or ketoacids (pKa about 4.8)  may contribute to the titratable acidity.
Standard measurement of the titratable acidity with the standard solution of sodium hydroxide spans pH range up to 7.4. Therefore:

Ammonium is not measured as part of the titratable acidity because the high pK of ammonium means no H$^+$ is removed from NH4$^+$ during titration to a pH of 7.4.

Source

I am answering more to the second part of your question as to why Ammonium is not considered a titrable acid.
The pKa of Ammonium is approximately 9.25.
By definition the titrable acidity of a solution is the amount of base (NaOH) that is required to neutralize the solution. On being neutralised the pH of the solution becomes 7 (neutral pH). For neutralisation to happen, the hydrogen ion(H+) from the acid should react with the hydroxyl ion (OH-) of the base to form water (H2O). For this to happen, the acid should be in its dissociated form.
However the pKa of Ammonium is higher than the neutral pH. It would mean that at a pH of 7 (which is the end point of titration) Ammonium ion still retains its hydrogen ion (H+), thus its contribution to the titrable acidity of the solution is minimal, if any.
This is why Ammonium is not considered a titrable acid


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Why there is no neurovascular drug-eluting stent?
I'm researching on neurovascular stents and I'm wondering why there is not much about drug-eluting neurovascular flow diverters in the literature? I read in an article that it's because of complex shape of cerebral arteries in comparison to cardiovascular system. But it doesn't look satisfactory to me. Any suggestion or idea is appreciated.

Despite some superficial similarities, the design of coronary stents and neurovascular stents are quite different. Coronary stents are hard metal, made out of stainless steel. They are quite solid, and if you crush one, it will remain crushed. They are deployed by expanding a balloon at potentially very high pressures (10-20 atm). Coronary stents are relatively short, and are deployed in vessels that are relatively straight given the length of the stent.
Drug-eluting variants of coronary stents are additionally coated in a polymer (i.e., plastic) matrix that contains the active ingredient and releases ('elutes') it over time. The common commercially available drug-eluting stents release anti-proliferative agents to prevent neointimal growth.
The purpose is also somewhat different: you mention flow diverters, so you are likely thinking about the context of aneurysms, where they may be used alongside coils to seal off the aneurysm from the normal flow. They are not providing structural scaffolding to prevent vessel occlusion from atherosclerosis.
Neurovascular stents, including flow diverters, are often made of self-expanding metals like nitinol. They are more flexible, but try to keep their nominal shape. These stents are deployed by retracting a sheath and then they themselves pop out to their nominal diameter. Because of this different deployment strategy, they can also sometimes be retracted and repositioned. The way these stents deploy is a lot more gentle, and they are also typically longer than the coronary varieties. They also may be placed in vessels that can be accessed superficially, such as in the neck. A stainless steel stent in the neck would be a disaster: if you laid pressure on that part of the neck you could permanently collapse the stent. A self-expanding stent will bounce right back open.
Back to your actual question...
The actual purpose of coronary vs flow-diverting stents are different; the purpose of drug-eluting coronary stents, preventing neointimal hyperplasia, is not as relevant in the neurovascular context. Additionally, there are lots of good reasons to use self-expanding metals in the neurovasculature because of tortuous anatomy and superficial vessels in the case of the carotids. The hard plastics that are coated onto steel stents can't be easily placed onto self-expanding stents, so other techniques would need to be developed.
The article you read talking about the complex shape of cerebral arteries is in large part correct.

I read in an another article (https://www.tandfonline.com/doi/abs/10.1179/016164105X35459) that another concern of using DES in the neurovascular interventions is that it is possible to have a therapeutic drug leakage into cerebrospinal fluid or more disastrously into the brain, which limited the applicability of DES to prevent neointima hyperplasia (i.e. in-stent restensosis) in the intracranial arteries. Any idea or suggestion about this claim?

@MehrdadYousefi It could be an issue of concern, just not one of the first I'd have on my list. I'm not aware of any neurological-specific worries with DES drugs like paclitaxel and rapamycin. Pharmacodynamic models that I am familiar with suggest that concentrations of DES drugs are low even in the media, let alone getting through the adventitia, and would be way less than the exposure when those drugs are taken systemically. The study you linked brings it up as an issue but then shows it did not occur in their study (at least not to an extent that they could detect drug in CSF).

So, I take the last reason that you mentioned in your answer as an interesting argument "The hard plastics that are coated onto steel stents can't be easily placed onto self-expanding stents, so other techniques would need to be developed." As a result, it's pretty much like that coating techniques are not capable to coat self-expanding stents (e.g. Nitinol) with polymeric drug coatings? Am I understanding this correctly? Do you have any reference to support this argument? I really appreciate your help because I need it for my PhD proposal.

My knowledge in the field might be outdated, and maybe it is now possible to do, but for example I do see the "Zilver PTX" stent is apparently a nitinol stent with paclitaxel, but it does not use a polymer. One of my concerns would be with how the flexibility of the material would be maintained when coated in plastic, or what would happen to the plastic during flexing (i.e., it could crack and release drug too fast, or produce a surface that is bad for hemocompatibility, etc). That also means that all of the drug is released within 72 hours, however, so not the same as polymer coated.

Thank you so much for your help! The Zilver PTX gave me a really good keyword to find useful references. Regarding the flexibility of drug coated stents I believe it will not change their flexibility so much because the coating thickness is thin in comparison to other stent's length scales. But for microscopic cracks I think it's possible to develop a polymeric coating with comparable mechanical properties to Nitinol to distribute bending stresses more homogeneously across the stent and its coating to prevent micro-cracks formation.

If I remember correctly, I think the polymer coating on a DES about doubles the thickness of the struts. But again, my memory may be incorrect. I see lots of results on Google Scholar for 'polymer coated nitinol' where you can start in your research. Best of luck.


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Why don't fish get hurt with so many sharp fish bones?
Why don't fish get hurt with so many sharp fish bones? And why don't fish feel pain when they swim? Don't those sharp fish bones stick into the flesh while swimming?

...Why don't we get hurt with so much sharp  roots of our tooth? And why doesn't  those sharp roots stick into the flesh while we eat?  Something like that...

https://en.m.wikipedia.org/wiki/Connective_tissue

Connective tissues prevent fish from being hurt by its bones. They surround the sharp bones so that the bones do not hurt its organs/flesh.
However Of course the bones can hurt the fish, but the situation is quite imaginable.
If a fish is smashed or gets too much force, its connective tissues cannot protect its organs much(like our clothes cannot protect us from bullets, or our broken bones penetrating our organs when we encounter a serious car accident despite our connective tissues covering the bones - the bones just damage our connective tissues and organs, and so on...) and its organs get hurt.
Your worry can happen in human case too (but much weaker version), we can think of our hip bones sometimes pressing our flesh between the bones and the chair we are on.


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are there any species that we can identify as being 'mid-way'though an evolutionary change?
I have just learned that dolphins evolved from a dog/cat like land mammal (Mesonix) that became ever-more water venturing. I understand and can visualise how the arms legs and tail slowly evolved into the fish-like ones of dolphins. The necessary transformation appears complete, with no benefit to further change of these limbs. So, I'm wondering if when you look at a seal, are they at a sort of intermediary stage, with the tail kind of like two little feet, which might 'improve' over time? Eitherway, when I read that the nostrils of Mesonix 'slowly moved' upward to the top of the head, I wonder why is there no sea-mammal that is only part way on this evolution, with a nostril between its eyes or something? (Is that even possible?) Or has evolution tended to happen in relatively short periods of accelerated  rates relating to climate changes as opposed to arbitrary and consistant rates, and we are now in a 'dormant' period? Also, surely there are some evolved biological characteristics that are only beneficial once 100% arrived at (eg nostril on top of head) and any intermediary form/position has no benefit and so cant be assumed to have been a natural/obvious path for evolution to have followed, yet how else do we explain how the transformation occurred?

you mean like the pygmy right whale, who's nostrils are about half way down its snout? http://rspb.royalsocietypublishing.org/content/280/1753/20122645 and http://scienceblogs.com/tetrapodzoology/2010/11/08/caperea-alive/

Also that seal's "tail" IS its feet, you can even see the seperate tail in many species, https://biologicalmarginalia.wordpress.com/tag/pinnipeds/. You seem interested in marine mammals you would do well to actually learn something about their anatomy before speculating.

I think there are a couple of issues that make this hard to answer. I find it very hard to think of a "half" evolved animal since it is a tree of life rather than a linear scale. This is close to an offshoot of "why didn't a beneficial trait evolve?"

Every species in existence is "midway through its evolution"
This is because evolution is a never ending process. Technically, we humans are still evolving. Evolution only ends when the species dies out.
Evolution is a very long process spanning countless generations. In a way its also an incredibly democratic process with voting in the form of reproduction. The populace tends to vote for things that increase survival or looks good.
The main cycle of evolution involves mutation and selection.
Selection is in my opinion the most misunderstood part of it. In order for a select trait to gain adoption by a populace it has to push out inferior traits. This normally means inferior members dying off by various means.
Let me give a scenario that starts to tie into your question:
Imagine a dog like creature that can only hunt on land, we'll call them a scruffy. Say one day a scruffy is born with webbed feet which makes it able to swim better allowing it obtain food from water. Now say something kills off ALL of the scruffies land based food sources. The scruffy with webbed feet can obtain food and provide for his progeny while the normal scruffies die off from starvation. Flash forward a few generations and now say a scruffy is born with longer toes (more like fins) which makes him an even better swimmer. That scruffy can be a better provider to his family making him a more desirable mate.
Flash forward MORE generations and the scruffies have become mostly aquatic since that's been their best food source.
One last distinction, it's considered a breed until one breed cannot successfully reproduce with another breed, that's when technically it becomes a new species (or so I've heard the argument). This is also the current great ambiguity with evolution because we don't know when or where this has happened for any species. Not to mention I read somewhere that Neanderthals did successfully copulate with humans which bares the question of whether they were a breed or a species (is a great Dane compared to Chihuahua a breed or species).

Also, surely there are some evolved biological characteristics that are only beneficial once 100% arrived at (eg nostril on top of head) and any intermediary form/position has no benefit and so cant be assumed to have been a natural/obvious path for evolution to have followed, yet how else do we explain how the transformation occurred?

Trait development is a very complex process. Things as arbitrary as sexual attraction play in. Mutation alone is incredibly random and can sometimes be dramatic. Something like a nostril on a snout could have migrated up the head over generations as a quality that was deemed sexually appealing. Or a mutation could have created a hole on the back that decoupled breathing from situational awareness and over time that hole was refined to be a more effective breathing apparatus.
NOTE: to all whom want to debate the breed vs species aspect. Lets not and just agree that it is an ongoing debate to be settled by doctoral thesis.
Clarification: In my opinion, as well as others, the biological classification system is not a very defined or very concrete with various cases breaking the system. This is especially the case with the category known as species where one begins or becomes another. The common, yet still fallible definition of a species, is members of group who are capable of producing reproductively viable offspring. There are many cases where this categorization breaks down or becomes blurred.

Thank you for taking the time to answer this. I did also find a helpful post title "where are all the evolutionary inbetweeners". I still find it amazing that the mutations coincide with the opportunities. Its seems like a child being potentially born gifted in some activity, but that activity actually hasn't been invented yet! and then if by chance they did coincide, the child would have to successfully procreate, and the gene successfully be carried on?

"since no one has actually recorded an evolution" ...this statement makes no sense. I also don't find this answer treats the issue of what a 'species' is correctly. -1. That said, the overall answer "Every species in existence is "midway through its evolution" is correct.

Sigh, and so the species debate begins, even though the hole biological classification system is continuously being challenged at various levels.

@BryanKrause how would you describe what a species "is".

@anon Species are just labels we put on a group of similar organisms that can breed with one another. There is no line where a species becomes another.

@BryanKrause that's abstractly part of my argument. Except the part where you say there is no line because there is and your own definition even hints to it. If we go far enough back into our ancestry we could not mate with whatever we were related to that was hiding from the dinosaurs. So there is a line its just ambiguous much like the sticker we call 'species'.

@Bryan Krause: Re "since no one has actually recorded an evolution", it not only makes no sense, it's (arguably, anyway) no longer true.  See e.g. https://www.bbc.com/news/science-environment-42103058 where scientists have recorded the evolution of a new finch species in the Galapagos.

@jamesqf Agreed. The obvious falsehood of the statement in one of the possibly poor ways you could try to interpret it is part of what means it makes no sense, especially because "an evolution" is not a unitary thing. "Evolution" broadly is observed constantly.

No, because that assumes evolution has some "end goal" which of course is not the case.
The statement "surely there are some evolved biological characteristics that are only beneficial once 100% arrived at..." is a fallacy.  I would recommend checking out Dawkin's The Blind Watchmaker and/or Climbing Mount Improbable for some very nice elaboration on this exact topic.


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Why Cerebrospinal fluid is not heated for VDRL?
For performing VDRL of serum , we heat serum to inactivate complement proteins which may otherwise interfere , but why don't we do same for CSF even though it too has complement proteins in it?
Is it because of lesser stability of WBCs in CSF( which is hypotonic) and on heating may rupture to release cardiolipin? But I can't comprehend how its worse than having complement proteins?


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Why are the cells the smallest unit of life?
Please Tell me why the cells are called the smallest unit of life. According to me I know that they are called so because they are smallest entity which is alive that is they show the properties of life on their own but if we divide them then the life will be destroyed. If that's the case so why they need to stay in a body why they can't be alone. I want to ask that if we separate a human cell from its body then can the cell be alive. If there is any better explanation that can explain why are the cells called the smallest unit of life please tell

Lots of cells exist that don't need to be in a body.  Bacteria, protozoa, single-celled algae, and many others.

An individual living being, whose material body consists of one or more cells, is the unit of life. The cells are not the units of life, but the units of the material body.
Multicellularity leads to specialization leads to dependence leads to loss of autonomous existence of an individual cell.


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Why are the first and last amino acids of an alpha helix not hydrogen bonded?
I am studying protein structures and in alpha helix I found out that one amino acid residue's carbonyl oxygen is linked to the nitrogen of amino group of 4 residues ahead.. However the first and last amino acids are not H bonded.. My question is why so? Shouldn't the first amino acid's carbonyl oxygen 5th residue's amino nitrogen like every other one.

In general, an absence of the alpha-helical backbone hydrogen-bonding interactions in an X-ray crystal structure of a protein can be due to (1) incorrect detection of the beginning and end of the alpha-helix, (2) local structural disturbance in the regularity of the alpha-helix, (3) low resolution of the X-ray crystal structure, (4) incorrectly modeled atomic coordinates into the electron density map.
But none of the above is your case . . .
The picture below shows the first alpha-helix in an X-ray structure of human DNA polymerase beta (PDB code: 2FMP). The alpha-helix is composed of 18 amino-acid residues (Asn-12 to Val-29), here numbered 1 to 18. All the "CO"..."HN" hydrogen-bonding interactions (black dashed lines) are present (blue, "N"; red, "O"), i.e., only the first four "N" and the last four "O" atoms are not involved in the hydrogen-bonding, because there are no -3 to 0 and 19 to 22 partners for them (because those amino acid residues do not belong to the alpha-helix).

Hydrogen bomd  forms between alpha  carbonyl group of 1st peptide bond with alpha amino group of n+th  amino acid residues away towards c terminal direction. Each and every amino acid residues in alpha helix should be inolved in H bonding it is the first 4 alpha NH2 group and last four alpha  carbonyl groups which are not involved because for first four alpha amino group there is no preceding carbonyl groups and also for there is no alpha amino group for last  four carbonyl groups.


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loops in neuron synapses
If we see at the connectome of c.elegans, it is easy to find "loops", in the simplest case, a neuron that synapses to another and this one backward to the first.
By example, neuron RIAR has 13 synapses to SMDVL (pre-synaptic is RIAR, post-synaptic is SMDVL) and this one has 8 synapses backward to RIAR (pre is SMDVL, post is RIAR).
Which is the scientific term to denote theses structures? Moreover, main hypothesis about its purpose?

"Recurrent" might be the term you are looking for, i.e.:
running or turning back in a direction opposite to a former course —used of various nerves and branches of vessels in the arms and legs
https://www.merriam-webster.com/dictionary/recurrent
If you observe a recurrent network within a single pair of neurons, you could also refer to this as a reciprocal connection, in that a pair of neurons are both post-synaptic and pre-synaptic to each other.
More generally, you could also talk about feedback as a general motif in neuronal circuits.
The function of recurrent connections likely depends on the specific network you are talking about, but they can be used for predictive coding, pattern generation, computation, and more. In organisms with 'simple' nervous systems like C. elegans, however, these connection patterns can be even more complex, because they have evolved to perform a lot of behavior with very few neurons.
Try searching Google scholar for recurrent neuronal circuits for some more information.


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How can humans taste saltiness in an aqueous solution of salt (saltwater) if the anions and cations in the salt are dissociated in the solution?
This may sound like a dumb question, but I've always wondered why we can still taste saltiness in a dissolved mixture of saltwater. In an undersaturated, aqueous mixture of salt and water, the salt ions are completely dissociated from each other, meaning that the salt is dismantled into its constituent parts. If this is the case, then why do we taste saltiness when drinking saltwater and not taste the individual tastes of the constituent cations and anions? Why do we taste NaCl instead of Na AND Cl individually?

Why do you think you are tasting the NaCl combined rather than either Na+ or Cl- separately?

And in what context do you think your mouth would ever be exposed to solid NaCl?

Note that there other things besides NaCl that taste salty, like potassium & lithium chlorides.  Also, at least as far as I understand the mechanism of taste (but I am not an expert), things have to be dissolved in water (saliva) for the receptors in the taste buds to work.


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Why are the hormones dopamine, adrenaline, noradrenaline and serotonin so ubiquitous across the animal kingdom?
As far as I know there is no reason for the makeup of a given hormone to be universal as it merely serves as a carrier from one part of the brain to another. So why are the above hormones seen across the entirety of the animal kingdom, and used in more or less the same way?

Evolution.
This is not special to hormones: receptors and ligands of all types are highly conserved across not only the animal kingdom, but also to single-celled organisms. The degree of conservation is typically dependent on the closeness of evolutionary relationship: more related organisms share more homology.
Because species evolve from common ancestors, they tend to share a lot of the same 'tools.' Changing the purpose of a hormone would likely require some sort of selective pressure, some new reason to use that molecule in a different way, and if the old and new roles conflict then there needs to be a replacement. This can happen, but it's complex and requires just the right conditions. More often, minor changes occur: among the steroid hormones, for example, you will find many small biochemical tweaks that make new molecules that have different functions.
Certainly the functions of some hormones are not entirely conserved, and if you look at the nervous systems of, for example, insects versus mammals, you will find some major differences, but the closer in evolutionary time you look the more similarity you will find.

Thank you for the answer, I assumed it was something like that, I just had trouble with the idea of a shared ancestor between all these animals that still retained the complexity of hormones and neurotransmitters, do we have any idea what animal that is?
P.S. I'm new here, is there anything I need to do to close the question or am I fine?

@ShmuelNewmark If an answer is helpful you should upvote it with the up arrow next to the answer; if a question has been solved by an answer you should accept it with the check mark. Sponges are the simplest extant animals, though they may or may not be in precisely the same lineage as the other animals, but even they have some rudimentary use of molecules like serotonin and dopamine - the purposes are almost certain different, but these things are very very old. C elegans is a roundworm and common model organism - you could start there. The actual common ancestor is long gone.


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VC06 neuron of c.elegans
My understanding was that all neurons and their synapses of worm c.elegans are already listed.
As source of this map I'm using following databases (both should contain same information):
Connectivity Data
Database of Synaptic Connectivity of C. elegans for Computation
In both databases, neuro-motor neuron VC6 (aka VC06) has no synapses to any other neuron. This is surprising for me.
Is connectome of this animal finished? If it is, are these two databases up to date? Finally, if answer to previous questions is "yes", any explanation about this "isolated" neuron ?


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How to determine if the amount of manganese chloride will change neural resting potential
If I am treating an organism in MnCl2 dissolved in water, how do I determine if the amount of Cl (in MnCl2) will change the neural resting potential Oor if it will influence motoneurons?

For theoretical calculations with other ions, you need to know the concentration and permeability of each of the major ions inside and outside the cell, both with and without the added substance (in your case MnCl2), and then use the Goldman equation/GHK equation to calculate resting potential before and after. Approximations would probably be sufficient.
However, chloride can be a bit complicated because the intracellular chloride concentration can fluctuate with extracellular chloride moreso than the other major ions. Therefore, depending on the sensitivity of your experiment, you may need to perform whole-cell patch clamp recordings to measure the resting potential directly.
If the change in chloride is a small percentage of the total, you can probably consider the influence to be negligible.

As the previous answer states you will need to know, or estimate, the concentration of ions and their relative permeability.
Knowing these values you can estimate the change using the following link:
http://www.physiologyweb.com/calculators/ghk_equation_calculator.html
Do you only have MnCl2 in your solution? Are there any other ions?

My solution consists of MnCl2 in water

Then you will greatly affect the resting potential. Probably since you don't have potassium or sodium outside you'll  generate an hyperpolarization.


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What makes red meat less healthy than seafood, after millennia of evolving to eat meat?
We are told that red meat is carcinogen; fish and white meat are not. What make us not "compatible" to red meat after thousands of years of evolution and meat eating, and yet seafood is opposite ?

Compatible is not a biological term in this case. We're compatible with red meat, and all the other good stuff, because we can eat it, derive nutrition from it, and survive long enough to reproduce. That's all it takes to be a viable member of the biosphere. Also, please consider that the Sun is a carcinogen too. Being carcinogenic does not disqualify it from being consumed by humans. Think cigarettes and barbecue.

Right. Even if compatible is not a correct term, I suppose the question is understood by everyone. Beside, you made a good example for my point : The sun is carcinogen, destroys tissues and we are exposed daily, therefore evolution drives the darker skin of certain race to counter that.

@Kenny - Please cite a reliable source that states red meat is a carcinogen. To my knowledge, it is not. What are co-carcinogens, though, are the products of grilling/frying/searing it over high heat. The same is true for grilling/frying/searing fish if there are any fat drippings (either from the fish, or from the sauce used to baste the fish. Since most fish isn't fatty, this is less of a risk.) Red meat can cause other problems, but a direct link

http://www.who.int/features/qa/cancer-red-meat/en/ "Red meat was classified as Group 2A, probably carcinogenic to humans" (limited evidence), and the fact that several renowned doctors in France recommend some friends of mine to stop eating red meat while treating cancers.

"We are told..." by people with quasi-religious agendas, like vegetarianism.  It's a good idea not to believe everything you're told without considering the source and/or looking for independent confirmation.

I've also voted to close because the question seems to be based on an incorrect assumption (that red meat is a carcinogen).

Sorry, but read meat IS a carcinogen that contributes significantly to colon cancer. Also, charred meat, as you mentioned, is a co-carcinogen. Kenny should not have to provide evidence for some of the minor details of his question. I have edited the question so that it makes more sense, but it seemed clear to me from the start.

If you read that article carefully, it supports my position quite clearly. There is no convincing evidence of a link, the only possibility is colorectal cancer, and who knows but that may be gut flora, etc. @KarlKjer - It is presumed to contribute to colorectal cancer. There is a great difference between presumption and fact.

@jamesqf True.But aren't all knowledge in the form of "we are told",or are you born knowing how to count? Second,human will never agree 100%, see round-earth fact. It's a good idea to take into account,not blindly,expert opinions in the fields we don't know when a large amount in that group agrees, especially in highly controlled domain like medical. Until agreed otherwise (e.g religion-never debunked, or slavery-agreed otherwise). Will you follow advices to treat syphilis according to the majority of medical advices now,or let it grow with a yet unproven chance of becoming superman later?

@anongoodnurse bolstering my point about "majority" against "convincing evidence". Even for agreed treatments, there is no 100% success rate. Clinical trial is always a statistical "majority acceptance amongst subjects". People are still debating if smoking is linked to cancer. That's because the number of known and unknown variables affecting health outcome is so huge, noone is certain and have to rely on "majority". Look at how we have thousands years of weather info and still cannot tell with certainty if it rains tmr. Talk about butterfly effect...It's a gray area and never definite.

The fact that there's no 100% success rate in treatment has absolutely nothing to do with causation. And, fyi, no one is seriously debating that cigarettes (or asbestos, or alcohol) cause cancer. Rain tomorrow? These are false equivalencies. They don't bolster your argument, they weaken it.

I beg to differ. First, about your argument Noone is seriously debating about the effect of cigarettes or alcohol, please refer to last month 's http://time.com/5376552/how-much-alcohol-to-drink-study/ "A New Study Says Any Amount of Drinking Is Bad". Wouldn't you call it debating over a 'fact' people seem to agree for years ? Aren't clinical study to prove a causation "Is drug A effective (more effective than drug B) for disease D ?" Rain tomorrow : ever noticed rain forecast tomorrow changes when it suddenly rain tonight ? The fact of raining today causes the chance of raining tmr to change.

@Kenny: No.  To use your example, we can deduce counting from observation.  WRT "we are told", it seems that there should be an obvious difference between "told" meaning the (repeatable & testable) results of scientific studies, and someone making up claims because it fits their agenda.  So where are the scientific studies showing that red meat causes cancer?  Whereas a couple of minutes with Google finds studies like this one https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691673/ showing no overall difference between vegetarians & meat eaters.

Interesting question that reveals a very common misconception about evolution. Evolution is not the same as optimization or advancement. It is about selection. Cancer and heart disease mostly kill people AFTER they have had their offspring. Selection does not generally act upon post-reproductives. So anything high in fat, calories and proteins would be likely to help humans survive starvation, and live to reproduce. We do not evolve to beat the diseases of old age, and our genes can be 10,000 years behind present optima. We don't evolve to be happy, live long lives, or be nice, unless these things help more of our offspring to survive.


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L-selectin in white blood cells
The white blood cells' function is mainly to fight off external antigens. However, another one of its traits is its ability to bind to vascular endothelial cells with the help of L-selectin. What is the purpose of this, and how does this help us？

Fighting of harmful microbes (and not antigens per se, although specific antigenic recognition is important), involves a lot of processes which require several lignad-binding molecules and ligands on the WBC surface. While the whole array of these proteins and their functions is very complex, we can take the case of a neutrophil trying to defend the body against microbes in a local wound, the so-called acute local inflammation response.
1. Adhesion to the endothelium
Here is where several selectins play a role. The simple broad idea is that in presence of microorganisms, as sensed by the local immune cells (tissue macrophages, blood cells in case of a vessel breach etc), there is an upregulation of chemokines in the local environment which causes the endothelium to increase the expression of certain adhesion molecules (ligands with receptors on WBC and vice versa) as well as other hemodynamic changes causing the neutrophil to come in close contact with these in the vicinity of the wound and bind to the endothelium. This is ften subdivided into three processes, margination, rolling and adhesion. L-selectin is one of these adhesion mediators, along with other selectins and integrins.
2. Migration through the endothelium into the tissues (diapedesis)
3. Chemotaxis towards microbes
4. Action on the microbes
Points 2,3 and 4 have their own mediators (see CD31, chemokines - AA, C5a, leukotrienes).
Reference:
Robbins and Cortran: Pathologic Basis of Disease, 9e
Other sources:
Wikipedia page


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How much variation is there between DNA molecules from the same organism
If different but in tact molecules of DNA were extracted from my body, for example hair sample, blood sample, and mouth swab, how much variation would there be between DNA molecules?

That would depend on age since we accumulate mutations our entire life.

From my understanding, individual DNA molecules would have those mutations, passing them on, but I see no way in which all DNA molecules uniformly change, like they're quantumly entangled. I may be wrong, but how do individual DNA molecules communicate their code to all other DNA molecules in the body?

Yes, it is extremely unlikely that one would find two genetically identical somatic cells in one adult human body.

The phenomenon is called mosaic single-nucleotide variations (SNVs) in somatic cells and it is an active area of scientific research (e.g., Abyzov et al., 2017, Genome Res. 27: 512-523):

We estimate that on average a fibroblast cell in children has 1035
  mostly benign mosaic SNVs.
Similar analyses in adults revealed no significant increase in the
  number of SNVs per cell, suggesting that a major fraction of mosaic
  SNVs in fibroblasts arises during development.

One, how rigorous is this research? I.e. extensively peer-reviewed vs. how new is the area of research. And it seems like the quoted text is saying that cells mutate a bit as a child but stabilize as adults. Also, this doesn't seem to answer how much total variation among DNA cells. Perhaps I should ask how identical are DNA cells?

(1) This field has been progressing lately with advances made in the accuracy and efficiency of genome sequencing; the study i quoted is not the first of this kind; Genome Research is a peer-reviewed scientific journal; they have a website where you can learn about the publishing process: https://genome.cshlp.org/; (2) the study i quoted explores SNVs in fibroblasts; different cell types may have different average number of SNVs and different mutation rates at different stages of human life; (3) knowing the size of human genome and knowing the number of SNVs means knowing the similarity.

I believe you may have answered my question, but I think my grounding in DNA is lacking. Thank you for your answer, I think the fault here lies with me.

There are several answers to this question, depending on exactly what you mean.
Cells in the body will accumulate random mutations as they divide and multiply
The cells in the body that are not part of the reproductive line are referred to as "somatic cells". These cells are typically derived from a single fertilised egg. Every time the cell divides, DNA must be duplicated, and each time it is duplicated there is a chance that there will be a random mutation. These random mutations will be passed on to any cells which are later derived from this cell. Most work in this area is on single-nucleotide variations (see the answer from Martin Klvana) but there can also be insertions, deletions, and duplications as with other mutations.
Damage from radiation and other mutagens can cause DNA mutations
Cells are subject to damage all throughout their lives, and some forms of damage cause breaks or alterations to the DNA of the cell. There are complex repair mechanisms in place to deal with this damage but they are imperfect so over time this damage can result in differences in the DNA sequence of the cells in your body. This will increase with age.
Some cells have mechanisms for deliberate, random mutation
Certain cells in the body have evolved to be randomly different from each other. The most obvious example of this is in the immune system where random re-arrangments of specific sections of DNA are used to create a vast array of different antibodies.
Mobile genetic elements can activate and re-arrange through the body
The human genome, like that of other organisms, is full of transposons and other genetic elements that contain genetic machinery for relocating themselves within the genome. The activity of these elements in the somatic cells of the body can lead to differences in DNA sequence.
Not everyone has all their cells from a single fertilised egg
It can happen that rather than deriving from a single fertilised egg, a person is derived from two or more fertilised eggs, so that their body is made up of cells of distinct genetic origin that are effectively siblings to each other. This can result in large genetic differences between cells.
Furthermore, in women who have had children, it is common (found in around 50-75% of women) for some cells from the fetus to enter the mothers' body and permanently take up residence in a phenomenon called fetomaternal microchimerism. Again this can lead to large genetic differences between cells.
Differences in DNA go far beyond mere differences in sequence
All the mechanisms I have discussed so far will lead to differences in DNA sequence, however the DNA in a cell is more than a mere repository of sequence information, and its function is mediated both through chemical modifications, most notably DNA methylation, and interaction with proteins, most notably through the histones which mediate DNA folding in the cell, or through the selective inactivation of one X chromosome in the Barr's body if you are female. These modifications have profound effects on the activity of the DNA within the cell and shouldn't be ignored.
All of this means there is no single answer to your question since it changes with time, varies between individuals, and depends on exactly what you mean.

II love this answer but I got confused when you said DNA was a cell. I had always thought of DNA as a molecule within a cell.

@JimmyG Yes, DNA is a molecule within a cell. Where do you think I was unclear about that?

I must have misread. Follow up question: what are the "non-somatic" cells? You mentioned somatic but not their counterpart, which I assume exists.

@JimmyG. Non-somatic cells are germline cells, that is sperm or eggs - and their precursor cells - in humans.

So are they called germline cells or non-somatic cells? Or both?

@JimmyG. Both. And some other names besides :)


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Do all Fungi have similar cells?
I know that most fungi are not differentiated into tissues. And tissues are groups of specialised cells aiming to perform a collective function. Does it, then, follow that most fungi do not have distinct cells for distinct functions, and that all their cells are essentially the same? I am slightly skeptical of arriving at that conclusion; but if it is true, then I believe that it would be reasonable to say that there is no difference between the cells that give rise to spores and those who don't. How is it possible, though, for cells to be structurally similar but capable of performing varying tasks?
To summarise,

Do tissue-less fungi have no dissimilar cells and all are exactly the same in all respects? I believe that the answer to this question would also be applicable to other multicellular organisms as well.
Can it be possible for two structurally similar cells in fungi to be adept at two different tasks? This too seems to be extendable to incorporate all other multicellular organisms.

No. Only a small group.

@Marzipanherz I did not know that. My textbook didn't mention it, perhaps to be in accordance with the naive standard that I happen to be with respect to the study of Biology. I think I should edit my question to reflect what you made me to learn.

@Marzipanherz Done. I hope it's answerable now. Thanks for feedback. :)

An absence of tissue does not mean an absence of specialized cells.

@MartinKlvana I would be very grateful to you if you could add a full answer. It's been days and there's no answer still. Thanks :)

Months now......

More than 2 years now... I'm still waiting.

You are an unusually patient and (gently) persistent user!


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How does collaboration on reconstructing metabolic networks work?
I am a researcher in psychology and I am trying to come up with a framework/platform in which psychological phenomena can be studied from a dynamical systems / computational perspective in collaboration with many labs. To be more concrete, the question is how to organize knowledge about psychological variables and how they are coupled by functional relationships on different time-scales that may be a function of additional variables.
My hope was to learn from disciplines that already work with a dynamical systems/computational framework for a long time. The first interesting analogy I came across were metabolic networks. I read this review about their reconstruction and while many things are different, the task is very similar to ours in that a given network of entities and functional relationships is continuously refined by the scientific community.
I saw that there are many data bases with genes, pathways, annotated graphs etc. but my main question is:
How is the scientific process of refining such a metabolic network organized? Are there platforms for this? Is there anything in place to quantify the uncertainty associated with parts of the network or to resolve disagreements? Are there any standards for implementations? Or is each group simply creating their own version based on previous literature and then publishing their new network in a paper?
I realize that this is a rather broad question and I apologize if I posted this in the wrong stackexchange forum. But I didn't know where else it would fit. I'd appreciate a lot if someone could give me some basic insights about how this field works or if someone has some pointers to relevant reading material.

In your comment to the answer from @Nicolai you refer to " a (formalized) dynamical system with many variables and many more parameters which render it impossible for a single research lab to map everything out alone". I don't think this is so. It does not strike me as dynamic and a single person usual writes the program that a single lab uses. One generally works with a network of pathways that is well established and stable, takes a bacterium, sequences it, runs the program to see which enzymes hit the network, and whether they join up to give particular pathways. Game over.

A bit of a preface:
A lot of this large scale collaboration (which I would maybe rather describe as the work of a whole [sub]field over a given time frame) often ends up in some sort of database. Really, there A LOT of those in modern biology - and often with minor but sometimes important differences. One of those would be the level of curation: are results gathered automatically from other sources, or always manually checked before being added? Another thing about databases is that (with certain exceptions of course) they often are only relevant for specific sub field, in some cases this can mean that only one lab maintains a website with a databases that is used by a few others, but that's it.
What I'm trying to get to is that there isn't really a 'one size fits all' solution and that especially the size of your field will impact which kind of solutions are both feasible and actually useful.
Now to answer your actually state question (as far as I can):
Most known biochemical pathways (including the metabolic ones) are described in the KEGG database. Initially this project was started by a single lab (and is still run by that group as far as I can tell), but of course it contains a lot of published information from other sources (I couldn't find information on how they update the networks in the database, you may have to read the papers for this). The database can also be accessed remotely, so it allows people to use the same network for a given reaction, and by incorporating sequence data it also has information on which organisms even contain the given enzymes in the network.
One thing the database does not contain is information about dynamics in the network. In this case I think most groups will generate and publish their own models (e.g. based on ODE's).

I think the poster is talking about computationally determining which metabolic pathways are present in an uncharacterized organism from the genes detected, using the full set of possible pathways in KEGG or the like as a reference. So the info about the KEGG database isn't particularly relevant to the fitting process. I imagine @jmb should try SE Bioinformatics where there may be someone who knows the approaches used in the programmatic fitting..

@ Nicolai thanks for the answer and @David thanks for checking in. I was less interested in the specifics of the field but rather in how efficient collaboration works in fields in which the phenomena of interest is modeled as a (formalized) dynamical system with many variables and many more parameters which render it impossible for a single research lab to map everything out alone.

@jmb — Sorry I misunderstood. I thing you have it wrong, but I'll comment on your question.


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growth stages of Maize
I am reading about growth stages in Maize and found this image.

I downloaded a brochure of a maize variety grown in Brazil.

On the right column, it says male flowering 63 days after planting (947 degree days) and female flowering 63.5 days after planting (955 degree days).
When stage does the male and female flowering happens in the first image?

In the first image, flowering occurs in the stage labeled "Pollination", which is when the male releases pollen and the female accepts pollen.  It give the time as 56-63 days after emergence, but note the asterisk ("*"); the footnote for it says their given times vary by "growth class" (such as "early" or "late"), indicating that these numbers are just a guide and actual times will vary by the cultivar (breeding strain) selected.


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Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?
I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables that can be filtered & searched for specific entries.
I would like to publish such a table as supplementary to a paper (e.g. preprint version) however usually data repositories allow for uploading files and text. I intend to deposit the first version of my main manuscript to Bioarxiv, where they primarily publish .pdf files.
Would anyone here know an official data repository with a format such that would enable publishing online an interactive table?
A good example of such a table is given here.
Disclaimer: I have also asked this question at SE BioInformatics. Like me, they are unsure which would be the best fitting SE Community.

Your example seems to be hosted on the website of an institute. Is there any reason you can't do/try something similar?

Journals and services where you can submit your script and manuscript and get DOI:

PLOS One
F1000
Zenodo
CodeOcean


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Is there mismatch in injures or death numbers for carnivores that hunt during day time and night time?
Is there significant mismatch in injures or death numbers for hunters (when hunter was killed or injured by its prey), between day time and night time hunts (carnivores that hunt during the day time and night time)?

Such animals could be:  lions, leopards, hyenas, wild dogs, wolfs. Basically I am looking for such type data (if there is one) that could give me insight into  the night time hunt as a risk factor for hunter.


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What is the signal that indicates which neurons Schwann cells should myelinate versus which should remain unmyelinated?
Schwann cells are neuroglial cells that produce myelin in the peripheral nervous system.
However, not all axons are myelinated - some will remain unmyelinated.
There must be some signal that indicates which cells are to be myelinated - what is it?

Are you asking what the signal is that makes some neurons remain un-myelinated? "Unable to form" seems to imply that they should be myelinated but somehow fail to be, rather than that some should be myelinated and others should not. Or are you asking why myelination is not necessary for all neurons?

I m asking that why schwann cells donot form myelin sheath around axon in non myelinated neurons?

Are you asking what the signal is that makes some neurons remain un-myelinated, or are you asking why myelination is not necessary for all neurons?

Yes I m asking what the signal is that makes some neurons unmyelinated?


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Is there any liquid that can replace water?
I understand this is a little futuristic but water freezes and damages cell causing cryostasis yet a reality. Is there any liquid that can be added to the blood synthetic or not that either plants and animals can live on instead of water? Synthetic water?

No. Water is essential both as a solvent and major component of biochemical reactions.
Imagining 'alien life' not based on water, not based on carbon, etc., is only for speculation and science fiction.


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What is this fruit?

There is a hairy hard shell (looking like a small kiwi), which naturally breaks, and under it there is brain-shaped red sweet flesh, half-covering the smooth black seed.
Picture taken in the Mediterranean coast of Israel in August

Kinf of Morus : https://en.wikipedia.org/wiki/Morus_(plant)

I think this tree is not native to the Mediterranean (cause I've never seen it). Was it located in a garden? Can you ask the owner of the house?

@RHA I have seen it mostly in public places, along roads, in a hopital, etc.

Might it be Alectryon tomentosus?
To me, the fruit looks the same and also the leaves have the same look.
It is an Australian tree whose common name is "wooly rambutan" and is used as a street tree as you observed. I did not find instances of this tree in Israel, though.

Kind of Morus, I have seen this in Morocco and it is delicious : https://en.wikipedia.org/wiki/Morus_(plant)

No. Morus has many small seeds, this one has one big seed. Morus has no shell around the fruit.

@Anixx I didn't say it is Morus, I said kind of Morus, which means Morus Family


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What determines the metabolic pathways that a biological cell is able to carry?
For example:

human cells (eukaryotes) can utilize the Krebs cycle pathway to generate more
ATP after glycolysis, but most bacteria cannot utilise the Krebs
cycle
plant cells can utilise the Calvin's cycle for
photosynthesis but human cells cannot.
yeast can utilise the ethanol fermentation pathway but human cells can only utilise the lactic acid fermentation pathway.

Why can't humans use the Calvin's cycle? Or why can't yeast use the lactic acid fermentation pathway instead? What determines the metabolic pathways that a biological cell is able to utilise?

Metabolic pathway is a sequence of enzyme-catalyzed reactions . . .

It is fortunate that many bacteria can utilize the Krebs cycle and oxidative phosphorylation or eukaryotes would never have acquired this capacity through their endosymbiotic capture to produce of mitochondria. And the answer is trivial — evolution. Metabolic pathways are no different in this respect from the elephant's trunk, the giraffe's neck, the birds wings or the fishes' fins. All are a result of evolution of the genome under environmental pressure.

Is it possible to genetically engineer new pathways in bacteria cells the

Yes, it is possible to genetically engineer new pathways in bacteria — this is called Synthetic Biology and you can search for articles about it. Putting in the genes for a pathway is not enough, though, you need to consider how they will be induced and regulated etc.

The determining factor is the hereditary traits that are passed on to the organism. Metabolic pathways require protein catalysts of which the instructions to make are stored in DNA. In other words humans can't use the Calvin cycle because our parents can't/couldn't, but plants can because their parents can/could.
In the long run though, very slowly organisms can gain or lose the ability to use pathways that their ancestors had.

By protein catalysts, do you mean enzymes?

That's right. Enzymes are catalytic proteins.

In that case, if the enzymes were manually added to the cells in a bioreactor environment, would the reaction be possible? For example, human cells cannot utilise the carboxylation pathway that converts PEP into oxaloacetate since the instructions to make the enzyme PEP carboxylase is not stored in our DNA. However if we isolate and manually add PEP carboxylase to a human cell, would the carboxylation reaction be possible?

If by "manually" you mean to purify the enzyme and literally add the powder in the reactor then probably no. Because the cells will likely not transport it in and the enzyme will likely get denatured. If you add the gene for that enzyme then probably yes. There are other factors too like if the gene is expressed properly and the enzyme goes to where it needs to go. Modifying metabolic pathways is something people do right now. For example researchers are genetically modifying fungi to ferment all the sugars in plant biomass and inhibitors in the medium. This involves adding new genes.

Thank you. So the only way to make new metabolic pathways is to genetically modify the cell, and more specifically, isolate the desired gene and insert it into a cell plasmid? (making recombinant DNA)


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Delay of sleeping on cortisol cycle
I was told that cortisol has to be measured at 9am or 4pm, because those where its peak level. But I wonder if changes on sleep patters affect the cortisol cycle.
I mean, if I usually go to sleep around 11pm, but certain day I go to sleep at 4am.
My cortisol cycle would vary according to my change in sleeping?
Probably the same question can be done using other hormones as example.


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ATP production via aerobic respiration
Just started learning about aerobic respiration today, specifically Glycolysis.
We were told that aerobic respiration produces 38 ATP, while anaerobic respiration produces only 2.
However, we're also told that:

Glycolysis produces 2 ATP
Link reaction produces 6 ATP
Krebs cycle produces 24 ATP (18 from NADH, 4 from FADH, and an extra 2)

This only adds up to 32 ATP, so where is this other 6 coming from? Or is this information incorrect.

In short, the difference stems from different values regarding the number of ATP attributed to the electron carriers in the electron transport chain (ETC).
My guess is that your class didn't go too far in depth on the subject, and also that your class or text is using mixed sources of information.

I have overviewed (general) glucose metabolism here, but feel free to skip this section if you don't need it.
Glucose metabolism is generally composed of 4* processes:

Glycolysis: a 6-C glucose molecule is broken down to 2 pyruvate molecules producing a net gain of 2 ATP and 2 NADH (electron carrier) molecules. Note that this is a net gain.
Pyruvate Dehydrogenase Complex (PDC): Here Pyruvate is made into Acetyl CoA, which enters the Krebs Cycle (step 3). This is the Link reaction step that you mentioned. This step produces a 1 NADH molecule per pyruvate.
Krebs Cycle (TCA): The Krebs cycle is central to cell metabolism and produces a lot of electron carriers, netting 1 GTP (ATP energy "equivalent"), 3 NADH, and 1 "FADH2" (electron carrier) PER Acetyl CoA entering the TCA.
Oxidative Phosphorylation (ETC): This step converts your electron carriers into ATP. It does this by using the energy released by electron transfers (e- are transferred from your electron carriers NADH, FADH2 to intermediate compounds to oxygen. This provides the energy to actively transport protons) to pump protons (H+ atoms) across a semi-permeable membrane to create a electro-chemical gradient. These H+ atoms will flow down this gradient through the channel of the ATP synthase, creating ATP. Currently, it is pretty widely accepted that an NADH molcule provides enough energy to net 2.5 ATP, and a FADH2 molecule provides enough energy to net 1.5 ATP.

As a result, we get the following:

+2ATP, +2NADH
+1NADH x2
(+1GTP, +1FADH2, +3NADH) x2
-10 NADH, +2.5ATP x10; -2FADH2, + 1.5ATP x2

This yields 2+2+25+3=32 ATP, which is what you obtained in your calculation.
However, a previously accepted value states that the 4th step nets 3 ATP/NADH molecule and 2 ATP/FADH2 molecule. Running the same calculation, we obtain 2+2+30+4, netting 38 ATP, causing the discrepancy you notice. I wouldn't say either set of values is universally accepted, but I would say that 32 ATP is generally recognized as the "right" answer.

In other words, 32 ATP is the result of the more recently accepted equivalences of 2.5ATP/NADH and 1.5ATP/FADH2 in oxidative phosphorylation, whereas 38 ATP is the result of the older pair accepted equivalences of 3ATP/NADH and 2ATP/FADH2.

Some notes and caveats:
Please note that in (most) Eukaryotes, the NADH produced in the cytosol (Glycolysis) is "reduced to FADH2" via the mitochondrial shuttle as the high energy electrions enter the ETC. This means that each NADH produced by glycolysis only nets 1.5 ATP, resulting in 30 ATP/glucose in majority of eukaryotes.
It is also important to note that the numbers that I have provided are mostly used in classroom calculations for general systems. Real organisms will often deviate for a multitude of reasons. Further, some organisms may not follow this rule at all.
*A few sources might classify the PDC as part of glycolysis or as part of the TCA.

Fine, but you misuse the word “convention”. You are takling about “accepted values” for the equivalence of NADH and FADH2 with ATP. At one time they were thought to be 3 and 2 (i.e. these values were generally accepted), but more recent work gives values nearer 2.5 and 1.5 (which are now generally accepted). It is now usual in eukaryotes to consider the mitochondrial shuttle, so a value of 30 (rather than 32) is cited, e.g. in Berg et. al.

@David I went back and edited out the word "convention." I'm usually pretty bad with choosing my words, so I'm not surprised to hear that I misused the word. However, I was wondering what made you say that "convention" was used wrong?

A "convention" refers to a normal or usual manner of proceeding, and in science usually refers to nomenclature or representation. The reason for not using it in the way you did originally is that it concerns the representation of an object rather than the object itself. Examples are 1. Writing nucleic acid sequences (e.g. GTTC) — 5′ to 3′ direction, phosphodiester linkages omitted; 2. Writing of species in papers — italicized, first mention in full with second part in lower case (Escherichia coli) subsequently first part abbreviated (E. coli).

I think that sort of makes sense to me. Just to check, the object itself is a convention, but a representation of the object is not a convention?

— I would put it the other way round. The object is a tetranucleotide and its representation is GTTC according to the current convention. If you look at early books on nucleic acids it would have been written GpTpTpC — an earlier convention, but the object is just the same. However as an analogy for the values for NADH/ATP conversion, consider that this was a discrete molecule the structure of which had been wrongly determined and, say, the C was later found to be methylated. Then the object has changed.

@David: How can a molecule of NADH give rise to 2.5 molecules of ATP? (i.e. how can 1/2 ATP be formed). Or is it like, 2 molecules of NADH gives rise 5 molecules of ATP.

@user237650 —  SE would regard this as a side discussion, but, in brief, it relates to the way ATP is synthesised by the chemi-osmotic mechanism and the structure of the ATP synthase. If you have access to it and your background is appropriate this paper might help. Otherwise it is a valid query and you should consider asking it as a separate question.

I dont know how much do you know this metabolic paths but i am going to try to get that 32 ATP out of 38 ATP step by step.

First off all in glycolysis you have to activate sugars with phosphate (glucose;fructose). This process is done by hydrolysis of  two ATP. So we have 36 ATP left.

I am going to move forward to the ratios of kofactors. Ratio ATP:NADH+H and ATP:FADH2 in oxidatice phosphorylation is not actually 3 and 2 ATP, but 2.5 and 1.5 ATP respectively.

ATP synthase produces 1 ATP from 3 H+. However the exchange of matrix ATP for cytosolic ADP and Pi (antiport with OH or
symport with H+) mediated by ATP–ADP translocase and phosphate carrier consumes 1 H+ / 1 ATP due to regeneration of the transmembrane potential changed during this transfer, so the net ratio is 1 ATP / 4 H+-

The mitochondrial electron transport chain pump 10 H+/1 NADH+H+ and 6 H+/1 FADH2. In the end it is that 2.5 ATP for NADH+H and 1.5 ATP for FADH2.

Sum it. FOr 1 molecule of glucose comes from substrate-level phosphorylation 2 ATP and 2 ATP (GTP) from Krebs cycle dicectly. 2NADH+H from clycolysis (2x 1.5 ATP or 2 x 2.5 ATP from malete aspartate. 8x 2.5 ATP from dekarboxylation of pyruvate and last but not least 2x1.5 ATP for FADH2 from Krebs cycle.
4+3 (or 5)+20+3= 30/or 32 ATP.

Source: https://www.saylor.org/site/wp-content/uploads/2013/04/BIO101A-6.2.3-CellularRespiration.pdf


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Are there examples of non-pathogenic RNA viruses?
There do seem to be some non-pathogenic DNA viruses, for example Foamy virus. Non-pathogenic viruses would be great to use for gene therapy applications, except DNA viruses incorporate themselves into the genome, which could drive oncogenesis. RNA viruses that are non-pathogenic would be great, but all RNA viruses seem to be especially pathogenic. Rabies, Ebola, Bas-Congo, Smallpox, etc.
Do there exist "gentle" RNA viruses?

Does it count if their pathogenicity is species specific?

The alphaviruses typically move between an arthropod host and a mammalian host. In the arthropod, they seem to be harmless. In the mammal, they are pathogenic. If there were some way to make them treat mammalian cells like insect cells, they would be very useful for gene therapy applications.


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Why is history not called science even though palaeontology is?
In the scientific method, we propose models to explain a phenomenon and propose falsifiable tests for it. In palaeontology, we cannot do direct tests to verify our models, but we still make predictions that this particular kind of fossil would be found within a particular time period, or a rabbit wouldn't be found among the Cambrian  fossils. I assume that's why, even in the absence of experiments, we can call palaeontology science.
But in history also, we do a similar thing. We propose models (Jesus existed, let's say), and then make (implicit) predictions that no future discoveries would contradict that hypothesis, or better, mention him by name in a non-theological context.
Then, why is doing history not considered science, when palaeontology is?

Because of this

I'm voting to close this question as off-topic because it is about the philosophy of science and not biology.

Tests need not be direct to be scientific 2. Direct tests are common in Paleontology. For example, the prediction that non-avian dinosaurs went extinct from an impact event can be directly challenged by finding a dinosaur skeleton above the impact layer.

Paleontology is not only guessing and estimating how old a fossil is... And it's also not only imagining how dinosaur XY may have looked like during lifetime.
Paleontology also is:
Paleobiology
Understanding the biology, physiology, anatomy, reproduction, evolution, and whole way of life of prehistoric animals, including trophic networks, life communities etc.
Taphonomy
The way from a biocenosis to a thanatocenosis and a taphocenosis. What happens after the death of an animal? How it is transported (allochthonous/autochthonous), what changes in chemistry lead to decay and preservation of hard and soft tissues? E.g. the principles of local self-eutrophication for phosphate-based soft-tissue preservation. How is the fossil embedded in the rock? Is a fossil spirit level preserved? What diagenetic processes happen after embedding?
Paleoclimatology
Understanding prehistoric climate changes by studing e.g. isotope levels, paleo-monsoon conditions during the formation of huge continents like Pangaea or Gondwana, the influence of plate tectonics on the conveyor belts of the oceans etc.
Paleobiomechanics
The mathematics and physics part... Breaking down animal locomotion to equations and calculations of forces and moment arms. This helps to understand how animals of giant sizes or with a completely different locomotory musculature were able to walk and to take a look at the forces, which were exerted on the joints during locomotion/mating/standing up etc.
So you see... Paleontology uses so many different natural sciences disciplines like physics, chemistry, biology, and mathematics, that practicing it becomes a natural science itself. Can you say the same thing for history?
My list could have been much longer... There are so many sub-disciplines in paleontology that it would habe taken too long to mention them all.


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Snake with orange spots found in South Florida
I found this snake near my doorstep. What species is it?

Although there's an answer with what looks like a very plausible ID, it would probably be helpful to give more information, such as the approximate size of the snake, what it was doing when you found it and so no.

corn snake.

Looks very much like a red rat snake (Pantherophis guttatus). Nonvenomous, and wonderful.

First I thought that the coloration was off, but an image search showed a big variation and some of them looked exactly like the picture in the question.


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Are bananas C3, C4, or CAM plants?
Are bananas C3, C4, or CAM plants? I have been researching for some time and cannot find the answer.

First of all, we have to think about the ecosystem in which banana exist. Obviously, the banana is in a rain forest. Rain forests are a very interesting ecosystem with lots of species. The climate is really hot and the atmosphere has high humidity.

Banana is definitely not CAM plant, because this kind of photosynthesis has usually cactuses and succulents. CAM plants usually have closed stromas during the day and open at night to protect from possible loss of water, carbon dioxide. This type of photosynthesis doesn't suite into the rain forest.

C4 plants are well known for Kranz anatomy of a leaf. They have special sheets to do secondary fixation of carbon dioxide. So according to this web I personally believe that banana is not C4 plant.

So according to this article the banana has C3 photosynthesis.

Anyway according to wiki there is a lots of cultivars and specious of bananas so i really dont know if its true for all of them.

The PDF you linked to is broken. You may want to link to the original article page instead of the PDF itself.

You can find a list of families known to have C4 plants here. [based on Sage 2016]1.
Although many other monocot species do exhibit C4 photosynthesis (and C4 photosynthsis does seem to have evolved independently multiple times)2, the banana family, Musaceae, consists of C3 plants3.
This includes the most commonly consumed variety of banana in developed countries, the Cavendish banana.

Sources:

Sage, R. F. (2016). Journal of Experimental Botany 67(14):4039–4056
Ehleringer et al (1997). Oecologia 112:285299.
Biocylopedia


text:
Why does blood come out of leach when salt is put on it?
I know osmosis is the reason for the water to come out of cells - When you sprinkle salt over a leech, it creates concentration gradient and forces the water out of the cells. But why does a lot of blood come out too ?


text:
How do the bacteria producing bacteriocins protect themselves from it?
Whenever there is Col plasmid in a bacteria it will produce bacteriocins which will kill other bacteria around it. Why will the bacteriocin not kill the bacteria which has produced it? How does the Col plasmid also help protect the bacteria from its own bacteriocin?

Keywords: colicin, immunity, operon, genes, proteins, mechanism.


text:
Molecular animations of, say, protein synthesis, are simplified, but how exactly?
In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein as if drawn by a magnet. As far as I know they move randomly. But still, translation occurs at a rate of about 15 amino acids/second and 75 ATP/second, so the rate of gobbling shown in the video clip is not off the mark.
I can think of two explanations:
1) The microscopic world is counter-intuitive. It is so frenetic that normal diffusion is enough to supply the hungry protein. The video simply doesn't show all the input molecules in order not to clutter the picture but essentially it is correct. However, amino acids are not small, and they are attached to the much larger tRNA, so they must be moving relatively slowly by Brownian motion.
2) There are additional helper proteins that concentrate or channel amino acids and ATPs in the vicinity of the ribosome or replicator. Never heard of these.
What is the real explanation?
Edit: To clarify, the question is not about the simulation side of things as such, such as how hard it is to actually make a true simulation. Most simulations, including weather prediction, involve a certain degree of approximations and simplifications. But in this case, there is something definitely untrue in the video clip, namely the molecules being attracted to the ribosome. As explained by a moderator, this means that it is not a true simulation but a "cartoon". So the question is: what would an ideal "non-cartoon" true simulation look like? Would the tRNA be diffusing in at a very fast rate, or are there helper proteins that, for example, tether tRNA in the vicinity of the ribosome? The moderators seem to indicate that diffusion is enough, but I would like to see a reasoned out answer with numbers that show this is the case.

tldr:

Making these things accurate representations is really hard
Accurate representations can be hard to look at anyway, so aren't always good to convey understanding

Molecular dynamics simulations that span long periods can be really expensive because of how computationally demanding they are, and they rely on accurate structural information about all of the molecules involved which isn't always available. The animation you linked might not be an actual simulation for that reason, but you'd have to check for yourself. Really fine grained accuracy probably isn't a priority for making a cool teaching tool like this one, you just want people to understand the just of it and the Brownian motion there might be a stylistic choice. Again, you'd have to chase it up for this specific example, I just want to give you something generalizable to other animations.
To make macromolecules like this actually interpretable by humans it's important to simplify them. One of these simplifications is normally called a 'cartoon', I don't think they guy in your comments was taking a dig at credibility of the video. It's also important to hide all the water molecules because they get in the way of you and seeing what's going on, so that's another way in which it's been simplified.
If you haven't already, have a look at some proteins in the PDB on the structure viewers and switch the mode from the cartoon/ribbons to other models like ball and stick. Ribbons are a useful way to simplify the structure representation so that you can see what the backbone is doing.
Here's one that I like:
https://www.rcsb.org/3d-view/4KEY/1
And you're right, at the systems level of something like protein synthesis, lots of stuff is involved and it's not practical to show all of it. For something like that it's easier to show these processes a a graph (term for connected nodes), check out the KEGG database for examples:
https://www.genome.jp/kegg/pathway.html#cellular
Hope this helps

What I don't understand is, why exactly is it so hard to simulate accurately? Is it because there are many more tRNA molecules than can be shown clearly (they would clutter the visual), or is it because the molecules are moving much faster than in the video clip (you would hardly see the tRNA fly by)?

It's more the number of time steps and the number of atoms in the simulation. So in that video we have a few different proteins, some DNA, tRNA etc and a lot of water molecules (which are hidden). That's a lot of atoms and for each one you need to calculate its new coordinates between each time point based on its local environment. So the demand on a computer is really huge. Also all the parameters are based on measurements taken from model systems like dialanine (maybe, out of my comfort zone a little bu here),  which might not be perfect. If this doesn't help, could you restate the question?

From David Goodsell's The Machinery of Life:

To get an idea of how fast this motion is, imagine a typical bacterial cell, and place an enzyme at one end and a sugar molecule at the other. They will bump around and wander through the whole cell, encountering many molecules along the way. On average, though, it will only take about a second for those two molecules to bump into each other at least once. This is truly remarkable: this means that any molecule in a typical bacterial cell, during its chaotic journey through the cell, will encounter almost every other molecule in a matter of seconds.

The Baffling Intelligence of a Single Cell by James Somers and Edwin Morris says if we scaled up a cell to a football field, basketball-sized proteins would fly at 1,800 km/h (1,100 mph).
Imagine how fast you smell burnt toast. And those molecules had to cross meters. The cell is tiny. Even with entirely random movement, every possible molecular alignment happens pretty quickly.
In a visualization, of course, we only see the one molecule that arrives at the correct place and angle. We don't see the millions of other collisions that didn't result in a reaction.

The good explanation is the second part of your question which you never heard of.
Actually for every movement in the cell, proteins play important role rather than nature of solvent (hydrophobicity, hydrophilicity or other forces) play any significant role. Brownian movement is also insignificant as you know AA (Amino Acids) can be more polar or less polar. Also they can't guide themselves to the desired location in the cell. Proteins which relocated them, cause their faster efficient and direction movement (may be due to formation of gradient or some sort of pulling pushing force due to interaction with other proteins.)
[UPDATE]
Exploring more into this, I came to know that the movement of anything is dependent on a gradient (May be concentration, electrochemical, pH etc...). So everything inside the cell is well planned and well documented inside the genome.

Please cite peer-reviewed papers or reviews that provide evidence for your assertion that there are proteins that relocate amino acids in a cell.

Better I move to researchgate or some other place or I try to publish my review paper than arriving here. You are continuously engaged with my interaction.

That is your decision, however it may be worth your while reminding yourself how SE works. It is a Q&A site in which answers are assessed, not only by the poster but also by other members of the site. If you make an assertion without providing evidence in support, the poster has no way of knowing whether or not you are right. Nor can other list members who may know something on the topic assess your answer properly. In this case I could have just said "this is wrong", but perhaps there is some recent work I have missed. So it was more appropriate to offer you the chance of providing evidence.

So there should be instruction to search on PubMed, Sciencedirect or Scopus should all those answers. Why to create redundant text?