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Why there is swelling when skin doesn't break visibly?
I had read that swelling occurs as result of blood vessels pouring watery fluid in the affected area to help in fighting the incoming pathogens, when we our skin is cut open. However sometimes like stubbing toe, or getting hit in head, our skin doesnt breaks, but still swelling occurs on the affected region. Whats the point of swelling in that case, when pathogens obviusly are not invading, as our skin is not cut open?

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details. (NB: A causes B, does not imply there can't be a C also causing B.)


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The Contradiction in Soy Production: Livestock Feed versus Human Consumption?
I'm not sure if this is the right place to ask this ecological question. I apologize for any inconvenience, and please let me know if it is.
There is a contradiction regarding soy production and its effects on the environment:

According to Our World in Data, more than three-quarters (77%) of global soy is used as feed for livestock, primarily for meat and dairy production. This means that only about one-fifth (23%) of soy is used for direct human consumption or other purposes.

The article also mentions that only 7% of soybeans are directly fed to livestock, while the remaining 70% is processed into soy cake, which is used as livestock feed. Soy cake is a by-product of soybean oil extraction and is classified based on its crude protein content.

Now, the question arises: what happens to the extracted soybean oil? Is it not used for human consumption? If it is used for human consumption, then humans are also directly responsible for 70% of soy consumption. Additionally, direct human consumption (including food and industrial uses) accounts for more than 24% of soy consumption.

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Is pyruvate considered a high energy molecule like ATP or NADH?
ATP, NADH and FADH2 are high energy molecules. The second half of glycolysis is known as the pay-off phase, characterised by a net gain of the energy-rich molecules ATP and NADH.
In fermentation, for example, pyruvate still has energy into it. If you had oxygen around, you could have cellular respiration, you could go into the Krebs cycle, the citric acid cycle, and derive more ATP from pyruvate. But the term 'high energy' or 'energy-rich' is not commonly used to describe pyruvate. Is it wrong to use such terms to describe pyruvic acid?

Summary
Do not use the term ‘high-energy’ to refer to biochemical intermediates because many people (including the OP) do not understand what it is supposed to mean. However, if you insist in using it in its historic biochemical sense, pyruvate does not qualify,
The terms ‘high-energy’ and ‘energy-rich’, although traditional in biochemistry, are best avoided. This is because they are meaningless to a chemist and misleadingly imprecise to a biochemist. This question is a good example of the misunderstanding of the term.
What is important is not to stick ‘labels’ on molecules (leave that to undergraduate politics) but to understand and articulate the energetic role molecules have in metabolism. As regards ATP and NADH, I have already provided such an explanation in the answer to another question. I will only summarize here to make a comparison with pyruvate.
However one thing should be emphasized at the start. Statements about molecules containing ‘energy’ are sloppy:

A change in Gibbs Free Energy only occurs when a molecule reacts with other molecules, and the magnitude of this change depends on
which molecule(s) it reacts with.
The biochemical usefulness of a molecule participating in a reaction with a negative change in free energy depends on the availability and ubiquity of
reacting partners and the magnitude of the free energy change compared with that of the reacting partners.

Historic use of the term ‘energy-rich’ with respect ot ATP, NADH and pyruvate

In the case of ATP, the hydrolysis reaction to ADP + Pi has a high enough negative change in Gibbs Free Energy to drive many biochemical reactions that have a positive Gibbs Free Energy change, and enzymes have evolved to couple ATP hydrolysis to such reactions. The latter is key — there must be a way of using this energy!

In the case of NADH, its oxidation to NAD+ has a standard redox potential of +0.32V, which is, in effect, a negative standard free-energy change. However it can only occur in conjunction with another redox ‘half-reaction’ with a redox potential that will result in an overall negative free-energy change. In fact the redox potential of the NADH oxidation half-reaction sufficient to drive many biochemical reductions, and enzymes have evolved to couple NADH (and NADPH) oxidation to such reactions. Furthermore the oxidative phosphorylation system has evolved to allow production of ATP from NADH.

In the case of pyruvate, its reduction to lactate has a standard redox potential of –0.19V, so it has a positive standard free-energy change. Clearly quite a different situation to NADH, with which it reacts to regenerate NAD+. So pyruvate could only be considered in relation to half reactions of even higher redox potential. In fact, it plays no general role in metabolism for driving thermodynamically disfavoured reactions.

The cause of the confusion
The explanation above shows that pyruvate does not conform to the description ‘energy-rich‘ in its (discouraged) historic biochemical usage. What caused the OP to think so? He states:

…pyruvate still has energy into it. If you had oxygen around, you could have cellular respiration, you could go into the Krebs cycle, the citric acid cycle, and derive more ATP from pyruvate.

What this is actually saying is that pyruvate is a metabolic source of energy in the form of ATP because it can be metabolized aerobically (in the pyruvate dehydrogenase reaction) like glucose and a host of other intermediates. This is not the usage of the term ‘energy-rich’. All one is saying here is that when pyruvate, glucose, fatty acids etc. etc. are oxidized to carbon dioxide and water the C–C bond energy etc. can be utilized in biochemical reactions (reductions) rather than being released as heat.
Appendix 1: Other phospho-compounds with a high group-transfer potential
An alternative to ‘energy-rich‘ for compounds such as ATP is that they have a high ‘group-transfer potential‘ — the free energy change in a particular reaction. The student of biochemistry will be aware that particular reactions in glycolysis and the tricarboxylic acid cycle can phosphorylate ADP to ATP, and so must have a high group transfer potential. Some examples (taken from Berg et al.) are listed below. These are all ΔG0′ (kJ/mol) for the hydrolysis of the phospho/phosphate group.
Phosphoenolpyruvate        –61.9
1,3-bisphosphoglycerate    –49.9
Creatine phosphate         –43.1
ATP (to ADP)               –30.5  ------------------
Glucose 1-phosphate        –20.9
Glucose 6-phosphate        –13.8
Glycerol 3-phosphate        –9.2

Thus, phosphoenolpyruvate, 1,3-bisphosphoglycerate and creatine phosphate have a higher group transfer potential than ATP, as expected from their role in phosphorylating ADP. They can be considered ‘energy-rich‘ in the historical usage of the term. However, unlike ATP, they play specific — rather than general — roles in biochemical energy transfer.
Appendix 2: Other biochemical reducing agents
Although biochemical reducing agents play a central role in overcoming the energy barriers to synthesizing reduced compounds such as fatty acids and steroids, the historical term ‘energy-rich‘ has not been applied widely to them. To provide a perspective on the reducing power of different biochemical compounds, some examples (again taken from Berg et al.) are listed below. The standard redox potential (E0′) is expressed in volts, and n is the number of electrons transferred in the oxidation/reduction
OXIDANT             REDUCTANT         n    REDOX POTENTIAL
Succinate (+ CO2)   α-ketoglutarate   2       –0.67
Ferrodoxin (Ox)     Ferrodoxin (Red)  1       –0.43
NAD+                NADH              2       –0.32
Glutathione (Ox)    Glutathione (Red) 2       –0.23
FAD                 FADH2             2       –0.22  ---------
Pyruvate            Lactate           2       –0.19
Cytochrome c (+3)   Cytochrome c (+2) 1       +0.22
Oxygen (O + 2H+)    Water             2       +0.82

Oxygen to water is a 4 electron process

@VincentFourmond — Not with reference to one atom with the product 1 molecule of water. I've clarified. (The problem is that if you try to lay out a table you have to use pre formatting that renders everything literally. Hence you can't use subscripts or superscripts etc.)

This is a related conversation between me and David Harrison, Course Director of Biochemistry for Pharmacy since 2009:
David:

Amir,
There is a problem with your nomenclature. I would describe NADH as an electron carrier not as a high energy molecule. Its reductive potential is only relevant in the presence of a molecule that has oxidative potential (say pyruvate). Similarly, I would say that ATP has a high energy phosphate bond meaning that the free energy of hydrolysis of ATP to ADP and phosphate is -7.3 kcal/mol (-30 kJ/mol) whereas a typical phosphate bond’s hydrolysis (glucose 6-phosphate) is closer -3 kcal/mol (-12 kJ/mol).
Pyruvate has a higher reduction potential (-0.19V) than NAD+ (-0.32V) which explains why it is readily reduced by NADH, but the free energy for the reaction producing lactate is only -2.5 kcal/mol. So, no pyruvate is not a particularly high energy molecule under reductive condition. However, when you consider the reaction of pyruvate and oxygen to give CO2 and water the free energy is huge. But again, if you want to talk about high energy bonds neither pyruvate nor NADH have them.

Amir:

Thank you. I know my question is semantic. I don’t think that terms like ‘energy-rich molecules’ and ‘high energy molecules’ are exclusively used to describe molecules that contain high energy bonds. For example, I read this in Wikipedia: The second half of glycolysis is known as the pay-off phase, characterised by a net gain of the energy-rich molecules ATP and NADH.

David:

The reason the NADH is considered high energy in this context is that, in the presence of oxygen, NADH can be restored to NAD+ via the electron transport system (Complex I, III, and IV) to produce a proton gradient across the inner mitochondrial membrane. That gradient is then responsible for driving the F0F1-ATPase (complex V) to produce ATP from ADP and phosphate. [I should mention that there are two different mechanisms for delivering the reduction potential of NADH from the cytosol to the mitochondrial matrix, but that is a different story] But again, the energy of NADH is dependent on context. In an anaerobic environment, it is the NAD+ that is necessary for the formation of ATP and the NADH is restored to NAD+ by converting pyruvate to waste products (lactate or ethanol).

Three cheers for David Harrison

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Does galactose occur before or after galactose transferase?
The follow shows a protein pathway pathway.

The question is "where does galactose (GAL) first occur" i.e. which block above is galactose first contained in?
A transferase is defined as (wikipedia):

any one of a class of enzymes that enact the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule (called the donor) to another (called the acceptor)

This definition of transferase is confusing as:

The question doesn't show any functional groups does it?
From it, I can't figure out whether the galactose transferase is the molecule that is the donor or acceptor

I can't decide if galactose first occurs in S (as a donor) and is transfered into an acceptor upon reaching T, or if another donor forms galactose (as an acceptor) after S, causing T to contain galactose.

Can you please explain this diagram and cite its source? I think it depicts the processing of a glycoprotein and shows how different sugars are added stepwise.

Yes, this is a biochemical pathway showing a scheme whereby proteins in the endoplasmic reticulum and Golgi apparatus become glycosylated on their way to the cell surface. The square boxes labelled with letters represent a generic protein substrate as it moves along the pathway. The arrows between the boxes are labeled with the names of the enzymes that are performing the post-translational modifications. Galactose is a carbohydrate, specifically, a hexose with a 6-carbon backbone. It would be one of the substrates for the Gal transferase enzymes.

You need to google for galactosyl transferases and find out what kind of reaction they catalyse. Then, if S and T represent proteins with growing polysaccharide chains (as @RosieF states, although I personally would have no idea) you should be able to work this out for yourself. But I think the question is unclear because of the schema and am voting for it to be closed.

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Insect Identification Request -- brown and white flea-like bug
So for context, this is a bug I found on the leaf of one of my young ginger plants, which I found a few days after watering. I have a few other tropical plants next to it, like a vanilla bean orchid -- which has the original soil from the garden store, unlike the ginger. (No bugs on the orchid btw).
The bug I found is a small (around the size of a pencil tip) jumping beetle. When I put it on a piece of tape to take a picture, it bends the end of its abdomen over its back so much that it is almost folding.It is also the only one on the plant that I found.
Some photos below (sorry about the poor quality):

hard to say from the photos; could you do ones which aren't washed out?

Where are they from?

@bob1 What do you mean by "washed out"? Do you mean the brightness/contrast of the photo? If so, I don't have any like that, because unfortunately this was the best I could do with my crappy phone camera.

@bathyscapher I'm not sure where the plants are from, but I live in central Canada.

Great, thank you. The location is usually more important than the origin of the plants (but latter sometimes might help as well) :)

These are clearly the larvae of the suborder Auchenorrhyncha, to whom cicadas, leafhoppers, treehoppers, planthoppers, and spittlebugs belong:

the have an (usually) elongated body shape, often with a triangularish abdomen which is often bent up at the tail
they have a well-developed, sclerotized pronotum
they have characteristic piercing-sucking mouthparts located on the front of the head used for feeding on plant sap
they usually have relatively short antennae
their eyes are well-developed and positioned laterally on the head
their legs are adapted for jumping, with hind legs being particularly muscular
as hemimetabolous insects, their larvae lack wings and their segemented bodies are visible all around their abdomen

These characteristics can be seen here in this (german) labeled image of an adult Neophilaenus lineatus (image credits:  Elke Freese | CC-BY-SA-2.5,2.0,1.0:

All these characteristics match well, therefore I conclude they must at least be Auchenorrhyncha. But even more, it is possible to identify them as leafhoppers (Cicadellidae):

both adults and larvae, have a slender and elongated body shape
usually, they are small insects (few mm to around 1.5 cm)
they have each pair of compound eyes and of dot eyes (ocelli) on the top or front of the head
the thickened part of the antennae is very short and ends with a bristle (the so-called arista)
the femora are at front with, at most, weak spines.
the (mostly squarish) hind tibiae have one or more distinct keels, with a row of movable spines on each (so-called setae)
the tarsi have three segments
the front wings not particularly thickened.

Here is a close-up of a leafhopper larvae (image credits: Patrick_K59 | CC-BY-2.0) depicting most of the named characteristics:

Thanks for the help! Just to add something too, it looks like leafhoppers (especially the larvae) curl the end of their abdomen like what I was seeing

Indeed, some species do curl their abdomen.

I think this is a springtail which lays it's eggs in young plant and moist soil and as you said, It bended it's abdomen by placing it on tape ,when they are stimulated ,they open their hidden tail known as furcula to save themselves from predator. I hope it is

Thanks, I think that is right. I searched a bit for some coloured springtails, and I found one that looks somewhat close, at least in terms of legs and hair (and that it is a springtail with a pattern; I haven't heard of that before):  Entomobrya nivalis (https://tinyurl.com/4xs3rsse)

Also, is the furcula the thing that looks like another leg, but singular, in the right side of the insect's body, on the first picture?


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Can someone with a positive test line and a negative control line in a Covid lateral flow test be Covid-negative?
If someone does a Covid lateral flow test and the control line is not visible, the test is invalid regardless of the visibility of the test line. A missing control line could be due to insufficient buffer volume or damage to the membrane coating in the area where the control line should appear. In either case, the visible test line would be true-positive. Is there a scenario where the test line is visible, but the control line is not visible, and the sample is Covid-negative? If so, how does this work on the molecular level?

I’m voting to close this question because it is a question about the interpretation of a clinical test, and not about a problem in biology.  It may be appropriate for our sister site, SE Medical Sciences

@David I'm not asking for the clinical interpretation of the test. This is something I already know. I am asking about how such a result can occur on the molecular/technical level.

Indeed, but that is neither a problem in biology or a in a laboratory research technique. It  is about the operational details of proprietary clinical tests, which falls within the remit of the newer SE site I mentioned. Please move it there.

If someone does a Covid lateral flow test and the control line is not visible, the test is invalid regardless of the visibility of the test line.

Your first sentence is your entire answer. If there's no control line, one or more of many possible issues have occurred, making that test's results null and void. The test should be rerun using fresh reagents 100% of the time. That's it. Without control, you cannot trust the appearance (or lack thereof) of the test line.
The same is true in laboratory settings. If I'm running an assay and my control doesn't work, I toss the entire thing and start over.

As far as how this could happen, as I said there are many possibilities, some of which could have influenced others. Typically the tests are arranged so that the buffer reaches the test area first, then the control area. As you say, lack of a control line could indicate that there was not enough buffer present to successfully diffuse the detection reagents to the control area.
However, you claim that the sample is supposedly "COVID-negative". I would first question how that conclusion was arrived at. PCR testing is the gold standard, and viral load can change relatively quickly in the body, so unless both types of tests were performed at the same time, you can't draw any conclusions about presence or absence of detectable levels of SARS-CoV-2 in the lateral flow test.
Let's assume, for the sake of argument, that the sample truly is negative for SARS-CoV-2. The most likely cause of this test pattern is some sort of manufacturing deviation, most likely several that worked together. Multiple possibilities come to mind - incorrectly formulated reagents, reagents being applied to incorrect areas of the strip, damage to the strip itself, possibly leading to the removal of the detection reagents, and so on. Most if not all eventually lead to human error of some sort, whether it is imperfect quality control, lack of verification/validation of all manufacturing steps, machines not working properly due to lack of maintenance, etc. An awful lot of complexity goes into producing these tests, and there are many steps where errors can occur. Without having access to the test strip in question and the manufacturing facility itself, it is impossible to definitively identify the cause(s) of the erroneous result.

I'm aware of how it should be interpreted. I'm interested in how this (positive test line, negative control line) can happen on the molecular level of the test, and whether/how this can happen if the sample is Covid-negative.

@AnjaM my apologies. Please see the edited answer above.

Thanks, this answers my question! As a context: The sample was indeed Covid-positive, as confirmed by another test. I wondered about the theory behind this since the manufacturer claims that a T-line without a C-line is not a valid test, but I couldn't think of a situation how a sample with a T-line would not be positive (except for if additional errors happened, like you listed - but they wouldn't influence the C-line). So in the case of T-line positive, it seems to me that chances of the sample being positive are the same independently of the C-line being visible or not.


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Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?
Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for "variable heavy domain of heavy chain". I assume the reason for this name is that the variable domain in the heavy-chain camelid antibody is heavier than other domains. However, I haven't been able to find the weight of each domain in the camelid antibody in order to verify my assumption.
Why are single-domain antibodies derived from camelids called "variable heavy domain of heavy chain"?

Do you know how "normal" antibodies are composed?

@Chris thank you for your reply. I am familiar with how normal antibodies are composed but I am not an expert in immunology. Normal antibodies have two heavy chains and two light chains, whereas camelids also possess antibodies with two heavy chains. The VH domain of the heavy chains of normal antibodies is somewhat equivalent to the VHH of the chains of a camelid antibody. I don't understand where the second "H" in VHH comes from, and I was wondering if it comes from the fact that the VHH domain is bigger/heavier than other domains in the chains of camelid antibodies. Thanks!

Apologies. Quite frequently computing scientists enter bioinformatics without realizing the need to acquire the background molecular biology. Clearly this is not your situation. I was misled by your suggestion of the VHH domain being "heavier", which doesn't make sense to me. However I agree the additional H in the nomenclature is strange. I'll see if I can track it down.

No problem @David, I could have made my question less ambiguous to reduce confusion. Thanks a lot!

First, the definition of VHH (and VH) from the article by S Muyldermans
— “Nanobodies: Natural Single-Domain Antibodies” in Annu. Rev. Biochem. 2013. 82:775–97.

VHH: antigen-binding variable domain of the H chain of heavy-chain
antibodies

VH: the variable domain of the heavy chain of
immunoglobulins

So the poster’s definition is incorrect — the term VHH refers to a single domain of the antibody, not the (single-domain) antibody itself.
Why use this acronym, rather than VH, which seems equally applicable? The key point, of which I admit I was not previously aware, is that camels possess both ‘normal’ antibodies composed of heavy and light chains, as well as these special ones with only heavy chains. This is shown in the diagram below, adapted from the original Nature paper describing these antibodies. It actually uses VH in both cases:

So one can imagine that  the term VHH  was introduced for convenience when talking about the variable heavy domain of both camelid types. (I haven’t searched for the original myself.) This also emphasizes the point that (presumably) emerged later, that the VH region of the two types of camelid antibody had different genetic origins (IGHV3 and IGHV3H) shown in the diagram below, taken from the Muyldermans review.

In conclusion, the poster’s assumption was incorrect: the additional H stands for “(of) Heavy-chain antibody”.


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How to tell if something is an organ or apparatus?
An apparatus is defined as

Physiology. a group of structurally different organs working together in the performance of a particular function.

An organ is defined as:

Biology. a grouping of tissues into a distinct structure, as a heart or kidney in animals or a leaf or stamen in plants, that performs a specialized task.

The below shows the Juxtaglomercular apparatus (JGA). Without knowing its name, how would I tell if it is an apparatus or an organ?
There is a question in my book (which asks: which organs are necessary for the continuation of the Renin-Angiotensin-Aldosteron-System) and to answer it correctly requires that we know that JGA is an apparatus and not an organ.
Is there any giveaways that show it is an apparatus and not an organ, based on the diagram alone?
I can't really tell based on the definitions above e.g. based on the diagram, I cannot tell if JGA performs "a specific task" or a "particular function".

It seems like a largely semantic argument and a poorly reasoned question from your book.

Thanks. I thought it was a bit dodgy too, but I haven't done biology before and am trying to learn it at home, so wanted to double check I didn't miss something obvious.

Usually apparatus is used to group some components that together do a specific work, but as said by @kmm and AlwaysConfused it's a syntactic question. I'm not completely sure about that (will check that asap) but the word apparatus (generally speaking of the animal/human body but not limited to that) etymologically (Latin) was considered as a group of organs that are involved in a specific function of the organism.

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Harbor Seal behavior and personality
I'm doing some research on Harbor seal behavior, but I haven't been able to find much on general behavior such as personality,  quirks, ect. Does anyone have anyone have any firsthand experience with harbor seals that could tell me what their general demeanor is? Are they playful? Curious? Shy? What are some behavioral actions that you see them do often? How do they react with their social groups? Do they have obvious hierarchies or do they mostly ignore each other? Any information is helpful, thanks!

Was this that question on Worldbuilding where they said people in the Biology SE could help?

Welcome to SE.biology! This paper looks like it might be useful

@DanPar yes it is

@user438383 Thank you this is perfect!

I think that the first to do is an ethogram about the behaviors of the Harbor seal...
Do you search for previous publications about Harbor seal behavior? See:
de Vere, Amber J., "Do Pinnipeds Have Personality? Coding Harbor Seal (Phoca vitulina) and California Sea Lion (Zalophus californianus) Behavior Across Contexts" (2017). Master's Theses. 273.
https://aquila.usm.edu/masters_theses/273


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Found possible bone on St Pete beach in Flordia
What is this bone from? Looks like a vertebrae but not sure. What marine animal could it be from? It’s about an inch Long.


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Does my dracaena marginata have spider mites?
I'm trying to determine if my dracaena marginata has spider mites. A little history about the plant: I got it about 5 months ago and it seemed to be an outdoor plant with the previous owner. Since bringing it home with me it now lives only indoors. I noticed some small cob webs as seen in the photos but I think those have been there since I got the plant. I recall seeing those little webs when I got it. As seen in the photos there are some small holes on the leaves but those have been there since I got the plants. I don't think the holes got bigger. I'm thinking the plant had spider mites at one point but they might be dormant now? I don't see any moving things on the plants at all. I sat and looked at a lot of the leaves but haven't seen 1 moving thing on it. This makes me think the plant once had spider mites but now it doesn't. I'm very new to houseplants so any info is appreciated

Short answer: probably not.
Longer answer: Spider mite infestations present with very fine webbing coating whole areas of the plant, generally whole leaves and the stem. Within this webbing you should be able to see small ~1 mm (0.04 in) dots moving, but it does take some observation and helps if you know what you are looking for. You will be able to feel this webbing if it is present, but may not be able to see it, as it is very fine and best seen by holding up against a dark background with a light source shining on the leaves at an oblique angle.
Holes in the leaves are not indicative of spider mite activity - at least not holes of that size. Spider mites are so small that they feed off the contents of single plant cells, which range from 10 to 100 micrometres in size (that's a 100th to a 10th of a millimetre). This kills the cells, leaving a small pale yellowish dot on the leaf, but not an actual hole that you can look through.
A good example of a heavy infestation can be found on the Wikipedia page for spider mites. I've reproduced it here (file attribution: Paramecium, CC BY-SA 3.0 https://creativecommons.org/licenses/by-sa/3.0, via Wikimedia Commons):

In this picture, you can see the webbing between the stem and the leaves, but note the difficulty seeing it on the leaves themselves, even though it is there. You can also (if you look closely) see the damage caused by the mites themselves as the pale yellowish speckles on the leaf to the top right and middle left.


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I found a mossy thing on my plant
I was just wondering if this is a moss and if so what type of moss

looks like a moss to me. A bryologist or local botany expert would be best suited. Where are you located? What plant? Having a picture of this directly on your plant would be best.

I agree it's moss. Like most plant ID, a close up (I know it's tiny; can you crop and enlarge?) and in its habitat (on your plant) is important. Thanks! (Pretty, too.)

Definitely moss. Which one depends strongly on where you are in the world. There are about 12,000 species in total. For proper ID we would need to be able to see the leaf, particularly the nerve (if present) and cells at the base of the leaf under magnification with a hand lens or microscope, as well as habitat (what type of environment you found it in) and habit - how it grows.


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Hello, i was wondering if this is an isopod or a springtail

I want to make a terrarium so i was in need for a springtail is this it or is this something else

Springtails are generally about 5 mm (1/4 inch). Photo is too blurry for me to tell what that might be. Possibly a woodlouse.

I say the same, regular woodlice, 4 of, so, isopods.

Those are isopods. Springtails are hexapods.
Some of them are superficially similar, such as Podura aquatica:


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Why using Fokl as an enzyme in the zinc finger nuclease method?
I started reading about CRISPR, and then about older methods of gene editing. I recently learnt about zinc finger nucleases, where Fokl (a restriction enzyme without specificity) gets specificity, thanks to the zinc finger domains, and can do one stranded breaks. So my question is, why do we need an enzyme which only cuts on one side of the DNA? Is there no other restriction enzyme which has no specificity and can cut on both sides of the DNA? I tried to research on my own, for example in papers, where the zinc finger nucleases method is described like in “Genome Engineering With Zinc-Finger Nucleases”, but I didn’t find the answer to this question.

In short, yes, there are restriction enzymes that induce double stranded breaks. In fact, unmodified FokI is a  restriction endonuclease (indicating it creates double-stranded breaks) ¹. Modified domains of FokI can turn it into a nickase (single-stranded breaks) ².
The reason these nicks are desired is because the repair of single-stranded breaks (SSBs) promotes different DNA repair pathways, I quote ²:

"Here, we demonstrate that site-specific DNA-nicking enzymes (nickases)—constructed by engineering the FokI nuclease domain of ZFNs—can induce SSBs in the genome, whose repair via highly accurate HR gives rise to targeted genome modifications. Importantly, SSBs are not repaired by error-prone NHEJ, and, therefore, do not give rise to indels at both on-target and off-target sites. Thus, SSB-inducing zinc finger (ZF) nickases could serve as highly specific mutagens with no or little off-target effects."

Nicks can be repaired via the less error-prone Homology Directed Repair (HDR) pathway. It is important to note that (in humans) the HDR pathway may be different between double- and single-stranded breaks ³.

https://www.neb.com/en-gb/products/r0109-foki#Product%20Information | 2024/02/12
Kim, Eunji, et al. "Precision genome engineering with programmable DNA-nicking enzymes." Genome research 22.7 (2012): 1327-1333.
Davis, Luther, and Nancy Maizels. "Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair." Proceedings of the National Academy of Sciences 111.10 (2014): E924-E932.


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Will “ground hornets” come back to the same place after winter?
We recently moved into a new house and when we mowed the yard we were being stung by these huge hornets. We couldn’t find anyone to remove them and I am terrified they are going to come back this year. They are in the ground and are about 1-2 inches long and chunky. They also come out at night when we are trying to sit on the patio. I need some advice. If they will be there this year, what can I do to rid of them.

Welcome to the Biology Stack Exchange. Please take a [tour] and visit the [help] page for more information on this site and how it works. There are quite a few different wasp/hornet species world-wide and this question will probably need an ID to be able to answer properly. If you can, can you please edit in a picture of the insects in question and a location in the world - something like your nearest major city and/or state and country usually works well.

Yes, they are likely to return to the same zone and garden if it is a good habitat for them.
Knowledge of them will protect you, and give you confidence that you can reclaim your garden.
1/ research dissuasion of ground hornets.
2/ put together some protective clothing, in case you have to spray a biocontrol agent or another deterrent. I don't know what your budget is, but you could get by with a hat protected by netting, from some instructions online, and some gloves, they won't swarm you in great hives.
3/ Invest in a lot of diligent research, to know what month they start burrowing, what day temperature they prefer to wake up to, how to protect yourself physically if you have to approach an active nesting hornet, if it's ok to keep a good long-handle net near the porch and intercept them when they venture too close in the evening. Read stories of others who have had the same adventure.
I am an experienced zoologist I have been stung by wasps many times, and fortunately not a hornet.
I climbed a tree with 20 in nest just above me and climbed down again, and many other encounters.
The biggest danger is that a wasp or bee falls in a cola when someone is briefly distracted.
Folk should know to be conscious of not mouth-breathing when running near them, and what to do if your friend is stung inside the throat on a hike far from help and breathing becomes difficult.
With this knowledge, I am became confident to let wasps and bees forage and walk on my hands and face which can be annoying after a minute or if they insist on foraging over an eyelid or a nostril, however it is better than startling them, I know how to tell the difference between more and less aggressive lookalikes based on their flying patterns, leg length in flight and other markers, It's a good thing to teach children. I became confident to stay very calm near a hornet nest and try to avoid it, to immediately suck a wasp sting and very fast put cola, or vinegar is better, on a sting, to greatly diminish its effect, and run fast if a nest is disturbed so they go into an aggressive mode.
Good luck.


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Insect Identification - Ecuador
I took a picture of this bug while I was in Chucchilán Ecuador in June. I am wondering what type of insect this is?
It was about 1-inch long.
This was the only good photo I was able to take, sorry for the poor angle.


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What's so special about nitrogen?
I understand why carbon is essential for life. It's able to form long chains and has four binding sites. But what about nitrogen? Proteins are the most important class of molecules for life (except maybe DNA), and they require nitrogen. Why can't we make enzymes and other structures without nitrogen? What's so special about nitrogen?

…or oxygen or hydrogen or carbon or sulphur or … You could ask this question on SE Chemistry, but I think they would expect you to study some chemistry first.

I think you need to distinguish between "why do OUR major functional macromolecules (proteins) require nitrogen?" and "would any similar life require nitrogen, or could alternative macromolecular chemistries be possible?".


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What species is this fly? Look like mosquito with unusually long legs
I found this in Bangalore, India. It looks exactly like a mosquito but with extremely long legs, first I confused it with long legged spider (which are common here) but it's not, Can someone tell me what it is?

Welcome to the site, the insect is too small and blurry in the picture to make out. For ID we ideally need several high quality photos of the organism of interest. Having said that, looks like it might be a crane fly.

Crane flies look like larger, long-legged cousins of mosquitoes, but are beneficial insects, and harmless to humans. Look for pictures of crane flies in your region and see if it resembles te critter you saw before it became...smooshed.


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How to calculatie frequency of recombination between two genes based on their coordinates in ENSEMBL?
I have two genes:
https://www.ncbi.nlm.nih.gov/gene/326619 and https://www.ncbi.nlm.nih.gov/gene/326620
both are mapped to chromosome 13. First is at position 23944778..23945232 second is at positions 23940920..23941369. Is there a way to compute approximate recombination rates between the two based on position? I need this for predicting efficiency for maintaining stable linkage between genes for a mouse cross.

I would strongly recommend consulting a mouse recombination map. Hopefully no need to compute anything, as you should be able to just look up recombination rates between named SNPs.

Here is one mouse map publication.
Here is another one.

I'd suggest taking a look at those and figuring out if they have the information you need.


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Are coding DNA and invariant DNA independent as subsets of the human genome?
Within the human genome we can identify the coding DNA and the invariant DNA i.e. the DNA that is shared by all humans. For example here the authors claim to identify a sequence that is shared not only by all humans but some other species as well.
What is known about their intersection?
Can they be considered as probabilistically independent (i.e. the chance that a random base pair is in both coding DNA and invariant DNA is the product of the chance that it is in coding DNA and of the chance that it is in the invariant DNA)?
I found a relevant preprint but additional references would help.

Related: Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

The more common related concept here is "highly conserved", meaning a sequence that is difficult for an organism to change and still remain viable.
Every base pair of DNA is potentially subject to change via copying errors and other sources of genetic perturbation.  Many such changes, however, will break something important and not produce a viable organism. This is true both for big, complex organisms like people and also for small, simple organisms like bacteria.
The more fundamental a region of DNA is to the operation of a cell, the more difficult it will be to change without breaking, and thus the more highly conserved the sequence is likely to be. That generally means that the conserved regions are either protein coding sequence or functional RNA sequence. Likewise, the most highly conserved are the ones involved with core cellular activities such as transcription, translation, and replication (see citations below) --- which are exactly the type of sequences identified in the reference that you link.
Now, since 2007 we've dramatically increased the number and diversity of organisms whose genomes have been sequenced, and it's not clear to me whether their purely invariant sequences will have held up. Those areas are certainly quite highly conserved however, and that is only to be expected.
Bottom line: the probability that a DNA region is conserved is highly dependent on it being a coding sequence or functional RNA.
Some relevant citations on the nature of highly conserved sequences:

Isenbarger, Thomas A.; Carr, Christopher E.; Johnson, Sarah Stewart; Finney, Michael; Church, George M.; Gilbert, Walter; Zuber, Maria T.; Ruvkun, Gary (14 October 2008). "The Most Conserved Genome Segments for Life Detection on Earth and Other Planets". Origins of Life and Evolution of Biospheres. 38 (6): 517–533. doi:10.1007/s11084-008-9148-z
Harris, J. K.; Kelley, S. T.; Spiegelman, G. B.; Pace, N. R. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803.

Do you have any data that bear on the question? As far as I can see you are merely expressing an opinion, which does not constitute an answer on this site.

Then please include them in your answer.

@David I have added them.

The problem (at least for me) is that the references are not linked to any of your statements, so I don’t know which supports what.

I've added a pointer.


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Why are sunflower seeds so much smaller than their shells?
I was snacking on some sunflower seeds recently when I noticed the large disparity between the size of the seed itself and the woody shell surrounding it. Why is this gap present? Is there some evolutionary advantage to making a seed pod larger? Or did the seed shrink over time?

I’m assuming the seeds you were eating were roasted and therefore dehydrated. Crack open a fresh seed and see if you observe the same thing.

Ahhhhhhhhhh that would explain it. Thanks!


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How does sea plants undergoes photosynthesis?
Since most of them do not have the chloroplast.
And if they undergo how do they perform it ( thus the light stage)

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please take the [tour] and consult the [help] starting with [ask] for details.

Who says they don't have chloroplasts?


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If protein is mostly used by the body for purposes other than extraction of energy, why are calories from protein relevant?
Non-biologist speaking here. As you can probably see from the title, I'm having trouble wrapping my head around concepts related to the body's energy balance amd the role of macronutrients. Let me explain in more detail.
If a person consumes excessive amounts of calories for a certain period of time (i.e. more than they need) they will start to gain weight in the form of fat. Conversely, an extended caloric deficit will lead to weight loss. So far, so good.
Now, each macronutrient has a certain amount of calories per gram of nutrient - if I'm not mistaken 1 g of protein has 4 kcal.
On the other hand, according to different sources that I've been reading lately, the body does not really use protein for energy gain unless in extreme circumstances. In other words, carbohydrates and fat can readily be "converted" to ATP for energy gain while the conversion of protein into glucose and then ATP is very inefficient. At least that's my understanding, if there's already a misconception here feel free to correct it.
Proteins are mostly used to build and repair different structures in the body. I will use the reparation and buildup of muscle tissue as an example. And here comes my main question: if proteins aren't being "burned" by the body to extract energy in the form of ATP, why are the calories consumed in the form of protein really relevant? In other words, if the protein that I eat is being used by the body to build stuff such as muscle, haemoglobin etc. and not being burned, why do I care about the calories that protein has? Why will excess protein calories make me fat?
I obviously "know" that calories from protein matter, but I don't understand why this is the case. I feel like I'm really not grasping something essential here. I hope that the question is clear and that an interesting discussion could follow. If anyone could give a more detailed explanation of what's going on in the body in this scenario, that would be much appreciated.

Relevant to what? Please provide context, i.e. a scientific source in which the energetic values of different foodstuffs are presented with implied relevance to something. Be aware that this site cannot provide dietary advice as questions about medicine and health are specifically off-topic. Also note that this is a question and answer site, not a discussion site, nor is it intended to replace standard textbooks in which metabolism is described for those wishing to know "what's going on in the body". Please cite the texts that you have consulted.

I tried to give an answer "in the spirit of your question," so to speak, but feel free to ask for more biochemistry

Preamble
I had not intended to answer this question as I felt it lacked the clarity required for this site. However I now think that it is necessary to correct the assertion that “protein has to be converted into glucose to generate energy”, especially as this is echoed by the answer from @ThatGuy. I shall clarify the question by interpreting the word “relevant” primarily to mean general “purpose” or “utility”, and shall consider this in relation to the Food and Agriculture Organization of the United Nations (FAO), one scientific body that has published values for energy values of nutrients.
Summary

The dietary nutrients carbohydrate, fat and protein can have
different metabolic fates in the body depending on individual
circumstances. The assumption that “protein is mostly used by the
body for purposes other than extraction of energy” does not apply
in many circumstances.

Energy values for food are concerned only with the situation in which the nutrient is used to produce its maximum biological energy yield as ATP, using the appropriate metabolic pathways.

These values  are not simple bomb calorimeter values. They are calculated separately for protein, carbohydrate, and fat, taking into account their different metabolism. For proteins this takes into account the different metabolism of the 20 amino acids, although it should be emphasized none of these need to be converted to glucose to generate energy.

There are several different purposes to which these values can and are used, but the FAO is primarily concerned with their use to assess basic nutritional needs and their fulfilment in the countries of the world in which malnutrition may occur.

The FAO and standard energy values for nutrients
As mentioned above, I will consider this question in relation to the FAO, the Food and Agriculture Organization of the United Nations, a body that has produced energy values of different nutrients — values that appear to be used by government organizations and commercial food groups in many countries. The source of my information is this report on the subject, produced in 2003, to which the reader is referred for fuller details.
What did the FAO envisage that the results of their work would be used for?
To quote from Section 1.1 of the report:

assessment of the energy needs of countries… living under
different circumstances;
assessment of food availability within regions and countries;
assessment of the potential ability of available food supplies to meet a country’s … needs,
assessment of individuals’ diets (although the recommendations are not meant for this purpose));
as a basis for food labelling, with implications for consumer information/education about specific foods, regulatory compliance regarding nutrient content and claims, and trade.

This should answer the original poster’s concern with the “relevance” of energy values. The purpose envisaged was clearly with energy requirements in countries in which energy malnutrition was a problem, not affluent Western countries suffering from easily preventable diseases caused by overconsumption of food (although they are not irrelevant in the latter).
Did the FAO take into account the different metabolic fates of different energy supplying nutrients?
Yes. It was constituted of personnel who, unlike the poster, were biological scientists with a sound understanding of the physiology and biochemistry of metabolism. To quote from section 1.3 of the report:

“Energy requirement recommendations remain “theoretical” and of little practical value until they can be related to foods… Two pieces of information are needed in order to translate individual foods, and ultimately diets, into energy intakes that can be compared with the requirement recommendations…
…amounts of components must be converted into energy content using an agreed set of physiology-related factors that correspond to the energy-producing potential of the components in the human body. Thus, in order to make accurate estimates of energy intake, it is essential to have energy conversion factors for each component that denote the energy per gram for that component. However, it has long been recognized that the energy contents of protein, fat and carbohydrate differ, both inherently in the compounds themselves and owing to their different digestion, absorption and metabolism.”

So the scientists on this body were well aware of the problems in producing energy values for different nutrients, and the paper considers proteins, fats and carbohydrates separately and in detail in sections 2 and 3 of this report. For each of these (and for different sources of the same constituent) they produced separate values of various measures, with final values in Section 4.
However the value of 17 kJoules per gram protein (=4kcal/g)) quoted by the original poster is the FAO value of Net Metabolizable Energy (NME) — i.e. the energy produced in circumstances when all the protein amino acids are oxidized to produce ATP. This is relevant to individuals in protein equilibrium but in net energy deficit.
(The overall energy values they suggest for fat is 37 kJoules/g, and for carbohydrate 17 kJoules/g).
Summary of metabolite interconversions in obtaining metabolic energy from proteins, fats and carbohydrates

The diagram above is my own attempt at a biochemical summary for the situation when carbohydrate, fat or protein are being solely used to generate energy. Although some ATP is generated directly in one pathway, most of the carbon skeletons are oxidized in the TCA cycle, shown. Not shown is the NADH produced in the TCA cycle and its oxidation in the electron transport chain to produce a proton-motive force which drives the conversion of ADP to ATP — a molecule that can be considered as a source of metabolic energy.
In the energy-deficit scenario carbohydrates are converted to glucose, then to pyruvate in glycolysis (with some direct generation of ATP) and then to Acetyl CoA which for oxidation in the TCA cycle.
In this scenario fat (triglyceride) is converted to fatty acids and glycerol, the latter feeding into glycolysis, and the former being oxidized to Acetyl CoA, and hence to the TCA cycle.
In this scenario, in which they are not required for protein biosynthesis, each of the 20 amino acids from protein undergoes different metabolic conversions, as shown. All these can lead to the TCA cycle, and, as is evident, none involve conversion to glucose†. (The removal of nitrogen from the amino acids, actually consumes energy, but this is allowed for in the FAO calculations.)
Analogy (for those that find them useful)
If I buy a gold trinket in an antique shop it will (in Britain at least) bear a hallmark indicating the purity of the gold. If I am interested in keeping the piece until the price of gold increases and then selling it for its gold content (perhaps after melting it down) then the hallmark information is of primary relevance to me. If, however, I am interested in the trinket because of its beauty or because it may be a rare piece from a famous designer, the hallmark, although reassuring, would have little “relevance” to my purpose.
Even shorter analogy (to demonstrate my sense of humour)
One man’s meat is another man’s poison.

†The misconception about protein and glucose may have arisen in the following way. In extreme starvation the primary metabolic consideration is to supply the brain with glucose, on which it is absolutely dependent. To do this muscle protein is broken down to amino acids, some of which (e.g. those in the diagram that go to pyruvate) can be converted to glucose in the liver by the reversal of glycolysis (gluconeogenesis). However in a normal diet this is unlikely to happen because there will be a plentiful supply of glucose from carbohydrate, and it is certainly not the scenario in which energy values of protein are calculated.

Thank you for the detailed answer, this cleared up some of my misconceptions. In retrospect I should not have asked this question on this site because it is too "unscientific", or at least I should have formulated it more precisely.

When I asked why the calories from protein are "relevant", I meant why their energy value of 4 kcal/g should be counted when keeping track of consumed calories (in a diet for example). My reasoning was that bodybuilders, for example, require high amounts of protein merely to build their muscle mass – therefore the caloric value of their protein intake is irrelevant as they do not metabolize this protein to gain energy but rather build body tissue with it.

On the other hand the reasoning often promoted in dieting tips is that they need to keep track of every calorie they consume – regardless of its origin – to avoid eating more calories than they need, otherwise they will gain fat. Apparently this misunderstanding is very common since it is very often asked on numerous forums. I resorted to this forum not because I wanted dieting tips but rather because I wanted to understand the mechanisms behind protein metabolism in this scenario, but you are right, this question probably doesn’t belong here. I apologize

Side note: A biochemistry professor answered this question (asked by someone else, not me) on a non-scientific forum called quora (https://www.quora.com/Why-count-calories-from-proteins-if-they-are-not-intended-to-be-used-as-source-of-energy-but-to-build-and-repair-body-tissue, answer by Mark Roseman). I also found his answer very interesting and in case anyone with the same misunderstanding as me is reading this, go read Prof. Roseman's answer and the comments to his answer on that site.

I should also note that your answer sparked a deeper interest in biochemistry. I found some very good textbooks that I am hoping to study soon if I have the time to do so. I know that comments shouldn't be used to say "thank you" here on stack exchange, but in this occasion I'll do it anyway: Thank you David for catalyzing my interest in a very fascinating scientific discipline!

@ilovemaths — Thank you for your kind remarks. Good luck with biochemistry!

Think about it this way: if you're compiling a budget or asset report then you want to know about cash flows - income vs. expenditures - regardless of what form that "cash" might take. Sometimes, you want to know how much "cash at hand" you have, and you'll count only the most liquid assets, but often you'll also need to know the total value of any assets that can be converted into cash at all - not just stocks and bonds, but real estate, let's say, and a lot of other possible in-betweens.
In that they are used here (in the context of nutrition), calories are basically like energy currency with varying degrees of liquidity. You might have some assets, like carbs, which are like publicly traded stock shares that can be fairly easily converted to ATP with little commission. Proteins, then, might be more like specialized assets. But the crucial point is, proteins are still energy assets. When you are evaluating your wealth for the purposes of taxes or to take out a mortgage, the bank/IRS will still want to know your net worth considering any property contributing to that net worth. Because proteins can be converted to energy, they still add up to the overall energy budget.
Imagine you have a financial portfolio where you're investing more into stocks (proteins) than what is optimal for your growth targets. The same way that if you have excess cash in your financial portfolio (after meeting your investment and savings goals), you might invest it into more stocks or bonds, the excess energy provided by proteins will need to be stored somewhere.
In the body, consuming more protein than needed for muscle repair and other functions leads to excess calories. Since the body sees this as an "excess cash flow," it converts proteins into glucose (sort of- the details are complicated) and stores it as fat (which is, in our parable, like the savings account).


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The Portion of the Earth's Biomass Attributable to Ants
An exterminator came to the house today (bad ant problem).
He claimed that 20% of the earth's biomass is comprised of ants.
I was surprised by this statement.
I figured that I would post the question here (hope that's OK) and ask if someone can, generally speaking, either confirm this assertion or refute it.
If the exterminator's statement is false, what would be a more accurate estimate? If you can provide a reason or two, I would appreciate it.
Thank you.

I've suggested this question as a duplicate of the one linked above because, even though it doesn't specifically refer to ants, the graph in the answer shows that arthropods (which includes ants) are a measly 1 gigatons, compared to the 450 gigatons of plants. If you dig into the supplemental information, you find that terrestrial arthropods are less than 0.2 gigatons, and a lot of that isn't ants (e.g., 0.07 Gt termites), so ants are way under 20% even just of animals.

This is an incorrect statement. According to an answer to a question in a different SE, https://skeptics.stackexchange.com/questions/7602/is-the-total-biomass-of-ants-roughly-equal-to-the-total-biomass-of-humans, ants comprise roughly 15-20% of the (terrestrial animals), which is only a small percentage of the total biomass that includes sea life and plant life, among other forms of biomass, on earth.

If you read the sources for that Skeptics post carefully, they claim “On average, ants monopolize 15–20% of the terrestrial animal biomass…”. So, that excludes all aquatic life and non-animal terrestrial life, including plants. So I’d say the 20% figure given by OP is likely off by orders of magnitude.

@Alex K Thank you for providing the link to the Sekptics posting. It is helpful.

@acvill I said "total dry biomass" to mean terrestrial animals, thanks for the suggestion.

@AlexK in a biological context, "dry biomass" typically refers to dehydrated mass (that is to say, organic material minus water weight). Also, there is nothing about the phrase "dry biomass" that suggests it refers to animal biomass exclusively. Your answer could be a good one if you correct the language to accurately reflect your linked source, and rewrite your conclusion ("This is a possibly true statement") to reflect the fact that terrestrial animal biomass is a small fraction of earth's total biomass.


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Which area of neuroscience\biology deals with the effects of genetics and drug discovery based on brain microcircuits?
So the title I chose might be a bit too broad or even misleading compared to the specific example I have in mind, but I couldn't choose something longer or more specific than that, so I apologize if that's the case!
Due to its close connection to Autism Spectrum Disorders (ASD) and even some personality dimensions in psychology and my interest in these topics, I was reading an article about the reward circuit (cortico-basal ganglia reward network: microcircuitry, Susan R Sesack and Anthony A. Grace, 2010) which in my opinion is a pretty nice article and as the title suggests talks about the different parts of the cortico-basal ganglia network mostly at a fairly high level of detail (e.g. nucleus accumbens, ventral tegmental area, prefrontal cortex, etc), their interconnections, some physical characteristics of those interconnections, the associated neurotransmitters for the different parts and connections, and some of the functional implications of these topics, and also presents a couple of nice diagrams depicting the afferents and efferents of this circuit. as far as I understand and perhaps obviously, most of this data comes from primate and mouse data, however I would imagine there could be a lot of similarity in humans, and we also approximately know from cognitive neuroscience or other disciplines the general function of some (if not most) parts of this circuit.
The question that came to my mind is, which area of neuroscience or biology deals with modeling and simulating this circuit at this level (not necessarily at the neuron to neuron level) to understand it better, and also understand the effects that genetics or environment could have on it, so that ultimately we might for example come up with a treatment for ASD? is it more related to systems neuroscience, computational neuroscience, systems biology, or even bioinformatics and computational genomics?
Thanks in advance!

Basically you are sketching a situation where:

Brain circuits are modeled (Computational Neuroscience), which often depends on anatomical (Neuroscience, Biology), structural imaging and functional imaging (Neuroimaging) and electrophysiological data (Electrophysiology). Various other disciplines may come into play (Histology, Pathology, Anatomy, etc.).
Genetic (Genetics, Molecular Biology, Cell Physiology) and environmental effects (Behavioral Psychology, Medicine, Psychiatry) also encompass a wide list of expertise, out of which a small handful is mentioned in bold.
The realm of drug discovery harbors Medicine, Toxicology, Organic Chemistry, Pharmacology, perhaps even Physics and likely a host of others.

In short, your question could, perhaps, better be phrased as 'What Biomedical fields of research disciplines are not related to Drug Discovery?

Thanks for the answer. I know all those fields you mentioned might be related to the problem I sketched, however, perhaps I should have explicitly said I meant which field is more directly related, or which field could have the final or biggest contribution to this problem?

@en1gmatic I think this answer addresses your question perfectly, it isn't possible to say "more directly related" or to know where the final contribution will come.

@BryanKrause - thanks for that reply. I'm growing slack in replying on comments - a sign of the dreaded 'I've stopped caring' phase evident in a lot of longer-time users in the Stack network. I'll try to reply more often :-)

No worries - just trying to settle an unanswered question that should be marked answered that got bumped to the top.

@BryanKrause - You're right at the place where Bach-y-Rita worked, right? I've visited Madison a while ago for a visit to Wicab, Bach-y-Rita's commercial legacy.

@Christiaan At the university, yes, but I came here after his death and did not know him; there is a room used for graduate and undergraduate courses in neuroscience and seminars named after him, and his lab continues doing similar work under the direction of other faculty, though I don't know those individuals well either. It's a big place :)


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Difference in rose seedlings with red or green seed leaves
I tried to sowing roses from rose hips the first time. (In autumn I collected some rose hips random from different bushes in the neighborhood. I mixed the seeds while sowing.) Now the seedlings grow one after another. Thereby I noticed, that some have their first leaves in a more red color, and others in a clear green.
Could I conclude some characteristics of the grown up plant out of this?
(I tried to search for "roses red or green leaves" but only get an amount of results with red petals...)

The first leaves of dicotyledon plants are called the cotyledons. Similarly, the scientific word for colour is pigmentation. Even searching with those terms though, I haven't been able to find an answer - I guess you'll have to find out for yourself!

@smartse If there is no answer here in around 6 month - AND I am remembering my question - I will write an answer myself ;)


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Does Invertase catalyse the hydrolysis of other sugars other than sucrose?
I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a colorimeter. Our results indicated that lactose and maltose were more effectively hydrolysed than the sugar alcohols sorbitol, inositol and mannitol. I'm guessing this could be because lactose and maltose are similar in structure to sucrose, which it normally hydrolyses, however, I was hoping there was a more concrete answer.

Welcome to the site. What research have you done on your own to answer this question? The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.

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Why is electroporation not the prefered choice transforming for Mammalian Cells (HEK)?
I see a lot of folks using different techniques for transforming mammalian cell (specifically HEK) instead of doing electroporation like I see with E.Coli (bacteria). Is there a reason for this ?

Viral methods are just more efficient and give you a higher viability in the end. Electroporation works but you'll have a low yield of viable cells after. Here's a nice paper looking at the effects of buffer composition on cell viability/transfection efficiency: https://www.nature.com/articles/s41598-020-59790-x with the general take away being, if electroporation is working well enough to transfect the cells, it will also kill a fair percentage as well.
Hek cells in particular are pretty easy to transfect through viral methods for stable integration of your plasmid or Fugene/lipofectamine for transient expression.

The reason mild electroporation has low transformational efficiency in eukaryotic cells is because they  sequester their DNA behind a nuclear membrane, right?

I'm pretty sure that all transfection techniques like electroporation/CaCl2/Lipofectamine are designed just to break the hurdle of getting it into the cytoplasm not the nucleus. The nucleus is a barrier to transfection but the prior mentioned methods aren't responsible for getting it there. Another shout out to retroviral based methods which will bring it to the DNA for you and integrate it into the genome

@yp66t89 I guess my followup question would be: "Why don't people use the retroviral methods for bacteria ?" Is there something that makes it not work, or is it just that electroporation would just be cheaper.

I'd assume bacteria tend to be more efficient at both integrating plasmids than mammalian cells, no one cares if most of your E.coli die as long as one bacterium survives with your plasmid, and I don't actually know if you can use virus on bacteria, I think you'd need a bacteriophage

@yp66t89 A bacterialphage is a virus --- that's the name for a virus that infects bacteria.

@jakebeal thanks for the clarification on my wording. Most people who work in mammalian cell culture refer to lentivirus and AAV as virus as a generic term and its easy to forget it can be confusing for others

By the way, @yp66t89: you seem to have some good synthetic biology knowledge: would you like to join the SynBio SE site proposal?


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Can we dilute PureExpress Cell Free Mix to increase number of reactions?
Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use.
From this image I found:

It seems like by just adding more 3PGA, amino acids we should be able to get more reactions out of a diluted solution. From my understanding, this would mean that 3PGA and the amino acids are the only consumables here. Would diluting just change the amount time it takes for the reaction to occur or is there something else that I'm missing here.

Really interesting question, but your image seems to show a crude cell free system and not a pure cell free system, unless I’m misunderstanding something!

Yeah, this was the best picture I could find to represent my understanding.

The PURExpress system from NEB is incredibly expensive, for this reason I have avoided it all costs during my experiments with cell-free systems.
This is the paper I've used to create my own cheaper cell-free systems while also discussing reasons why using the NEB PURExpress system is not recommended:
https://pubs.acs.org/doi/10.1021/acssynbio.8b00427

"Although NEB provides a few different formulations of
the PURE system, the commercial system can’t be customized or optimized by the user, and the precise formulation of the commercial PURE system is not publicly available."

This might answer your question as to why I would not dilute the PURExpress system since the precise formulation is not publicly known. Thus, we can hypothesize what would work at various concentrations, but at the end of the day it is unknown what they specifically use in this reaction and how one could optimize it for their own purposes. It would take some trial and error if you really wanted to dilute/change the formulation.

"Our method co-cultures and induces all 36 protein producing E. coli clones in a single flask followed by a single Ni-NTA purification."

This is the method I personally use and it can be time intensive, however the payoff is the cost and ability to optimize your system for your specific experiment.

"The PURE system consists of several different components [7], that can be separated into three main categories: proteins (transcription, translation, and energy regeneration),ribosomes, and small molecule components (salts, buffers, NTPs, creatine phospate, and folinic acid)

If you were to go down the dilution route, I would suggest reaching out to NEB before hand to receive consultation for the purposes of your experiment and any consumables you may need to also purchase. This quote from the paper shows how your system has many considerations for consumables you may need to further research to maximize the expression of certain proteins. As for how this affects the reaction time, dilution shouldn't affect time, it will however affect the amount of product you get out of your reaction.

I guess in a macroscale, it wouldn't really affect the reaction time but in the scenario that there are reusable components then shouldn't it affect the reaction rate? (Thinking back to high-school physical chemistry)


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Blood samples in cell lysis
I will be joining a team of field biologists on a trip to some uninhabited islands in the tropics. We will be collecting bird blood samples for some genetic research. We will be out there for two weeks. Will blood samples in lysis buffer last for two weeks with out refrigeration or freezing them? Or should we do our sampling closer to the day we leave so they have less time in tropical heat?

The exact answer to this greatly depends on the lysis buffer used, what you are lysing the cells for (DNA/RNA isolation, protein analysis, etc.) and how you intend to quantify your samples.
https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Roche/Bulletin/1/11814389001bul.pdf
This is a link to a standard red blood cell lysis buffer and handling recommendations. Note the following:

Lysis buffer must be stored at low temps prior to use
Use blood stored in EDTA, citrate or heparin anticoagulants
To obtain RNA use fresh blood only
For best results in DNA applications, use fresh blood or blood stored for less than 3 days.

Here is another paper describing the effects on DNA/RNA extracted from blood in ranging temperatures and storage methods
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184692


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How to convert a genus name to a noun or adjective
Consider the crayfish family Cambaridae.  As I understand it, this familial name can be turned into an English noun or adjective by changing the first letter to lower case and dropping the "ae." An example use is "Responses of cambarid crayfish to predator odor" (adjective). Similar conversions from generic names are widely used as well.  For example, for the crayfish genus Procambarus, the english conversion "procambarid" is widely used, primarily as an adjective, but also as a noun. A google scholar search for this word turns up hundreds of uses.  A search for "id" conversions for other generics names for hermit crabs, and snake genera turn up uses of them as well. I cannot find any information that actually describes this conversion and it's rules.  Can someone point me to a reference, or otherwise help clarify the issue?

some resources note the capitalization but not the rules themselves: https://scientistseessquirrel.wordpress.com/2020/10/13/why-dont-we-capitalize-taxonomic-names-used-as-adjectives/ (i left a comment there asking)

I think that it boils down to taking a Latin name and removing the case ending to get an acceptable English adjective. Given that it might be a purely linguistic situation, it's possible another SE site would be better (English language?), but this topic is definitely relevant to biologists, as they're probably the ones who run into it most frequently.
We can look at IAPT article 60.10 and it suggests a systematic way to do this, albeit for an unrelated reason. I don't see that they directly address the anglicized Latin adjective form:

A noun or adjective in a non-final position appears as a compounding form generally obtained by
(a) removing the case ending of the genitive singular (Latin ‑ae, ‑i, ‑us, ‑is; transcribed Greek ‑ou, ‑os, ‑es, ‑as, ‑ous and its equivalent ‑eos) and
(b) before a consonant, adding a connecting vowel (‑i- for Latin elements, ‑o- for Greek elements).

I think that we want to apply step (A) but not step (B) here, as their goal is the formation of compound names, and step A alone will get us -id, which is an anglicized adjectival ending (-idus --> -id).
Taking your examples:

Cambaridae --> remove Latin genitive suffix -ae --> cambarid.
Procambarus --> make Latin noun into the adjective procambaridus --> remove suffix -us --> procambarid.

Unfortunately, it looks like there are a ton of possible Latin adjectival endings- the -id examples seem pretty straightforward because you can get an English adjectival ending directly, but other taxonomic names don't resolve so neatly. For example, if I want to use "Lachnospiraceae" as an adjective, I could imagine the following (applying only step A above doesn't seem to work well: "lachnospirace"):

lachnospiraceid
lachnospiraceal
lachnospiraceous

and I don't really know how to pick among them!
I have left a comment on a blog post from Stephen Heard on a related subject (comment above), perhaps he'll see fit to weigh in here.


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Curious what this bug is
I just found this little guy crawling on me after coming in from the garden in Northern VT.  We live in a narrow grassy valley in a pretty wooded area.
This bug was crawling up my neck and when I tried to sweep him away he clung the way a tick does.  He also has a very flat profile and kind of a "hard" feeling body, but otherwise bares no resemblance to a tick.
I took this photo with my phone so it's not great.  The eyes are distinctly roundish and black. His mouth parts were visible and moving around slightly, but while I watched him he didn't appear to be trying to bite into me.
That's all I've got.

It looks like a wingless fly. I've seen something like that in an insect book.

The blurry picture makes it hard to be sure, but I'm guessing it's some sort of louse fly (family Hippoboscidae). They are typically very flat, and can lack wings. They can bite humans, but the different species are dependent on their specific hosts to reproduce.
Image of a louse fly (found on someones neck) for comparison:

(image source)

That's totally what my bug looked like.  Well done!

Found a good general-interest article about louse flies: entomologytoday.org


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Method to estimate age of a variant from genotype data
I will obtain array genotype data from approximately 60 related individuals who all share a rare pathogenic variant, which is at such a high frequency in the enlarged family due to a founder effect.
Is there any software that I can use to estimate the "age" of this founder effect i.e. how long ago there was a "most recent common ancestor", basing on the haplotypes observed from genotype data?

Welcome to Biology.SE. Coalescent theory is what you need. Take a look at this list of available software.

You will need genome-wide data to make a good estimate of the time to founder effect. If you only genotyped individuals for the single locus explaining variance for the disease, you won't be able to estimate much. What kind of data do you have exactly?

ABC to the Jensen style might be useful but it won't be as easy as feeding your raw data to a software.

I am not sure on the exact array version on which samples have been genotyped, but it will be genome-wide (I guess it'll be Illumina Omni Express, approx 700k SNPs). Thanks for the suggestions, please let me know if you happen to find some other software....I am also looking in the literature but there seems not to be anything particularly user-friendly to do this...


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How many Laws does Mendelian inheritance have?
I know of 3 laws of Mendelian inheritance :
1.law of segregation
2.law of dominance
3.law of independent assortment
But, I've also come across a couple other "rules" of Mendelian inheritance such as principle of unit character/factor and principle of paired factor. I cannot understand what these other rules actually mean and whether they are a part of the Mendel's law of inheritance.
Further is there a distinction between the words Law,Principle and Rule or they mean the same thing.

Welcome to Biology.SE. The last question Further is there a distinction between the words Law,Principle and Rule [..] is a question of philosophy, not of biology (have a look at philosophy.SE).

Principle of unit character/factor
To understand this concept, it is good to fall back into the era in which Mendel lived, an era where we knew so little about the nature of genetic information. Consider a famous (and highly racist) argument by Jenkins against the hypothesis of natural selection as formulated by Darwin.

Jenkins supposed that a white man was wrecked on a desert island inhabited by Africans. The shipwrecked European would kill many black men in struggle for existence. He would have many wives and children. Many of his subjects would live and die as bachelors. In the F1, there will be some intelligent young men who are mulattoes (mixed race) more intelligent than negroes. Eventually instead of the beneficial white characteristic rising in frequency through natural selection acting on intermediates, Jenkins said that the European alleles and genes will be diluted out.

Putting aside the obviously racist and false assumption that whites are superior to blacks, the argument is not silly. Why would not the beneficial characteristic of an individual just dilute into the majority unadapted population? The answer is in the long forgotten Mendel's work. Individual characteristics are not 'fluid'. Characteristic of parent don't just average to give the characteristic of the offspring. There are actually particular unit of heredity (a gene) which has some seemingly atomic property in the sense that its effect will be diluted by crossing individuals carrying a given allele (an allele is a variant of a gene) with individuals carrying different alleles.
Principle of paired factor
Here is the underlying discovery of diploidy. Of course, by far not all living beings are diploids (or diplontic) unlike Mendel may have thought but he still discovered that diploidy is a thing.
Mendel discovered that it is the combination of two 'alleles' (the terms 'gene' and 'allele' did not exist at that time yet) that would determine the 'phenotype' (this term did not exist yet either) of an individual.

thank you for clearing things a bit , but going back to my basic question do these principles hold as the principles of inheritance or not ? Moreover do you perceive that there maybe a difference in what Mendel's law and principles ? also is the principle of unit character a repetition of the principle of paired factor or are they separate for they all seem to be overlapping to me

Answering your 3 questions in order. 1) Sure, they relate to inheritence. It is a human decision to call them one way or the other then. 2) The difference between principle and law is a question of philosophy, not biology. 3) No, they are different. Maybe try rereading my answer and if it does not help, you can try to specify what is unclear to you.


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Difference between bacterial chlorophylls
I understand that bacterial chlorophylls are of the form a, b, c and d.
But i read in my textbook about pigments like bacterio purpurin and bacterio viridin; are they a part of the 4 types of chlorophylls and if not how are they different and what actually are they?

What research have you done before asking it here?

@another 'Homo sapien'  i looked through a couple pages on the internet about bacterial photosynthetic pigments along with a wikipedia page and also a couple books but none of them were very clear about the relationship between bacterio purpurin/viridin and bacterio chlorophylls.  Thus,  my question is simply to ask for the relationship between them and if someone could explain the difference between


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Is carbon dioxide dissolved in plasma same as carbonic acid?
Carbon dioxide is transported through blood via 3 methods :
1. Dissolved in plasma 2. As bicarbonate  ion 3.through RBCs. The carbondioxide when transported as bicarbonate ion i.e HCO3- and H+.  What i dont understand is that dissolved carbon dioxide in plasma should also yield H2CO3,  so is writing co2(aq)  the same thing as writing H2CO3? Further shouldnt this carbonic acid also dissociate and form bicarbonate ion and proton? Doesn't this make both the processes equivalent?
What i found out is that H2CO3 has a low   ionisation constant of the order 10-4, is this tbe reason why they are separate events? Implying that carbonic anhydrase  catalyses the formation of bicarbonate ion while some part of H2CO3 is not ionised and that is what refers to co2(aq)

Please put more effort into presenting your questions in a readable manner. You can do this by: 1. Using paragraphs to separate different ideas or different points. 2. By making sure that you capitalize the letters representing chemical elements (CO not co), 3. More difficult subscripting or superscripting chemical formulae. There are two ways of doing the latter. I use HTML markup e.g. numeral and +. This will work in questions and answers (not in comments) 4. Capitalize "I" in English.

Im sorry for being sloppy,  i typed it on my phone and didn't pay much attention to details, what do you think about the answer?

Well if you can find a computer and take the trouble to clean the question up as I suggested — and if nobody has answered in the meantime — tomorrow I might look out the lecture notes I used to use on carbon dioxide transport and bicarbonate buffers and provide a comprehensive answer. In SE the idea is not to provide a limited answer for one person, but to provide answers to biological questions that will be of use to many.


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Birds with overlapping summer and winter ranges
My question is about bird species with overlapping summer and winter ranges, like fieldfares. What happens in the overlap area? Do the birds that breed there also stay there, or do they migrate to the south while their place in winter is occupied by their relatives who breed in the north?

It's possible that ranges don't actually overlap for individuals but that ranges between individuals overlap. If I live very far north and you live very far south, my southern range for me might just be your northern range.


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How to measure tone of the cerebral cortex?
There is a lot of information about the "tone of the cerebral cortex". Some scientific papers describe that the tone could decrease or increase. However it's not clear how do they measure the tone of the cerebral cortex. Any ideas?
In case if they use EEG for that purpose, could you please specify what exact frequency ranges(alpha,beta,etc.) should have to alter to indicate that the tone is to be decreased or increased?
Thank you!

Welcome to Biology.SE. Please [edit] your question to include some examples of this usage. Please also take the [tour] and consult the [help] starting with [ask] for details about what is expected on this site and update your post accordingly.

Tonic is used to describe constant muscular contraction; this word has also come to refer to neural activity that leads to constant muscle contraction, and further to mean constant neural activity more generally, in contrast to "evoked" activity produced by some stimulus.
When they say "tone of cerebral cortex" they mean "tonic activity of cerebral cortex", or in other words, they refer to background firing activity at rest/not specifically evoked by some experimental stimulus.
Action potentials are most associated with gamma and high gamma bands, but you can also speak of tone in other bands. It's quite possible they simply mean EEG amplitude. It's not possible to say for sure, you would want to refer specifically to the methods sections of papers mentioning "tone"; they need not all measure the same thing.


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Is plastoquinone not an electron carrier?
In my book, under the topic chemiosmotic hypothesis, it is given that proton gradient is created by accumulation of protons in the lumen of thylakoids. One of the ways by which the gradient is created is mentioned as below....
' As electrons move through the photosystems protons are transported across the membrane. This happens because the the primary acceptor of electrons which is located towards the outer side of the membrane transfers its electron NOT TO AN ELECTRON CARRIER BUT TO AN H CARRIER. Hence this molecule removes proton from the stroma while transporting an electron.
I suppose they are calling plastoquinone as the H carrier, but then, why is it not an electron carrier? It is involved in electron transport isn't?

By 'H carrier', I think the author means 'a proton plus an electron carrier' or a H atom carrier.
When PQ accepts an electron, is may also pick up a proton from the outside (it now has accepted a H, that is a proton plus an electron).
If the electron is donated to another acceptor, a proton may be lost on the inside. PQ is now back in its original state, but the net result is that a proton has been 'transported' across the membrane (but it is almost certainly not the same proton) and an electron has been 'carried' from donor to acceptor.
(Oxidation is the loss of an electron or electrons. Reduction is the gain of an electron or electrons. But accepting or losing a proton is neither an oxidation nor a reduction, but an ionization)


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Overlapping atomic radii in data of experimentally observed protein assemblies
I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M
When taking the atom centers of a monomer and applying the transformations specified in the .pdb file, I get a structure where the VDW radii of different proteins overlap. I have tested a variety of sets of radii and it happens for all of them. I tested with Bondis radii, ProtOr radii and several radii taken from popular force fields (AMBER, PARSE, CHARMM).
I am wondering:

What is the least wrong set of radii to choose here and why?
Is there a popular way to resolve this?
The Clashscore depends on overlaps within a protein right? What radii are chosen for this measure?

Thank you in advance
Ivan

can you give us the chain ID, residue number, and atomID for the atoms in the .pdb file that are overlapping in the linked TMV structure? Is this something you've noticed in other structures as well, or just this one?

In the example behind the link, the chain ID is 'A' and considering two adjacent monomers transformed by the specified BIOMTs we get an overlap between Atom IDs 164 and 72 by 0.3 Angström for example, when choosing Bondis VDW radii for the atoms. There are around 20 of these overlaps in total.
So far every assembled TMV structure I checked has these overlaps.

Looking at the validation report for model 6R7M, we see that there are no symmetry-related clashes listed. (Although there are two clashes within the asymmetric unit, HA of ASP20 - HD3 of PRO21 and HG13 of ILE95 - HB2 of ALA111)
The relevant portion of the PDB's validation explanation page is here:

All-atom contacts within the ASU are calculated by the Reduce and Probe programs within MolProbity (Word et al., 1999; Chen et al., 2010). This method was developed to quantify the detailed non-covalent fit of atomic interactions within or between molecules (H-bonds, favorable van der Waals, and steric clashes). Since most such interactions involve H atoms on one or both sides, all hydrogens must be present or added (Reduce optimizes rotation of OH, SH, NH3, etc. within H-bond networks, but methyls stay staggered). At present, in order to ensure comparable scores between NMR and X-ray, hydrogen atoms are removed from the analysed structure, and replaced by a different set placed by Reduce in idealised and optimized nuclear-H positions. All-atom unfavorable overlaps ≥0.4Å are then identified as clashes, using van der Waals radii tuned for the nuclear H positions suitable for NMR (rather than the electron-cloud H positions suitable for X-ray).).

(bolding mine)
The main takeaway is that MolProbity does not consider that amount of overlap to be a problem. So to your second bullet point, I don't think anything needs to be resolved.
As for which radii should be used, I don't have good advice. It looks like that is still being debated. However, looking up the original paper for the MolProbity tools used by the PDB for validation, the radii for O and non-carbonyl C are 1.4 and 1.75 Angströms, respectively. That sums to 3.15, I measure 2.92 between the atomic centers, so slightly less overlap than you got.
My initial assumption was that these would be poorly-resolved residues near the edge of the macromolecule and that the VDW overlap would be due to fitting errors, but it looks pretty good to me:

As noted in comments, some nonbonded atoms in model 6R7M have more than 0.4 Angströms overlap, but are not tagged as clashing, e.g. the sidechain oxygens of THR29 and TYR73. This is because these overlaps are not unfavorable; that is, molprobity predicts hydrogen bonding between them. I couldn't find any specifics about how molprobity determines if a particular overlap is unfavorable. The best description I found is in the documentation of the chimera tool findclash:

The Clash/Contact Parameters control what will be considered a clash or contact. The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

overlapij = rVDWi + rVDWj – dij – allowanceij

Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify favorable contacts.

Subtract [ allowance ] from overlap for potentially H-bonding pairs - an allowance > 0 reflects the observation that atoms sharing a hydrogen bond can come closer to each other than would be expected from their VDW radii. The allowance is only subtracted for pairs comprised of a donor (or donor-borne hydrogen) and an acceptor. This is equivalent to using smaller radii to characterize hydrogen-bonding interactions (for example, see Li and Nussinov, Proteins 32:111 (1998)). As in FindHBond, possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair.

Thank you  for the detailed response. Follow up question: Between Atoms 217 and 590 I am calculating a distance of roughly 2.3A. Both are oxygen atoms so no matter the set of radii that would be a symmetric clash no?

the bolded text in the 1st quote of my answer says 'unfavorable overlaps'; if a bond is expected, some overlap is expected, so it doesn't register as a clash. I don't know the specifics for molprobity, I'll add it to the answer later.

This is really interesting. I did not know, that bonds between different proteins form at all during self assembly.

to be clear, these are hydrogen bonds, not covalent bonds. Bacteriophage HK97 does form isopeptide covalent bonds in the final stages of its self-assembly, but that is unusual.

Thank you for clearing that up. Is there a way to identify the hydrogen bonded Atoms from a PDB? And also if it is easy to explain: how do hydrogen bonds lead to oxygen atoms being closer together?

It's probably best to read about hydrogen bonds separately, but it is an attractive interaction between donor and acceptor atoms, so the repulsive interactions between them will be offset more than when an H-bond isn't present. To predict H-bonds, I would use the FindHbond tool in the program chimera, but there are probably many other options for different software packages.


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Is this snake hazardous around children?
This snake lives in a small rock dam in a residential retention pond in Chattanooga, TN.  Children play in the area at times.  It is approximately 30 inches in length. Is this snake a hazard or can it be ignored?

This appears to be a northern water snake.

 TN.gov
Nonvenomous. Not dangerous if left alone, From tn.gov:

When threatened Northern Watersnakes will make a silent retreat, but are aggressive when captured. They will flatten their head and neck, try to strike and bite, and discharge a foul-smelling musk from glands at the base of their tail.

See https://www.tn.gov/twra/wildlife/reptiles/snakes/northern-watersnake.html

The fat body is quite reminiscent of a cottonmouth, but it doesn't have the mottling I associate with them.


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Nerve Impulse Process
In the process of re-polarization, when we have achieved the normal membrane potential, why does K+ voltage gate dont close at -70mv and rather at -90mv when its hyper-polarized?

There is a key difference in Na+ and K+ ion channels:  Na+ channels are quick to open and inactivate, while K+ channels are both slow to open and close.
Shortly after the peak of depolarization is reached, the inactivation gate structure of Na+ channels stops the inflow of Na+. However, the voltage gated K+ channels that have been activated by depolarization allow the membrane to repolarize from K+ outflow.
The K+ channels are slow to close and thus they allow some more K+ to escape (afterhyperpolarization) before finally closing.

They do, but they are slow to change state and the membrane voltage is changing quickly.
You can think of ion channel gating like a chemical reaction, with the channel in equilibrium between different states: open and closed (and frequently other types of states as well, like "inactivated"; there can also be multiple distinct open and closed states).
Like a chemical reaction, in addition to the concept of "equilibrium" (what would be the average state of the channels given a very long time) there is also "rate": how long does it take to get to equilibrium.
The equilibrium of closed versus open voltage-gated channels is, by definition, a function of voltage, but equilibrium is not reached instantly. In the Hodgkin-Huxley model, the rates $\alpha$ and $\beta$ represent the opening and closing reaction rates. I'd highly encourage playing around with a Hodgkin-Huxley simulation and tweaking those parameters to see the results.