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Identifying a spider very similar to a brown recluse
I took this pic tonight when I saw what I thought to be a Loxosceles reclusa or brown recluse. But when I looked closer, the typical pattern on the back of its cephalothorax seems to be upside down! I tried to compare with lots of pics and I was not able to identify this one. Plus, its abdomen is kind of velvet greenish.
Could anyone help identifying this spider please? Last precision : the body size (excluding the legs) is around 1cm.
Thanks Folks!
Photo taken on June the 24th 2018 around 10pm in Toronto, South Ontario, Canada.
PS: Even if one of its leg is fully missing, it was still running very quickly...

I think this a nice male Cheiracanthium inclusum, the familiar "yellow sac spider" (outdoors edition).  The abdomen is what you would expect, the very long first pair of legs, the obvious eyes at the front of the head (middle two of the top row).
I'd feel more comfortable if I could see the usual very dark 'face' and chelicerae, but the angle of the photo is such that it might be just hidden.  The carapace pattern looks interesting, but it may well be that the flash of the photo is giving us a different look there.
Here's the link to the Bug Guide page, with a representative photo of a similar male:
https://bugguide.net/node/view/80427


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What is this aquatic organism in Fiji?

I found them under reefs in Fiji. The hand-like structures moved slowly. I was not sure if it was an animal or plant. I was not even sure if they were several individuals or it was a whole.
The part that was not hidden by the stone was about 50cm length. I did not touch them, since I was not sure if it was dangerous.

What size is this?

the part which was not hidden was 50cm length.  I did not touch them, since i was not sure if it was dangerous.

They seem like sea-cuecamber (Holothuroidea).

It is probably Holothuria leucospilota
Holothuria leucospilota is a medium-sized sea cucumber reaching a length of up to 40 centimetres (16 in) when relaxed but it can stretch to about a metre (yard) when extended.
Holothuria leucospilota is found in shallow water along the east coast of Africa and in much of the Indo-Pacific region. It is a common species on the north east coast of Australia where it is found on reefs and rocky coasts, often partly concealed under a boulder.
References
https://en.wikipedia.org/wiki/Holothuria_leucospilota

Please provide more explanation, links, etc., that help others understand why you think this is the answer.

source: Stack Exchange

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

sort: votes


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Can anyone identify this seed or nut?
I found many of these nuts in a botanical garden in Sweden (outside, not in a greenhouse) but was unable to find the plant it belonged to. The garden has species from all over the world. I don't recognize it as a native plant, but I could be wrong on that.
I've tried to use various identification webpages to find it, but failed. I would love to know the species, so that I can get more info on the plant and its seeds! The Bic lighter is there for scale.
The nuts (or seeds, or whatever they are) are very hard, like a peach stone or other drupe stones.
This is a crosspost from Reddit where no-one has answered the post(yet).

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


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Isolation of Intact Granules from Mast Cells
How to isolate intact granules from mast cells without using sucrose and percoll?


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What happens to Km when enzyme concentration is *very* high?
Let Km be an empirical measurement of a certain enzyme with concentration [E]. Theoretically, this value is constant and shouldn't vary when [E] goes up or down. Now let [E']=10*Km. Under this concentration of enzyme, it's clear that if [S]=Km, V0 cannot be 1/2*Vmax (as there's only enough substrate to saturate 1/10-th of the enzyme molecules). What's happening here, and how does this relate to the derivation of the Michaelis-Menten equation?

I can imagine if your Kcat is sufficiently high and your Kr for the reverse reaction of [E][S] ↔ [ES] is sufficiently low, the assumptions that Michaelis-Menten kinetics work on begin to break down, like reversibility and equilibrium.

@CKM maybe, but those are not affected by concentration (and if they are, how?).

Michaelis-Menten is often challenging for students because of the importance of the conditions that must exist in order for the model to hold. Walking through the derivation and the relevance of the assumptions can be helpful. Berg's Biochemistry is available via NCBI, and the section on Michaelis-Menten kinetics does a good job here, illustrating the following points:
Assumption 1:  The rates of all the relevant reactions are linear.
This assumption is what allows us to write down the equations the derivation starts with. We look at each separate reaction, and say that the rate of that reaction is equal to some rate constant times the concentration of each thing on the left side. From the equation $E + S \rightleftharpoons ES \rightarrow E + P$, we get the following

$E + S \rightarrow ES$

$Rate = k_1[E][S]$

$ES \rightarrow E + S$

$Rate = k_{-1}[ES]$

$ES \rightarrow E + P$

$Rate = k_2[ES]$

This assumption (the rate is linear) only matches the experimental evidence early on in the reaction, while most of the substrate is free $[S]$ (rather than bound up in $ES$).  Remember this. It will come into play when we evaluate assumption 3.
Assumption 2: The $ES \rightarrow E + P$ reaction is irreversible
In order for us to combine the above rate equations to derive the Michaelis-Menten equation, the only source of ES should be from $E + S \rightarrow ES$. We can't have any measurable $E + P \rightarrow ES$. Experimentally, for enzymes that follow Michaelis Menten kinetics, this is true when $[E]$ and $[P]$ are small relative to [ES]. So here we have our first requirement that $[E]$ be small. Biochemical reactions tend to not involve very high changes in free energy. The in situ free energy of ATP hydrolysis is the high end for a reaction in the cell, and that releases about $50kJ mol^{-1}$. We're not talking about combustion here. So in fact, these reactions are often reversible at appreciable levels of $[E]$ and $[P]$
Assumption 3: ES formation and breakdown is at steady state
This assumption is often described in a confusing way, i.e. the entire reaction ($E + S \rightarrow E + P$) is at steady state. Lets drill down to what we're actually talking about. In order to derive the MM equation. We need the rate of formation of $ES$ to equal the rate of breakdown of $ES$, that is, for $\frac{d[ES]}{dt} = 0$. That is steady state. Let's say that in words: the change in $[ES]$ needs to be zero. We only achieve steady state at an early point in the reaction (remember, we need most of the substrate to be free $[S]$ for assumption 1 to hold), if $[S]$ is substantially greater than $[E]$. $E$ needs to be saturated with $S$ while $S$ is still mostly in the free form. This is the key combination of assumptions that the situation you described violates.
Once we meet the three assumptions above, we can write down the following equality:
$k_1[E][S] = (k_{-1} + k_2)[ES]$
This equation says that the rate of formation of $ES$ (the rate from equation 1 at the top) is equal to the combined rate of the breakdown of $ES$, either into $E + S$ or $E + P$ (equations 2 and 3 at the top). Once we have this equality, we can derive the Michaelis-Menten equation: $V_o = V_{max} \frac{[S]}{[S] + K_m}$, where $K_m = \frac{k_{-1} + k_2}{k_1}$. Again, see Biochemistry to walk through this.

@user1136 these are interesting comments, and may be true, but I would note that your statements do not match how Michaelis-Menten kinetics is described in Berg and other Biochemistry textbooks I'm familiar with. I appreciate your answer, and would be curious to see you fill it out a little more.

The derivation of the Michaelis–Menten equation makes a number of assumptions. The exact assumptions depend a bit on how you actually do the derivation, but most modern formulations depend on the steady state approximation. (For example, see here.)
In your situation, where the concentration of enzyme greatly exceeds the concentration of substrate, that assumption is violated. You'll never reach a steady-state. As such, applying the Michaelis–Menten equation to this particular situation gives inaccurate results. You certainly can model the kinetics of the reaction in these conditions, but you need to use other equations and approaches.
That's not to say that the Km doesn't apply in those situations. The Km of an enzyme is a property of the enzyme that applies even in the high-enzyme regime - it's just that the "conventional" interpretation of Km ("the concentration of substrate at which reaction rate is half maximal") doesn't apply. That statement is only true in the particular conditions which the Michaelis–Menten derivation holds.

I don't know if I'd agree that Km somehow applies in the situation the OP described. Km characterizes the reaction an enzyme is involved in, and concentrating the enzyme, for example in a pellet in a centrifuge, doesn't change the theoretical property of the enzyme, but there is no application, or use of Km that is valid unless [E] is low relative to [ES].  It's a constant you get when you write down the steady state equality. See my answer

The effect of high concentrations of enzyme on the Michaelis-Menten equation has been considered by M. F. Chaplin, "The effect of enzyme concentration on the Michaelis-Menten equation" published in the January 1981 issue of Trends in Biochemical Sciences, page VI, under the heading 'Textbook Error' (but, as far as I can determine, this article is not indexed in Pubmed or the like).
The author draws two important conclusions:

The assumption that the total enzyme concentration, $E_o$, must be less than the initial substrate concentration ($S_o$) is unnecessarily restrictive. The Michaelis-Menten equation holds, to  a very good approximation, when $E_o$ is greater than $S_o$ but is less than the Michaelis constant (!)
At high enzyme concentrations, a modified equation is proposed
$$ v_i = \frac{V_{max}[S_o]}{K_m + [S_o] + [E_o]}$$

The derivation of this equation is given in the cited reference.
Edit

A Dropbox link to the Chaplin reference. It does not seem to be available from anywhere, including the TIBS site (and it does not appear to be indexed in PubMed or the like)
A user asked (question now deleted) if $K_m$ is in any way dependent on E${_o}$

Setting
$$ K^{'}_m = K_m + E_o$$

it is seen that the substrate concentration at half-V$_{max}$ is $K^{'}_m$

that is the 'true' Michaelis constant will indeed depend on $E_o$ 'just a little bit' as the User suggested under the less restrictive assumptions considered by M.F. Chaplin (where $K_m$ is defined algebraically above).

Perhaps the User would consider un-deleting this question? IMO an interesting one.

Interesting. Is there experimental data in  this TIBS article?

@user1136 - I did look up at this question before asking that one, but this was about when the enzyme concentration was very high.  undeleted that one https://biology.stackexchange.com/questions/87870/why-does-not-km-change-with-enzyme-concentration


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If the human atlanto-axial joint is pivotal only, what accounts for the craniums additional degrees of freedom?
The atlanto-axial joint is supposedly a pivot joint. I assumed it would be considered a ball-and-socket joint, based on a) the physical shape of the dens, and b) the degrees of motion of the cranium relative to the spinal column.
A pivot joint is distinct from a typical ball-and-socket joint because it only allows for a single degree of freedom; yaw - to rotate about it's own axis or diameter, like a spindle. A typical ball-and-socket joint allows at least one additional plane of limited movement.
I can think of (or observe) at least three degrees of freedom of the cranium, relative to the spinal column; pitch & roll. Pitch allows you to direct your gaze from the ceiling, to the floor. Roll allows lateral movement in a similar manner, so you can point your left ear to the ground, and then your right.

The additional degrees of freedom are provided by the entire cervical spine, rather than the atlantoaxial joint alone, which is the joint between C1 and C2. What you're describing as roll (when you point one ear to the ground), is provided by contraction of the sternocleidomastoid. The sternocleidomastoid muscle pulls the mastoid process (behind the ear) down and in, toward the fixed clavicle and sternum.  The joint that provides lateral flexion in response is the entire cervical spine.
Here you can see the sternocleidomastoid muscle (the SCM):

And here, a drawing with a reasonable approximation of the way the cervical spine responds to lateral flexion (due to contraction of the SCM). I can't find a good c-spine film at the moment to demonstrate it in a human person, rather than an artists imagination. But this drawing is accurate to my recollection. You can see the space between C1 and C2 on the right is quite limited (that atlas and the axis are in close apposition). C2 and C3, as well as the other cervical vertebrae, have more space between them on the right:


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What are these balls in meshopyll cells? [Plant biology]
Anybody knows what are these small balls? The picture was collected with a confocal fluorescence microscope. These balls have a green epifluorescence and they are in mesophyll cells of rice leaves.


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Is plaque formed even if you do not eat anything?
Some people report that their gum and dental health improves when they are fasting. Many forums contain crazy amounts of misinformation and claims which are unsupported by serious scientific research, so many people attribute various effects of fasting to their body being "purged of toxins" and all sorts of other nonsense.
I have noticed one of these effects on myself when I'm fasting - my teeth get somewhat sticky in the evening. The same effect is reported by many people on the aforementioned forums. On normal days when eating food, this does not happen.
It's pretty certain it's not some sticky toxins being excreted by the teeth. So what is it? I strongly suspect that it's just normal plaque, which would otherwise be abraded by chewing on food. But I always assumed that plaque is formed by food remains in the mouth, so it leads me to the question:
Is plaque formed even when one does not eat any food?
Citations of scientific literature are welcome.

But I always assumed that plaque is formed by food remains in the mouth

It's not surprising that you'd have this assumption. The clinical term, dental plaque, refers to soft deposits on the teeth. While is often described to the lay public in connection to eating (without brushing), it is not food, or the remains of food, it is a biofilm. Biofilms are complex masses of bacterial colonies in a gel-like matrix produced by those same colonies. The matrix typically, helps the colonies adhere to some surface and protects them from external threats.
Good supporting electronic references of what, exactly, a dental biofilm is and how it impacts the health of your mouth and body are behind a paywall, but you may be able to access them at your local public or school library. Socransky and Haffajee have a good review in Periodontology. You can find it on Pubmed (behind a paywall).
As you suspected, not eating does not prevent plaque formation, but it is not because your teeth are excreting sticky toxins. Your mouth is full of bacteria, most of which lives peacefully without causing any problems. They're the ones that make the plaque, and they will make it whether you eat or don't. Whether or not those bacteria are more likely to cause problems (e.g., cavities and gum disease) if you fast is a question for future research.
There is some evidence that the bacterial composition in the mouse gut changes when they fast, and that obesity is associated with periodontal disease in humans. There is some interesting evidence in support of effects of intermittent fasting that would make it reasonable to ask a research question about the impact on dental caries and periodontal disease, but that evidence isn't enough to support fasting as a treatment for any disease.
tl;dr
Plaque is (caused by) bacteria, not food. It's produced whether you eat or not. Fasting is certainly not an approved treatment for periodontal disease or cavities, and I'm not aware of any direct evidence supporting it.


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Large spider identification, Kentucky USA

What kind of spider is this I live in KY and it was found on my stairs.

It's not a widow, false black widow,  or a brown recluse, and you're in Kentucky, so it is not a spider that could be a medical threat to a human. Since all I can do is rule that out, I'm not posting this as an answer.


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Bee Identification, Rochester NY
bee I found in Rochester NY, any guesses what species?

Some kind of Halictidae. You can tell by the pollen-collecting ventral side of the abdomen.

It is a bee in the genus Megachile, in the family Megachilidae, not Halictidae.
Megachile are leafcutter bees, and have scopal (pollen carrying) hairs on their bellies (ventral side of their abdomen).
Most bees in the family Halictidae have scopae for carrying pollen on their legs, though they may have hairy bellies with substantial pollen carrying capacity.


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Addax in the Land of Israel
The Addax (Addax nasomaculatus) is critically endangered species of a desert anetelope with impressive long horns. Today there are small populations in the Sahara desert and the Arabian desert (Saudi Arabia). The addax is mentioned in the bible ("Dishon"), though the identification is not uninomous. Today in Israel there are breeding centers for the addax, one in Hai-Bar Yotvata (near Eilat, the rift valley, bay of the Red Sea) and the other in the Zoological Center at Ramat Gan ("The Safari"), but as far as I know, there are no plans to release addax in the wild in Israel (although I think it can survive and flourish there).
The question is: was the addax native to the Land of Israel (before it was eradicated from it by overhunting)? Do the conservation organizations support reintroduce it to the wild in Israel (in addition to the Sahara and the Arabian desert) addax herds from the breeding centers? The reintroduction of Oryx to the wild in Israel was pretty successful.

According to Yossef Braslevi, "HaYadata Et HaHaretz - Yam HaMelach Saviv Saviv" ("And you shall know the land - The Dead Sea and its Surroundings", 1956, Vol. C, page 199 -- the answer is positive. There were native addaxes in the Land of Israel.


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If a person is infected with an RNA virus what percentage of the RNA in the blood of the person contains RNA of the virus?
Karius uses DNA sequencing of everything that's contained in a sample to detect all bacteria and DNA-viruses in the sample. Given the way that costs of sequencing are falling this approach seems to be the future of detecting bacteria based infections.
It would be great if the same approach would also work for RNA-based viruses. For it to work it would of course be necessary that there's enough RNA of the virus in comparison to the other RNA.
How much virus RNA is there in a person who's infected by an RNA virus in comparison to the other RNA?

You didn't get an answer to your specific question, though @de_novo answered a related one. It's not possible to give an answer to How much virus RNA is there in a person who's infected by an RNA virus because it's too general; RNA viruses are wildly diverse and include viruses that are highly localized and don't enter the blood at all, as well as some that are blood-borne and can reach fairly high concentrations. So the answer to your question would be cover at least a billion-fold range if not more, which isn't helpful.

I think your question is:

Can you diagnose someone with an RNA virus by looking for that RNA in their blood?

The use of nucleic acid tests, or NATs in diagnosis has been around for a long time. The specific for profit company you mention is not the first to use them. Almost all NATs work by first amplifying the genetic material with PCR or other methods, so there does not need to be a large proportion of pathogen RNA vs total RNA in a sample in order to use a NAT.
NATs, rather than culture or antigen/antibody based tests, provide the definitive diagnosis for many viruses, RNA viruses included. As the CDC describes, NATs (among other tests) are also used to screen donated blood for RNA viruses (HCV, HIV, and West Nile).
Incidentally, the for profit company you mentioned does NOT detect all bacteria and DNA-viruses in the sample as you said. It screens for a large number of specific pathogens in their

proprietary micro-organism reference database

If there's a new bacteria in the blood of patients then if enough of the bacteria is in blood samples that are given to Karius, Karius automatically gets the DNA of those bacteria through their process. Snippets of all DNA in the blood are picked up by their process even when the software analysis might not match all the snippets to organisms.
NAT's in the sense that Wikipedia describes the term you actually have to know what organism you are looking for to choose the right primer. More importantly it's price increases linearly if you are looking for more organisms.

@Christian you still have to know what you're looking for in the Karius test. It matches the non human DNA in a sample to its "proprietary micro-organism reference database." If it's not in the database, it doesn't get identified.

@Christian moreover, you don't have to have a large proportion of a nucleic acid for this same type of test to work. Karius's methods are a change in scale from standard of care, not type. If you read the studies from their group, they are not using a novel amplification or detection technique.

There test is based on next generation DNA sequencing. That's a technology that recently got a lot of cheaper. The Wikipedia page on NAT speaks about probe-target binding and not about next generation sequencing.


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Identification of a bug, Anobium punctatum?
At first I feared that our old building was attacked by Anobium punctatum. But now, I'm not so sure.
Each week we find 2-5 of them around our apartment. What are they? and should we worry?
The bugs were found in our apartment in Denmark.
UPDATE Added Picture of Antenna

If you can get a photo with a clear view of the antennae, that would help.  At the moment, I'm thinking Dermestidae (Carpet and Larder Beetles, among others), but am not certain.  Mind, if I'm right, you DO have a problem, and WILL want them gone ...

+1 for a great and detailed photos!


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What arthropod is this?
Location: Johannesburg, South Africa
Colour: Brown/Grey
Legs: 6 or 7 pairs
Size: ~10mm
I've been finding these guys in my bath tub the past two mornings. I've caught and released them. I'd like to know what they are so that I can decide whether pest-control measures are needed.

That is an Isopod crustacean, in the suborder Oniscidea https://en.wikipedia.org/wiki/Woodlouse. These are harmless, so I would not worry about contacting pest control. They are also known as "pillbugs".

It should be mentioned that they are a good indicator of moisture problems as they only like very damp conditions, if you are continuing to see them you may want to start looking for leaks, rot, and mold. they also indicate easy access for other insects so you may want to start sealing cracks. https://pestcontrolcanada.com/sow-bugs-pill-bugs/


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Amount of animals to use for animal trials
I am working on an independent research project involving animal models. I am unsure how to deterine how many animals (rats) to use for the project. The rats will be injected with different solutions to examine the effect on a target. There is nothing in the literature about trying any of the solutions in rats. How do I determine the amount of rats to use?

I might be wrong, but I don't believe we consider general stats questions to be on-topic here even though we allow questions on technique. What you are asking about is called a "power analysis" in statistics; to do a power analysis you do need to have some prior expectation or knowledge of the estimated magnitude of the effect and variability or at least what magnitude of effect would be 'interesting' to you.

I'm voting to close this question as off-topic because it is about statistics and not biology. As Bryan said, you are interested in power analysis, the type of analysis for which you will need to estimate (eventually just a gut feeling estimate) the effect size that you're expecting.

The topic pertains to biostatistics which is a valid tag.

This paper should help https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826013/

@Remi.b this is a completely valid question for here many factors for this have little to do with statistics and a lot to do with the animals physiology.


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What causes DNA gel electrophoresis bands to swirl?
I recently ran a gel on a new system and came out with something I've never seen before.
I loaded the first three wells with a ladder in the first and an uncut plasmid in the next two. There are no bands, just swirls all over the gel.
It's a 10 cm gel, 0.7%, and I ran it at 80 v for 1.5 hours. Part of the new system is the buffer, lithium borate,  which I've never worked with before.
Any ideas as to why this is happening?

Edit: thank you for your answers. I followed the regular protocol closely and used the same bottle of buffer for both making and running the gel. I did this twice and got similar results both times.
I had the power supply tested and discovered that the voltage may have been fluctuating between 77 and 83 volts during the run. Could this have caused it?

Are you sure you used the right buffers or prepared the correct (dilution, concentration)?

I didn't prepare the plasmid, but I know the ladder is correct. Yes, lithium borate was all it called for, and I diluted it as the instructions said.

What length of DNA fragments are you expecting to see? What is the power (Watts) or current (Amperes) in your region?

It can possibly be one of two problems:

Either the gel poorly prepared, in that it was cooled for too long, resulting in parts that solidified before pouring it into the mold.
This I have seen before, the pH of the electrophoresis buffer and the buffer used to make the gel was not the same. It has to be the same throughout the gel to ensure that the DNA moves evenly to the positive electrode.

Do you perhaps have a gel image of the bio-transilluminator? It could provide more insight.
Hope this helps

Because the question says that a new lithium borate buffer was used, we should also make sure that the gel was made up in LB buffer with the same final concentration as the running buffer.

It seems that the gel was not prepared properly and does not have a homogenous  texture as it should, which then affects its pores and prevents the sample from traveling through (hence be absence of bands).

Electric potential (voltage) should apply equally across the gel. This should not cause DNA to run unevenly. In gel electrophoresis, the electric forces affect all (negatively charged) DNA molecules and the flow in the same direction.
What causes differences in their flow is the resistance to diffusion or flow of DNA molecules by the gel. Larger molecules are more likely to collide with the polymer matrix and will therefore move through the gel more slowly. If you have DNA prepared in varying sizes, they should form well-defined bands. There are several parameters that you can optimise, depending on the sizes of the bands that you want to distinguish:

concentration of the gel: a denser gel will slow DNA molecules more and is useful to prevent smaller molecules running off the end of the gel
time or voltage: smaller molecules running on a denser gel will take longer to separate so you may need to adjust the running time or voltage accordingly.

It is possible that the gel or input DNA has not been prepared correctly. A gel needs to be mixed and poured while it is still liquid (before it cools) to ensure that the polymer forms evenly. However, the absence of a positive control or DNA ladder even in the wells shows that the DNA is not present in this gel at all: It has run off either end of the gel. Therefore either:

the DNA ran through the entire gel: it was run for too long or the polymer was not a high enough concentrate. Prepare a gel with a higher concentration or run it for less time.
the DNA ran the wrong way: please check that the electrodes were connected in the correct orientation (negative by the wells and positive at the other end). These should be colour-coded (usually red and black).


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Are Restriction Enzymes obsolete with CRISPR?
Are Restriction Enzymes obsolete with CRISPR?

No.
While CRISPR allows you cut a piece of DNA anywhere, you need to order a guide RNA to target your desired cut site. All standard plasmids still carry traditional restriction sites, and it's often convenient to use these. Using CRISPR as a restriction enzyme is probably more expensive and more complicated than using traditional restriction digest. Additionally, there are limitations about PAM sites with CRISPR. And you can always PCR a plasmid using whatever primers you want to produce a blunt end product that is "cut" where ever you want, and I'd bet the DNA oligos needed for PCR are cheaper than the guide RNA you need for CRISPR.


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Do all retroviruses evolve into dna viruses?
Since even nonprocreative sex transfers genetic material it seems redundant for viruses to destroy the host. Retroviruses are sufficiently simple to fit into DNA. So why not just become DNA viruses?

Why is this question tagged proteins? Unrelated, I've been contemplating that life change myself...

First of all we need to be clear with the differences between DNA and RNA.

This is the typical picture that comes to our mind after high school biology classes when anybody mentions RNA and DNA. But this is actually not 100% accurate. Fact that in DNA is only 5-methyluracil (thymine), not uracil and in RNA is only uracil, not 5-methyluracil is not true.
Uracile
One of the example of Uracil occurring in DNA is deamination of cytosine. Basically it's a type of mutation. But the occurrence doesn't have to be just by mutation. According to this article:

The other main source of uracil in DNA is by incorporation of dUMP instead of dTMP during DNA replication. dUTP is a normally occurring intermediate in nucleotide metabolism, but the level is kept very low due to an efficient dUTPase which prevents incorporation of dUMP. Although incorporation of dUMP into DNA was demonstrated both in bacteria (Tye et al., 1977; Wist et al., 1978) and isolated mammalian nuclei 25 years ago (Wist et al., 1978), the extent and significance remains unclear.

Double helix structure
Even the claim that only DNA has double helix structure is not true. You can easily disprove it by seeing tRNA´s 3D structure.
2C ribose ring
So the only difference is on the 2C of ribose ring. In RNA there is one extra -OH group which makes it more unstable than DNA (which doesn't have an extra -OH group). Although, C-OH has more bond energy than C-H, the true reason that it is so reactive is in the electronegativity of Oxygen (2nd most electronegative element after fluorine).
Why RNA viruses use RNA?
So, why is it better to be RNA virus for the HIV?  According to this study:

Multiple factors influence evolutionary rates, including
  generation times, fidelity of copying genes, and selective
  pressures. Microbes often have very short generation times.
  Ribonucleic acid (RNA) viruses, typically lacking proofreading,
  have high error rates when they make copies. As a result,
  evolution rates in microbes tend to be rapid, and RNA viruses
  are the most rapidly evolving organisms. This is useful
  for rapid adaptation to novel selective pressures such as immune
  selection and antimicrobial drug use. To compensate,
  the most rapidly evolving genes in vertebrates are immune
  related.

Basically, it says the  RNA form can increase your evolution rate and your chance to avoid the host immune system. In the end take it logical. Viruses have special life strategy (technically viruses are not living form of matter so apologies for that). They wanted to replicate itself as much as it can. So if the virus is made from DNA the proces takes much more time (it has to be transcribed into mRNA and after that translation). So RNA virus have to only translate the RNA to make as much as it can (my claim is confirm by viruses classification on wikipedia).

You have to remember that evolution has no logic, in the sense that "if it works, it ain't stupid"! There are many creatures that, by our perspectives, we would ask the question, "why?".
What makes retroviruses so well evolutionary adapted is their high mutation rates with each replication cycle and destroying the host cells are like leaving no witnesses. High mutation rates are associated with RNA molecules, because they are   not as stable as DNA. This can make the virus difficult to identify by a host cell and initiate defense mechanisms because they are changing all the time. We see this with the HIV virus, which is why we can't seen to find a cure, we cant lock on a single version on the virus.
The take home message is that if an organism, even viruses, have evolved in a strange way, it is probably because they function uniquely and efficiently within their niche. Natural selection knows best!


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Acidity and Alkalinity of Foods
Some foods leave an acidic effect on the body such as meat and dairy, while others leave an alkaline effect, like vegetables. However, are these effects significant enough to greatly alter the blood pH that seems to be strictly monitored by the kidneys, which keep it around 7.4?

Extracellular acid base homeostasis in human physiology is maintained primarily by the bicarbonate buffer, as regulated by both the kidneys and the lungs (and to a certain extent, the intracellular phosphate buffer). Outside of illness or injury, (arterial) blood pH is kept between 7.35 and 7.45. There is an excellent review of acid base homeostasis in Pubmed central that covers these points. Be aware before diving in, though, acid base homeostasis is one of the most complicated topics in human physiology.
As discussed in the reference above, a healthy pair of kidneys can usually compensate for a dietary acid or alkaline load. In these cases, what changes is not your blood, but your urine. There, is, though, some evidence that high blood pressure, diabetes, and possibly poor bone health may be associated with a chronic dietary acid load. Though an alkaline diet is being investigated as a treatment for chronic kidney disease, it is not currently approved for the prevention or treatment of any disease in the US.


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Query regarding KEGG KGML pathway files
With respect to the the Wnt pathway in KEGG, the KGML file of this pathway has description of each interaction between a pair of genes. These interactions are designated in the form:

  entry1="46" entry2="41" type="PPrel"
  subtype name="inhibition" value="--|"/
  subtype name="phosphorylation" value="+p"/

In some entries, the reaction "subtype" entries are 2 in number while in some, it is one, as for the above-mentioned interaction. Another entry is as follows:

   entry1="47" entry2="46" type="PPrel"
      subtype name="phosphorylation"
    value="+p"/   relation

Why do some of the entries have 2 interaction types while some have one? What does this signify biologically?
There is an interaction type called "compound". What does a compound interaction signify biologically?

  <relation entry1="17" entry2="16" type="PPrel">
    <subtype name="compound" value="4"/>
    </relation>

have you looked at this description?

@DanHall yes but they have not explained why one entry can have 2 subtypes or how 2 genes are contributing to the formation of a compound...

See the manual:
PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother.
For the first and second example, the subtype(s) give more information about the interaction. They aren't necessarily mutually exclusive. For example, phosphorylation can result in activation, inhibition, something else, or unknown. For the first one, there is phosphorylation and the effect is inhibition.  For the second one, the interaction is phosphorylation but the effect is not characterized.
When compound is under subtype for a PPrel relation, the value is the entry element ID for the compound (so go look for entry element 4), and it refers to an intermediate of two interacting proteins.

Why can't the first one be " it is inhibition and the effect is phosphorylation"?

@girl101 that just happens to be the causal pathway --  phosphorylation of a protein causes inhibition (in some cases... in other cases it is activation).


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Could large plants grow out of large, solid rock in some way? What is primarily stopping them?
Roots of plants are known for being able to pierce through the firm soil and even solid stone to some extent. However, it occurred to me recently that I might be overestimating this ability as soil isn't the continuous material it seems from a large scale, but rather it is made of many small but firm granules connected by softer organic material which got me wondering just how important the granulation of soil is.
Typically, I don't see large stemmed plants growing out of solid rock despite that many granules of soil have a similar hardness to solid rock. But, could a plant that normally grows in soil grow instead in solid rock under the right circumstances? Soil is granulated, whereas solid rock is not.
I'm no expert, so I can only imagine different possible scenarios.
Could a large solid rock support a large and stemmed plant if it was porous enough? In other words, is it unimportant that the rock is very firm so long as there is enough exposed surface area to allow the chemical reactions that take place during the ion exchange at the roots and possibly break down the stone?
Or alternatively, it may not even be the porous or granule nature, but it might simply be the solution water carries. Could an large plant grow off of a large and smoother solid stone alone with roots rested near the base, but, if there was water running fast enough and warm enough to dissolve the surface of the rock and allow the ion exchange to take place in roots once the water was carried downstream to those roots?
Perhaps it's neither of those possibilities and it is solely the ability of a plant to anchor itself that matters the most in this issue. Even if a plant could pierce through the stone with its microscopic roots, since its stem also grows proportionately, if a plant can't anchor itself then it will just be blown away or washed off, so only small plants can anchor themselves to rocks.
Which of these traits is the most important factor in why plants don't typically grow out of larger solid rock, and can it be overcome to successfully grow large stemmed plants out of large solid rock?


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How do you check how many cones you have in your eye?
Following my previous question: What color does the other cone in Tetrachromacy correspond to?
People with normal color vision posses 3 cones in their eye. But there are some rare cases when people can have 4 cones (Tetrachromacy). These people, some of them will notice the shades difference in the scene through their eye. And the rest won't notice it, because simply their 4th cone is activated in the close peak value with the the L-cone. Therefore eye will not find any difference and will encode only one color even if it's coming from 2 cones stimuli.
How do you check, to know how many cones you have in your eye ? If the case is, even people who posses 4 cones can't even notice the shades difference ?

Regarding your last question: article.

One of the two confirmed cases of tetrachromacy was confirmed genetically:
From this Popular Science article:

Based on Antico's genes, Jameson has determined that Antico's fourth
  cone absorbs wavelengths that are "reddish-orangey-yellow, but what it
  appears to Concetta is uncertain at the moment," she added. Since the
  tests aren't calibrated for this wavelength, empirically demonstrating
  tetrachromacy is still really difficult.

Color vision is connected to the X chromosome and mutations in the X chromosome cause less or more color vision.  In the above case, the theory that people with 2 mutated X chromosomes could have four cones instead of three was tested.
This image from Scitable by Nature Education articles simulates regular vision on the left and tetrachromatic vision on the right:

As far as how to test to see how many cones you have, there are some online test that may or may not be very reliable.  This Metro news article has a test produced by Professor Diana Derval, author of "DesigningLuxuryBrands: The Science of Pleasing Customers’ Senses.  However, due to the limitations of computer screens it would not be reliable to test for tetrachromacy.

Thanks a lot! Very informative. And the reference, the reference also very interesting.

Well, this article says one can't check if [s]he is tetrachromat using LED displays. In the original image I could see 37 colors but I hardly have some kind of outstanding vision. This means it is not just not reliable test, but that any trichromat can finish as tetrachromat. And the article says that many of those who have 4 cone types may be trichromats.


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Metatranscriptomics Extraction
I am attempting to perform metatranscriptomics analysis of a cleanroom. The DNA input is known to be rather low (<1pg). Despite this, I want to still attempt to try it. I am thinking it might be best to perform extraction trials before hand where certain parameters are manipulated. I can then determine from these extraction trials which values for which parameters are best.
As an example, I am reading a peer-reviewed paper called "Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics" where they used the Illumina Nextera XT DNA library preparation kit on low biomass samples. Two of the parameters they manipulated were:
1) PCR cycle numbers (Values = 12, 14, 16, 18, 20)
2) ATM dilution (Values = undiluted, 1:5, 1:10, 1:20, 1:50)
I am hoping to use the same type of extraction trials to determine which combination of values from these two parameters is best for a clean room. My first question is: How can I determine which combination is best (as there are 25 combinations)? I have two ideas (but am open to others):
1) Check the amount of RNA derived
2) Check some quality metric on RNA
As I hope to do triplets of each of the 25 combinations, I will have 75 samples. I am hoping not to have to do sequencing as it is time consuming and possibly expensive in order to chose the best combination. Is there a way to chose which combination works best without having to sequence?
My second question is: Are there any other parameters in this workflow that I can also test for if I am not getting decent results in these low-biomass cleanrooms?
(As you can tell, I do not have too much direct molecular biology experience, so feel free to correct or question any of my post and/or "dumb down" your response). Thank you for sharing advice (for either question)!

Consider doing triplicates of just 4 combinations of cycle/dilution: low+low, low+high, high+ low, high+high.  Simpler.
Most important: prove you can extract DNA from a clean room.  If you extract from a real clean room and get no result from the PCR, maybe it is because you failed to collect anything or maybe nothing was there.   Idea - spray a known quantity of DNA into a room that will serve as your sham clean room.  Then do your extraction protocol.  You can test the cycle / dilution parameters with the sham clean room extraction and have those variables optimized for when you collect from a real "wild" clean room you did not dope with DNA.


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How do metal ions acting as enzyme cofactors "find" their respective enzymes?
Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells by the ribosomes and metal ions are exogenous materials, i.e. are obtained from food, how would a metalloprotein and its respective metal ion find each other in the body? Are the metal ions taken inside all body cells? Does the meeting take place in the blood?
A quick Google search retrieved nothing useful.

The metal ions are transported across cell membranes by various mecanisms like channels, pumps or extracellular receptors for carrier protein.
The loading step mostly happens in the cell. Once transported inside, some ions just diffuse into their binding site on the protein; others, like iron, need a scaffold.
Some essential enzymes are metalloproteins, for example most ATP-using enzymes need magnesium; and the respiratory chain needs iron. Thus most cells will have transporters for these metal ions.


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Book recommendation for studying biology for neuroscience
I will be starting a double degree in neuroscience and mathematics very soon, and I realised that an understanding of human biology can really help me out, and so I'm looking for an introductory level biology textbook that also covers things in great detail. I have no background in biology whatsoever.
Also, am I supposed to learn about the biology of plants for example before diving into human biology or can I just get started with human biology straightway.
By the way, I'm not looking for a biology textbook that has a mathematical approach, just the traditional approach can suffice.

Book recommendations are off topic for the biology stack exchange

Will you be an undergraduate student?

@BryanKrause yes

Presumably with those majors you will take a general biology course your first year, and subsequent courses in genetics, cell biology, and physiology most likely your second year. Each will come with an a textbook no doubt.

Yeah well, from my experience with mathematics for example, the textbooks recommended in the course outline were not really great, they were very surfaced level and focused more on application rather than theory and rigour. The textbooks I found most useful were actually recommended to me by the maths overflow community. So I'd naturally assume that it'll be the same case for neuroscience, hence the reason I posted this question, plus I'd also like to start studying these subjects early, even though i'll be introduced to the fundamentals once I commence my degree. @BryanKrause

It is not clear to me whether you are looking for a general biology (as you've indicated in your question body) or neuroscience (as you've indicated in your previous comment) textbook. The two most popular neuroscience textbooks are arguably Kandel's "Principles of Neural Science" and Squire's "Fundamental Neuroscience". Both devote a few introductory chapters discussing topics that could be described as general biology.

I agree with @vkehayas, you could add Purves to the list as well. I just don't think there is going to be a good answer for what you are looking for though: a introductory textbook that covers things in great detail is kind of an oxymoron, and it's going to be entirely a matter of opinion to resolve the conflict between the two. There is far more to understand in biology than there is in the foundations of mathematics.

Ok, Fine. I'll join. Kandel is excellent. I took his class back in the day. If you had one nueroscience textbook, I would definitely recommend that over Purves. Sorry @BryanKrause . You'll want Albert's MBoC as well.

I never said Purves > Kandel just adding it to the list :) @DanHall I haven't personally used Kandel ever but have certainly heard good things.


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NADP and NADPH in in vitro metabolisme test
I did an in vitro metabolism test using chicken liver S9 as the source of the enzyme. I did two different of method experiment. one was using NADP and second was using NADPH as the co-factor. my compound was fipronil, and I expect it to be metabolised become Fipronil sulfone (through oxidation reaction). The results, when I use NADP, fipronil sulfone formed was very low concentration, but in contrast, when using NADPH, I got high amount of fipronil sulfone.
what is the different using NADP and NADPH in this experiment?
Thank you for sharing the informatio.
Kind regards
Alex

Your question is unclear. What do you mean by an "in vitro metabolism test"? What is chicken liver S9? What enzyme are you assaying? What is your assay? Fipronil is hardly a compound that the average user of this site will have heard of — I had to Google for it. If you want us to help you, you should write down the equation of this reaction, showing what you expect to happen. At the moment you seem to be telling us that you are assaying an oxidation reaction but you only get results with a reducing cofactor. You are obviously doing something wrong. We need more information to help you.

Are you sure your question is accurate?
NADP in solution does not exist... it can either be NADPH which is the reduced form (has gained an electron in the form of a H atom and now has the potential to give that electron to another molecule in the solution) or NADP+ which is the oxidised form (has lost an electron in the form of H atom and now has the potential to gain an electron from the solution).
In your experiment, Fiprinol to Fiprinol Sulfone is an oxidation reaction, so the enzyme catalyses the removal of an electron from Fipronol, and it does that with the help of NADP+, which is missing an electron itself and therefore takes it from Fiprinol (oxidises it) to give a high Fiprinol Sulfone yield.

This is really a comment rather than an answer. You are explaining what the reaction is but not why his assay isn't working, which was his (unanswerable) question.


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How do biologists estimate that there is 8% of protein coding genes in human genome?
In class, the professor said that there is about 8% of protein-coding genes in human. I wonder how biologists estimate this without annotating all of human genes. Thank you!

What do you mean by "without annotating"?  Without a minimal annotation of the transcriptional and translational features this is obviously not possible. After they got the sequence they had to read it. What is your question exactly?

S/he's off by about 6 - 7%.
As per the national human genome research institute approximately 1% of the human genome encodes proteins. We can tell this by looking at the sequence (which we're now able to do quite quickly) and identifying those portions of the sequence can be translated to protein using the genetic code.

Scientists have been able to identify approximately 21,000 protein-coding genes, in large part by using the long-ago established genetic code. But these protein-coding regions make up only approximately 1 percent of the human genome...

You are taking some wrong assumptions. There are plenty of regions that contain open reading frames in the human genome and a high fraction of them are translated into "proteins". This was recently seen in ribosome profiling experiments. That does not mean that these translated ORF are proteins in the sense that they perform a function. Most of them are noise as they are transcribed and translated in small quantities.
Additional evidence to consider a translated region as a true protein is usually conservation. However very recent proteins will not appear even in closely related species.

@biojl This is a statement by the NHGRI, the institute at the NIH that oversees genomics research. It represents consensus in the field. There is, of course, more to that goes into it, but you find out how much of the genome codes proteins "in large part by using the long-ago established genetic code". We use conservation of these ORFs as well, but recent work suggests we should be a little more liberal with what we consider a functional protein.

The consensus in the field of genomics (where I belong) has changed quite a lot since 2012... Those statements were true back then but the beauty of science is that it changes when new data or new ways of looking at it appear.

@biojl personally, my time in the lab is remote, but I like to think I'm still on top of things, and current research is relevant to me. Do we really not think that 1-2% of genome encodes proteins anymore? Do we not start that estimation by looking for ORFs?

It is important to remember that protein-coding genes have a start and an end, exons and introns, and identifiable promotors. Knowing that these factors exist and how to identify them (usually by their unique DNA sequences, the frequency they occur and their sequence lengths) we can identify these sequences as part of whole genome analyses.
Next-generation sequencing made it possible to sequence the entire genome of a human in a matter of days, if not hours. This massive database makes it possible to identify it's variable elements. Now, knowing where a promotor is, the following start codon of a gene can be found along with its stop codon. This leads to identifying open reading frames (ORFs).
Now it is simple, in that simply counting all the ORFs in relation to the other structural and "nonsense" DNA and the percentage of protein coding sequences can be determined. Remember that this is the norm, however there is still much we do not know about the human genome. There may be more protein-coding genes with unknown promotors that we do not know of. So always keep on asking!


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Do all bacterial cells have a double membrane?
I’m reading that gram positive and negative bacteria have an inner plasma membrane surrounding the cytoplasm, then a periplasmic space, then an outer membrane.
How does this compare to my general knowledge of bacterial cells having one plasma membrane surrounded by a cell wall?!

Some bacteria, e.g., Mycoplasma spp., lack a cell wall.

Do all bacterial cells have a double membrane?

No. There are a number of bacterial membrane and cell wall structures. Some of them have a double membrane, some of them don't.
In microbiology, we often make the initial distinction between two groups of bacteria based on whether or not they take up an iodine based stain called a Gram stain. Gram negative bacteria have an inner membrane, a rigid cell wall, and an outer membrane around the cell wall, so they don't take up that stain. Gram positive bacteria have an inner membrane and a rigid cell wall, without the outer lipid membrane, so they do take up that stain.  There are other bacteria that don't stain well with either the Gram stain or its red counter stain (typically safranin), but most medically important species of bacteria fall into one of these two categories (gram positive: blue, no outer lipid envelope, or gram negative: red, has an outer lipid envelope).

You can read about gram-negative and gram-positive bacteria on Wikipedia, but it's surprisingly technical. This biologywise post might be a more approachable introduction.

How does this compare to my general knowledge of bacterial cells having one plasma membrane surrounded by a cell wall?

When the concept of prokaryotes and eukaryotes is introduced, you're taught about key distinguishing features between the two. One of the key distinguishing features of (most) prokaryotes is a rigid cell wall. This is present in both gram negative and gram positive bacteria. They just didn't tell you about the outer lipid envelope in gram negative bacteria. At that point in your education, the idea is to introduce you to the concept of prokaryotes vs. eukaryotes, not to catalogue or understand all the different kinds of prokaryotes.
The more you learn, the more you'll see that life is quite varied. Many eukaryotic cells are coated in a layer of complex sugars and proteins that is in some ways similar to the cell wall of prokaryotes. It just doesn't provide rigidity against an osmotic challenge like prokaryotic cell walls. On the prokaryotic side, mycoplasma don't have rigid cell walls.


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If a venomous snake somehow gets it's own venom in its body, will it be affected by it?
Here is a hypothetical situation I had been thinking about that sparked my curiosity:
Let's a snake is just slithering around, not being attentive for some odd reason. It happens to pass a mouse, in which it didn't see (this is all just hypothetical), and the mouse freaks out and starts to run. When it does, it trips over the snake's tail, and, not knowing what is happening, the snake snaps back bites the mouse and gives it a good dose of venom. (Now, to my question).If the snake ate the mouse, would it's own venom, now in the mouse, hurt the snake?
(Since they are native to where I live, let's say the snake is a Water Moccasin)

An excellent question.  This fun mental floss article addresses that question, but from the perspective of one snake biting another snake:
Snake on snake violence

“The conventional wisdom is that they have circulating antibodies in their blood,” says Stephen Mackessy, Ph.D., a Professor of Biological Sciences at the University of Northern Colorado and an expert in venomous snakes. “This would protect them from their own venom, as well of venom from another snake in their own species.”
Hypothetically, if a speckled rattlesnake bit another speckled rattlesnake, the immunity they’ve built from being exposed to low levels of their own venom—kept in glands behind their eyes and secreted when they bite—would protect them from a fatal wound. (Even though the glands are closed, they still contain blood vessels that allow the venom to circulate in their system, causing mild exposure, Mackessy says.) But a speckled rattlesnake that meets up with a cobra might have a different day entirely.

The same principle should apply to venom ingested in dead prey. Antibodies against the venom would protect the snake. For what it's worth, I think your way of phrasing the question is more interesting and relevant than the way it was phrased in the mental floss article.

Thanks! (If no one else answers, I will probably check mark this one)

@TheMattbat999 I think it's safe to say no one else is answering this one. If there is anything this doesn't address for you, let me know.

@DeNova I am so sorry. I totally forgot! I will accept it!


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What kind of beetle is this (found on landing windowsill)?
 found this beetle on my landing windowsill, would like to know what it is, very small, this was a zoomed picture on my phone.

Please provide your location. Also, please add an aproximate size if possible

Thanks, in the UK and 3mm.  Found another one yesterday, same windowsill, I've uploaded a couple more pictures.

After researching I think it's a furniture beetle or biscuit beetle?

@Angel if by "furniture or biscuit beetle" you mean a species of Anobiidae you're probably right; the third photo down shows (admittedly somewhat blurrily) that the last three antennal segments are longer than the others, which is characteristic of that family.  Which species IN that family I can't help you with; I don't know the British fauna.


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Golden Brown Flying beetle identification
Bug (probably a beetle) flew into my house tonight with golden body and black stripes. I live in pacific asia.

.

Pacific Asia could be a bit vague as a location. As well if you can specify the season (you just saw it now or few month ago) and what kind of habitat your living (urban area, jungle, desert and so on).


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What does it mean for a type of plant to "vegatatively dominate" as opposed to "taxonomically dominate"?
I'm reading Plants and the K-T Boundary, by Douglas Nichols and Kirk Johnson. On page forty-seven the authors write the following: "By the Campanian many floras were vegetatively co-dominated by angiosperms, conifers, and ferns, but taxonomically dominated by angiosperms."
My first intuition was that this means angiosperms, conifers, and ferns were equally dominating the available resources in many ecosystems, but that at the same time the angiosperms had become more evolutionary diverse. But I'm very new to reading about paleobotany, and biology in general, so I thought I'd better check that. Thanks for your time.
What is the difference between vegetative and taxonomic domination in the above example?


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Can multiple antibodies bind the same antigen?
Given the size difference between small molecule antigens and antibodies is it ever possible for multiple antibodies to bind to the same antigen if they recognize different domains on that antigen? When the antigen is a protein rather than a small molecule is it more likely that multiple antibodies can bind?

Does this answer your question? Can more than one antibody bind the same antigen

Not only is it possible for multiple antibodies to bind a single antigen, when that happens, it's more likely to trigger a full immune response.
Here's a description of the concept from a company that sells antibodies for research. To help understand the quote, you'll need to know that the portion of an antigen that an antibody binds is called an epitope.

Because an antigen can have multiple different epitopes, a number of antibodies can bind to the protein. When two or more antigen binding sites are identical, an antibody can form a stronger bond with the antigen than if only one of the antibody’s sites is bound. Antigens with multiple identical binding sites are called multivalent, and antibodies are able to bind it more strongly.

Here is an article that describes, among other things, the importance of clustering in B-cells when multiple B-cell receptors bind to a single multivalent antigen.

Thanks! Does that only work for large antibodies though? I'm worried that the relative size of a small molecule compared to the antibody means that even with multiple epitopes only one antibody will be able to bind it. I reached out to novus and they were unable to give an answer

@ike that's going to depend on the antigen. Is this for something you're working on in a lab?

Yes--We're looking to work with aflatoxin, a small molecule produced by Aspergillus flavus that has multiple antibodies which recognize it.

Oh yes, that's an intercalating agent. I wouldn't be surprised if you got more than one antibody binding to one molecule of aflatoxin, but you'd have to test it. Are you trying to measure a quantitative signal?

it's more of a binary on/off as to whether both bind or not.


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Is the heart more relaxed when stretched or contracted, and how does it affect cross-bridge interactions?
In the heart, are stretched muscles during the diastole more relaxed or are the contracted muscles more relaxed? Depending on the answer, are there then more cross-bridge interactions in cardiac muscle cells when the heart is stretched or contracted?

Can you clarify your question? What do you mean by "more relaxed". There are a few things to consider here: the contracted or relaxed state of cardiac muscle, as well as the baseline stretch in that muscle. But your use of "relaxed" in your question isn't standard.

Well that is the question itself. When the heart is contracted, is that when it is more relaxed? Or, is it more relaxed when it is expanded? Which state is the resting state of a heart?

Relaxed is the opposite of contracted, so when it is contracted it is exactly not relaxed, by definition. Are you referring to the pathological state of stretching that occurs in some forms of heart failure, e.g., dilated cardiomyopathy?

It's completely possible I have terminology mixed up, I'm not biology expert and different sources gave conflicting descriptions. I'm not referring to any kind of disease, what I want to know is which state, expanded or "smaller", is the heart's resting state when it is not exerting energy to pump blood, and thus, which other state must then be the one that takes more energy to allow more cross-bridge interactions to maintain. Is the heart more relaxed when it is expanded? Or when it is...I guess I can only say "smaller" since contracted could be for either direction.

Contracted literally means to shrink in size: "contracted" cannot mean "either direction"

@BryanKrause I used to think that too before Dan commented. But, for instance, when muscles in your biceps contract, part of them becomes shorter, but then another part of them bulges up and becomes larger. So muscle "contracting" could cause surround tissue to expand.

Nothing in Dan's comment suggests that contracted could mean anything but shrunken in size.

@BryanKrause They said relaxed is the opposite of contracted, but there is nothing in biology that says a larger or smaller structure has to be either in general. Just hold out your fingers, they are moderately suspended from your hand, not completely dropping to a 90 degree angle, but not completely risen up either. When the muscles in your fingers contract, your finger can either rise, Or Also curl. Either way, a muscle "contraction" occurs.

I should correct to say length instead of size: length is the important dimension of size in the context of muscle action. When your fingers extend that is not because the muscles that bend your fingers are lengthening in some way, it's because another muscle pulls the back of your finger taut.

@BryanKrause You mean the length of the sacromere. Yes, I imagine that always decreases during muscle contraction which is what allows the ratcheting to occur in the first place based on what I had found.

@BryanKrause But your finger description is exactly my point. Even though muscles always contract to exert force, they can affect surrounding tissue in different ways. So, I can't simply say that the heart shrinks just because I read cardiac muscles contract since as you pointed out, contraction can lead to different kinds of movement, more information is needed.

I mean the length of the whole muscle. More information is not needed to answer your question "Is the heart more relaxed when stretched or contracted": you are asking "Is the heart longer when it is longer or shorter?"

@BryanKrause We just agreed that just because one muscle contracts, it doesn't mean all the surrounding tissue shrinks. In the finger example, some of the tissue shrinks, but also the opposite part of it expands. So, simply stating cardiac muscles contract isn't enough to be 100% sure that that is what causes the heart to shrink in size, especially when we're dealing with all kinds of different contractions in different 3D directions.

The muscular portion of the heart is comprised of cardiac myocytes, elongated cells filled with bundles of actin and myosin called sarcomeres. These cells are similar in many respects to skeletal muscles, but are shorter, have only one nucleus, and slightly different isoforms (versions) of the proteins involved. The purpose of this cell, like the skeletal muscle cell, is contraction, or shortening on activation.
This image of cardiac muscle cells shows how full they are with long bands of proteins (proteins stain pink).

Because the heart is a muscular chamber, instead of simply a band of muscle (like the bicep), the relevant dimension for the organ is volume instead of length. Where your bicep gets shorter when it contracts (and pulls your forearm toward your upper arm, bending at the elbow joint), when your heart muscle contracts, it twists and squeezes against the fibrous part of the organ, decreasing the volume of the chamber.
Since there is no air in a healthy live heart, when the heart contracts, reducing the volume of the container, the blood is forced out of the heart (ejection) through whatever opening is available. This is called systole. When the heart relaxes, the volume of the container increases, and blood enters the container through whatever opening is available. this is called diastole.

Now, how is this related to cross-bridge interactions?
The mechanism for contraction itself, in both skeletal and cardiac muscle, is cross-bridge cycling. Those pink bundles of actin, myosin, and associated proteins in the picture above form bonds, change conformation, break bonds, change conformation, and form new bonds:

This cross-bridge cycling occurs during contraction when $Ca^{++}$ enters the cell as part of the cardiac action potential. Relaxation occurs when $Ca^{++}$ concentrations decrease, through the action of the $Ca^{++}$-ATPase, causing cross bridge interactions to decrease.

Okay, so just to make it clear before I select it as the answer, when the heart is expanded, that is it's natural resting state, and when the cardiac muscles exert force through contraction, it is only to shrink the size of the heart? I just want to make sure on whether it is the expanding or the shrinking that requires the cardiac muscle to contract, and so far it seems like it's the shrinking action.

You are correct. Contraction causes the volume inside the heart to decrease (the volume inside the chamber shrinks).

You're putting a lot of work into the question and I appreciate that, but I don't want you to over-invest when I am focused so much on a singular question. I can infer the cross-bridge interactions depending on what the answer is and I am familiar with the theory behind it.


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What did the evolution of multicellular animals look like?
What did the evolution of multicellular animals look like?
Aspects of this question include:
(1) Are there any living organisms that might be helpful in visualizing "transitional forms" between unicellular organisms and multicellular animals? E.g. I have heard of slime molds as one example. Would love to hear of as many good examples as you can come up with. Not looking for strict hereditary relationships here, and I am fine with plausible but unproven theories. E.g., mudskippers might help a person visualize the evolution of amphibians, even if they aren't in fact closely related to amphibian ancestors.
(2) Do we think that the first animals evolved into sponges, or cnidarians/ctenophoroans, or something else? Did sponges and cnidarians/ctenophoroans evolve multicellularity separately? As this is probably a big topic, feel free to just post a link or two.
(3) For any examples that you can think of for #1, would love to hear of any good citations of articles or books for me to read, but keep in mind that I am not a scientist and not looking for anything extremely technical.

Welcome to Biology.SE. I am afraid your question is way too broad to be answered here. A SE post must always be restricted to a single, clearly defined question that can ideally be answered without having to write a whole book!

http://www.bbc.com/earth/story/20150112-did-snowball-earth-make-animals

Evolutionary biologists have frequently cited volvocine green algae, which include both unicellular and multicellular members, as a useful model system (your point #1), e.g. see this article

Thanks, that article looks like what I needed, and contains a few details I hadn't thought about -- e.g., the development of more than one cell type within an organism that has unicellular living relatives.

The life cycle of myxobacteria (e.g., Myxococcus coralloides, Myxococcus disciformis, Myxococcus flavescens, Myxococcus fulvus, Myxococcus macrosporus, Myxococcus stipitatus, Myxococcus virescens, Myxococcus xanthus---for references to the original articles describing these species, see Bacteria I. Taxonomy: Genera and Species) includes the formation of fruiting bodies, which is an obligate multicellular process requiring cooperativity between individual bacterial cells (see, e.g., Cao et al., 2015).

Thank you! I had heard of fruiting bodies among slime molds, but had never heard of such a thing amongst bacteria.

What did the evolution of multicellular animals look like?

There is no agreed scenario of evolution of animals. Molecular evidence is ambiguous, early fossils are puzzling in form, and even more in relations.
Molecular phylogenies agree that closest unicellular relatives of animals are choanoflagellates. Most (nearly all) researchers interpret it that our distant ancestor was choanoflagellate-like organism. However there are people that think that choanoflagellates are sponges that "returned" to unicellular life.

Do we think that the first animals evolved into sponges, or cnidarians/ctenophoroans, or something else?

Molecular phylogenies of animals are not clear. I write below few examples of most basal taxa from different articles, all based on molecular evidence. Most basal is on the left.

ctenophora, porifera, placozoa, cnidaria, bilateria ref
ctenophora, demospongia, placozoa, homoscleromorpha, cnidaria, bilateria ref
porifera, ctenophora, placozoa, cnidaria, bilateria ref and ref
porifera, placozoa, ctenophora, cnidaria, bilateria ref
porifera*, placozoa, ctenophora, cnidaria, bilateria ref

Porifera are sponges, I marked with porifera* paraphyletic reconstruction, and with porifera monophyletic. Groups homoscleromorpha, and demospongia are subgroups of sponges. As we see the most basal are either sponges or ctenophora (comb jellies), after them usually placozoa are second. Cnidaria with bilateria are least basal.
Most animals except most sponges and placozoa have basement membrane. It is a non cellular collagen matrix under virtually all epithelial tissues (tissue organized as 2d sheet of cells). In sponges only one group, called homoscleromorpha in larval stage was reported to have this membrane. This would suggest that all other animals derive from that group. However other source contradicts that finding: https://www.elsevier.com/books/book-series/advances-in-marine-biology vol 61.
Fossil evidence of most basal animal is even more problematic. There are plenty of early sponge fossils, some of them going even before Marinoan glaciation (about 90My before Cambrian), check this one, however none of the Precambrian fossils are uncontested. This is especially significant as sponge fossils with their robust spicula, and macroscopic sizes, are usually quite well-preserved fossils. Moreover, there are great richness of soft-bodied animals preserved from Ediacaran, but sponges are missing. This suggests that sponges before Cambrian would have to be very small, and without spicula, what is possible, however not very likely.
If precambrian sponges are rejected then sponge-like animals could not be basal animals. Scenario consistent with sponges being most basal is that they either evolved multicellularity independently in Cambrian, or that they evolved in Cambrian from animals of different form that separated from our lineage in Precambrian.
If we reject sponges, then most basal living animals are either placozoa or ctenophora. Placozoa taxon contains just one genus Trichoplax with few species of a very weird animal. Ctenophora (comb-jellies) is a small group with about 100 species of slowly moving marine predators.
Earliest unquestionably animal fossils are from Avalon assemblage from Ediacaran period (about 30My before Cambrian). Figure 1 from here is quite telling. Those earliest fossils seem to be sessile  growing on surface of bacterial mat, bound to the ground with gelatin-like substance produced by bacteria. They were likely filter-feeders, possibly with symbiotic algae, just like modern sponges. However their form is very different from sponges; in shape they are more similar to plants or fractals. You can read about those sessile forms here, and here. Later mobile animals evolved, most iconic of them Dickinsonia. Here is an album of many of Ediacaran forms, that could be a good starting point. First mobile animals like Dickinsonia, or Yorgia were probably feeding on biomats. They didn't have mouth, probably digesting bacteria externally under bottom of their body. Only extant animal that feeds that way is placozoan Trichoplax. There is possibility that they are related.
There are plenty of sources to learn about Ediacaran biota, a lot is known about them. However question which one of them, if any, was the most basal animal was not answered till now. In other words you can read a lot about those fossils, but still you will not learn how the first animal looked.

For any examples that you can think of for living organisms that might be helpful in visualizing "transitional forms"

Though probably not the most basal animal, it will be helpful for you to read about Trichoplax. I suggest this, especially figure 7 is nice ilustration.

Choanoflagelates are single-celled eukaryotes that are almost identical to the flagellated cell type in sponges, and are thought to be the sister taxon of Metazoa (Multicellular animals) http://www.ucmp.berkeley.edu/protista/choanos.html

Thank you! I had heard that choanoflagellates were likely related to sponge ancestors, and it intrigues me that free-living unicellular organisms might go from using their flagella to swim around, to using their flagella to draw a current of nutrient-rich water through the body of a sponge. Truth be told, I am a fiction writer and was hoping for more details of this sort to inspire me to write a story about the evolution of multicellular animals, even if the story is not documentably accurate in all its details. I was hoping for more examples, but thanks, this is a good one.

One thing you could think about it how evolutionarily difficult (and thus rare) multicellularity is, because evolution favors selfishness. For a colony of individual cells, each independently reproducing, to become a multicellular organism, then some of those cells must give up their own reproduction to support others. This is "against the rules".Choanoflagellates do congregate, but remain reproductively independent.


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What is the mechanism by which quitting smoking causes increased appetite?
I guess it has something to do with  sugar regulation.
Does anyone know something more about this?

please feel free to add relieble source of information for your claim or i think your post is going to be close because now its too opinion based,

@L.Diago Every internet site which mentions symptoms when someone quits smoking (nervousness per example) mentions also increased appetite

http://www.eje-online.org/content/170/2/219.short

But still i would be rather skeptical about this than making some generalization about this phenomenon.

@LDiago weight gain is a clear and consistent finding with smoking cessation. Where are you reading that it causes appetite suppression?

What is the mechanism by which quitting smoking causes increased appetite?

Research has generally focused on weight gain, rather than increased appetite, since it's a more objective outcome.
Smoking cessation has been clearly and consistently shown to be associated with weight gain, in both retrospective and prospective studies, and nicotine replacement seems to reduce some, but not all of the effect, at least while it's used.
There is an excellent, though now aging review of both the effect and potential mechanisms behind a paywall by Filozof. One of the most cited early articles is free at NEJM.
The mechanism of this weight gain is an active area of research, and, as discussed in Filozof, includes increased appetite with associated increase in calorie intake, decreased resting metabolic rate, and decreased physical activity.
Leptin, a hormone that increases both satiety and energy expenditure, is actually increased in people who stop smoking at the same time they are gaining weight. This finding has been convincingly demonstrated and replicated. Leptin insensitivity is a strong candidate for the primary driver of the increase in appetite (and weight gain) after smoking cessation.
Of course, since cigarette smoking causes profound changes in gene regulation, smoking cessation likely does as well. The full answer is almost certainly multifactorial.


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BMI limits in interpretation in people with high/low heights
In a study, I measure BMI of a large sample of adult people.
Among them, there is some who have very low and very high height.
As I can read on the internet (like here or even in the wiki, for instance), BMI is not relevant for very short or very tall people.
Some math professor even wrote an article with a "better" calculation of BMI, but with a very low impact in science world (didn't find it on pubmed) so it's not really peer-reviewed.
Let's take some examples, assuming "normal BMI" is 21:

for a 110cm tall adult, ideal weight is 25kg
for a 130cm tall adult, ideal weight is 36kg

These weights appear really low to me. Note that dwarfism cutoff is 145cm in France.
My question is then the following: How could I choose a cutoff on height to exclude BMI values ?
NB: I didn't find anything on pubmed nor on google scholar, but maybe I missed an important article

I don't really know much about this subject, but I doubt there is a precise cutoff. Isn't it simply a continuous thing? Gradually, the more you move away from mean height (in either direction), the less value the BMI measurement has. One thing you could do is a weighted analysis, with more average height people having heigher weight.

I don't think this has been studied this precisely but I agree, it should be continuous. Still, I guess it is not linear (x3 maybe?), so there should be a value or a range of value where it become reasonable to think BMI is not relevant anymore.

The best procedure is going to depend on what exactly you're going to do with your data. Regardless, you should NOT exclude the BMI values. Just include the height, weight, and BMI. If you're simply reporting BMI as a characteristic of your study population, you can annotate that figure and let your reviewers and readers decide what to make of it. This follows the principles in Chapter 4 of Hulley's Designing Clinical Research. You want to get and maintain all the data.
If you're going run some further analysis on BMI, or if BMI is an outcome in your study, then you can evaluate the impact of a cutoff on your results, but you have to decide ahead of time how you'll do your primary analysis. I recommend using the entire data set (no height cutoff) for your primary analysis (because *there is no established practice for a BMI height cutoff in the general medical literature), and then running a secondary analysis that excludes those research subjects above some threshold (you can pick it, but depending on the size of your sample, 2 standard deviations could be reasonable). That secondary analysis would be a hypothesis generating analysis. If excluding very short and very tall people changed the results of your analysis, that's something to mention in your discussion and something to consider for the next study.
*If you're in a specialized field, then follow the practice of that field for your primary analysis.

Very interesting answer. Keeping height along with BMI is a very good idea. Still, I don't understand why excluding people is such a bad idea. My outcome is overweight and I don't have any other measurement than BMI to assess it, but I know BMI is a bad overweight assesser for very short people. Thus, by keeping short people in my analysis, I think I'd induce bias (I would not really measure my outcome for this very population), wouldn't I ?

If you're not going to apply your results to people below a certain height, then you have an excellent argument for excluding those people from your study. I was under the impression you already had the data and it included people who were very short (who, presumably, had other measurements taken that were used in other parts of the analysis).


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Turbulence in blood
Turbulence in blood flow is known to indicate diseased or obstructed arteries. Techniques to measure turbulence in blood flow are mostly based on turbulence kinetic energy measurments using MRI [e.g., Ha H et al., PLOS ONE 11(3), (2016) (1)].
Are there any other well known techniques to measure turbulent blood flow, besides those based on MRI?
(1) https://doi.org/10.1371/journal.pone.0151540

Whatever constricts an orifice, whatever dilates a cavity, whatever establishes an orifice or cavity where none shall be, will disturb the even flow of blood and produce vibrations and a murmur.
—Samuel Jones Gee (1839–1911)

Turbulent blood flow is classically detected by auscultation (listening). Turbulent flow across the valves of the heart causes murmurs. A certain amount of external pressure applied to a brachial artery allows turbulent flow, which you can hear, which is how you measure blood pressure. Carotid bruit's are a sound produced by turbulence in the carotid artery.  You can reference any physical examination textbook, e.g., Bate's for information on this method of detecting turbulent flow. There's an NCBI books Clinical Methods textbook that you can search for turbulence.
Turbulence can also be detected by one of a variety of ultrasound methods. The specific measurements taken using these methods are typically anatomic measurements (e.g., thickness of a tissue, distance across a valve), peak flow, overall direction of flow, and gradient measurements, since those are the markers that have been used to characterize disease and/or outcomes. However they can detect turbulence. Quantitative measurements of turbulence just aren't used experimentally.


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What flying insect is this? Resembles Wasp / Crane Fly / Moth?
What insect is this?
Found this in southern Bangalore, India. Looked dangerous, flew really slowly with its body upright and legs spread out and landed on a wall.
Size: about 1.5 inches tall, 1.5 inches wide, when spread.
These photos are zoomed in and rather dull colored, but the actual color was a bright orange, like #FF9050 and dark black.

The long legs suggest one of the crane fly families (Tipulidae, Cylindrotomidae, Pediciidae, Limoniidae, Tanyderidae most likely; Ptychopteridae and Trichoceridae less so); the pointed abdomen tells me your subject was female.  The patterned wings might make identification a little easeir--if India has a version of bugguide.net, that would be your next stop.

@ArthurJFrost: Thanks, you pointed me the right way. I dug it up. See my posted answer! Cheers!

Pselliophora laeta, a species of crane fly (Tipulidae) in the Ctenophorinae subfamily.
Route to discovery: Reverse image searching my own photo on Google led me to a matching image on Naturalista (Familia Tipulidae), and in-turn to iNaturalist, which showed me to Genus Dictenidia. Further Googling for "Genus Dictenidia" brought up many families of crane-fly, which I visually scanned until I spotted it -- Pselliophora! That led to Wikipedia, and to this image, which mentions its source to be whatsthatbug, where the discussion cites Pselliophora laeta on India Nature Watch.
--

Source: https://www.inaturalist.org/observations/299363
Observed: Thiruvananthapuram, India; Jul 28, 2012 5:13 PM IST
Mating Crane Flies from India

Source: https://www.whatsthatbug.com/2010/09/30/mating-crane-flies-from-india/
Observed: Mumbai, India; Sep 30, 2010 1:43 AM IST


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Are all mammals capable of sneezing?
I only know dogs and humans sneeze... so do other mammals sneeze as well? Is it possibly an evolutionarily-determined immunological trigger?

Are you really asking about all animals (including  jellyfish for example)  or rather about mammals, as your examples imply?

Dogs and cats sneeze. My dog sneezes of excitement every morning when we're going out. A sponge - having no nose - obviously does not sneeze.

@Marzipanherz Yes, I’m asking about all animals. I know about humans and dogs (examples of mammals) hence why I asked if “other animals sneeze as well”.

@P.SN Note that to a biologist, "animals" is quite a broad taxonomic grouping, and as Marzipanherz and Remi.b point out includes plenty of organisms that have no lungs or nose or respiratory system at all.

@Marzipanherz give the OP a break. Sponges sneeze. It's a reasonable question. This is why I like beginner questions. They aren't closed off to ideas that seem implausible to experts.

@DanHall Unclear questions are unclear. They are not open-minded because they are unclear. It is at the core of the SE format to require the question to be clearly defined by the OP. We don't want a discussion in a post, we want a clear question and a clear answer.

@Remi.b The question wasn't unclear. It was very clear. Are all animals capable of sneezing? That's a clear, interesting, answerable question. No, not all animals sneeze. Yes, some animals you might think of as not being able to sneeze can.

@Remi.b  A dog and a human both happen to be mammals, but they are also both animals. The reason the original question was interpreted as unclear was that the "savy" readers didn't think non-mammals could sneeze.

@DanHall I never doubted the question was reasonable- On the contrary, I find it very interesting. I just wanted to make sure that there is no misunderstanding due to the potential different use of the term animal by a beginner and an expert. I used to believe that this what comments are meant for.

Just curious.  Why/how did the title of the question change?  I thought the OP said all animals in the comments above.  Did the OP change their mind?

@wanderweeer Yes OP improved the post based on the comments and modified "animal" to "mammal".

@DanHall To double on what marzipanherz said, I never meant that the question was fundamentally crap. I meant that some elements of this question were unclear. OP still has not fully addressed them IMO but I removed my vote close when OP edited its post. Anyway... Let's not fight any further on it.

This national geographic post discusses many mammals that sneeze. It doesn't come right out and say all, but suggests most mammals have a cough and sneeze reflex:

Mammal coughs and sneezes come from throat and nasal passages, respectively, says Bill Milsom, a comparative physiologist at the University of British Columbia.
Mammals, he says, are the only animals that process food in the mouth by chewing. In other types of animals, like reptiles, "food is swallowed whole or by chewing, and breathing is suspended during the event."

The same expert discusses non-mammals that sneeze, marine iguanas and fish.
You don't even need nerves or muscles to sneeze, per this Cell Press article

Sponges 'sneeze' without the benefit of nerves or muscles


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replenishment of wild salmon
I understand fish from salmon farms are inferior, so I am wondering if it would be better to 'seed' the original waterways with wild caught roe/milt?  I am sure it is complicated, but so is salmon farming!

What do you mean by "inferior"? Also, once the claim is clarified, can back it up with a reference (and make phrase it as a hypothetical scenario)?

The process you propose is called 'stocking', and has been carried out for many different fish species for many years. The practice is, as you suggest, complicated, and more than a little contentious.
In the specific case of Atlantic salmon, Young et al. (2014) provide a non-technical overview of the conservation, population-genetic, and infectious-disease factors at play in stocking decisions. In general, fish raised in hatcheries are often wild-caught, which decreases the wild population, and once they are released, they sometimes have lower survival rates and reproductive success than truly-wild fish. If fish are raised in captivity for multiple generations, they can show evolutionary adaptations for captivity, and once released, captive-adapted fish can introduce harmful genes to the wild population. Similarly, captive-reared fish may be at an increased risk of communicable disease, and may introduce diseases to wild fish after their release.
A further complication from stocking is the impact of the stocked species on the local ecosystem. Many commonly-stocked species are non-native in the areas where they are released, and have negative impacts on the native species in that area. For example, brown trout have been introduced to many waterways in New Zealand, and they are predators of many native species, and compete for food with others. The New Zealand government has trialled an eradication of brown trout from some high-value conservation waterways in order to minimise the ecological damage caused by trout.


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Oxygen in the earth’s atmosphere
If CO2 only makes up about 0.04% of the earth’s atmosphere how do trees and organisms in the ocean produce oxygen to 10% of the earth’s atmosphere?

Short answer: They had a very long head start

Some places the atmospheric Oxygen is nearly 20 %.

A very long head start
To elaborate on Drake Johnson’s comment, CO2 used to be much higher in concentration. During the Great Oxygenation event, when cyanobacteria (ancestors) began photosynthesizing, they converted much of the CO2 into O2, driving CO2 concentrations down as they drove O2 up.

When was this and what temperature was the atmosphere in then? Good sources?


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Background selection and hitchhiking effect
As I read the maintenance or removal of an allele from a population is dependent upon the alleles in its linkage group; so, when an advantageous mutation occurs in the population, variation in nearby alleles that linked to that mutated allele is reduced to fix (maintain) the mutated allele in the population (hitchhiking effect). This is true for deleterious mutations and background selection. But, I cannot understand how background selection can remove the deleterious mutation from the population? Could you please kindly explain to me about it?
Thanks

can you clarify your question at all?  The focal, deleterious mutation is being removed by plain old natural selection (e.g. it would be removed even if it were on a chromosome by itself, unlinked to anything else). "Background selection" is the term for the loss of diversity/alleles in the linked region around the deleterious allele.

The phrasing in your question is a little unclear which makes it hard to know exactly what is unclear to you. But I'll give it a try hoping that it helps.
Background selection (BGS) is the process by which deleterious mutations reduce genetic diversity at nearby loci. When you say

I cannot understand how background selection can remove the deleterious mutation from the population

I would like to highlight that BGS does not remove the deleterious mutations per say. BGS is caused by deleterious mutations and has for consequence to reduce genetic diversity whether this diversity represent any variant for fitness.
An easy way to get an intuition of this effect is to think of the effective population size. In a Wright-Fisher population, where all individuals have the same probability to reproduce, the effective population size is equal to the population size. Imagine now that half of the individuals in the population carry a mutation that make them completely sterile. If this is the case, then the effective population size is reduced to half the population size. As the effective population is smaller, so is the genetic diversity. Hence, deleterious mutations (and fitness variance in general) reduce the effective population (in comparison to the actual population size).
Now, a single deleterious mutation that disappears in the next generation will affect the entire genome equally. However, repetitive deleterious mutations at specific loci (conserved regions) that stay around for a few generations will affect the effective population size at this region more than at other regions. Yes, the effective population size, for a population, can vary along the genome.
The strength of BGS to affect various statistics such as expected heterozygosity, $D_{XY}$ or $F_{ST}$ is hard to estimate as both hitchhiking (selective sweeps) and BGS leave very similar genetic signature. See for example Matthey-Doret and Whitlock (2018; bioRxiv) (shameless self-citation).