text:
BLASTN in NCBI strand Plus/Minus
I am a newbie in Bioinformatics. I am trying to understand terminologies used in NCBI BLAST system. Here is what I am trying to align:

So effectively I am trying to align two sequences with the following property.

So the query is part of reverse complement of the subject sequence. Now BLAST is throwing me the following result:

My confusion here is with the numbering system with query sequence starts from 1 from left side whereas the subject sequence starts from 1 from right side. Now I am assuming the numbering system starts from $5'$ end of any sequence and from the handwritten note above, it is clear that to align these two sequences I have to further reverse the subject string so that the $5'$ end of both sequences match up and hence numbering for both sequences should start from left side as opposed to what is presented in BLAST result page. BUT, I am suspecting that in my handwritten note in the reverse complement of subject sequence I have mentioned the $3'$ end in left side as is the case in DNA. But if I just take the (non - reverse) complement of the subject sequence keeping the $5'$ end towards left side, then and only then the numbering system works. But why we want to take complement of a given nucleotide sequence in non-reverse way!
Can someone kindly throw some light on this?

Yes, BLAST is making a best alignment, which is to the complement of your ‘Subject sequence’. That is how BLAST works, especially as other subject sequences may be genomes with genes oriented in different directions. And BLAST seems to be assuming that the numbering of your ‘Subject sequence’ is ‘official’ in some way (as it would be if it had been deposited in a data bank), and hence retaining it.
But as a “newbie in Bioinformatics” you should consult a suitable book and read about pairwise sequence alignment — which is what you appear to be attempting. An implementation of the Smith–Waterman algorithm, such as that on the EBI site, would seem more appropriate. This gives the alignment of the strands you entered:
EMBOSS_001         1 ATTGGCATT      9
                     |.||.||.|
EMBOSS_001         1 AATGCCAAT      9

If you want to check both strands, you need to do the reverse complementation yourself here.
There is also an EBI implementation available for the Needleman and Wunsch algorithm for global sequence alignment.


text:
Function of coenzymes: do they act as substrate shuttles?
My biochemistry textbook, "Harper's Illustrated Biochemistry", states:

Coenzymes serve as recyclable shuttles that transport many substrates
from one point within the cell to another. The function of these
shuttles is twofold. First, they stabilize species such as hydrogen
atoms (FADH2) or hydride ions (NADH) that are too reactive
to persist for any significant time in the presence of the water,
oxygen, or the organic molecules that permeate cells.
Second, they increase the number of points of contact between
substrate and enzyme, which increases the affinity and specificity
with which small chemical groups such as acetate (coenzyme A), glucose
(UDP), or hydride (NAD+) are bound by their target
enzymes."

To be specific I don't understand the meaning of the words in bold, above:

what are these so-called small chemical groups?
are they already bound to the enzyme or are they substrates?
what does increasing the specificity mean?

Summary
Co-enzyme is a general term employed early in the development of biochemistry and applied to non-protein components required for enzyme activity. Thus the term is not a chemical or mechanistic description and is of limited contemporary importance. Nevertheless a group of molecules designated as coenzymes, though differing in chemical structure, share the function of being activated carriers for particular chemical groups (not substrates).
The term “shuttle” neither describes, nor is generally applied to, this function: indeed it is reserved for the process of moving molecules back and forward between cellular compartments. This is quite distinct from whether or not the reactivation of the coenzyme occurs within the protein or after dissociation into the surrounding milieu. (Incidentally, the fact that both situations are found illustrates the limitation of defining cofactors tightly bound to proteins as prosthetic groups, and those that are not as coenzymes.)
The basic reason for the other molecular portion of a coenzyme of the activated carrier class is to provide a thermodynamically activated structure — a chemical bond to the group being carried that ensures its reactivity. Other features differ quite widely and may relate to the specific type of interaction of different coenzymes with proteins.
Cofactors, coenzymes, cosubstrates and prosthetic groups
For historical reasons the terminology in this area is generally descriptive rather than chemically systematic, but is best considered first as it has tended to influence perceptions of function (specifically the term “shuttle” in the quotation in the question). The all-embracing term ‘cofactor’ was coined for non-protein components of proteins that were necessary for their activity. There was then a fairly clear-cut distinction made between cofactors that were metal ions and those that were organic molecules. Here the terminology becomes somewhat less clear. Organic cofactors were designated ‘coenzymes’, but then a distinction was made betweeen those which are loosely bound to the protein and those which are tightly bound, the latter being termed ‘prosthetic groups’. Initially prosthetic groups were regarded as a sub-class of coenzymes, but some authors now consider coenzymes and prosthetic groups as a subdivision of organic co-factor, perhaps influenced by the haem prosthetic group in the non-enzymatic protein, haemoglobin. Furthermore, coenzymes such as NAD can be regarded as co-substrates in an enzymic reaction, and it is difficult to argue that they are distinct from co-substrates such as ATP and SAM, which are not generally termed coenzymes. This state of affairs is illustrated in the table below.

Name
Co-enzyme?
Prosth. Gp?
Co-sub.?
Act. Carr.?
Group

NAD, NADP
Y
N
Y
Y
electron

Coenzyme A
Y
N
?
Y
acyl

FAD
Y
Y
N
Y
electron

Lipoic Acid
N
Y
N
Y
electron

Tetrahydrofolate
Y
N
?
Y
1-C unit

Pyridoxal phosphate
Y
Y
N
N
—

Thiamine pyrophosphate
Y
Y
N
N
—

Haem
N
N
N
N
—

ATP
N
N
Y
Y
phosphoryl

S-adenosyl methionine
N
N
Y
Y
methyl

UDPG
N
N
Y
Y
glucose

[Source of designations: Coenzymes — Berg et al., Prosthetic Group — Wikipedia, Cosubstrate — own judgement, activated carrier — general literature]
‘Activated carriers’
It is possible to find a functional chemical communality among many — although not all — of the cofactors and cosubstrates in the table above by considering that they function as ‘activated carriers’ of chemical groups that are transferred to a substrate during the enzymic catalysis. Such groups range from single carbon units to larger acyl and phosphatide groups. It is usual also to include cofactors involved in redox reactions in this category. For species such as NAD and FAD one can argue that the activated group is a hydride ion, although it is necessary to consider electrons as the activated species if one wishes to encompass all redox reactions.
For repeated use of a cofactor it is necessary to reactivate it, which in different cases occurs within the enzyme (e.g. FAD-containing enzymes) or after release in solution (e.g. NAD-containing enzymes). Activated carriers of the former type illustrate that Harper’s statement of the function of coenzymes as “shuttles that transport many substrates from one point within the cell to another” is quite incorrect.
Harper’s chemical explanation of coenzyme structure in terms of stabilizing reactive species is unhelpful and, indeed, misleading as it implies such species are generated in cells. Instead, this should be considered from the opposite viewpoint: that the groups being transfered are more ‘reactive’ than in the target molecules, although the word ‘reactive’ is best avoided as it is ambiguous. The common feature of the molecular structure of cofactors is that the chemical bond between the group that is being transferred and the rest of the molecule is such that its breakage involves a decrease in Gibbs Free Energy sufficient to drive the formation of a stable bond to the target substrate. An illustration of this is the reaction of acetyl-CoA in which it is a thio-ester bond (red) that provides this activation.

Non-catalytic components of coenzymes
One aspect of the structure of cofactors that serve as activated carriers for different chemical groups is obviously the region of the molecule containing the group to be transferred and the ‘activate bond’. Parts of the rest of the cofactor structure will be involved interaction of the cofactor at its binding site on the enzyme, and contribute to the strength and specificity of the binding. That much is self-evident, and is the gist of the second point in the Harper extract in the question, including the emboldened text. The reference to ‘groups’, which the poster did not understand, are those listed in the table above, and encircled by red rings in the composite of co-enzyme structures, below.

It can also be seen how extensive the ‘rest’ of the structure of the coenzyme is in most cases, far more extensive than would seem necessary for simply enabling specific and strong binding. It is also remarkable that in many cases the ‘structural extension’ involves a nucleotide (generally adenosine) diphosphate moiety (yellow background).
Why? The student is warned that what follows is speculation (not original on my part) for which there is — and can not be — any evidence. However, it has been suggested that the nucleotide phosphate moiety is a relic of a postulated RNA world, in which the functional part of the coenzyme was covalently attached to the RNA of ribozymes. When the transition to protein enzymes occurred a nucleotide binding site evolved on proteins to attach the coenzyme, rather than an alternative molecular change, which perhaps occurred in other cases (tetrahydrofolate? lipoate?).
Coenzymes that are not activated carriers
Because of the emphasis above on cofactors/coenzymes that are activated carriers, it seems to me necessary to give an example of coenzyme that does not work in this way. I have chosen pyridoxal phosphate, which is actually covalently bound to the enzymes in which it is a coenzyme. These catalyse quite variety of different types of reaction — the racemization of L-alanine to D-alanine is illustrated — but the important point is that there is no group transfer involved, with the coenzyme being in the same state at the end of the reaction as at the beginning. In this respect it is similar to, say, the catalytic triad of serine proteases, and can be thought of being chemically more sophisticated and versatile for catalysis than a combination of amino acid residues.

[From the Wikipedia entry for pyridoxal phosphate]
…and shuttles?
“The original meaning of the word ‘shuttle’ was as a noun, referring to the device used in weaving to carry the weft thread. By reference to the continual to-and-fro motion associated with that, the term was then applied in transportation to both the vehicle involved, and as a verb, to the motion itself” (adapted from the Wikipedia entry).
The author of the chapter in Harper from which the quotation in the question is taken seems to be using a metaphor in which the coenzyme is equivalent to the shuttle, and the activated group to which it is temporarily covalently bound is equivalent to the weft thread. There are two problems with this. He goes on to say that such shuttles “transport many substrates from one point within the cell to another”. There is confusion about the way that the term ‘substrate’ is employed — rather unusually it appears to be equivalent to what he refers to as ‘species’ or ‘small chemical group’. However the reference to transport from one point within the cell to another is just plain wrong. Some coenzymes diffuse into the containing milieu (usually aqueous) where they are reactivated in a different enzymic reaction, but others stay bound to their holoenzyme. And transfer of groups during chemical reaction can hardly be regarded as transport between points. The second problem is that the term ‘shuttle’ is already in widespread and specific use in biochemistry in relation to surrogate transport of metabolites across membranes such as the inner mitochondrial membrane. This author‘s use of the term is particularly confusing in relation to one particular coenzyme: for NADH in aerobic cells  the malate–aspartate shuttle transfers its electrons from cytoplasm to mitochondrial matrix.

This is a long answer, which is why I started with a summary. I have tried both to answer the poster's question and provide a general perspective on coenzymes in the hope that it will be of wider interest. An answer this long will, no doubt, have deficiencies in fact, clarity and typography. If these are pointed out to me I will endeavour to remedy them.

source: Stack Exchange

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text:
Are stable isotopes ever used in pharmaceuticals?
Carbon has two stable isotopes, C-12 and C-13. Since they both have the same electronic structure they can both make up the same molecules, but presumably they may perform different functions in biochemistry due to different mass.
Q: Have various stable isotopes of the same atom ever been put to use in pharmacology?
Basic internet research only yielded information about unstable, or radioactive isotopes.

I think you'll find that the chemistry is more important than the mass,  but I don't know if there has been any pharmaceutical made that that specifically used a stable isotope, so not writing this as an answer.

@bob1 MRI works on precession of the nuclear spin, and that varies dramatically. Consider 12C (spin 0, no (useful) magnetic moment) vs 13C (spin 1/2 like a proton, but heavier) Now whether medically approved contrast agents used in human MRI are considered a pharmaceutical per se or not is a different question.

29Si Isotope-Enriched Silicon Nanoparticles for an Efficient Hyperpolarized Magnetic Resonance Imaging Probe and Use of 13C Isotopes in MR Research and MRI/MRS: Use of Isotopes in Hyperpolarization

@uhoh It looks as if the FDA considers them to be  intravenous drugs, so, yes, pharmaceuticals

@SimonCrase excellent! The last task of showing that stable isotopes are used as pharmaceuticals (rather than just explored as possible candidates) remains and I'm probably not quailed to assert that with supporting sources. Perhaps someone else can/will. Thanks!

@uhoh I didn't think of contrast agents; wouldn't have thought they are pharma, but apparently they are.

@bob1 well if someone is going to inject a substance into your blood, you'd like it to be safe, and therefore its manufacture and distribution carefully regulated. Doesn't really matter whether it's for diagnosis or treatment.

Could you change the actual Question title to reflect the explanation in the exposition, Q: Have various stable isotopes of the same atom ever been put to use in pharmacology?
Either way, isn't the real Question, 'Have different isotopes of the same atoms been used in pharmacology?' and isn't the different wording in both title and exposition simply confusing?

You should check the Wiki articles:

Isotopes in Medicine
Radiopharmaceutical

If we solely focus on carbon-13 based drugs then there is carbon-13 labeled ibrutinib, carbon-13 labeled midazolam/1′-hydroxymidazolam, carbon-13 labelled aspirin.
Lastly, you can reads this papers:

Schellekens RC, Stellaard F, Woerdenbag HJ, Frijlink HW, Kosterink JG. Applications of stable isotopes in clinical pharmacology. Br J Clin Pharmacol. 2011 Dec;72(6):879-97. doi: 10.1111/j.1365-2125.2011
Gregg, C.T. Some application of stable isotopes in clinical pharmacology. Eur J Clin Pharmacol 7, 315–319 (1974). DOI: 10.1007/BF00560350
Bodamer OAF, Halliday D, Uses of stable isotopes in clinical diagnosis and research in the paediatric population, Archives of Disease in Childhood 2001;84:444-448, DOI: 10.1136/adc.84.5.444

Deutetrabenazine.
As the linked article from Wikipedia notes:

Deutetrabenazine (trade name Austedo) is a vesicular monoamine
transporter 2 inhibitor which is used for the treatment of chorea
associated with Huntington's disease and tardive dyskinesia.
Chemically, deutetrabenazine is an isotopic isomer of tetrabenazine in
which six hydrogen atoms have been replaced by deuterium atoms. The
incorporation of deuterium slows the rate of drug metabolism, allowing
less frequent dosing.

Whilst what you have in the above is an isotope of hydrogen, the effect this gives is seen in other compounds belonging to the bioisosteres (chemical substituents or groups with similar physical or chemical properties which produce broadly similar biological properties in the same chemical compound), the purpose being to:

enhance the desired biological or physical properties of a compound
without making significant changes in chemical structure

The different mass of the deuterium in the case of deutetrabenzine is thought to tweak the chemistry in useful ways:

However, the C–D bond is a bit shorter, and it has reduced
electronic polarizability and less hyperconjugative stabilization of
adjacent bonds, including developing an anti-bonding orbital as part
of the newly formed bond. This can potentially result in weaker van
der Waals stabilization, and can produce other changes in properties
that are difficult to predict, including changes in the intramolecular
volume and the transition state volume

The urea breath test for Helicobacter pylori uses urea labelled with carbon-13 or carbon-14 to detect the presence of the bacteria, which would metabolize it to carbon dioxide and be exhaled.

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text:
How many GTPs are used in prokaryotic translation?
Here is the question: How many GTP are necessary to synthesize 2 linear peptides of 11 amino acids each using an in vitro prokaryotic system? Assume the tRNAs provided are already loaded with their proper amino acids. All 3 steps of the protein synthesis reaction must be completed.
My answer was 46. I thought that translation initiation uses 2 GTPs (the GTPs on eIF2 and eIF5B are hydrolyzed). Elongation involves 2 GTPs for each amino acid after the first methionine (the GTPs on EF1 and EF2 are hydrolyzed) - there are 10 amino acids left, so 2x10=20 GTPs are used. Termination involves 1 GTP (the GTP on eRF3 is hydrolyzed). So for one linear chain of 11 amino acids, 2+20+1=23 GTPs are used, and for 2 chains, 46 GTPs are used.
The correct answer is 44. I'm not sure where in my reasoning I went wrong. In what steps were there less GTPs used, and which proteins instead did not actually have GTP hydrolysis? Thank you.

Welcome to SE Biology. Please finish reading the [Tour] to learn how this site works and what sort of questions are suitable. The question specifies prokaryotic translation but all the factors you mention are eukaryotic (that's what 'e' stands for). Despite that, you are correct. It looks as if whoever set the question forgot about termination. However I am voting to close this question rather than answering it because the usage of GTP in protein sythesis is standard text-book material, and this site exists to answer points about biology, not to discuss poor or sloopy teaching.


text:
What happens if a lysosome is pierced and it's enzymes are made to get released
I am confused the results be same as it happens when lysosome gets damaged during some metabolic activity or different . If same  the cell will die by the actions of those hydrolytic enzymes slowly or immediately , I think the results might differ from the accidental case

Enzymes of lysosome are usually inactive and are activated only in low pH environments, so I guess, randomly puncturing a lysosome wouldn't affect the cell to any serious extent unless the cell is an acid secretory cell or It's membrane is easily permeable.


text:
What are Palomena prasina doing in my home?
I live in eastern Europe, and every autumn, ever so often a Palomena prasina flies inside my home.
I have an avocado plant that I put them on to live - I currently have 5 of these on my plant
However, I have noticed they hardly if ever eat the plant and they hardly if ever move, and I haven't noticed poo either (they are alive). I was thinking that they are waiting the winter to pass and kind of hibernate, but if this is the case, firstly - how can they tell, and secondly - isn't their lifespan too short to wait for the spring?

Many people call many different things 'stink bugs.' You will have to be more precise with what bug you are referring to (species ideally, genus is probably okay). I don't know if they can be "hibernating" (overwintering) on your indoor plant - is your indoor avocado plant kept at room temperature?

I believe it is Palomena prasina


text:
Hardy-Weinberg Equilibrium Test Result for Merged Genotypes
I was curious if two populations are in Hardy-Weinberg Equilibrium (HWE), and if they are merged, then what happens? To find out, I considered populations from the 1000 genome project data. For example, at first, I considered the genotypes of the American (AMR) population from a specific SNPs and checked whether they were in HWE and found that they were. Then I selected the East Asian (EAS) population and found that the genotypes were also in HWE. However, when I merged the genotypes from both populations and checked HWE, I found that it was not in HWE. Surprisingly, when I added 50% of genotypes from each population, they were in HWE. So, I did it for different combinations, for example, 80% genotypes from the AMR population and 20% from the EAS population and vice versa, and found that they were also in HWE. I used the chi-squared goodness of fit test and the Haldane Exact test. The allele and genotype frequencies for each combination are different from the initial populations. What conclusion can I draw from my findings? Should I check to see if there are any assumptions about the test that are violated?

Welcome to Biology StackExchange! If I understand your question correctly: Imagine a limiting situation with two alleles and two populations, one of which only has one allele present ($p_1 = 1, q_1=0$) while the other has only the other allele present ($p_2=0, q_2=1$). Even if both of these populations are in HWE, when you merge them, they won't be ($p = 1/2, q=1/2$ but there are no heterozygotes).

Here are the allele frequencies and genotype frequencies: G T GG GT TT 0.408 0.592 0.184 0.447 0.369 → AMR Population || 0.651 0.349 0.427 0.448 0.125 → EAS Population || 0.550 0.450 0.327 0.447 0.226 → Combined all || 0.550 0.450 0.327 0.446 0.227 → 50% each combined || 0.471 0.529 0.247 0.447 0.306 → 80% AMR and 20% EAS || 0.614 0.386 0.390 0.448 0.162 → 80% EAS and 20% AMR @Domen

your initial question was: I was curious if two populations are in Hardy-Weinberg Equilibrium (HWE), and if they are merged, then what happens? I have given you an example which tells you that merging allele frequencies from two populations in HWE will generally result in a population not being in HWE.

Thank you very much! I get your point. My question is: how can I draw conclusions? Since different percentages of merging of genotypes result in HWE, except for all of them combined. Can I say something from the allele and genotype frequencies? Or do I need to take any further steps to reach the conclusions?

@statm I suggest that you look into the idea of statistical power. More extreme deviations from HWE will naturally be easier to detect by your test; "in equilibrium" is not a binary after all, every population is somewhere in a continuum of disequilibrium. I'd also suggest consulting prior attempts to test for HWE in stratified populations. I think that you can safely reach the trivial conclusion that well mixed populations are closer to HWE than stratified populations, but no more.

You may want to recheck your calculations. The fully combined and 50% combined groups should be the same, and I got G 0.52925, T 0.47075, GG 0.3055, GT 0.4475, TT 0.2470.

Why would you expect the result to be in HWE in the first place?

As @Domen points out, there is no expectation that adding two populations that are each in Hardy-Weinberg equilibrium will initially create a new population in HWE.
OP's procedure of combining different proportions of the initial populations, then checking for HWE, is essentially like asking how much of one population can be added to another before HWE is lost. This vaguely gets at the question of how different the two populations are to begin with, but doesn't provide any information on whether the assumptions underlying HWE are met.
A better function to ask about the initial difference between populations, and that can be calculated from the initial allele frequencies, is the fixation index, FST.
Incidentally, if the assumptions of HWE are still met after the two populations are merged, then after one generation of mating HWE will be reestablished across the whole population.

Well, the absence of migration is one of the assumptions of Hardy-Weinberg law. By merging the two populations you are basically simulating migration, violating the assumption, and thus (as @Domen and @Darlingtonia correctly pointed out) there is no reason why you should expect that the two populations are in HWE (https://www.nature.com/scitable/knowledge/library/the-hardy-weinberg-principle-13235724/).
The fact that you get different results when mixing different proportions may be due to different factors, such as (but not limited to):

Lower number of individuals obtained when mixing a fraction of each population may influence the power of the chi-square test. Seeing the numbers used in the chi-square test may help to understand.
The difference in frequencies between the two populations is small enough that only a total mixing brings to a significant deviation from equilibrium.
When you mix a large proportion of one population and a small proportion of the other, you likely get a final population which is sufficiently close to the first one, and thus does not significantly deviate from HWE.


text:
Why are the ducts of pancreas lined with compound epithelium?
Most other places with compound epithelium are in contact with the outside world, and that of course makes sense. So why would a duct snugly placed inside our body need stratified epithelium? Is it to protect against the protein digesting enzymes passing by?
edit- i still havent found a satisfactory answer...

Do not bump your post with trivial edits. You can always edit to include new background you find even if it doesn't answer your original question.


text:
What's this aquatic bug?
I have a small freshwater aquarium at home with only some aquatic plants at the moment. In the summer, I put some mud and sand from a local pond into the tank. At some point, I noticed a strange moving "segment" of plant:

Here is a video of it moving right under the surface of the water:
https://www.youtube.com/shorts/QbXv4QFDJpE
If you look closely, you can see that the "segment" is actually made from several smaller segments of a stem of an aquatic plant. In other words, this little creature chopped up the plant, then assembled this little "tube" for itself to hide.
Few weeks later, it apparently disassembled the little house and created a larger one from leaves:

Here is a video of it:
https://www.youtube.com/shorts/sraLS-XHfrM
It basically this little leafy house everywhere and can move up and down the water column. I think it feeds on different plants because I can see some visible damage in the tank.
Can you identify this creature? The location is northern Europe.

Those videos are great! It's some sort of caddisfly larva, known for the cases they create, but as there are ~14,000 species, I can't begin to say which one. Maybe someone else will know. :)

@anongoodnurse I would be quite content with just knowing the order or family! And yes, I think you are exactly right after reading the wikipedia page :)

in norwegian we call them vårfluelarver(spring fly larvae),one way to identify them is from the materials they use in their "house"different types use different materials,some use grains of sand other ones use dead leaves or as in your picture green parts of plants.


text:
Is the amount of pigment in one feature (e.g. hair, eyes, skin) connected to the amount of pigment in another?
Let's say, genes allowing it, you have a red-haired child with hazel eyes. The hair is a darker/deeper orange color, so (if I recall correctly) having some degree of eumelanin—not much compared to phenomelanin but enough to darken it to that deeper red shade. Would the hazel eyes be connected to this trait, being a mix of pheomelanin with some eumelanin akin to the hair, or is eye color’s “pigment pool” entirely independent from hair color’s “pool?”
Also another perspective, if the head-hair and the facial hair (eyebrows, etc…) are that red color, does the body hair (arms, legs, etc) always have to match those and be reddish too, or is it more likely to be blonde/clear/etc?


text:
Can Gravity convection incubators negatively affect the growth of strict aerobic bacteria?
Background
Gravity incubators rely on natural convection for heat distribution. There is no fan or blower system, and the heat rises from the heating element at the bottom of the incubator.

https://www.thermoline.com.au/blog/fan-forced-vs-gravity-incubators#:~:text=Gravity%20incubators%20rely%20on%20natural,as%20in%20fan-forced%20incubators.

Problem
I'm working on a strict aerobic bacteria. I have a problem with the growth rate of broth cultures; the growth seems too light in comparison to the inoculum size (4-5 colonies), low broth volume (4-5ml), and incubation conditions (24 hrs). The incubator available to me is of the type gravity convection incubator with no mean of shaking. I use screw cap test tubes for the broth cultures,  the degree of tightness of the caps greatly affects the produced turbidity. However, even after learning about this and making sure the caps are loosened, the growth rate is increased but still inadequate.
I have a colleague that has access to a fan-forced incubator and they seem to have a higher growth rate.
Question
Can Gravity convection incubators negatively affect the growth of strict aerobic bacteria?
Prior work
I have not found any text on the internet that discusses this matter. I have great experience in searching.

Can you update the question to include details about shaking?

Done (mentioned that no shaking incubator was used, as it is not available)

Hard to make a definitive answer without more information. I would confirm the temperature where your cultures are growing in the incubator with a thermometer. Flasks are generally better than tubes for gas exchange, but not sure if that applies to static cultures. Pre-warming the media can help. And best practice is to inoculate from a single colony whenever possible. Even minor genetic variations between colonies can result in competition between two or more clonal lineages, slowing outgrowth during the lag phase.

I used to do single colonies before afriend suggested doing more. I don't intend by using definite values in some of the givens I mentioned to build a complete scientific picture, all I need is the effect of using gravity convection incubators on the growth of broth cultures of aerobes, from practical experience.


text:
How can I find out where the holotype of a species is?
When I visit the Wikispecies page for Synapturanus zombie, it tells me where the holotype is, as does the paper which describes the species. But on visiting the page for Quercus gambelii, the holotype is not listed and the article where the species is described is not named (though I am given the journal, author, and year of publication). Can I find out where the holotype for this species is without hunting down the journal article in person?
Q: What's the process in general for me to find out where the holotype is stored for an organism?

In general, one would hope to find the depository that holds the holotype as a part of the formal description article published. However, with many, especially older (1800's or earlier) descriptions, this isn't necessarily the case. Often major collections, such as Kew (UK) or the National Academy of Sciences (USA) will hold collections from important researchers, but this is not always the case. Nowadays, you often have to do a bit of searching to find this information. I've put a description of my process below.
The Journal article in question is:

Nuttall, T. 1848. J. Acad. Nat. Sci. Philadelphia ser. 2, 1(2): 179.

The link provided on the Wikispecies page doesn't take you to the article directly, only to a page for the journal, which links to series 1, volume 1.
I did a bit of link sleuthing and was able to link from the wikispecies page, through the International Plant Names Index (click on the top listing to take you to this page, where you click on nomenclatural link to this page, click on publication, which takes you to this page, where you need to click read this publication under heading BHL). All this finally takes you to the Biodiversity Heritage Library listing for the journal, where you need to access the right volume there (Volume: ser.2:v.1 (1847-1850)), listed as 1847, but covering 1847-1850. You want to look at page 179 under the heading Quercus for the description.
The article doesn't provide any information on the location of the holotype, so a bit more, very easy, sleuthing and you will find that Thomas Nuttall, the descriptor, worked at the Academy of Natural Sciences Philadelphia (now Academy of Natural Sciences of Drexel University), and unsurprisingly published in their periodical. This makes it highly likely he deposited his material with them.  From a quick search of their site, it seems they do indeed hold some 4,000 samples from Nuttall.
They also hold some records from W. Gambel, in their Historical collections. Nuttall's article in the Journal of the National Academy of Sciences, Philadelphia was a description of samples collected by Gambel, and Quercus gambelii is named for him, so they should(!) be with either Nuttall's or Gambel's collections.
So, long story short: The specimen is likely to be at Drexel University in Philadelphia.
I say "should(!)" because things get lost, sent off to other places and not returned etc. Nuttall also worked in the UK from 1842 onwards until his death, as he inherited property from an uncle, under whose will, Nuttall had to spend at least 9 months of each year in England. I don't know enough about the chap to say whether he still continued to work in Philadelphia, but he certainly continued to publish there, as evidenced by the article for the species in question. This could mean that some of his specimens are in the UK. There doesn't seem to be at Kew, at least not digitized, but there are quite a few other sites they could be in the UK.

thank you, you are awesome

Here is one specimen, from Harvard's Gray Herbarium, that is probably a type of Q. gambelii. Because the specimen doesn't have a collector's number (common for that era) and because Nutall didn't say anything about which specimen he used for the description, there's still some uncertainty. Note that L. R. Landrum, who studied this specimen, only says it is a probable isotype (an isotype is another specimen from the same collection as the holotype, called a "duplicate").

We know the above specimen was collected by Gambel in the right area. There might exist other duplicates of this collection at other herbaria, one of which might have a better claim to be the actual one Nuttall used for the description. If someone could convincingly argue that point, they could designate that specimen as the "lectotype", and it would have priority over other isotypes.

@Darlingtonia Kew has a specimen from 1847, A. Fendler collection it seems. Doesn't mention if isotypic or not though.

Since the Kew specimen was collected by Fendler, and Nuttall doesn't mention Fendler, that wouldn't be a type of Q. gambelii. (Well, theoretically, if you could show that Nuttall actually meant Fendler when talking about Gambel, maybe it would have a chance. Like, if Fendler was the botanist on the hypothetical Gambel Expedition to New Mexico, that could maybe be argued.) If one could show that Nuttall consulted the Fendler specimen when writing the description, and then all of the existing Gambel specimens were lost, one could then designate the Fendler specimen as a lectotype.

The Fendler specimen is a type in its own right, but for a different taxon. That specimen, and a few others, are syntypes of Q. douglasii var. novomexicana. A syntype is a specimen listed in the original description, but where none was designated as a holotype. It looks as though taxonomists generally consider this taxon to actually be a part of Q. gambelii, meaning they just don't think that it's distinct enough to be called a separate species. Other taxonomists may disagree, and if they were to use the name Q. douglasii var. novomexicana, then that specimen would be the syntype.

Incidentally, JSTOR Global Plants helped me track down the Gambel specimen.

@Darlingtonia Sounds like you can write a better answer than me - please do! It's only a hobby for me now (since >20 years ago), so I don't know much of how it is done these days.


text:
How do birds concentrate their urine?
I've read that birds have shorter loops of Henle in their kidneys, and their primary strategy of water conservation is expelling nitrogenous waste in the form of uric acid.

However, the nephrons of birds have loops of Henle that extend less far into the medulla than those of mammals. Thus, bird kidneys cannot concentrate urine to the high osmolarities achieved by mammalian kidneys. Although birds can produce hyper-osmotic urine, their main water conservation adaptation is having uric acid as the nitrogenous waste molecule. (Campbell Biology, 11th edition)

However, I still can't quite understand how uric acid could make birds excrete white paste-like urine with less water than mammalian urine. I know that uric acid is not very soluble in water, and birds reabsorb some water in the cloaca, but this still doesn't answer my question.

I don't know, but perhaps a better question is, "How do birds conserve water?" Their excrement is paste-like because it is both urine and fecal matter, and if you've ever owned fowl, you'll know that their production of excrement is... well, nearly prodigious.

First off, I think it's helpful to go backward a step and figure out why an animal might make and concentrate urine in the first place. There's no usefulness in itself to having concentrated urine, it's just waste. Rather, for mammals (which, being mammals, we have a bit of a bias of thinking about the world from a mammal's perspective), urine concentration is part of the solution to the problem of needing to get rid of nitrogenous wastes: humans, like other mammals, flush soluble nitrogenous wastes into our kidneys with a bunch of water. This strategy creates a new problem of water loss, and the mammalian solution to this new problem is to collect a lot of that excreted water back so we can get the waste flushed out.
I think that the paragraph you quote is taking the mammal-centric position a bit too far and therefore the ordering of the statements in this paragraph is a bit misleading. I'll rewrite it using most of the same words but a different order. Though the meaning is the same I think it'll be easier to understand:

Although birds can produce hyper-osmotic urine, bird kidneys cannot concentrate urine to the high osmolarities achieved by mammalian kidneys. That's because the nephrons of birds have loops of Henle that extend less far into the medulla than those of mammals. Instead, their main water conservation adaptation is having uric acid as the nitrogenous waste molecule which they can excrete as a solid rather than flushing with water.

I think "hyper-osmotic urine" misleadingly suggests "really really high solute concentrations" because of the prefix "hyper", but in this context "hyper" just means "greater than (blood/plasma)", it doesn't actually say anything about the degree.
Orosz, S. E., & Echols, M. S. (2020). The urinary and osmoregulatory systems of birds. Veterinary clinics: Exotic animal practice, 23(1), 1-19. mentions birds concentrating urine to 2-3 times plasma.
In contrast, "high osmolarities achieved by mammalian kidneys" seems to be using "high" relative not just to plasma but also to what birds can achieve.
Nawata, C. M., & Pannabecker, T. L. (2018). Mammalian urine concentration: a review of renal medullary architecture and membrane transporters. Journal of comparative physiology B, 188, 899-918. mentions urine concentrations in mammals relative to plasma in the range of 4-30x depending on species.

Back to worrying about the mammal-centric thinking: there is a causal implication in both the original and my edited version that is not warranted, which is that the anatomy of the loops of Henle is somehow determining the nitrogen excretion strategy that birds use. It's equally reasonable to presume that birds don't need long loops of Henle since they evolved an alternative excretion mechanism that makes it unnecessary to concentrate urine to a great degree.
The "trick" of that alternative excretion mechanism is using uric acid and excreting a paste. Because uric acid crystalizes and comes out of solution, it doesn't "count" toward osmolarity of the urine, it's excreted as a solid. Birds don't need to remove water to crystalize uric acid, and don't need to use water to flush it out at all, it falls out of solution on its own because it's not very soluble. You could add a bunch of extra water and it would still stay mostly solid rather than dissolving.
So back to your original question: how do birds concentrate their urine? Well, pretty much the same way we do as far as the kidney goes. They also pull some water back in through the cloaca before urine is released, similar to how mammals pull water in from stool in the large intestine. The important difference is not how birds concentrate their urine (because urine concentration isn't a goal/need in itself), but rather how birds excrete nitrogen waste. By not flushing soluble nitrogenous waste with water in the first place, they don't have as much urine to concentrate, so it's less important for them to be very efficient in doing so.

Having just read some papers on this, I agree with all of this. The main takeaway seems to be 'hyperosmotic relative to plasma', which is easy because of excretion of larger amounts of NaCl. Also, it seems there are other water conserving machanisms birds use that mammals don't, including in the cloaca. Interestingly, there are entire books devoted to just this topic of avian osmoregulation.

Thanks for your detailed answer! I would just like to ask how do birds reabsorb most of the water in the filtrate if they have shorter loops of Henle? If uric acid is not very soluble, and it does not count in determining osmolarity, would this mean that water would diffuse out of the nephron quicker, since the filtrate has higher water potential?

@Nibelung Are you looking for an answer for an assignment? Those questions are not bringing you closer to understanding.

No, I'm in high school and this is way deeper than what my teacher would give me. However, I would just like to know how bird kidneys reabsorb all that water in the filtrate. But I'm curious why are those questions useless?

@Nibelung Urine concentration isn't done for fun, it's done to avoid water loss specifically when you would otherwise need to use water to get rid of a lot of waste. Birds don't concentrate their urine any special way. They don't need to, because they don't need to flush a bunch of soluble nitrogenous wastes. They get rid of excess nitrogen by using a non-soluble, non-water-requiring method by converting it to a different chemical.

Unlike mammals, birds excretory matter is not liquid but a semi-solid matter which is concentrated uric acid (this is not to be confused with feces which is the dark solid matter). Their urinary system (consisting of kidneys, lower gastrointestinal tract and nasal/orbital salt glands) is somewhat different that can conserve water and produce hyperosmotic urine:

Unique aspects in the avian (urinary) system include the presence of loopless and looped nephrons, lack of the thin ascending limb of Henle's loop, a corticomedullary osmotic gradient primarily consisting of NaCl without contribution of urea, and significant postrenal modification of final urine. The countercurrent multiplier mechanism operates between the descending and ascending limbs of Henle via recycling of a single solute (NaCl) with no water accompaniment, forming an osmotic gradient along the medullary cone.
—Urine concentration and avian aquaporin water channels

Birds do not have any urinary bladder, so they don't store water anywhere. Instead they have aquaporins. In the absence of the bladder, the renal output enters the lower gastrointestinal tract, where it is significantly modified. Birds consume prey that is high in salt content or intake fluids high in salinity. So, they have functional salt glands that are capable of eliminating excess ions, usually sodium chloride, and in the process produce free water. Aquaporins come into the picture and facilitate transfer of water between cells, so they get absorbed and not get excluded as waste matter.
You may find more details of the avian urinary system and the osmoregulation process in the references below:

Nishimura H., Urine concentration and avian aquaporin water channels. Pflugers Arch. 2008 Jul;456(4):755-68. doi: 10.1007/s00424-008-0469-6
Yimu Yang, Hiroko Nishimura, Bird aquaporins: Molecular machinery for urine concentration, Biochimica et Biophysica Acta (BBA) - Biomembranes,
Volume 1863, Issue 10, 2021, DOI: 10.1016/j.bbamem.2021.183688
Eldon J. Braun, Chapter 12 - Osmoregulatory Systems of Birds, Sturkie's Avian Physiology (Sixth Edition), Academic Press, 2015, DOI: 10.1016/B978-0-12-407160-5.00012-9
https://avesbiology.com/bird_excretion.html


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Cladistics question - species of non-terminal nodes
I understand that in a cladogram, the terminal nodes of a full tree are species (or subspecies), while parent nodes represent a branching event in an ancestral population.
It makes sense that in general we won't know what the actual ancestral species was, so the having no species assigned to the parent node makes sense.
But what about a case where we actually knew this? For instance if we directly or indirectly observed some members of a known species rafting to an island and far in the future observed that they had diverged and had no gene flow with the original population.
I'm guessing that we would not assign a new species name to the still existing original population. In that case, what would the cladogram look like in terms of labeling?
I can see that it would make sense to assign subspecies names to both halves of the split as the ancestral population will have also diverged. But what if we had specimens from before the split- how would they be classified?

First: tips are best thought of as individuals, not species. One might have multiple members of the same species even in a phylogeny. Recall that species / subspecies are fundamentally arbitrary groupings, and the higher levels of classification even more so.
It is not very rare to use fossil information to inform phylogenetic modeling, see for example here. This can be helpful for time calibration or character modeling for example.
What I'm not sure that I understand is your questions about subspecies/species naming. It is common for us to apply species names even to long-extinct organisms such as dinosaurs.
If we have sufficient information to decide that an ancestral population constituted a distinct species, why wouldn't we label them as such? Paleontology is very rich in examples of species named in the absence of living "tips".

I suspect OP was given a "rule" by someone without that "rule" being fully explained.


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Why don't membrane potentials violate the principle of electroneutrality?
The principle of electroneutrality states that the number of anions and cations in a solution must be the same, i.e., that there will be no charge excess in any side of the membrane separating two solutions.
Despite this, a membrane potential of (e.g., of -70 mV) must mean there must be a charge excess on one side of the membrane.
My texts say that this does not violate the principle of electroneutrality since the number of potassium ions that moves to create the membrane potential is very small. I appreciate this fact,  but it seems unconvincing to respond to "there will be no charge excess" with "there will be, it's just very small".
As a follow up question: when we discuss "injecting Na+ into a cell" does this also not violate electroneutrality? How can we get a solution with only sodium ions dissolved in water in the first place?
Thank you.

Whose principle is this and under what conditions does it hold?

@BryanKrause this is part of my confusion as the principle is mentioned in several of my texts and in places online but I can't find where it comes from. It does seem to hold in macro solutions, e.g., a solution has 140 mM of K+ and 20 mM of Na+ then it would be the case it has 120 mM of some A- ion. But in micro it seems counterintuitive when considering membrane potentials

In bulk aqueous solution, the principle of electrical neutrality strictly requires that the sum of n(i)z(i), summed over all i, be zero.  But is it generally agreed that local violations are allowed.  One the the brickbats aimed at the chemiosmotic theory of Peter Mitchell was (and still is!) that it violated the principle of electrical neutrality. See Analysis of molecular mechanisms of ATP synthesis from the standpoint of the principle of electrical neutrality

There is perhaps Pauling's principle of electroneutrality "each atom in a stable substance has a charge close to zero" - maybe that's the principle referred to in your book? "Close to" is an important part, though, and this is not some law of physics, just an observation of how things tend to be, not how they must be.
Consider also a capacitor - that's how the membrane behaves. A capacitor features charges that are separated by some insulating medium.
Unfortunately, some textbooks do a really terrible job of explaining how membrane potentials work. I recommend starting from imagining no membrane potential at all, just ions of different concentrations, and then think about how those ions would move across the membrane according to those concentration gradients, ignoring charge entirely.
If, say, K+ is high inside a cell and low outside a cell, K+ is going to tend to diffuse out of the cell more often than it diffuses in. No charges needed to understand that so far, just concentration gradients. But, as a consequence of K+ ions tending to move out of the cell, you're creating an electric current: the K+ ions have a positive charge, so if a few more leave the cell than enter, the inside is going to be a little more negative than it was. And since it's a little more negative, there will be a little less tendency for K+ ions that have positive charge to leave that slightly negative space, even if the concentration gradient would make you expect K+ ions to keep moving.
How much more negative? And how many ions will move until it's "negative enough" that the electrical gradient holding K+ ions in is equivalent in strength to the concentration gradient letting K+ ions leak out? I posted some of the math for the number of ions here - as you mentioned, it's very small. Electricity is powerful stuff, and that's why Pauling has that principle that things tend to be roughly equal. For a membrane potential, things are equal enough that if you were just writing down the concentrations it would fit into the measurement error. For the "how much more negative?" question you can use the Nernst equation.
When multiple ions are involved you'll have to weight each of their contributions to calculate the overall membrane potential. Only ions that have some permeability across the membrane contribute to the membrane potential. You can both calculate the membrane potential and also see how ions that don't have any permeability don't contribute from the Goldman equation. You can also see it from the story above: the voltage across the membrane caused by potassium is only happening because potassium is moving.
When someone talks about "injecting Na+", they don't have a vat of sodium ions, rather they're using this for shorthand of "injecting Na+ and an unimportant anion", that is, something that's not important for the membrane potential.
Be careful about trying to add up charges on each side of the membrane to calculate a membrane potential: you want to think about concentration gradients, instead, and how ions move according to those gradients and what consequences that has for the distribution of electrical charge across the membrane. You also shouldn't think about the charge that moves across the membrane as being distributed throughout the cell: it's literally at the membrane. Remember, the membrane is a capacitor: the extra charge exists right along the membrane, and it doesn't just sit there without having an effect on anything, a bit of negative charge inside the membrane is going to pull any positive charges anywhere in the membrane a little closer to the inside, and push any negative charges a little further away.

Thanks, that makes sense. I went down a rabbit hole of some of your responses and they also helped clear things up. In this answer you mentioned you won't do the maths but such a charge separation would boil the apparatus - just for fun what equations would show the energy released?

@TheAnonymous https://en.wikipedia.org/wiki/Electric_potential would probably be a good place to start, it'll be easiest to do the calculations if you make some "uniform spherical cow of charges"-type physics classroom assumptions. Actually, probably easier conceptually to work from https://en.wikipedia.org/wiki/Capacitor


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Left digested peptides in speedvac for hours
I had done phosphopeptide enrichment of proteomic samples and digested the peptides with trypsin. However, I forgot and left the samples in speedvac to dry at 45 deg for way too long, about 10hrs. It does usually take a few hours to dry. Will it hamper my samples and the proceeding LC-MS analysis?
Another thing to ponder is that only one sample has a big round white powdery clump and the rest are transparent clear blobs, hard to see anything, as it should be. And this is also the tube which I eluted one extra time as well. If it is salt or detergent I don't think it would be that thick. Have any idea on what this could be? I will run it in the MS anyway. Thanks!

Sounds like it's unlikely to work, to me, though I'm not an expert in this stuff. Interested to hear what the data look like though!

Thank you for responding and for your insight. I will run it in the MS soon and see. I hope it somehow works and will update on how it looks, fingers crossed.


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Chloride Clamp and Nernst potential
The Nernst potential for chloride is -70 mV. The neuronal Resting Membrane Potential (RMP) is -70 mV. Under this condition, if the chloride channels are open (as it happens in Inhibitory Post Synaptic Potential - where chloride channels act as postsynaptic ionotropic channels), Chambers† writes that there is a movement of chloride ions along the concentration gradient i.e from outside to inside. However as the RMP and Nernst potential are the same, there is no hyperpolarization, as would happen were the voltage-gated potassium channels to open. However, the result is that there would be a need for much greater excitatory stimuli (influx of sodium) to cause an action potential in this cell. This is called a "Chloride clamp".
I am confused about two things:

Why is there a net movement of chloride ions when the RMP is equal to the Nernst potential of chloride?
As there are more chloride ions inside the cell, why is the cell not hyperpolarized?

Cl‾- mediated IPSP: binding of
neurotransmitter opens Cl‾ channels. The
resulting intracellular movement of Cl‾ ions
usually makes little difference to the
postsynaptic membrane potential, as the
Nernst potential of Cl‾ (–70 mV) is
approximately the same voltage as the RMP.
However, to reach threshold, an excitatory
signal must trigger sufficient Na+ influx to
exceed the combined effects of Cl‾ influx and
K+ efflux, making it much more difficult to
depolarise the cell membrane; this is known as
the ‘chloride clamp’.

† David Chambers Basic Physiology for Anesthetists Second Edition, chapter 53 - Synapses and NMJ Page 233

Can you quote from your book where it says when the membrane potential is equal to the Nernst potential for chloride there is a net nonzero movement of chloride ions in a particular direction?

For question (2), make sure you understand what causes the membrane potential. This answer I wrote yesterday addresses the same issue: https://biology.stackexchange.com/questions/113638/why-dont-membrane-potentials-violate-the-principle-of-electroneutrality

Also https://biology.stackexchange.com/questions/57064/why-is-it-possible-to-calculate-the-equilibrium-potential-of-an-ion-using-the-ne/57066#57066  https://biology.stackexchange.com/a/79623/27148 https://biology.stackexchange.com/a/60547/27148

@BryanKrause I have added the verbatim quote from the book.

I don't think your book is saying that there is net movement of chloride ions at the reversal potential for chloride (Nernst potential): you are correct, that is specifically the voltage where the net flow of an ion is exactly zero; if there is net flow of an ion you are not at the Nernst potential and vice versa. See also https://en.m.wikipedia.org/wiki/Nernst_equation
What your book says is "little difference" and "approximately" rather than "no difference" and "exactly": they're assuming that the resting potential is slightly less negative than the reversal for chloride, so there will be some small but negligible flow of ions and small but negligible change in membrane potential.
The chloride "clamp" or "shunt" will work by opposing any voltage change away from the reversal potential of chloride. The same is really true for any conductance that is open: membrane potential is a weighted sum of the contributions of all permeable ions, so when you open a conductance with a reversal of -70 mV the resulting potential with any other conductances open will be closer to -70 mV than it would be otherwise. See also https://en.m.wikipedia.org/wiki/Goldman_equation

Thank you. I understand what you are telling. So in other words, if an excitatory end synaptic potential were to arrive at this point, any movement of sodium ions inside will be accompanied by movement of chloride ions inside - in other words, as the membrane potential goes toward nernst potential for sodium, chloride starts moving in and tries to keep the membrane potential close to RMP (Nernst potential for chloride). This makes it difficult to excite the cell. Thank you.

@OneFace Yes, exactly.


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Insect(Ant?) Species Identification - location: Singapore

I saw this arthropod (I am not sure if it's an insect) on November 11 at 10:57, at the Berlayer Creek Boardwalk in Singapore. The Berlayer Creek is a mangrove creek flowing towards the sea. This ant-like arthropod was jaw-locked with a weaver ant for 5 minutes or more, and I found them on the wooden partition that separated the bushes and trees from the boardwalk. Both the weaver ants and the unidentified animal is about 1.2 to 1.5 cm long (head to tip of abdomen)
Does anyone know what it is, and maybe even what was it doing?

Can you please tell much more information about this insect like no. Of legs , body structure, winged or not

I see three ants here: two seem to be of the same species (in red) and are somehow in a fight (usual ant business) with another, larger ant species (in blue):

All three have an ant-characteristic habitus:

a flattened head with large eyes and strong mandibles
long (elbowed) antenna and legs
a distinct thorax
a petiole (connects thorax and abdomen)
a distinct, segmented (and usually large) abdomen

... which you already correctly identified for two of them (the "weaver ants").


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Sleep stages and rythm
I would like to get a rough understanding of sleep stages and their rythm, especially in relation to my experiences with sleep.
Disclaimer: I hope to get explanations to my experiences with this post. I do not seek medical advice here, for this i consulted a medical professional. But they couldn't give me satisfying explanations.
If i sleep 6 hours (+- 30 min) i have an easy time getting out of bed, feel well rested and energetic throughout my day. 6 hours has been my average for the past half year or so.
If i sleep more (e.g. 8 hours) i experience the opposite. I have to drag my self out of bed and feel tired for hours to come. I also don't "fully recover" to the point i feel like with 6 hours of sleep. In the past i used to have an 8 hour schedule. But i was aware of the 6 hour behavior and abused it on days i needed an energy boost.
If i sleep until i wake up by my self (10-12 hours usually) i do feel well rested, but have a slower start in the day than with 6 hours. I usually try to avoid sleeping in this long.
From what i understood this experience is related to the sleep stage i am in when i wake and 6 hours seems to hit the "sweet spot" for me. Altho i don't know any other span that would result in the same experience. So im asking my self the following questions

Which sleep stages are there and how do they influence you when you wake during them?
Are there ways to "schedule" these stages to shift my 6 hour cycle to 8 hours?

Sorry if this post isn't in the right place here. Let me know and i will remove it.

The background information you give and your second question place this post in the "medical advice" category, even though that may not have been the intent. If you remove all that, it boils down to a very broad question that shows no evidence of research, something this site strongly advises in order to get an answer. Sleep is complicated; you can start here. You can change your sleep pattern for the better, but you need a good sleep specialist's help.

I think there are some good questions in there but as anongoodnurse says you'll need to separate them from medical advice and also separate them from "tutorial":: Stack Exchange is for specific questions with specific answers, there are entire books written about sleep stages and their rhythms. It would be better to start reading about this on your own (Wikipedia is a decent starting place) and then as you come across things that are unclear you can ask questions here about those.


text:
Is there potential to modify GM crops to inhibit their reproduction with non-GM crops?
I've been reading on terminator gene sequences and was wondering whether the same technology could be applied to GM crops to prevent transgene flow. Turns out Monsanto had developed the technology but pledged not to use it in their crops, from what I gather because it would have forced farmers to keep purchasing new seeds from the company annually.
Thus my question is: how feasible is it to genetically modify GM crops so that their gametes produce healthy offspring when crossed with other GM crops, but produce lethal mutations to the embryo if crossed with a non-GM crop in order to eliminate the possibility of transgene flow?

I can imagine a couple of different ways to do it. One would be "terminator" seeds of the kind that you mention. Another might be a gene drive style system to make GM-wild hybrids sterile.
I would argue that it's feasible right now to use the GURT systems such as terminator seeds to prevent cross-breeding- after all, you'd just have to set up the genetic switch to respond to a stimulus that you can control, and once the seed grows feral without the right stimulus, it becomes sterile or non-viable (see figure from wikipedia).

The problem, as with any bioengineering, is that biology loves breaking rules and escaping from these kinds of systems in the wild under intense selective pressure.
This kind of mutational or epigenetic escape from the lethality system is probably rare enough to still make it worth it to Monsanto to develop the tech (especially when complemented with intellectual property legal instruments), but still plausible enough to freak out folks who don't like GM organisms.


text:
Insect identification request : is it any species from muscidae family or some another?
I belong to Haryana , India
Sudden I found this type of insect in my classroom
and it stung me suddenly because ,I felt itching in my hand for about 15 mins , so please tell me, is it poisonous or not and which type of Arthropod is it ?
Characteristics:-
Two horn like protrusions on its head ,
A stingy tail,
Eyes are not clearly visible,
Winged ,
1-1.5cm in size
(Sorry for blurred image )

The photo is far to unclear to be able to tell anything other than "winged insect" I can't even tell if it could be a bee or a fly.

I got it , it is a horned treehopper which is found in UK, US and India

From the wings, it must be an Auchenorrhyncha, likely a Membracidae species. So, I wonder how it could have bitten or stung anyone...
This one looks similar and occurs in India: https://www.projectnoah.org/spottings/16531012

I am also confused that , which type of eyes this treehopper has ..... These are not ommatidia not simple eyes but which type

It's a treehopper (membracidae) from the genus Oxyrachis. They do not sting or bite. Identifying the species is impossible due to the quality of the image, but here are a few:

O. tarandus

O. versicolor

O. sinensis


text:
What components of a neuron are impermanent during the host organisms's lifespan?
I understand that a neuron's dendrites can die, and new ones can grow. To what extent are other components of a neuron impermanent during the host's lifespan? Do we need to go to the atomic level to find impermanence in the soma and axon?


text:
What are the $2^{23}$ combinations in gamete fusion?
According to my textbook, when two human gametes fuse, there's $2^{23}$ different combinations of chromosomes, but I don't see how that is. The chromosomes are homologous, so they don't have any choice to make, and if they did have a choice to make, there'd be a different formula. Are there two oocytes perhaps, and each chromosome in the sperm can chose either one of the homologous chromosomes that exists in the respective oocytes, a choice available to each of the 23 chromosomes, thus yielding $2^{23}$ possibilities?
EDIT:
My textbook made the above claim as a sidenote to its explanation of meiosis. See my translated quotation under (bold made by me):

Therefore, four possible gametes can be formed (BR, Br, bR and br). If we take all 23 chromosome pairs into account, it will be almost 8.4 million ($2^{23}$) combination possibilities. And when two gametes are finally to fuse, the number of combination possibilities increase to almost 70 000 billion ($2^{23} \cdot 2^{23}$).

As you can see, my textbook says the fusion of gametes can happen with $2^{23}$ different combinations of chromosomes. Since I think I've read somewhere that the (pre?)fetus is triploid at some point, it makes sense to me that these combinations come from the fact that each chromosome from the sperm can pick a homolog from either of the two homologs available from the two oocytes. That's $2^{23}$ possibilities (assuming the sperm comes with only Xs).
My textbook is Naturfag Påbygging, by Aschehoug.

The book says when gametes are formed, not fused, is when there are 2^23 combinations. Where are you getting this triploid idea?

@BryanKrause No, the book says there are $2^{23}$ combinations when a gamete are formed and then another $2^{23}$ possibilities when they are later fused. Also, I got the triploid idea from double-fertilization, so nevermind that, I didn't read it properly the first time.

I think it is difficult to judge the original text on the basis of a translation, but it seems to me to be, at the best ambiguous, and, at the worst, wrong. I think that this ambiguous explanation is widespread and a source of confusion that is not easily remedied by "homework". I think that the question is useful in focussing on this and the downvotes should be reversed. Considering the nonsense we have to put up with from drive-by members of other SE sites, we should consider this question from a genuine student of biology. I have edited the title to fit the situation better.

The calculation is actually quite simple. Each gamete can contribute one of two sister chromatids for each chromosome, so that in humans (with 23 distinct chromosomes) the number of possible combinations in the progeny cell resulting from fusion of the male and female gametes is:

423 (aka approx. 64 trillion  — actually approx 70 trillion)

The number 223 (aka approx. 8 million — hence the erroneous 64 trillion in the source cited below), much loved by various sources including the poster’s text book, is the number of possible combinations of sister chromatids for each individual male or female gamete before fusion.
This is explained with illustration in Biolibre texts in the section entitled “Independent Assortment and Random Fertilization”.
I have no idea why there is an obsession with the number of pre-fusion combinations when the interest of the reader is surely the number of possible outcomes. As a non-biologist the difficulty for me in understanding the explanations I have read is the way that the genetics and cell biology are dealt with together. I admit that the cell biology is important, but if I had to lecture on this topic I would do the genetics first, and then the cell biology.
This explanation is hinted at in the comment from @BryanKrause, but I think that the textbook is at fault, and the poster’s confusion is justified.

The 2^23 number is useful in describing the meiosis process of gamete formation, which occurs before any interaction with any other gamete is relevant. With crossover it's of course also wrong, but still a useful starting point.

Shouldn't it be that there are 2^23 different types of gametes possible from a single individual with 23 chromosomes? The math behind it is as follows:
Case 1: Only one chromosome.
Let's say, from the diploid precursor with 2 homologs of chromosome 1. Half of the gametes would be with the 1A homolog, the other half with the 1b homolog. So, 2^1 types of gametes.
Further cases: More chromosomes.
Consider two chromosomes, 1 and 2, each with 2 homologs (1A, 1B and 2A, 2B). Because each chromosome assorts independent of every other, 2^2 (= 4) possible combinations are possible. 1A-2A, 1A-2B, 1B-2A, and 1B-2B.
Extending the math, this would amount to 2^23 combinations for 23 chromosomes, leading to these many (~8.3 million) gametes from a single human.
Each of these haploid gametes from a male, would combine with a gamete from a female. In each successful fertilization event, the resulting cell would have 46 chromosomes, restoring the diploidy.
I think your textbooks arrives at the 2^23⋅2^23 (= 70,000 billion) by taking into account all the combinations. Since each of the 2^23 male gametes can combine with each of the 2^23 female gametes, the overall combinations come out to be just that. I don't know where you got that fetus is ever triploid (will be happy if you share the source). I still cannot relate this to two oocytes. I'm saying this because your textbook also doesn't mention anything about 2 oocytes (I'm assuming). It just states a combinatorial fact.

This is not what I am wondering about, but it is related. See my edit. My textbook claimed what it did as side note to exactly this.

I think your textbooks arrives at the 2^23⋅2^23 (= 70,000 billion) by taking into account all the combinations. Since each of the 2^23 male gametes can combine with each of the 2^23 female gametes, the overall combinations come out to be just that. I don't know where you got that fetus is ever triploid (will be happy if you share the source). I still cannot relate this to two oocytes. I'm saying this because your textbook also doesn't mention anything about 2 oocytes (I'm assuming). It just states a combinatorial fact.

Ah yes of course, that makes sense. It is the only interpretation that makes sense thus far, so I will accept it if you make that into your answer :)


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At which point does the physical change in evolution occur?
So you go from homo erectus to human for example. At which point do the actual physical changes take place. Does it happen in the embryo, is it only a change in DNA at a very early stage in the new animal or does it happen when the animal is growing or has fully grown?
And which body parts change first, what is the order of sequence?

You've essentially asked, "Which came first, the chicken or the egg?" Obviously reptiles laid eggs, so eggs. But the first chicken egg, was it laid by a chicken? Chicken first? Or did the not-quite-a-chicken ancestor lay the not-quite-a-chicken-egg that became the first chicken? Egg first? The point is, either way, the two of them, the ancestor and the chicken, had to be extremely, exceedingly, unimaginably similar in appearance. That's the point at which physical changes in evolution take place.

It’s not clear to me what you are asking. Changes in DNA are required for changes in the organism, which goes through an embryonic stage. Are you asking at what stages or tissues a mutation in DNA can occur that will produce a heritable change in an animal? And the answer to the last question surely depends on the nature of the overall evolutionary change and even then can vary. And please finish the [Tour] to find out how this site works, and the Help on asking questions.

@anongoodnurse "Had to" is a tiny bit too certain.  Punctuated Equilibrium events do happen occasionally.  It's just sort of like winning the lottery.  More like "the two of them, the ancestor and the chicken, were so likely to be extremely, exceedingly, unimaginably similar in appearance that we can basically assume they were in any case where we don't have evidence to the contrary."

@Jeremiah - I agree that some changes occur suddenly, but those are so rare as to easily allow a "had to". The difference between the red jungle fowl and a domesticated chicken is that one gene changed enough to allow a harder shell. Look at a picture of the red jungle fowl and tell me it doesn't look like a handsome rooster to you. The mutation, btw, occurred several times in different locations. No one is recorded to have exclaimed, "Omg! A CHICKEN!"

@anongoodnurse Yeah I'm not really commenting on the chicken in particular.  The thing is though that a red junglefowl is just a wild chicken.  Domestic chickens are a subspecies of Gallus gallus.  They diverged from junglefowl solely as a consequence of domestication.  There was never some species of wild chickens unless you are talking about junglefowl.  Now, could the green and red junglefowl have gotten their different colored feathers all at once?  Yeah.  Color changes are one of the more common single generation shifts so it's totally feasible.  Did they?  Probably not.

@Jeremiah - I believe you and I are pretty much in agreement overall. I agree about feather coloration, but (always a but) having raised many breeds, especially rare breeds, of chickens, those feathers don't look at all different from some of the chickens I raised, especially the crosses.

I'm not sure where any of the "buts" are coming from if I'm being honest. I wasn't attacking your comment even from the start, just pointing out that punctuated equilibrium events occur and that evolution isn't always totally gradual. Like most species, the chicken probably has some stutters and jumps in its history if you go back far enough. An egg probably did hatch at some point that looked very different from its mom.  What this change was and whether it was in a junglefowl or before is kind of immaterial. I don't think we really disagree on anything. I was just clarifying a generalization

It's somewhat unclear what this question is asking, but it seems like it assumes that evolution is some sort of linear process, which it isn't.  You may as well be asking "at what point did latin turn into french".  People tend to overthink evolution, largely due to intentional efforts to obscure its simplicity by certain groups and individuals, but it's a very simple process at its core.  Evolution is just the name we give to the change that happens when selection acts on variable populations with transmissible traits.  If you have a mechanism for generating variability, like mutation and crossover, a mechanism for allowing traits to persist across generations, like heritability, and a selective mechanism, like natural selection, the population will change over time as new traits are generated and the ones that are selected against are pruned off while those that are selected for increase in frequency.
This isn't limited to biological systems.  Languages evolve over time, and are even mapped out using the same cladistic methods that biologists use.  Genetic algorithms like differential evolution are used to find the optimal solutions to complex optimization problems.  Even internet memes undergo a diversification and selection process that maps quite well onto biological evolution.  Any time you have diversity, transmission, and selection, you get the process we have come to call evolution.
Looking at it like this, you can see that it doesn't make sense to ask "what changes first" because that will be radically different from instance to instance.  The diversity generation processes in biological evolution are random.  Nonrandom selection will then prune that down, but what it gets to work with in what order is largely down to a roll of the dice.
There are some general tendencies in this regard.  Changes effecting non-vital systems, for example, are less likely to be deleterious in a way that would cause them to be selected against than more drastic changes, and so more "good" ones would likely pop up before a "good" change happens to show up for something easier to break.  Polygenic traits that are impacted by a number of different genes are also more prone to drift, since a change in any one of those factors will likely not break things too much when others can pick up the slack.  So one could predict that, say, changes to a polygenic, largely aesthetic trait like hair or skin color, would happen more often than something more impactful like a change in skeletal structure or an organ moving to a new spot, not because the mutations themselves are necessarily any more likely but because they are less likely to be selected out when they happen if they aren't immediately beneficial.
This doesn't necessarily help when talking about what changes happened "first" in the transition from one organism to another though.  This is partly because defining when such a change starts is usually very fuzzy, since evolution is generally a very slow, smooth process.  However, there are those occasions where a population diverges very rapidly into something that it makes sense to differentiate into two different species, sometimes in one generation.  On these occasions, it does make sense to talk about a "first" change in the evolution of that species.  The problem is that sudden, all at once changes that actually benefit the organism are extremely rare, and so are the exact opposite sort of "first" changes one would predict using the statistical logic above.  If the new species diverged from it's parent species slowly, but experienced some incidence of punctuated equilibrium during that process, that instance of punctuated equilibrium, statistically, probably happened later than a bunch of smaller mutations.  However, if that punctuated equilibrium event is what caused the speciation event to occur, then the least likely mutation to be first is, in fact, first.
Humans do have evidence of punctuated equilibrium events in our history.  One especially well documented one is the fusion of human chromosome 2, changing our chromosome number from the 24 seen in chimps and our common ancestor to the 23 we have today.  The markers of this fusion are very obvious (it has 2 centromeres) and this simply couldn't have happened gradually.  At some point, a parent with 24 chromosome pairs had a kid with 23, and that kid was probably distinctly different from their parent, though we don't know how.  If that led to a speciation event (actually pretty likely since it would problematize breeding with the parent species) that would be the "first" mutation in that new species history.  If it didn't, then there were probably a million virtually undetectable changes to stuff like fingernail growth and nose hair texture before anything big like that happened.

Human chromosome 2 doesn't actually have 2 centromeres. It has what appears to be remnants of a centromere, and genetic material identical to telomeres in the middle, whereas in "normal" chromosomes, the telomeres are only at the ends, suggesting a fusion (along with banding patterns). But this is a nice explanation, much better than my comment.

Good call.  I didn't really mean two functioning centromeres, but that's definitely worth clarifying, as two actual functional centromeres would make the chromosome nonfunctional and I don't want anyone repeating stuff that is going to get them hammered later when some creationist drills down into the details.  Thanks!

Pedantically, selection is not necessary for evolution to occur, though it is sufficient when combined with heritable differences in fitness and in most cases the more "interesting" contributor to evolution.

True, and I actually find nondarwinian mechanisms of evolution to be plenty interesting, but I thought diving into the weeds of genetic drift and spandrels and heffalumps and woozles was going to be more confusing than helpful when someone was asking a question like this one. Maybe the blue jolly ranchers are gone because they are your favorite, or maybe it's just because you happened to grab all the blue candies, but if someone still doesn't accept that a bag can be cleared of blue candies through random grabbing if you put the non-blue ones back, the second point just muddies the first.


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Could a geomagnetic storm disrupt the functioning of nerves?
It is known that geomagnetic storms can cause power grid outages. Can they also disrupt the functioning of nerves/the nervous system?

We expect questions posted here to show some evidence of prior research effort.


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Are Hardy-Weinberg equilibrium assessment for two alleles on one loci or two locus?
Are Hardy-Weinberg equilibrium assessment for two alleles on one loci or two locus? For instance, when the video says BB Bb bb https://www.khanacademy.org/science/ap-biology/natural-selection/hardy-weinberg-equilibrium/v/allele-frequency is it referring to two alleles, one of A/T/C/G on a position of a chromosome inherited from father and another from mother, or is it referring to two locus, one is one of {A,T,C,G} x {A,T,C,G} the other is one of {A,T,C,G} x {A,T,C,G}, choosing one of the  one from father and one from mother.

Welcome to SE Biology! feel free to take the tour etc. to learn more about the community. Usually we ask for some evidence of prior research via e.g. google or wiki before we answer stuff here. For example, there is a helpful explainer from nature that talks about HW in some detail. If that doesn't answer your question, feel free to come back and update the Q with what's confusing.


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What is the range of motion of a raptor wrist?
I have been trying to find out how much could raptor like dinosaurs move their wrists.
I know that this will vary between species, so let's say for example a deinonychus.
I am aware that the usual movie depiction of pronated wrists is wrong.
But I want to know the range of motion of the real animal.
Sometimes they are drawn with fingers pointing back to the tail, sometimes down to the ground and sometimes forward.
So were they able to rotate the wrist the full 180 degrees or where the truth is?
A couple of examples what I mean.
https://en.wikipedia.org/wiki/Deinonychus#/media/File:Deinonychus_Restoration.png
Fingers down:

Fingers forward (Same wiki page):

Thanks.


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Why are "alanine, cysteine, glycine, and serine" not ketogenic amino acids?
In the figure below,

Purple letters represents both glycogenic and ketogenic amino acids
Brown letters represents glycogenic amino acids, only
Green letters represents ketogenic amino acids, only

https://upload.wikimedia.org/wikipedia/commons/1/16/Amino_acid_catabolism_revised.png
So, the following glycogenic amino acids are also ketogenic;

Threonine, Tryptophan
Isoleucine
Tyrosine
Phenylalanine

However, as can be seen in the figure below, at least the following of these can be converted to pyruvate, which can eventually become acetyl CoA, and in this sense, their carbon skeletons can also be used in the synthesis of ketone bodies.

Alanine, cysteine, glycine, and serine

My question:

Why are "alanine, cysteine, glycine, serine" not ketogenic amino acids, even though they can be converted to pyruvate and thus their carbon skeleton can be used to generate acetyl CoA?

As I understand it, whether it is ketogenic or not should depend on "whether it can be used to synthesize ketone bodies or fatty acids". While pyruvate can be used for glycogenesis directly back through the glycolytic system, some metabolic systems go through acetyl CoA; of course, if acetyl CoA is produced, the carbon skeleton part cannot be used for glycogenesis.
Amino acids that can be converted directly to pyruvate should be able to be converted to acetyl CoA via pyruvate and thus be used in the reaction to produce ketones from acetyl CoA.
Those that must once go through pyruvate (alanine, cysteine, glycine, serine) are not traditionally included in the ketogenic amino acids?
Wikipedia has the following description；
https://en.wikipedia.org/wiki/Ketogenic_amino_acid

A ketogenic amino acid is an amino acid that can be degraded directly into acetyl-CoA, which is the precursor of ketone bodies and myelin, particularly during early childhood, when the developing brain requires high rates of myelin synthesis.1 This is in contrast to the glucogenic amino acids, which are converted into glucose. Ketogenic amino acids are unable to be converted to glucose as both carbon atoms in the ketone body are ultimately degraded to carbon dioxide in the citric acid cycle.

The answer to this question would depend on how one concretizes "degraded directly" in the quoted above.

It always helps to define your terms — so we know what the poster is talking about, and the poster himself does. Please do that — it will probably lead you to the answer to your question.

@David  I added a definition, as far as I know. If there were an additional clause such as "those that cannot become acetyl CoA without going through pyruvate are not included in ketogenic amino acids", then my question would be answered, but I have yet to see such direct language.

I think your definition is incorrect, and I suspect you are not aware of the physiological/pathological context — starvation or diabetes. And what effect does ketogenesis have on acid-base balance? Will expand later if necessary.

Does this answer your question? About the definition of ketogenic amino acid

I now find that your question has been asked before, and that I have already provided an answer from the context of starvation and provision of glucose for the brain. I think it is a much more pertinent answer than the other one, even though it  is losing 0-6 in the scoring stakes. Perhaps you and other readers might wish to reassess it.


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Metabolic significance of aspartate transaminase in mammalian liver
Aspartate transaminase (aspartate aminotransferase) is an enzyme that is abundant in hepatocytes and catalyses the reaction:

(Modified from https://en.wikipedia.org/wiki/Aspartate_transaminase)
There is ample literature available on its diagnostic use in liver disease (where it goes by the abbreviation AST) but much less on its metabolic role. (There is a SE question on its role in gluconeogenesis.)
It seems to me that the roles of aspartate transaminase in metabolism are as follows:

to convert aspartate to oxaloacetate so that it can be used in the citric acid cycle,
to generate aspartate from oxaloacetate and glutamate (in the reverse reaction) for supplying the urea cycle.

However, in the equation above, α-ketoglutarate is 1-carbon longer than its product, oxaloacetate. Therefore I would think that more energy can be extracted from α-ketoglutarate than from oxaloacetate.
So what is the benefit of converting α-ketoglutarate into oxaloacetate if there is a loss of potential for generating energy?

I have edited your question in the light of your explanation. The edits may seem extensive, but the SE philosophy is to try to rescue questions if possible, and I am keen on increasing the representation of biochemical questions. I will provide an answer in due course. If I have misrepresented you, do say. I would note that we avoid non-standard abbreviations such as AST in science (rather than clinical testing) and that all the acids are ionized at physiological pH (as in the formulae) so we refer to the ion (which is also shorter). And they are cycles, not circuits.

@David Thanks for the very nice edit. You have cleared up my questions. Perhaps the significance of the amino acid transferase-mediated input to the TCA cycle is not so much to get energy from the amino acids, but rather to get amino acids of various lengths. Is this understanding correct?

I've answered the question now. Amino transferases are to transfer amino groups, not to generate energy or to alter carbon skeletons.

Summary
The primary metabolic function of aspartate transaminase, like other transaminases is to transfer nitrogen, in the form of amino groups, between 2-oxo acids. These reactions are readily reversible, and so can function in both directions, i.e. in the context of both amino acid synthesis and degradation.
In the liver aspartate transaminase and alanine transaminase are especially important for feeding nitrogen into the urea cycle for disposal as urea. Alanine transaminase transfers amino groups to glutamate, from which ammonium ions are liberated. Carbamoyl phosphate, formed from the ammonia, and aspartate, produced by transamination catalysed by aspartate transaminase, are the nitrogen inputs to the urea cycle. Thus, the poster’s second postulate is correct.
However the poster’s first postulate is incorrect. Aspartate transaminase is not concerned with energy generation, and the demands of the urea cycle ensure that aspartate is normally a product, rather than a substrate, of the transamination in the liver. In certain situations aspartate does feed into the tricarboxylic cycle as oxaloacetate, produced by transamination as shown in the question. This is to replenish oxaloacetate removed for gluconeogenesis, but does not short-circuit the tricarboxylic acid cycle as the α-ketoglutarate consumed in the transamination is subsequently replenished from the glutamate produced.
The central role of glutamate in transamination
The diagram in the question shows an example of transamination, which is a reversible reaction between two amino acid / keto-acid pairs: the amino group of the first member of the pair replaces the keto group of the second member, with a reciprocal replacement of the amino group of the first member by the keto group of the second. In general this allows the distribution of nitrogen to different carbon skeletons to form a balanced distribution of amino acids for protein biosynthesis.
The poster’s question concerns aspartate transaminase, in which one of the pairs is aspartate/oxaloacetate; but before considering this particular enzyme in the context of the liver, I think it useful to emphasize the central role of the other pair — glutamate/α-ketoglutarate — in the uptake and disposal of ammonia. This is summarized in the diagram below:

It can be seen that the formation of glutamate from α-ketoglutarate is the entry point of ammonia into metabolism, and that transaminases allow glutamate to transfer its acquired amino group to produce a range of amino acids. In conditions where excess nitrogen must be removed, glutamate is formed from the transamination of α-ketoglutarate by other amino acids, typically with the liberation of ammonia. In aerobic organisms the α-ketoglutarate is available from the pool in the tricarboxylic acid cycle, but is regenerated and so does not drain this pool.
In simple organisms ammonia is released from the cell as such, but in many animals this is not possible and it must be converted to some other nitrogenous compound. In terrestrial mammals this is urea.
The mammalian liver and urea production
There is a cyclic sequence of reactions — the urea cycle — involved in the formation of urea, which occurs in the liver. It is important to realize that the two nitrogens in this compound, (NH2)2CO, come from two different molecular species.The first is the ammonium ion released by the reduction of glutamate, above, which reacts with carbon dioxide to form carbamoyl phosphate:

The second nitrogen input required for the urea cycle is aspartate, which is also formed from glutamate, but by transferring the amino group of glutamate to oxaloacetate in the aspartate transaminase reaction, but in the reverse direction from that shown in the question:

glutamate + oxaloacetate → aspartate + α-ketoglutarate

At first sight, this formation of aspartate would seem to drain oxaloacetate from the pool of the tricarboxylic acid (TCA) cycle. However the outline diagram below shows that carbon skeleton of aspartate is released from the urea cycle as fumarate. This is an intermediate in the tricarboxylic acid cycle, and regenerates oxaloacetate after conversion to malate.

Alanine transaminase
In the mammalian liver the main transaminase used to transfer amino groups into glutamate is alanine transaminase. This is because glucogenic amino acids produced from protein breakdown in the skeletal muscle are generally converted to alanine before transport to the liver through the blood.
Entry of aspartate into the tricarboxylic acid cycle
The primary role of the TCA cycle is to generate energy by the complete oxidation of the acetyl group of acetyl CoA, derived from fatty acids (especially in the liver) or pyruvate. Oxaloacetate is required for the acetyl group to enter the cycle, and must be regenerated at the end for the cycle to continue.  In the liver — especially in starvation — oxaloacetate from the TCA cycle can be converted to phosphoenol pyruvate for gluconeogenesis, providing essential glucose for the brain and nervous tissues (see this answer). This uses amino acids from the breakdown of muscle protein, as mentioned above, and is illustrated by the red arrows in the diagram below:

The TCA cycle also serves as a pool of certain intermediates that are starting points for biosynthetic pathways: e.g. oxaloacetate and α-ketoglutarate for the several amino acids, and succinyl CoA for porphyrins. When intermediates are drawn off for this purpose they must be replaced or the TCA cycle will come to a halt, and this is accomplished by input from other compounds such as pyruvate and aspartate, when they are available, in so-called anaplerotic reactions. In the case of aspartate, this is accomplished by the reaction catalysed by aspartate transaminase, in the direction shown in the diagram in the question (as pointed out by @user338907). It should be emphasized that this reaction alone could not maintain the TCA cycle, as it would remove α-ketoglutarate from it. The glutamate produced from this transamination must be converted back to α-ketoglutarate via glutamate dehydrogenase or transamination with some other aminoacid/oxoacid pair. Thus, it would be incorrect to think that α-ketoglutarate is being converted directly to oxaloacetate in these circumstances, forfeiting energy that could be generated from an oxidative conversion in the TCA cycle: the overall reaction is the conversion of (external) aspartate to oxaloacetate + ‘amino group’.
Literature
The topic of transaminases is dealt with in an organism/tissue-agnostic manner in most biochemical texts. I therefore suggest this review of the Urea Cycle that appeared in Biochemistry and Molecular Biology Education, and can be accessed without subscription.

Thanks for the great answer.  Your answer seems to extend to the next question, I'm preparing a new thread of questions on this.
The main point of the new question is: as long as we use transaminases, we can just use members of the citric acid cycle (alpha ketoglutarate, or sucinyl CoA) that were on the TCA-cyclethere originally; what is the significance of introducing amino acids from the outside, since it does not seem to increase the number of "molecules that will become OAA".

@BlueVarious — Could you do some reading before posting  more questions. Mammalian metabolism is quite complex and relates to the role of different tissues in different physiological conditions, and should be approached by looking at pathways as a whole and how they interact.

As for the question I was preparing, it appears that a significant portion of the answer is contained in your response to this question. Perhaps a little paraphrasing based on your answer would create a answer to the new question.

Maybe this is it.　https://i.stack.imgur.com/HJNGI.png

@user338907 — I see you've deleted your comment, but on reflection it is particularly relevant to an answer to a question about aspartate transaminase. And, of course, aspartate transaminase can be considered anaplerotic in conjunction with glutamate dehydrogenase (or another transaminase) to regenerate αKG. So I need to modify my answer again. Not a bad thing if it results in something more generally useful. My answer was based on undergraduate lectures I had to give ca. 30 years ago on a subject which was not in my research area. I could do it better now, but it's a little too late.