text:
Structure and reactions of the cofactors of oxidoreductases such as ferredoxin
I have seen the word flavoprotein being used in place of ferredoxin in few places and vice-versa. I have not found any source that mentions them both together and explains the relation between them.
Examples I have found are:
FAD-Flavin Adenine Dinucleotide/Ferrodoxin Adenine Dinucleotide
FNR-Flavo protein NADP Reductase/ Ferredoxin NADP reductase
Is there any relation between the two? Are they the same or do they serve the same purpose?

Have you tried searching for each of these terms on Wikipedia or the like? You need to search for flavoprotein, ferredoxin (not ferrodoxin), flavodoxin, FAD, FMN, NAD and iron–sulphur clusters. In addition, make sure you know what a protein is and what a prosthetic group or cofactor is. Although it appears from the tags you have used that you have encountered ferredoxin in photosynthesis, it is better to first consider these molecules in their general roles in oxidation and reduction reactions. Then tell us what you have found and any remaining difficulties.

i will try to but at max what i have found(and understood) is that they both are have Fe-S in it. i will do using the keywords provided and get back.

i searched using the keywords you have provided and found that the serve the same purpose as oxidants/reductants. so mainly they take up electrons and then release them. am i right? and the iron sulphur clusters also are co factors in this process. so basically they are present wherever there is a need to move electrons?

I have now provided a more general answer for which I modified the title of the question. I dealt with FNR briefly at the end.

Summary
Enzymes catalysing oxido-reductive reactions (oxidoreductases) do so with the aid of non-protein molecules (prosthetic groups or cofactors) at their active sites. The three main types of such prosthetic groups or cofactors are iron–sulphur clusters, derivatives of flavin (FAD and FMN) and nucleotide derivatives of nicotinamide (NAD and NADP). The groups of proteins incorporating these type of cofactors are often referred to by the general terms ferredoxins (also iron-sulphur proteins), flavoproteins, and NAD(P)-linked oxidoreductases, respectively.
Introduction
The vast majority of enzymes are proteins, linear polypeptide chains folded into specific but irregular spheroidal shapes. In addition to interacting with the reaction substrates, the amino acid side-chains of the polypeptide chains participate in the actual reactions catalysed by many enzymes, and in many cases are sufficient for the catalytic properties of enzymes. However for the catalysis of some sophisticated reactions, additional non-protein molecules are required — metal ions or organic molecules — known generally as ‘co-factors’, ‘co-enzymes’ or ‘prosthetic groups’. This is the case for the various enzymes termed oxidoreductases, which catalyse oxidation/reduction reactions, involving the transfer of electrons.
Nucleotide derivatives of nicotinamide in NAD(P)-linked oxidoreductases
The cofactors found most frequently in oxidoreductases are nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP). The pyridine ring of the cofactor is the electron acceptor, and the oxidized and reduced forms are termed NAD+ and NADH, respectively.

[Own diagram]
Proteins with bound NAD or NADP (non-covalently) are the most common type involved in oxido-reductions, and have systematic names composed of the cofactor, substrate and ‘oxidoreductase’. e.g.
Systematic Name: lactate:NAD+ oxidoreductase
Common Name: lactate dehydrogenase)
Flavin Nucleotides in Flavoproteins
The other common cofactors in oxidoreductases are flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN). The isoalloxazine ring is the electron acceptor, and the oxidized and reduced forms are termed FAD (FMN) and FADH2 (FMNH2), respectively.

[Adapted from section 14.3 of Berg et al.]
Proteins containing FAD or FMN are called flavoproteins, and are less abundant than NAD(P)-linked oxidoreductases, and a few of them actually perform non-redox reactions. Example of nomenclature:
Systemic name:  short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
Common name: short-chain acyl-CoA dehydrogenase
Iron–Sulphur Clusters in Ferredoxins
Whereas the above two oxidoreductases are common in intermediary metabolism, those containing iron–sulphur clusters (some of which are known as ferredoxins) tend to be involved in more specialized and ancient reactions, such as photosynthesis, tagged in the question. The diagram  shows one particular type (2Fe–2S) of iron–sulphur cluster and its covalent attachment to the ferredoxin through cysteine residues. 4Fe–4S stoichiometries are also found, as well as some others.
The electron transfer involves changes in the oxidation state — Fe(II)/Fe(III) — of the iron.

[Adapted from section 19.3.3 of Berg et al.]
The figure also provides a good illustration of the relationship between a co-factor and the protein in which it resides.
Example of nomenclature:
Systematic name: hydrogen:ferredoxin oxidoreductase
Common name: ferredoxin hydrogenase
The situation here is complicated by the fact that iron–sulphur clusters are found in other proteins besides those termed ferredoxin, including some specialized oxidoreductases involved in the electron-transport chain, and in nitrogenases. The term ferredoxin is historical rather than systematic.
Differences between these oxidoreductase cofactors
The specific roles played by these three cofactors in oxidoreductases is a topic of its own. However, it should be mentioned that an important difference is their standard reduction potentials, the biochemical background to which can be found in Section 18.2.1 of Berg et al., available online.
Ferredoxin-NADP+ reductase (FNR)
Electron transport occurs between the different cofactors in certain circumstances, one of which is photosynthesis where electrons are transferred from ferredoxin to NADP+. The enzyme catalysing this — Ferredoxin-NADP+ reductase — uses the third type of cofactor — FAD!


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What causes midcycle FSH surge in the menstrual cycle?
I have encountered contradictory attributions to the causal factor of midcycle FSH surge. Whereas some sources attribute it to the relatively high estrogen levels (1), others say it is because of increasing amounts of progesterone (2).
I am confused.
(1) http://www2.hsc.wvu.edu/som/physio/classes/pcol260/classroom/notes/reproductive.htm
(2)
https://www.ncbi.nlm.nih.gov/books/NBK279054/#!po=1.17188

The LH surge is began by a impressive rise of estradiol produced by the preovulatory follicle and results in subsequent ovulation.
The LH surge stimulates luteinization of the granulosa cells and stimulates the synthesis of progesterone responsible for the midcycle FSH surge.

If this is true, why are FSH levels kept low by progesterone and estrogen secreted by the corpus luteum in the mid- and late-luteal phases of the cycle?

source: Stack Exchange

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

sort: votes


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Can a virus infect a virus?
As far as I know a virus can infect any cellular organism from a bacteria onwards, including protists, algae, plants, and so forth.
But can a virus infect a virus?

No, it cannot. Viruses infect cells, in order to use the cellular machinery to replicate themselves - viruses themselves do not possess such a machinery, so speaking of one virus infecting another is meaningless.
This does not mean that viruses do not interact: when two viruses co-infect the same cell, the progeny virions may contain parts of the genomes of both viruses. This is how genetic recombination occurs in HIV.
An even more famous example is gene reshuffling of influenza viruses, where an animal virus exchanges its genes with a human virus, producing a new human strain. In the popular culture some of these a famously named after animals whose virus contributed or animals where the reshuffling has occured (bird's flu, swine flu, etc.)
Update
It is worth mentioning the satellite viruses, which are viruses that lack the proteins necessary to catalize the replication and possibly even the genes coding for their capsid proteins (in which case they are more properly called satellite nucleic acids rather than satellite viruses). These viruses are dependent on a helper virus to carry the missing genes. This is not characterized as parasitism, but it is rather close.
Update 2
A special type of satellite viruses, called virophages, actually do exhibit characteristics of parasitism in respect to the helper virus:
Unlike satellite viruses, virophages have a parasitic
effect on their co-infecting virus. Virophages have been
observed to render a giant virus inactive and thereby
improve the condition of the host organism.

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


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SPR TRIS or PBS buffer
Hey guys I want to ask why I can't get any binding interaction if I use TRIS-NaCl buffer for protein quantification using aptamer as its bioreceptor. But I can see the binding interaction if I use PBS buffer
The procedure step for my experiment :
1.) Self Assembled Monolayer (24-48 hrs) - NHS/EDC Activation (wash with acetate) - Streptavidin (Acetate buffer) - wash with acetate - wash with TRIS - ETH Blocking - wash with TRIS - Aptamer biotinylated (TRIS buffer) - Protein (TRIS buffer)
all washing buffer are using TRIS or PBS
And down below (my other method) I tried to exchange the buffer from PBS to TRIS after aptamer injection
2.) Self Assembled Monolayer (24-48 hrs) - NHS/EDC Activation (wash with acetate) - Streptavidin (Acetate buffer) - wash with acetate - wash with PBS - ETH Blocking - wash with PBS - Aptamer biotinylated (PBS buffer) - Buffer exchange (PBS to TRIS) - Protein (TRIS buffer)
I can see my aptamer signal in 1st and 2nd method, but still no binding occurred between my aptamer and my protein in TRIS buffer.

I don’t quite understand your protocol, but EDC/NHS activated carboxylates react with primary amines. Tris contains a primary amine and will be present at a much higher concentration compared to streptavidin.

Are the pH and ionic strength of the two buffers the same?

I presume the aptamer is biotinylated; if not, that’s a likely reason for the outcome.
Have you used a biotinylated positive control to confirm the surface is functional with PBS? I understand you want to buffer exchange to Tris, but this positive control in PBS buffer is important.
Amine coupling involves covalent attachment of the 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) to carboxylate on the chip surface, followed by replacement of this adduct with N-hydroxysuccinimide (NHS), thus creating an active surface to crosslink primary amines at slightly acidic pH. Then the unreacted active surface is quenched with ETH. Residual active surface would react with Tris that contains a primary amine.
Perhaps the ethanolamine blocking agent may not have completely inactivated the active surface following streptavidin amine coupling, enabling crosslinking of Tris buffer to that surface and impacting the ‘Protein’ capture?
Other possible reasons: Binding of the aptamer to streptavidin may sterically hinder binding of the 'Protein.' Also, the loss of the proper secondary structure of the aptamer may impact the 'Protein' binding. Perhaps refolding the aptamer prior to streptavidin capture may help?
Edit: Differences in pH and ionic strength may impact 'Protein' binding to aptamer when tested in Tris versus PBS buffers.

Yes, the aptamer is biotinylated thus it can bind with the streptavidin. Yes and I also know that NHS ester will be released because of the primary amine of the TRIS buffer and create covalent amide bond.
But I'm pretty sure right now that my ethanolamine blocking agent is deactivated all the NHS ester residue because I also double-check using BSA blocking to my SPR surface. That's why I'm pretty confused why with PBS my aptamer can catch the protein and with TRIS can't

It looks like the ethanolamine quenching may not have been sufficiently effective?

Oh I forgot to mention that I can see my aptamer signal, but when I inject my protein I can't see its binding interaction and the signal keep going flat (not indicating any changes at all)

OK. Increased RU counts is a good sign. Has this lot of protein been confirmed to bind this lot of aptamer by a different technique?

I got this aptamer and its protein from my co-worker and he said he already test and confirm it with ELISA.

But why I can see the binding interaction of my protein and its aptamer using PBS buffer?

I presume you have a control surface with no streptavidin, but everything else to confirm the ethanolamine quenched the residual active surface? Also, is the positive binding of the protein to its aptamer using PBS show reasonable dissociation rate constants?

Yes, and i see reasonable association and dissociation rate constants of different kind of concentrations

At what pH was the 'Protein' binding done in the PBS and Tris experiments?

Ah yes maybe because the pH and ionic strength difference, so because of that my aptamer cant bind with my protein properly even though my aptamer can bind with streptavidin.


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Did Mendel believe that proteins are hereditary substances?
Scientists first thought that proteins, which are found in chromosomes along with DNA, would turn out to be the sought-after genetic material. Proteins were known to have diverse amino acid sequences, while DNA was thought to be a boring, repetitive polymer, due in part to an incorrect (but popular) model of its structure and composition.
Was Mendel (1822-1884) one of these scientists?
Note that in 1869, Friedrich Miescher isolated "nuclein," DNA with associated proteins, from cell nuclei. He was the first to identify DNA as a distinct molecule.

Did Mendel really even know about proteins?  AFAIK they aren't really relevant to his work - just as Darwin didn't need to know the mechanisms of heredity to know, from observation, that it exists.

@jamesqf You ignored the note that I added to this question. He probably heard about proteins and nucleic acids in his lifetime.

I would say "possibly" rather than probably, given his apparently rather isolated life.  But the point I was trying to make is that (at least AFAIK) nothing in Mendel's work requires theorizing about the actual underlying mechanism of heredity.

Your sense of scientific history is a little disoriented. Few geneticists were interested in the chemistry of the phenomenon until after the second world war. Genetics textbooks in the 1960s hardly concerned themselves with this. Mendel was a monastic plant breeder with acute observation and deductive powers. He was not a scientist in the  modern sense, and cerainly had no interest in (and probably knowledge of) chemistry.

The first person to directly indicate a linkage between the hereditary material and enzymes was Garrod in 1902, based on the observation of the hereditary enzymatic disorder alkaptonuria. This is after Mendel's death.
The tetranucleotide hypothesis (i.e. DNA is not informative) that you refer to seems to have been formulated around 1910. So there is no way that Mendel knew about that.
It was not even proposed that proteins were composed of amino acids before 1902. No protein was sequenced before 1950. So Mendel had no idea what sequences or amino acids were, for any biopolymer.
It is formally possible that Mendel knew at some point about Miescher's result, but I'm not aware that he was at all interested in the chemical nature of Mendelian factors (what we now call "genes"). I agree with commenter @jamesqf on this point.
It was not immediately obvious to anyone that there was a discrete mapping between phenotypes and specific agents such as proteins. The major theories of inheritance at the time came from biometricians such as Galton, who believed that inheritance was driven by a blending-like mechanism (more or less), based on phenomena such as regression to the mean. They weren't really interested in the chemical basis either.
Mendelian genetics was only rediscovered around 1900 (Mendel was basically ignored during his lifetime), after which the debate started to consider the question of discrete genetic factors.
In short, I don't think that there is any evidence that Mendel had any interest in chemistry or the chemical relations of the organismal characters he studied.


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How can good Shine–Dalgarno or Kozak sequences enhance translation?
In prokaryotes the Shine-Dalgarno sequence, a polypurine consensus sequence near the initiation codon (usually AUG), is required for the mRNA to bind to the small ribosomal subunit, allowing initiation of translation.
In eukaryotes, the ribosome binds to the 5′ cap of the mRNA, and then moves along it until it finds an initiation codon — usually the first initiation codon — for initiation of translation (the Kozak ‘scanning’ model). In some cases the first initiation codon is skipped, and this appears to because the sequence context of the mRNA — sometimes called the Kozak sequence is in some way unfavourable.

I have read that either a Shine–Dalgarno or Kozak sequence that is
optimal for recognition by the small subunit will greatly enhance
translation. However I cannot understand why this should be so, as the
actual insertion of amino acids only occurs in response to base
triplets 3′ of these sequences.

In addition, for eukaryotes, it would seem that the scanning ribosomal
subunit is skipping the first AUG it encounters if a second or
subsequent one is in a ‘better’ sequence environment. If this is the
case, what mechanism enables such a selection to occur.

While this is a good question with plenty of detail, it's often helpful to cite sources (e.g. links to journal articles, textbooks, wikipedia, or other resources) to maximize clarity and reliability.

As what I regarded as a poor question has resurfaced with an answer, I have edited it to remedy its scientific deficiencies (other than in the logic).

I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions.
At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes happening at a single molecule. Thus, what changes with different sequences is a rate at which some step occurs (e.g. rate of ribosome assembly, rate of translation initiation, rate of start recognition); none of these steps will occur with 100% probability on every mRNA molecule.
What this means is that you can write down equations for kinetic models of translation, allowing us to apply principles of mass action and rates of reaction from elementary chemistry. Having a higher rate of ribosome affinity for a sequence is therefore similar in effect to just having more mRNA, in the sense that in both cases you will do more translation and make more protein.
Thus, it might be easier to use the terminology of "strong" and "weak" SD/Kozak sequences. A strong sequence has a high rate of reaction and a weak sequence has a low rate of reaction. Here, the "reaction" in question is ribosome binding, or translation initiation, or whatever process we're currently studying.
Now, as to the specific questions:

Sequences alter the rate at which downstream processes occur. So, e.g. a weak Kozak sequence will often simply not initiate translation, and the ribosome will fall off without translating anything. This will almost never happen with a strong Kozak sequence, so a strong Kozak is more "efficient" in the sense of more reliably leading to translation. A strong Shine-Dalgarno sequence increases the rate at which ribosome binding occurs.

Both ribosome binding and translation initiation are necessary for protein production, so if you increase the rate at which these processes occur, you increase translational efficiency in each case.

There is no "foreseeing". Think about this mechanistically. The ribosome scans 3' along the mRNA, starting at the point of attachment. Also, each ribosome attachment to an mRNA can only start one translation event. Once a ribosome stops scanning and starts translating, it does not recognize subsequent Kozaks.

Thus, if there is a strong Kozak sequence, then translation will almost always start at the strong sequence, and will never have the opportunity to start at a sequence further 3'. It is mostly only when a 5' Kozak is weak that further Kozaks get recognized at all ("leaky scanning"):

The first start codon closest to the 5′ end of the strand is not always recognized if it is not contained in a Kozak-like sequence. Lmx1b is an example of a gene with a weak Kozak consensus sequence.[22] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. Exceptions to the first AUG rule may occur if it is not contained in a Kozak-like sequence. This is called leaky scanning and could be a potential way to control translation through initiation.[23] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon. (Wikipedia)

So it's not that Kozaks are required, necessarily. You just need some set of circumstances which increase the probability that the ribosome starts translating next to a start codon. The Kozak simply happens to be an efficient way to get a ribosome to start translating. The closer a sequence is to the consensus Kozak sequence, the more efficient it is, because the probability of translation initiation is higher.

Oh thanks! So to clear my understanding, for q1: 'efficiency' means how strong are the interactions between the ribosome and the SD sequence. If it is stronger, the ribosome will less likely to detach during translation (i.e. higher processibility), hence a better efficiency? (i.e. higher efficiency = stronger ribosome binding)

for q2: when the ribosome slides to a strong Kozak sequence, it will start translation there no matter if there are even stronger Kozaks downstream? But sometimes when the first Kozak is too weak, leak scanning occurs i.e. subseuent Kozaks are selected?

@Questions comment 1: I would say that "efficiency" is a very high-level term that just means "how much protein do I make for a fixed concentration of all reactants". I would agree that higher affinity of sequence for the ribosome (what you seem to call "interaction") does lead to higher efficiency, but efficiency is a much larger outcome, really the product of (ribosome affinity of mRNA) * (strength of translation start site/kozak) * (ability to recruit co-translational helper complexes) * (...a lot of other stuff). A sequence on its own is not "efficient", it doesn't do anything.

@Questions comment 2: I believe that is approximately correct. There is always a small chance that the ribosome fails to start translation, and therefore downstream Kozaks get a chance. Likely there is some weird mechanism by which a downstream Kozak can conformationally constrain upstream Kozaks; for example viral translation is weird and there are often internal ribosome entry sites (IRES) and weird stuff like that. But for normal canonical translation, I think that a strong first Kozak dominates everything else. Though I could be wrong in some detail, biology is weird!

@Maxiilian Press Thanks a lot for the clear explanation :)

The argument regarding the insertion of amino acids in response to a section of the mRNA 3′ to the (usually) AUG initiation codon — an argument only applicable to eukaryotic translation — is easily refuted. If the ribosome isn’t associated with the mRNA it can’t translate it. This represents the extreme case — translation or no translation. However if there are factors that have an effect on the efficiency of this association, they will have a graded effect on the rate of translation. It is conceivable that different mRNAs may be translated at different rates or in different physiological circumstances.
It is important to realize that the mechanism of attachment of mRNA to the small ribosomal subunit is quite different in prokaryotes and eukaryotes, so each must be considered separately. This is important because the first unique step in any biochemical process is the step at which control can be exerted most efficiently†.
In prokaryotes the first step in initiation is the attachment of the mRNA to the small ribosomal subunit by base-pairing between the Shine-Dalgarno sequence in the mRNA and a complementary sequence in the 16S rRNA§. This positions the AUG for interaction with the initiating fMet-tRNA. A perfect base-pairing with the rRNA is not required, and Shine and Dalgarno sequences differ in the number of base-pairs, and hence the strength of interaction. If binding of the mRNA to the ribosome is rate-limiting, this provides a potential mechanism for regulating the rate of translation of different mRNAs. There are some examples of poorly expressed mRNAs with poor Shine and Dalgarno sequences, as well as mutational experiments, that provide support for such regulation.
In eukaryotes the first step in initiation is the attachment of the mRNA to the small ribosomal subunit by  binding the 5′ cap. This is a complex process involving many initiation factors and is a logical point for regulation to occur. In fact this is the case, the activity of cap-binding initiation factor 4E being regulated by the phosphorylation of a protein that binds to it. In contrast, it is difficult to see how the ‘goodness’ of the subsequently encountered environment of the first AUG could have a regulatory effect — either the ribosome stops and the met-tRNA it is carrying at this stage interacts with the initiation codon, or it continues to the next.
And, of course, it is incorrect to suppose that in the scanning model a mechanism exists for ribosomes to reject the first AUG in an otherwise satisfactory environment because the environment of a subsequent one is better. All that might happen is that a portion of the ribosomes skip the first AUG in a marginal environment and initiate at a subsequent one, producing an alternative protein — a different sort of regulation.

§This sequence is absent from the eukaryotic 18SrRNA subunit, so the Kozak consensus sequence is in no way analogous to the Shine-Dalgarno sequence. The mode of action of the Kozak sequence is, as far as I am aware unknown.
†It is recognized that other factors can regulate initiation. The tertiary structure of the mRNA can affect access of ribosomes to Shine–Dalgarno sequences in polycistronic prokaryotic mRNAs, and the phosphorylation of eIF2 (the initiation tRNA binding factor) can also regulate initiation of eukaryotic translation at a stage later than 40S ribosome binding.


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Do we find protein not of cellular origin in nature?
I read once that we have two sources for proteins:

Protein that is made in cells
Protein that is made in labs

However, based on Miller–Urey experiment, it's argued that amino acids can be made from initial Earth's condition, and from this link, it seems that protein-first world is a hypothesis.
Yet if we accept that proteins could be made before cells, then the process that made proteins in the first place is still out there. This means that we should be able to find proteins outside cells or labs in nature.
Do we find protein not of cellular origin in nature?

I would suggest rewording your question to refer to proteins/peptides/amino acids not of cellular origin instead of "in nature".

Viruses are composed of proteins. They exist outside of cells freely in nature.

Vituses reproduce in living cells and use host cell's machinery to replicate. Thus they don't count.

On our planet, there is such an incredibly massive amount of protein creation by biological organisms (as well as smaller peptide constructs) that it would be essentially impossible to identify any that was created by a natural non-biological process.
Moreover, now that there is life, any location with the right conditions for non-biological creation of protein would likely also be a good place for modern microbes  to take advantage of those same resources to grow themselves, diverting the necessary inputs or quickly eating the outputs.
It is for this reason that we search for precursors of life in space, and have long ago found the basic building blocks. This is also why probes to other planets are carefully sterilized, because otherwise we will never know if life found on Mars is just hardy colonist organisms transplanted from Earth.
To the best of my knowledge, however, no non-Earth molecule has yet been found that has the full complexity of a protein, as opposed to just isolated amino acids.

@user1136 Sure. But if you found material with L-amino acids, you wouldn't know.

We're in agreement: finding proteins based on D-amino acids would be interesting.  I'm saying that if we didn't sterilize spacecraft and we found proteins based on L-amino acids, we might have a hard time determining if it came from the planet or the spacecraft.


text:
What tests are available to detect C. Botulinum/Botulinum Toxin in fermented meats?
I am interested in the preparation of fermented dry-sausages (salamis, summer-sausages, etc) where due to the humid anaerobic atmosphere inside the salami. It is a good environment for C.Botulinum spores to grow.
The mainstream food safety practice is to use Sodium/Potassium Nitrate or Nitrate + Nitrite, which are suspected carcinogens.
I would like to prepare fermented dry-sausages without Nitrate usage and test the finished product after for the presence of C.Botulinum?
Salamis are usually 10-50cm, and if I were to consume or sell them it is viable for me to test each salami. Thus, I am also interested in the viability of taking a few cuts out of a salami to test for C.Botulinum presence, would a small cut on the sausage be sufficient, or it might be that there is a growth of C.Botulinum in a small part of the sausage not throughout the whole sausage making testing a sample not likely to reveal whether or not other parts of the sausage have C.Botulinum.
Also concerned about whether lack of C.Botulinum is sufficient proof that the salami is clear, or whether the bacteria might have died off after producing the toxin. The same concern about whether if there is toxin production should it be throughout the salami or in isolated pockets making testing a small sample from a large salami not viable.
Based on this situation what would be a test that is will allow me to detect whether a salami is likely to cause botulism?
Is it as simple as some gram stain and an optical microscope?

Isolated pockets is quite likely - so testing would be ineffective.


text:
Are antibodies removed before blood transfusion
I am an O blood group person meaning, I can donate my blood to all as I don't have any Antigen A and B. But my body does contain antibodies A and B right?
If they were along with the donor blood, wouldn't they cause clotting with the recipients blood?
We spent a whole period over this. My teacher said they probably remove the antibody before transfusion, but I couldn't find much info on that. I postulated that these antibodies can not work outside the donor body for some reason.
Thanks for the help

I quote from the below.
Groups and Red Cell Antigens
by
Laura Dean (page 7). Available at:
http://www.ncbi.nlm.nih.gov/books/NBK2265/
"Red blood cell incompatibility may also occur when the patient's RBC antigens are attacked by antibodies from the donor's plasma. This tends to be a minor problem because of the small amount of antibody present in the donated plasma, which is further diluted on transfusion into the recipient's circulation."
I dont think the antibodies are removed, but in countries with a good medical system I believe the matching blood type is always used.
http://en.wikipedia.org/wiki/Acute_hemolytic_transfusion_reaction

"I dont think the antibodies are removed" But isn't O group still considered universal donor. Thanks for telling me it's only a minor problem

O is universal donor.


text:
Hybrid seed production requires a male sterile parent. Why?
Hybridization is the process of crossing two plant species or varieties. In this case, two varieties of plants. In plant breeding, crossing is a very useful technique to improve the features of the offspring. For example, if a maize corn variety has lost yield over the years, it can be crossed to a variety with a higher yield and the offspring will also have a higher yield.
In order to cross these two varieties, the male needs to be sterile. Why is that? I don't understand how the process works and I cannot find the reason anywhere. The answer should be pretty basic, and I think I am missing something that everybody assumes I should know.

male-sterility is not required for breeding.
Male-sterility means that the female acting plant (the plant that will bear the fruit) has sterile male organs (either dysfunctional anthers or sterile pollen). and won't self pollinate. The male-acting plant is fertile.
In monoecious plants this is helpful for breeding because we can't easily provide a controlled pollinating environment by separating the female and male organs
Tomatoes are monoecious (hermaphrodites), self-pollinated. The pollination occurs (usually) before the flower opens. Male-sterility prevents pollination and allows the breeder to pollinate.
Corn is a cross-pollinated plant with some capacity for self-pollination, male-sterility in corn helps ensure that the corn plant is not pollinated by itself.
Male-sterility gives peace of mind and easier breeding techniques but is not a requirement.
You can expand your knowledge using Principles of Plant Genetics and Breeding, Second Edition by George Acquaah. Check chapters 5: Introduction to Reproduction and Autogamy.
Searching "male sterility in plants explained" in google yielded many relevant pdfs.

To get a hybrid you need pollen from a different plant. Corn is likely to self-pollinate if some action is not taken to prevent it. I don't know of sterile males plants - in the US corn belt the self-pollination is prevented by detasseling. Many young people get summer jobs detasseling (cutting off the tassels) for seed corn.

My kids did some tasseling ; It was a good paying summer job. Maybe I can get one to post what they did. I took their word for what they did. I just saw a group of teens in the corn rows ( if they were near the edge of a field.).


text:
How do cellular conditions change the Gibbs free energy of a reaction?
How do cellular conditions change the Gibbs free energy of a reaction?
Taking glycolysis as an example, how exactly would cellular conditions affect the free energy released from this reaction?

https://en.wikipedia.org/wiki/Glycolysis#Free_energy_changes

Standard free energy or actual free energy?

And this wouldn't be a homework question by any chance? In any case, what attempt have you made to answer it yourself?

To understand that, you must have a basic understanding of Gibbs-Helmholtz equation. it states-
$\Delta G'=\Delta G^{'o} +RT\,ln\,(Q) $
Here, $\Delta G'$ = biochemical free energy change & $\Delta G^{'o}$ = standard biochemical free energy change.
Suppose you have a reaction,
$x+FADH_2\rightleftharpoons xH_2+FAD $
So, $Q=\dfrac{[xH_2][FAD]}{[x][FADH_2]}$
Now let's assume that $\Delta G^{'o}>0$.
Hence the spontaneity of the aforesaid reaction (in forward direction) will be dependent on the $\Delta G^{'o}$, which is a function of reaction quotient (Q) as well as temperature (T).
Now, if the body is in lower energy state, i.e. fasting; $\dfrac{[FAD]}{[FADH_2]}$ ratio will be high. So, in order to make $\Delta G'<0$, the following condition must be satisfied $-$
$RT\,ln\,(Q)+\Delta G^{'o}<0$,
or, $RT\,ln\,(Q)< -\Delta G^{'o}$
or, $RT\,ln \dfrac{[xH_2][FAD]}{[x][FADH_2]}\,< -\Delta G^{'o}$
With this reasoning, be it any metabolic pathway; we can predict its spontaneity.

I don't see how this answers the poster's question. You are just explaining how the free energy change allows one to predict the direction of one particular reaction from the concentration of reactants. 2. Strictly speaking the prime indicates "at pH7". So one answer to the question might be that if the cellular pH changes this will alter the free energy change. However, the poster has not responded to either of my pertinent questions, so it is not clear what he is about.

I guess the poster has asked about free energy change in different cellular environment. So I briefly mentioned about different factors.


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Evolutionary selection pressure for human hair patterns?
Are there hypotheses or conjectures that postulate any selection pressures or benefits that account for the patterns of non-pubic human hair?  Particularly:

Humans do not grow notable (i.e., non-vellus) body hair until puberty.
Terminal body hair growth in adults is not only sexually dimorphic but also peculiar in its patterning:

Source
As with any trait: it is quite possible that the evolution of human hair patterns had no selective significance.  It could also have been the result of a sexually-selective feedback loop, and therefore are an arbitrary sex trait.
I am looking for hypotheses or conjectures that suggest some objective benefit to terminal body hair.  I struggle to imagine one particularly because of the sexual dimorphism in adult hair patterns:  E.g., if facial hair provides some benefit to men, why would it not provide the same one to women?
If we stipulate that the pattern is only fully expressed in males then it is still peculiar: For example, I can't see any functional characteristic that would make hair on the front torso beneficial while not conferring a benefit if present on the shoulders or top of the torso.

At least some of it is a side effect of the way human skin develops. Humans actually have the same number and density of hair follicles as great apes, it is merely that our hair develops as short vellum hair rather than the thicker, longer hair of great apes. This is a side effect of the same genes that control eccrine sweat gland development, turning on the genes causes the skin to develop more sweat glands at the cost of reducing hair thickness across the body. For humans, a primarily tropical species, having sweat glands was evolutionarily more useful than being hairy, so we largely traded hair for sweat glands. As a result, the distribution of hair across our bodied may be at least in part a side effect of where it would be most useful to have sweat glands. Hair is typically retained in the armpits and groin because it helps trap odors that may elicit sexual signalling.
Hormones may also play a role. Testosterone has been linked to changes in hair development, and may actually be related to male-pattern baldness.


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Can mRNA vaccine have flaws and generate the wrong spike protein?
Someone asked me if SARS-COV2 mRNA vaccine could create the wrong spike protein and have a negative effect on our immune system. Since I know too little about biology I couldn't answer that and started doing some deeper research than I did before on mRNA. But I can't seem to find anything to answer my question (it most probably is because I lack the knowledge in this field).
So here are the two main questions of this problem:

When created, can the mRNA vaccine have flaws and when injected generate a different spike protein than the SARS-COV2 one ?
If so can the spike protein be harmful to our system in any way ?

I am sorry for any term not correct in this context.

The mRNA won't be entirely perfect, but the imperfections will not matter.
The spike protein is big, encoded by thousands of base pairs in the virus. In the virus itself, it's not entirely homogeneous: there are always going to be small mutations that cause different variants to be produced, but nearly all of those are nearly identical.
The mRNA in a vaccine may also have some degree of copying errors introduced during amplification, which will produce some distribution of variants. Though the specifics are different, random copying errors in a synthetic process and random copying errors in natural viral replications will produce qualitatively similar types of distributions (more serious errors producing truncations and recombinations can occur in both as well, but similar arguments apply and they're even less likely to be functional).
Moreover, since only the spike protein is there, it can't actually produce a damaging infection, only teach your immune system what an infection looks like. Finally, since it's easy to validate a batch of mRNA via sequencing, ordinary quality control procedures should be fine to make sure what goes into the vial is what was planned (modulo the variances described above, when they are at a low enough frequency to fall below the threshold of discrimination).
In short: don't worry about the mRNA varying. If you're going to worry about something, worry about the virus varying enough that our nice, tightly controlled mRNA doesn't match it any more.

This answer providea no evidence in support of the statements made, so that although the poster may have accepted it, he has no basis on which to assess whether or not it is correct. Furthermore, by  repeating the unusual term "flaws", without any explanation of what is meant or how you imagine they arise, your answer lacks conviction.

@David What additional details are you looking for? I typically try to answer questions at a level appropriate to the apparent expertise of the asker, thus focusing on what I perceived to be the core of the question, rather than going into full details.

@David you are right I have no basis to really know whether or not this is a good answer. But Jake you can also go into full details, I will read and research terms I don't know of yet.

I would prefer a detail answer even if I can't get everything than an incomplete one.

I've added additional detail to explain the reasoning more thoroughly and precisely.


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Species Identification: Liberian "kiss-meat" snail
Before my wife immigrated to the US from Liberia as a kid, she loved eating "kiss meat". It's a freshwater snail they collect from the swamp during the rainy season and eat as a delicacy, so called because you suck the meat out with a kiss.
Here's a YouTube video of this process, so you can get a good look at the snail and see its habitat (mangroves).
This is the best image from the video that I could find. They've been washed and the rear of their shell has been broken off. I can't get Stack Exchange to let me add a second picture );

I have not been able to find any other references to these snails, except under the name "kiss meat". Would anyone be able to identify these?
(Note: There seems to be a similar looking brackish snail commonly called "African Periwinkle". I don't think this is the same thing.)

Welcome to Biology.SE. It is important that your question contain all the content that will help answer it, without relying on external links like videos that may be deleted sometime in the future. It's fine (and encouraged) to reference outside sources, of course, but it shouldn't be crucial to understanding the question to visit the link.

@BryanKrause Thank you for the feedback! I'll get some pictures added.

It's Tympanotonos fuscatus from West Africa. They harbor near the roots of mangrove at low tide. Due to their tendency to bioaccumulate heavy metals, they have been used in studies of environmental presence of heavy metals, and the samples taken from markets have been found to be excessively high in cobalt and manganese.

Thank you! So it seems they are the same thing as African Periwinkle...

Yes indeed, it's them.


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Questions about "parasite recursion"
So imagine a parasite of a parasite. Imagine a parasite of that parasite. Then imagine a parasite of that parasite, then a parasite of that parasite, and so on and so forth.

Is there a formal term for this?

How frequent does this occur in nature? If it varies, what does it vary by? How many levels down do parasites typically go?

What is the deepest level that has ever been observed, and with what organism?

Thanks

There actually are virophages https://en.wikipedia.org/wiki/Virophage or satelite viruses https://en.wikipedia.org/wiki/Satellite_(biology), so the level should be at least 4 or 5, maybe more.

Hyperparasitism is one possible term. According to the linked article it is commonplace in certain types of insects, but also in fungi. Apparently the cases of at least three levels are known: a fungus on a fungus on a fungus on a tree.


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What material is permeable for plant roots, but "impermeable" for fungi & bacteria?
I'm designing an experiment where the roots of the plant will grow in a sterile environment while the shoot will grow in a non-sterile grow room. For this reason the environments of the shoot and the root should have some form of physical separation.
Is there any material that allows roots to grow through it but will stop fungi and bacteria?

root and shoot grow in different directions. Why can't you sterilize your media and cover it with an impermeable material?

I might have found a solution! Kuijken et al. (2015) first germinate seeds in a sterile eppendorf filled with agar and nutrients. They then cut off the bottom of the eppendorf and stick it through the lid of a sterile plastic jar and pad it with sterile cotton. So I guess they are using the agar as a material that is permeable to the roots and "impermeable" to bacteria and fungi.
Kuijken, R. C., Snel, J. F., Heddes, M. M., Bouwmeester, H. J., & Marcelis, L. F. (2015). The importance of a sterile rhizosphere when phenotyping for root exudation. Plant and Soil, 387(1-2), 131-142.


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What kind of salamander is this?
This guy was found in central Virginia, under a flower pot. He's about 3 inches long, because part of his tail is either missing or it's just short. He looked dried out, so of course I wet my hand, scooped him into a small container, and moved him to our birdbath (which is on the ground and had been recently rinsed so the ground was plenty moist). I ran my hand (still wet) over his back and he seemed happier and started moving around.
However, I can't seem to find on Google just what kind of salamander he is. The VA Herpetological Society has an entry for a Jefferson Salamander, but those are only found in North/West VA. Attached is a picture of him (blurry, sorry) when I found him. I have a video of him coming out of the container and going under the leaves next to the birdbath, but it's too big of a file to put on here. Instead, here is a link to the file in my Google Drive: Salamander
Edit: I checked some pictures I had of him, and he has five toes on his hind legs. He is a dark gray-brown with faint mottling and a semi-light underbelly. Sorry that I didn't say this earlier. Hope this helps!
Can anyone identify him?

be careful of tapwater with amphibians, you probably know, because of the chlorine content.

yea i used spring water for my hand, but I used garden hose water for the birdbath. That should be okay, because chlorine evaporates out after 24 hours, and it's been about 48+

@PvParkour thanks for the updated clearer photo. I think you should keep it, but I still want to recommend that you [edit] to also add a gif of your video. EZgif is a very easy website to use.

Maybe it's a Mabee's Salamander, Ambystoma mabeei.  Unfortunately, I can't really see the underside in your video, but I have the sense that it is a lighter color.  The clubbed tail, with an apparent break, seems like it may have been autotomized or otherwise injured, making it harder to compare.  I had the impression your example had dark spots dorsally and lightening ventrally, as can be seen in the image above.  Some other images are a bit different.  However, Mabee's Salamander is only found in "six localities in the coastal plain in extreme southeastern Virginia: the cities of Hampton and Suffolk and the counties of York, Southampton, Gloucester, and Isle of Wight. It is also found in Newport News." and is considered threatened, so unless your location matches what you read there it is still not likely to be the answer.

i updated it for a better picture i you want to look at it again

The appearance seems similar to my eye, the frequently confused species suggested at the first site don't look like they could be options, but the range and rarity of Mabee's Salamander concerns me.  If you're not in the area they describe, I'm very likely to be mistaken.

no, Im close to richmond (central VA). its ok though, you're still helpful

ok since the bounty expires in one day, i dont want 50 rep. to disappear, so ill give it to you


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CAM Photosynthesis Oxygen Generation?
I've been looking into CAM plants - notably the snake plant which is native to West Africa.
Upon researching the CAM photosynthesis cycle, I've found it fascinating that the plant stores CO2 at night and photosynthesizes during the day. But I'm a little confused as to how oxygen is a byproduct of this reaction. There seems to be no images of the cycle where oxygen is involved in any of the diagrams I've seen.
There was one question somewhere online that explained it, but I was nowhere near smart enough to understand their technical language and so I didn't really get an answer.
So here's my question.
Does a CAM plant release oxygen during the day? If so, is there a specific ppm value or some other value that that is applicable to a snake plant or another similar plant that I can use to calculate the approximate amount of oxygen released?
Your help is  much appreciated.
Thanks!

In the process of photosynthesis light is used as as a source of energy to generate sugar from carbon and water. A by-product is oxygen.

This process can be broken into two cycles: light reaction and Calvin cycle. In the light reaction energy from photons is transformed into usable energy and reducing agents (ATP, NADPH) and water is used as a source of electron, this results in the release of oxygen. In the Calvin cycle this energy coins are used to produce the actual carbohydrates.
There are three known wide-spread mechanisms of photosynthesis: C3, C4 & CAM
One can think of C3 as the "common" system and C4 & CAM as adaptations.
The CAM adaptation is a way to overcome dry, hot climates. The problem is that photosynthesis requires CO2 but opening the stomata allows water to escape. This is not acceptable. CAM plants separate the time of acquisition of CO2 and the actual fixation. They open the stomata at night, allowing oxygen to get out and CO2 to get in but fix the carbon, and thus create the oxygen, during the day.
Although the Calvin cycle is not light dependent it needs substrates created in light conditions so it will not work in the dark under normal conditions.
This article has assimilation curves depending on temperature in different CO2 concentrations. You can use the above equation to estimate grosso modo the amount of oxygen released. They also supply graphs of oxygen change inside a bag following several hours.

Please remember that the amount of oxygen is less important that the concentration, especially compared with CO2

@user1136 This is the balanced equation. It caused a lot of confusion and many experiments were designed to prove your very important sentence in parenthesis. But We can't change the equation

@user1136 that equation isn't more clear for me but i'm not against. I think editing gives your internet points. If you want you can edit my answer and I'll will approve

The rationale behind CAM photosynthesis, as opposed to C3 photosynthesis, is to partition the "light" and "dark" reactions temporally to avoid production of phosphoglycolate by RuBisCO in the presence of oxygen. During photosynthesis, molecular oxygen is produced in the photosynthetic electron transport chain, or the "light" reactions. The components of the electron transport chain are very highly conserved across species, including CAM organisms. The enzyme responsible for producing oxygen, Photosystem II, uses light energy to oxidize water, in turn generating molecular oxygen. This means that light is a necessity for generating oxygen, and essentially constrains the highest levels of oxygen evolution to daytime.


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When should I use cryofixation and chemical fixation?
We know that the technique used in TEM sample preparation involves multiple steps, one of the most important of them is fixation.
Fixation can be of two types:

Cryofixation, that suggests that the specimen are subjected to freezing temperature to perserve the cell's living material before we observe them.

Chemical fixation involves the use of certain chemicals, such as formalin, glutaraldehyde, etc. for almost same purpose.

The question is when it is mandatory to use one of them only? Such as, cryofixation or chemical one? At some instances, have the researchers ever need to use both of the techniques at the same time?

Cryofixation usually preserves the organelles inside the cells better, but is more work and usually results in TEM images that are lower contrast. Chemical fixation is easier and gives good contrast, but is more likely to destroy details in delicate samples. Chemical fixation will usually be used unless it is found or expected to not work well for a particular sample. It is possible to mix the methods, for example by including glutaraldehyde in freeze substitution solutions. Here is an article that describes everything you asked about in more detail, if you can access it: A comparison of cryo- versus chemical fixation in the soil green algae Jaagiella


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If a "parasite" is growing on a dead part of the host or on a completely dead host, does it still count as a parasite?
What I mean is the case where the parasite does not contribute to the death of the host (tissue). Instead, the parasite may start growing after the host (tissue) is already dead.
I came up with this question when I was following the link in this answer and read the PDF about a fungus on a fungus on a fungus on a tree. In the PDF, the author first says that the Hypomyces was growing on the dead bracket mushroom, and then says again that Rhinotrichella globulifera was in turn growing on dead portions of the Hypomyces.
I'm not a mushroom expert and the author also does not mention whether the parasites caused the death of their respective hosts.
So suppose the parasites only started growing after the death of the host, do they really still count as parasites? My understanding is that a parasite should seek a host that is not dead and try to leech nutrients without killing the host too quickly (at least until the parasite is ready for the next stage of its lifecycle and no longer needs the host).

Related: Is spiders building webs on plants an example of mutualism or commensalism?

In parasitic interactions, one species (the parasite) benefits from the interaction while the other (the host) is harmed. So, whether an interaction is parasitic or not really depends on whether on the host species is harmed by the interaction. If something only grows on the dead remains of another organism, but causes no harm to living organisms in terms of growth and reproduction, it would not be a parasite, and might actually be beneficial to that organisms in some ways.
However, dead cells or tissues are not always useless to a still living organism. For example, the vast majority of cells in a mature tree are dead, but are still important for the survival of that tree by providing structure and water/nutrient transport. A hypothetical parasite could feed only on the dead cells inside of a tree and still cause harm to that tree by weakening it's trunk or impairing it's ability to transport water and other nutrients.
Not knowing much about fungal physiology myself, I can't say whether these "hyperparasites" are truly parasitic or not. But it is at least feasible for a parasite to only grow on the dead portions of a host and still cause it harm.


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A word that includes plants and fungi, but not animals
Hello biologists and biology enthusiasts!
I am working on a project which includes information about plants and fungi. It would be very helpful for me if there a word that means plants-and-fungi, but I'm not sure there is. "Flora" only includes plants, but "biota" includes animals.
Thanks!

Also, are you interested in a taxonomic term or a non-technical term?

Thank you for your response! I think if you think flora is OK, you can put it as an answer and I will accept it. I don't think a taxonomic term exists (please correct me if I'm wrong), so I suppose I'm looking for the best non-technical term.
Do you know why my question was downvoted?

I don't think "flora" is what you're looking for. I simply wanted to point out it's broader usage beyond plants. I think referring to "all plants and fungi" as "flora" is not clear and will likely not get across the meaning you intend.

 Short Answer
There is no such word that I can think of.
 Long Answer
Note: although fungi were once considered to be lumped with plants, such classifications fell out of favor 60+ years ago (or sooner). See here for a summary.
Nomenclature "dead ends"
Using the traditional taxonomic approach (including Woese's familiar 3-domain classification system)  will not provide the collective term you're looking for. Plants, Animals, and Fungi are all of the kingdoms rank in this system; the only higher rank than kingdom in this system is domain (in this case "Eukarya"), which would include all 3 kingdoms.
If we take a cladistics approach instead, we can investigate Phylogenetic nomenclature. This taxonomic approach lacks categorical ranks such as "kingdoms" and instead tends to use hierarchical group names based on nested ancestral synapomorphies. However, using this approach proves to be even less useful for finding the term you're looking for:

Generally ~6 (5-8) informal supergroups (sometimes called "suprakingdoms") have been recognized based on phylogenetic research. Importantly, 2 of these groups (i.e., clades) are the Opisthokonts (which include fungi and animals) and the Archaeplastids (which include plants). Since animals and fungi share a common ancestor more recently than plants, it's not possible to "lump" plants and fungi together without including animals (and a whole host of other organisms).
You can see a recent publication (Burki et al., 2020) discussing an even more recent proposed organization for classifying Eukaryotes that maintains this phylogenetic distinction and separation between animals/fungi and plants.

Comment on the usage of "flora"
FYI, "flora" has broader usage beyond plants. "flora" can also be used for fungi (e.g., search "fungal flora" on Google). In fact, in microbiology, "flora" (or sometimes "microflora") is used to describe microorganisms in/on a system/host, which would include fungi, bacteria, etc. (For example, see gut flora).
I don't think "flora" is what you're looking for. I think referring to "all plants and fungi" as "flora" is not clear and will likely not get across the meaning you intend without further annotation/clarification.
Other thoughts:
I momentarily considered if being sessile would be a possible trait to use for delineating these organisms the way you're trying since by definition animals are not sessile (at least not at all stages of their lifecycle). However, many "protists" are also sessile and therefore such delineation would not be exclusive to plants and fungi. Further, I'm not sure all fungi are in fact sessile (though I can't think of any reason why not).

The phrase "multi-cellular sessile organisms" is probably much more exclusive and encompassing, but probably not 100% perfect. (However, at the point you'd be considering such phrases, I'd just suggest sticking with "plants and fungi" :p).

Perhaps someone else can come up with something, but I couldn't think of any non-outdated ways to accomplish your goal off the top of my head.


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Can fermentation and aerobic respiration occur at the same time?
In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time?
The cell can't completely lack oxygen, which means that some of pyruvate will move into the mitochondrion, however, lactic acid is also produced which means that anaerobic respiration occurs. Is this reasoning correct or is there some other mechanism that I am skipping that doesn't allow these processes to simultaneously occur?
Also, the NAD+ used for glycolysis is regenerated and net 2 ATP is releaseD in glycolysis, but the NADH doesn't move into the mitochondrion, so if pyruvate moves into the mitochondrion at the end of glycolysis, then there will be less NADH in the mitochondrion, which makes sense because there is too little oxygen and too many electrons in the ETC.

You keep posting questions in which you provide no support for your statements, no context to your qustions and do not respond to requests for clarification. Please sort out the questions you have already asked before posting any more.

@David In this case I believe the question is self evident and clear to understand, what part of it do you need more information about?

By posting one is asking others to spend time and effort providing an answer which will be of value to the "library of detailed answers" that this site aims to build. The poster therefore has a duty to write a good question, one that shows research (including previous questions here), is specific and explains the context in which the question is asked. If clarification is requested it should be provided. One should only "answer well-asked" questions. Until you respond to the queries to your ΔG question, I see no reason to consider others.

What happens at rest is that the muscle relies on blood glucose for energy supply. This involves glycolysis, Krebs' cycle and the ETC. In short, glucose is split into two trioses. The two trioses are then completely oxidatively decarboxylated. This produces reduced coenzymes, carbon dioxide and ATP. The reduced coenzymes are reoxidised by the ETC which takes the hydrogens, splits them into protons, that leave into the matrix, and electrons that jump between electron carriers, the last of which is oxygen which unites with protons too to form water. The jumping of electrons generates energy. The energy is used to pump protons from the matrix to the intermembrane space to a certain level. Once this level is reached, electron transport and proton pumping are stopped by ATP synthase and the already pumped protons diffuse through ATP synthase to the matrix. The energy that was used to pump the protons is then used to make ATP.
What happens during excercise is that energy consumption is faster so we need to generate energy faster. We use three mechanisms to do so.

Phosphagen system
Aerobic system
Glycogen-lactic-acid system

The phosphagen system is the one we use first. It relies on the phosphocreatine store. Phosphocreatine can donate its phosphate radical to ADP forming ATP and creatine. This system is short-lived.
When the excercise becomes prolonged, we rely on the aerobic system to maintain higher energy supply than at rest. It's essentially the same as what we do at rest with the exception that we start breaking down glycogen stores to free more glucose. The aerobic system can operate indefinitely; as long as there are enough oxygen and glucose.
If we need more energy than what the aerobic system can provide (more than oxygen supply allows), we start employing the glycogen-lactic-acid system. This system involves glycogen breakdown and glucose splitting into the trioses with no net oxidation and no decarboxylation. This is because the trioses that glucose is split to are oxidised producing reduced coenzymes, but the coenzymes can't be reoxidized by the ETC because there's not enough oxygen supply, so the trioses take back the hydrogens so the coenzymes can be used for another cycle. ATP is only produced at the substrate level. The resulting non-oxidised trioses are lactic acid molecules. Lactic acid, being an acid, causes fatigue, which is gradual reduction in the ability of the muscle to do work.
So to answer your question, yes they happen at the same time.
You can also check this answer for a more in-depth explanation.


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Will Fst (inbreeding coefficient) always be a value close or at 0 in asexual populations?
FST is the average inbreeding coefficient of a total population. The equation is:
$F_{ST} = \frac{Var(S)}{Var(T)} $
$Var(S)$ = variance in the frequency of the allele between different subpopulations, weighted by the sizes of subpopulations
$Var(T)$ = variance of the allelic state in the total population
If $F_{ST}$ equals 0 that means there is no population differentiation and there is no heterozygosity in the population. The ceiling for $F_{ST}$ is one so there is population differentiation and the population is all heterozygotes.
If the population is asexual, meaning they are parthenogenetic, would $F_{ST}$ be at or close to 0? Can this not be assumed?
In the context of this question I am considering the whole genome or just one allele.

It depends on whether mutation exists. Generally mutation is happening in biology, but in its absence, yes it will be at or near zero:

Note that in the absence of any mutation, $F_{ST}$ would be defined but equal to 0, as all the genetic variance is within individuals and none between individuals and subpopulations.

From that paper, see this figure:

So, basically, the exact level of $F_{ST}$ in such cases will be controlled by the mutation rate. That figure shows a value above zero at 100% clonal reproduction because it does have a nonzero mutation rate. There is also nonzero migration between populations, so that will have the effect of reducing $F_{ST}$ somewhat. So here the value is controlled by those 2 factors. Another thing worth noting is that, if there is no initial variation between populations before the split, that will tend to increase $F_{ST}$. So it does matter how much variation exists overall.


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What is the consensus in the scientific community over COVID-19's mode of transmission?
I've read from many news and scientific sources that COVID spreads primarily through respiratory droplets, but I've also read multiple sources that have said we don't entirely know yet. Is it fomites, droplets, or aerosols? Is it some combination? Do we have a complete understanding of it?
With how infectious the B117 variant appears to be, it seems like it would spread through aerosols, since most other infectious diseases that are very contagious tend to spread through aerosols, like measles, tuberculosis and varicella. If that's the case, why do so many sources keep claiming that it's through droplets? I've also read an article on the Johns Hopkins website that suggested the scientific community was initially wrong about the mode of transmission for tuberculosis, so is that possible for COVID?
Thank you!

"I've read from many news and scientific sources that COVID spreads primarily through respiratory droplets, but I've also read multiple sources that have said we don't entirely know yet". Please can you try edit your question to include links to where you found those statements (ideally primary sources). It'll improve the question and any potential answers. Thanks.

The terminology really depends on the scientific field. You also have to be aware that sometimes terminology is simplified for the purposes of presenting information to the general public.
A droplet can really mean anything from a few micrometers up to several millimeters and it does not necessarily have to be spherical. The key point is that the virus may spread through droplets.
Aerosols typically refer to small solid particles or liquid droplets, maybe less than 20 micrometer in size, but again, it depends on the field.
In quiescent air, any heavy (more dense than air) particulates (solid or liquid) which are about 1 micrometer  or less will remain suspended in the air for several hours due to Brownian motion and also the fact that their gravitational settling velocity is small.


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What does ΔC and ΔN mean with regards to a protein sequence?
I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement:

Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the
amino-terminal half of Frat (ΔC Frat) localized predominantly to the
cytoplasm of transfected MDCK cells (Fig. 1, A and B, i and iii).
Unexpectedly, the carboxyl-terminal half of Frat (ΔN Frat) accumulated
preferentially in the nuclei of transfected cells (Fig. 1B, iv).

I am not sure why the amino-terminal and carboxyl-terminal half of the Frat protein are referred to as ΔC Frat and ΔN Frat respectively. I know that the amino terminus of a protein is also referred to as the N-terminus, whilst the carboxyl terminus of a protein is referred to as the C-terminus. I am not sure why in this paper ΔC and ΔN are used to refer to the amino-terminal and carboxyl-terminal half of the Frat protein.
Any insights are appreciated.

This is just a simple technical abbreviation. Δ is used to mean deletion, so ΔC is used for the N-terminal fragment  as the C-terminal part has been deleted. One shouldn’t write answers in comments, but this doesn’t need any more.

The Frat/GBP (frequently rearranged in T-cell lymphomas/GSK-3-binding protein) protein is a proto-oncogene that regulates the Wnt signalling pathway. (van Amerongen et al., 2004)
The cited paper (Franca-Koh, 2002) noted a correlation between some forms of Frat and GSK3 cellular localization. Without Frat, GSK3 is cytoplasmic. In the presence of Frat, the heterodimer Frat-GSK3 translocates to the nucleus. As Frat is phosphorylated, it was unclear then what mechanism(s) was(were) involved. To investigate the role of Frat, the authors hypothesized that a region of Frat may be involved, not necessarily the whole protein.
They engineered deletion constructs and added an N-terminal FLAG tag for easy affinity purification. They used the symbol delta (Δ) for deletion. The N-terminal region of residues 1 – 129 encompassing Domain 1, i.e. deletion of the C-terminal region is called ΔC; likewise, the C-terminal region of residues 129-274 encompassing Domain 2, i.e. deletion of the N-terminus is called ΔN. They also engineered a green fluorescent protein (GFP) tag fusion protein variant. Here are their constructs as illustrated on Figure 1 of their paper:

Human ortholog
I aligned the residue sequence of the murine Frat with the human orthologs: it has 79% identity to human Frat1 and 68% identity to human Frat2. mFrat residues 1 – 129 (ΔC) and 129 – 274 (ΔN) correspond to hFrat1 residues 1 – 132 and 132 – 279, respectively.
Added Note
Here is a co-crystal structure of GSK3β (N-terminal lobe in orange and C-terminal lobe in cyan) complexed with Frat1 peptide 197-226 (forest green) and an inhibitor (N-(6-(3,4-dihydroxyphenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)acetamide) (green) as deposited with RCSB as entry 5OY4.pdb . The presence of the inhibitor helps locate the active site in the image of the GSK3b protein kinase.

References
Franca-Koh, J., Yeo, M., Fraser, E., Young, N. and Dale, T.C. (2002) J. Biol. Chem. 277:43844-43848.
Van Amerongen, R., van der Gulfen, H., Bleeker, F., Jonkers, J. and Berns, A. (2004) J. Biol. Chem. 279:26967-26974.


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Why is the number of cells virtually a constant?
Going back to highschool, I learnt about mitosis: in order to renew their cells, eucaryots' cells divide themselves into two copies.
But my course didn't cover what moderate the replication. By moderation, I mean something that prevent the number of cells to grow forever.
So here is my question:
What phenomena are responsible for the moderation of cell replications?
I did some research on my own on both the internet and SE, but couldn't find anything (maybe because I don't know the correct keywords)

You want to try googling 'cell cycle control' - perhaps also in the context of cancer.

You have to understand this is a very, very, very, very broad question. Decades of research in multiple disciplines allow us to answer this question in a million directions. However, I would start by looking up information about the cell cycle and its checkpoints. Here of course I would point you - for starters - to this page:
Khan Academy's page on cell cycle checkpoints
For further reading, you can consult the college-level chapter on Cell communication and cell cycle regulation. Here the most relevant section would be Regulation of cell cycle, it's a great introductory read, well researched and well presented didactically.
A short tl;dr
In short, cells have checkpoints at different stages of their life cycle - both before and after they divide. You can imagine that, for instance, a nutrient starved cell incapable of copying its DNA prior to division, will arrest its progress through the cell cycle at the checkpoint before S (DNA synthesis) phase. And under the right conditions, it will resume its progress and get ready for division. This example is only one of many checkpoints that exist, and varying types of cells may have varying checkpoint requirements.


text:
How do plants prevent infection from retroviruses?
Why are plants not affected by animal viruses such as retroviruses? What prevents them from being infected?

I think your question is answered in my answer to: Can an infectious diseases come from a plant?. I also have an answer to another question in this area: https://biology.stackexchange.com/questions/90174/is-there-any-disease-in-common-between-human-and-insects/90493#90493

I think you have the question backwards.  Viruses tend to be pretty specific in what they attack: not only animals, but particular species of animals, and often only particular cell types.  So why would you expect a virus to attack such different things as animals & plants?

Plants do are not affected for the same reason that linux virus cannot infect windows computer: viruses work like a lock and key for specific infiltration methods in different hosts.

Virus are extremely host-dependent because they need to enter the host, move inside of it, use its replication mechanisms and codon usage. There are virus that cross the family boundry (ToMV for example) but crossing the kingdom boundry is less probable.  For example, animal cells don't have a cell wall, which is a major change and requires a change in strategy for entrance to plant cells.
For retrovirus, they simply are virus that can integrate into the host genome.  Several articles [1, 2, 3] describe retroelements that have been classified as retrovirus, retrovirus-like particles, and retroelements encoding coat proteins. This can lead to the conclusion that there are retrovirus in plants.
It is worth noticing that virus are not the major pathogens of plants (fungi are) and resistance to virus can be acquired even without understanding the mechanism.   This leads to a lower level of interest, funds, and researchers in the area, which leads to a lower rate of discovery of new virus.
In conclusion, we have not found a virus that crosses the kingdom barrier but have families of virus that contain both plant and animal virus.


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Cancer: what does it mean "at presentation"?
Unclear to me what this means:

"Objective The biological heterogeneity of hepatocellular carcinoma (HCC) makes prognosis difficult. We translate the results of a genome-wide high-throughput analysis into a tool that accurately predicts at presentation tumour growth and survival of patients with HCC."

Reference

https://en.wikipedia.org/wiki/Presentation_(medical)

"At presentation" means "when a symptom/diagnosis is observed/noted by a medical professional".
In the paper you cite, they are doing microarrays on biopsied tumor tissue. "At presentation" here effectively means "at biopsy", at which time that a patient is diagnosed with hepatocellular carcinoma. It's important to note that their sampling is based on presentation time because tumor age at presentation is not going to be the same for everyone - some patients may "present" with symptoms and be diagnosed when a tumor is relatively new, others may present when a tumor is advanced. Presentation is both a convenient and clinically relevant time point - it's the earliest time a prognosis can be offered.

"Presentation" is the event where the patient first visits the doctor.
For example, "the patient presented with yellowing skin and complaining of abdominal pain".
The paragraph you have doesn't make this clear, they assume you have already had your genome sequenced prior to visiting the doctor, who looks at the result, uses this tool and predicts what is likely to happen to you and your cancer based on your DNA.

This answer is a bit wrong; this is not based on prior genome sequencing. They're doing microarrays on biopsied tumor tissue and identifying particular genes for prognostic benefit. Presentation is when the patient is biopsied and diagnosed.

Thank for polite comment, Your answer covers it so I will delete mine tomorrow.


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3 primers to know if Homozygous, Heterozygous or WT
In this imaginary experiment, I am using T-DNA to make an insertional mutagenesis that will get randomly inserted into the DNA where it might get inserted within a gene, disrupting it.
In order to get homozygous individuals, If I working on plants, I could self-pollinate this particular plant that has had this gene disrupted making homozygous offspring.
In order to prove that, I can do a PCR using 3 primers.
My question is, why 3 primers? I would use 4 primers!
I have been researching it and trying to understand it for myself for a while, but I do not reach any positive conclusion. I think it should be pretty basic and I am missing something.
I think I need forward and reverse primers for the T-DNA, but what about the 3rd primer? If I only use these two primers, though, I will not be able to distinguish between the homozygous and heterozygous.
Thanks!

Does this imaginary experiment come frome an article or a book? Could you add a reference? Is the goal to disrupt a particular gene or to search for mutants with paticular phenotype? Do you know the sequence of the gene which has been disrupted in the parent plant before self-polination? If the gene is known one or two primers can be designed to bind the gene and not the T-DNA.

As an exercise: can you imagine any scenario under which 2 of those 4 primers could be combined into a single primer, for 3 total? (Genotyping T-DNAs is generally done with only 3, I can confirm). Also, any reference would be helpful. Is this a homework or study problem?

Maybe two different PCR tests where PCR gives positive results, one where the insert was successful, and one where no insertion happened.

This is from one of my lectures, where the professor introduced T-DNA mutations and said that I would need 3 primers with no explanation. I do not have any reference though. What I can add is the following: if I do an electrophoresis next, the WT would have a of 900 bp, the Heterozygous would have two bands, 900 and 400 bp, and the Homozygous would habve 1 band of 400 bp.

From statistical viewpoint, one needs at least three measurements to have a meaningful estimate of mean and variance . Even if you do no such estimations, these considerations are likely the reason for recommending 3 primers. If you can have more in a reasonable amount fo time and at reasonable cost, it is only better!

As I think that this is in danger of turning into an extended Socratic comments-fest without really getting anywhere, I'll just post [this link][1] which discusses T-DNA insertion confirmation. I'll note that this site is easily accessible by Google, which is a good place to look first, to help us help you!
[1]: https://bitesizebio.com/35392/genotyping-t-dna-insertion-mutants/

Thanks Maximilian! I found this website too when I changed my Google search strategy. Now I am trying to understand it properly.

@Laura can you point directly to e.g. a quote or a figure or other part of this site that is confusing you? Have you followed the links?

Thank you for reaching out again. This part confuses me: " Flanking primers [...] The chosen primer pairs span this insertion site. Furthermore, the primer pair needs to cover a region long enough that the PCR reaction will not be able to amplify the insertion mutant". The flanking primers are not  in the left and right border of the T-DNA but outside of it, in random positions of the DNA? The third one is it the T-DNA, as I understand. These random primers will be designed in a way that will give you 900bp band except if they fall where the T-DNA is?

If it is like that, it means that you will have to amplify every region of the genome in order to find the T-DNA, right?


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Could a vaccine injecting B cells theoretically work?
So I was in the car riding to school today when I was struck with genius. Each B cell is attuned to a different pathogen, am I correct? By that logic, would a vaccine injecting a dose of B cells attuned to the pathogen you're trying to protect against work?

Yes, take the cells out, purify, multiply them with the right stimulus and reinject.
You have been struck with genius, but I think some other people with the same idea got prizes already. Good to see you thinking, dont stop!
A review of just one application of this is here.
"Cancer Immunotherapy"
by
Wennhold K.a · Shimabukuro-Vornhagen A.b · von Bergwelt-Baildon M.
https://www.karger.com/Article/Fulltext/496166
permanent ref is http://doi.org/10.1159/000496166


text:
How does lactate produced in the intestines get transported to the rest of the body?
Some gut bacteria known as lactic acid bacteria(LAB) are known to produce lactate in the intestines and they confer beneficial effects such as enhancement of the immune system, but I assume not all of the lactate stay in the intestines and some of them will get transported to the rest of the body and used by other tissues (e.g. cori cycle). If that's the case, do these lactate enter the circulatory system? Are there any articles reporting it?


text:
Loss of taste and smell during a SARS-CoV-2 infection
In France the loss of taste and smell (la perte du goût et de l'odorat) is considered as one of the key symptoms of a SARS-CoV-2 infection (although googling shows that it is considered less definitive elsewhere). What causes such a loss of taste and smell?
More specifically, an infection by SARS-CoV-2 is rarely associated with nasal congestion, so one cannot blame mechanical obstruction (and it would not apply for the loss of taste). One can then think of the virus attacking the relevant sensor cells or a less direct effect via disrupting the relevant metabolic chains. I will appreciate clarifications/explanations/references.

Of peripheral interest: "There are angry ladies all over Yankee Candle’s site reporting that none of the candles they just got had any smell at all." (https://twitter.com/kate_ptrv/status/1332398737604431874?lang=en). Apparently there is a statistically significant down-hike in the scented candles ratings, complaint: No scent.

Is there really a loss of taste (i.e., no sour/salty/bitter/umami sensation) or is it just the lack of aroma because the sense of smell is gone, which makes everything taste bland? My google fu didn't give me any answers.

@Peter-ReinstateMonica Chris's answer addresses this in the third paragraph (starting "For the tasting") which refers to chemosensory defects separate from olfaction. It seems that there is true loss of taste as a physiological sense in addition to the overall perception of taste that includes smell. I don't know if there is good data on the prevalence of each, because there is some ambiguity if patients simply report "loss of taste" without further elaboration.

@Bryan Ah, thanks!

I’m voting to close this question because it should be migrated to SE Medical Sciences.

This is not completely clear to say the least, but there are some hints. Please keep in mind that there was not much time for extensive research, since this disease is still quite new. What seems clear (at least at the moment) is that most like the nerve cells (in the olfactory bulb as well as in the taste bud) are not directly affected, since they do not express the ACE2 receptor on their surface which is needed by the virus to enter a cell.
In the nose, there are two studies, which link the loss of smelling to massive damage of the epithelial cells surrounding the nerve cells. These cells have a lot of ACE2 receptors and are thus susceptible for an infection with SARS-CoV-2. An infection leads to the death of these cells, which disturbs the balance of ions for the nerve cells leading to loss of smell. Specifically this seems to affect sustentacular cells. Since the epithelial cells recover over time, smelling comes back. This also fits the description of affected people, who describe the loss of smell as a sudden event, while the recovery happens gradually.
For the tasting it is less clear, but it also seems that supporting cells (which carry ACE2 receptors) are affected. For sensing of sharp (for example Chili), which is not chemical sensing but via pain sensing, it seems that at least a part of the cells are also susceptible to the virus as they express ACE2.
Taken together this seems to indicate that important cells in the vicinity of the nerve cells are hit by the virus, causing anosmia and ageusia. It is also important to note that not all people who lose their sense of smell also lose the sense of taste.
For furter reading have a look at the references, the first one is a nice article in the scientific american, the second goes deep into the topic with a lot of nice images.
I will have a deeper look into the topic later and probably update the answer.
References:

Mysteries of COVID Smell Loss Finally Yield Some Answers
COVID-19 and the Chemical Senses: Supporting Players Take Center
Stage
Massive transient damage of the olfactory epithelium associated with
infection of sustentacular cells by SARS-CoV-2 in golden Syrian
hamsters
SARS-CoV-2 Receptor ACE2 Is Enriched in a Subpopulation of Mouse
Tongue Epithelial Cells in Nongustatory Papillae but Not in Taste
Buds or Embryonic Oral Epithelium
Real-time tracking of self-reported symptoms to predict potential
COVID-19

+1, this may be another good reference since I believe it may have been the first paper which rigorously showed the sense of smell was a distinguished symptom https://www.nature.com/articles/s41591-020-0916-2

@user438383 Thanks, I will add this in a second.

Apparently, pathological (autopsy) findings have shown "viral particles" in nerve cells. How could they possibly have entered the cells  - as it is true that nerve cells, in general, not only the cells of smell, do not carry the ACE2 receptor?

@PeterBernhard As far as I know, they have been shown on the surface of the cells. Do you have a specific reference for that?

Yours might be : "Clusters of extracellular viral particles adhering to the surface of the plasma membrane were also seen."? Here's my "German one":  https://www.charite.de/en/service/press_reports/artikel/detail/how_sars_cov_2_reaches_the_brain/

@Chris https://pubs.acs.org/doi/10.1021/acschemneuro.0c00122 Apparently, neurons, for instance, have the ACE2.

@PeterBernhard The Charite press release is interesting, as the state that they found the virus in the epithelial cells (as noted above) and also in the nerve cells. However, they also limit their own findings possibly to severe outcome patients: "It is not necessarily possible, therefore, to transfer the results of our study to cases with mild or moderate disease.” The problem is we don't know it yet in all details. We do know that the virus needs ACE2 as an entry door. I will look at the literature from time to time for updates.

"ACE2 is not present in olfactory neurons"  is in support of  your answer  ("surrounding cells" of neurons  being the only target),
https://erj.ersjournals.com/content/early/2020/07   /23/13993003.01948-2020
Interestingly, some neurons in the brain do have the ACE2. I understand that "being found in neurons" is different from "neurons carry the ACE2" . I think it makes sense to ask, if   "naked RNA"which comes as  cell debris is uptaken  by neurons and  by other body cells (in which  virus particle were  detected by electro-microscope - reference on request). Thanks!

@PeterBernhard We still don't know exactly, how this works. So far, all reports I have seen (which is most likely not complete) only report the infection of ACE2 expressing cells. However, it is possible that a part of the nerve cells carries this receptor and is therefore susceptible for the virus. More research will tell.


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Why do predatory mites have to be introduced multiple times?
I'm combating spider mite infestation using either Phytoseiulus persimilis or Amblyseius californicus. After extensive study of the literature, I'm still unsure why the producers of these predatory mites suggest that they have to be introduced several times (2-3 times depending on manufacturer). I know that adult predatory mites are very agile and scout for new prey. Phytoseiulus is also known to wipe out spider mite populations. So as long as spider mites are present, why should one introduce them at intervals rather than just introduce a large number of predatory mites at the beginning?

You are right that ideally it should be enough to apply them once, but predatory mites seem to be quite sensitive: If it gets too cold or too hot or the moisture is too low, they might die.
I applied several rounds of predatory mites in non-optimal conditions without any success. They just kept disappearing without any effect whatsoever. Funnily, some small type of Heteroptera came to save my plants. (from nature without my doing)
Next time I would try some Chryson instead.

Thanks for the input. This paper (https://www.eje.cz/pdfs/eje/1993/01/02.pdf)  suggests that P. persimilis can even survive temperatures below zero for brief periods of time. I think the problem is that it takes to long for the beneficials to arrive, because they are produced in the Netherlands and shipped to the distributor so it can take up two 2 weeks for the benefials to reach the target destination. Also a big producer (entocare) lists the shelf-life of 1 day.

OK, I see. From a non-biological and rather economical standpoint, it's always advantageous for companies to recommend triple use: They make more profit, there is a higher chance of success due to the duration of time alone, and it shuts down customer complaints, if it doesn't work the first attempt.


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Parameters that determines the thermal stability of DNA
Why a DNA with a high GC content more stable than one with a less GC content? Is it because of the three hydrogen bonds in GC base pair which is one more than a AT base pair or is it because of the more stable base stacking of GC base pairs?
In my book it is given that it is due to the hydrogen bonds but in a research article I found it is saying that base stacking solely determines thermal stability. enter link description here

Although taken in isolation GC bonds should be more stable than AT bonds, due to their higher binding energy (three hydrogen bodns versus two), it is the stacking energy that is considered the stabilizing factor of the DNA:

We find that temperature and salt dependences of the stacking term
fully determine the temperature and the salt dependence of DNA
stability parameters. For all temperatures and salt concentrations
employed in present study, base-stacking is the main stabilizing
factor in the DNA double helix. A•T pairing is always destabilizing
and G•C pairing contributes almost no stabilization. Base-stacking
interaction dominates not only in the duplex overall stability but
also significantly contributes into the dependence of the duplex
stability on its sequence.

The reason for that is that one can have the same number of pairs under many different configurations of strands, which means high entropy and instability, unless there are stacking interactions. This is why most models of DNA and RNA helices are based on adding the stacking energies, although there are some additional contributions, particularly in the case of RNA - initiation energy, energies associated to the inner loops, etc.


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What is the meaning of 'primary' and 'secondary' sympatric speciation in this paper?
Sympatric Speciation in the Genomic Era. Both terms are used throughout the paper.
I'm not able to make sense of these terms in the contexts used.
I've also heard the terms 'primary' and 'secondary' gene flow elsewhere on the same topic - are they related?
From the abstract:

However,  I  argue  that  genomic  studies  based  on contemporary  populations  may  never  be  able  to  provide  unequivocal  evidence  of  true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies in  to  this  field. This  inability  to  robustly  distinguish  cases  of  primary  and  secondary divergence-with-gene-flow may be inconsequential, as both are useful for understanding the  role  of  large  effect  barrier  loci  in  the  progression  from  localised  genic  isolation  to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to  shared  underlying  mechanisms  driving  divergence  and  potentially  leaving  similar coalescent patterns.

From the introduction:

Lastly,  I  consider  whether  primary  and  secondary  sympatric speciation represent a mechanistic dichotomy, I suggest that primary and secondary contact can leave a similar genomic signature, when speciation is driven by tightly clustered or  large effect loci. Arguably, the advent of affordable population genomic studies should place less focus on whether study systems result from primary or secondary contact and instead focus on the mechanistic aspects of the genomic architecture and making progress in identifying the conditions and processes under which natural and sexual selection can drive speciation, without extrinsic barriers to gene flow.

The paper is behind a paywall, which will mean that most readers cannot access it. Can you please extract some relevant fragments into your question?

Apologies, I've added some excerpts.

TLDR
Sympatric speciation and allopatric speciation with later migration into the same habitat were historically diffucult to distinguish without looking at palaeo-biological data. The paper argues that while palaeo-genetics has made this easier, it is still difficult to distinguish pure sympatric speciation (which it calls primary) and sympatric speciation with a geneflow from an geographically separated (allopatrically speciated?) subpopulation (which it terms "secondary sympatric speciation" or "speciation with secondary gene flow", "...with secondary contact" etc.).
Speciation
Speciation is the divergence of one species (with one gene pool) into two different species (with different gene pools). It is obvious that this will happen if subpolulations are geographically separated and continue to adapt to their local conditions (allopatric speciation).
However, Mayr suggested (back in the 1940s) that there is another type of speciation that happens while the speciating populations share a habitat, and, consequently, while gene flow between these subpopulations is maintained until the speciation process is complete. This requires strong selection pressure towards two different ecological niches each with their associated adaptations.
Empirical examples have been discussed and called into question again. One cool and frequently discussed example is that of the apple maggot in North America that has developed from the hawthorn maggot after the introduction of apples in North America.
Debate
Unequivocal examples for pure sympatric speciation are rare, leading to some debate about the merits of the concept. Sympatric speciation models (following Maynard Smith's models from the 1960s) as well as the reasons for skepticism towards them are illustratively explained for instance in this article (Felsenstein 1980), page 133-135.
The debate continues, today with additional, newer findings from genetics, palaeo-genetics, etc. This is what the article in the OP (Foote, 2018) was about. The pdf of the article (Foote, 2018) without paywall can also be found here. While Foote suggests that what pure sympartic speciation and speciation with secondary gene flow may never be unequivocally distinguished (without additional palaeo-genetic information), others are more optimistic, e.g. Richards et al. 2019 (without paywall on biorxiv). Coincidentally, Richards et al. have a very nice illustration (their Figure 1) that illustrates the issue the OP was asking about.