text:
How stacked rods / multibank retinas cells are layered out?
I read that some animals have stacked rods in their eyes, usually fishes, a feature that as far as I know has the name of multibank retina.
I'm trying to understand how that is laid out in the retina alongside neural cells and retinal pigments, but I'm not finding any representation I can comprehend.
For example, this is an image of a human eye:

But I can't find anything close to representing a multibank retina that satiates my curiosity about this.
For example, I can't find how retinal pigments reach all rods & cones if the first one is layered, and if not, how that affects the cells (as far I know they help recycle used light-sensitive proteins). Or if horizontal cells extend to reach the deeper rods or the rods extend themselves towards the horizontal cells), or the same with the retinal pigments. If ganglions and bipolar cells are layered together or the entire retina is doubled, having two sections of ganglion->bipolar->rod/cone->ganglion->bipolar->rod. Nor if cones are only found in the first layer, the last one, or all layers. Or if müller cells extend towards all layers since as far I know they help propagate light to cones. There are so many questions that I could answer with a single picture.
Since I could not find many papers which aren't behind a paywall or too complex for me to understand, I tried luck asking in a chat about biology, and I only got that they have "more photoreceptors layers that project further back up towards the ganglia layers", which I didn't understand much. Does that mean something like this?:

It sounds wrong, like some photoreceptors never get into contact with retinal pigment cells (which recycles photoreceptor disks), and now the wiring is much dense, blocking photons from reaching cones (which the eye doesn't have more to compensate). Is this correct?
Also, if photoreceptors are stacked, then the ones which are further from the choriocapillaris (the largest network of blood capillaries in the eye, which is located after the retinal pigmented cells) would receive less oxygen and I have understood that these cells consume an enormous amount of oxygen. Does the cell's layout take this into account in some way?
What about tapetum lucidum? Is it located after the last layer of rods or does each one have its own? The first one would increase the distance between the receptors and the reflective structure, blurring the image as photons bounce in different directions, but the second one would make the following layers quite useless as the layer mirrors light. Or do multibank eyes have no tapendum lucidum?
Seeing a representation of the layout would allow me to know what "tradeoff" has these types of eyes.

Why do photoreceptors need to contact retinal pigment cells? Does an animal that needs a bunch of extra rods to detect light have any use for cones anyways? What would make the photoreceptors further from blood vessels?

@BryanKrause Honestly my knowledge is limited, but AFAIK, (1) cones/rods remove old opsins and they are absorbed by pigment cells and recycled. (2) some teleost fishes have multibanks and they live in coral reefs, which have light, so I suppose they have color vision. (3) if roods are stacked, some layers will be closer to the outer blood vessels which surround the retina from the back, while others don't, isn't it?

Tissues get fed by capillaries, not larger vessels. Recycling opsins is not something I was familiar with, thank you. My understanding is that the multibanks are a specialization for extreme low light conditions. Of course, evolution isn't perfect and it's certainly possible that a fish that evolved specializations for low light moves into a different niche where those specializations don't make as much sense.

@BryanKrause I see, I may be wrong about how photoreceptors get oxygen. I know that evolution isn't perfect, so an adaptive trait may become maladaptive in a different environment, which in my opinion it only makes me more eager to know how evolution attempts to fix such details, if it actually tries and how that is reflected in the current layout of such organism. However, I still believe the rest of the question to be valid enough to ask if you don't mind.

@BryanKrause This is what I mean with blood vessels, or capillaries, they are next to pigmented cells, difficulting stacked rods to reach them. https://www.researchgate.net/publication/353406543/figure/fig3/AS:11431281212543395@1702652163031/Transport-mechanisms-for-delivering-nanoparticles-NPs-into-the-blood-retinal-barrier.tif

Capillaries run throughout the retina. They are not only next to pigmented cells. Yes, I think it's a valid question. Not sure this paper will answer all your questions but seems relevant: https://pmc.ncbi.nlm.nih.gov/articles/PMC10688437/

Let us continue this discussion in chat.

As far as I can tell, multibank retinas are associated with deep-sea or nocturnal fish. Here is a histology image from Multiple rod layers increase the speed and sensitivity of vision in nocturnal reef fishes (this is a BioRxiv paper, so you should be able to access it.):

Fig. 1. Retinal structure and cell densities.
A. Representative radial sections from the retina of i) O. compressus, ii) N. sammara and iii) M. violacea. Rod banks are numbered as Bn. Representative rod and cone outer segments are indicated by black and white arrows, respectively. B. Densities of different types of retinal cells in O. compressus (n=1), N. sammara (n=1) and M. violacea (n=1). PRL, photoreceptor layer; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer; GC, ganglion cells. Scale bars: 25 μm (Ai), 50 μm (Aii and Aiii).

O.compressus, pictured on the left, has a single rod bank, while the other two fish have multiple. Note that the scale bar on the left represents 25 microns while the center and right are 50, so while the single rod bank appears to be the same depth as the multiple banks, it is actually about half. This is outside the scope of the paper, but if I am interpreting their figure correctly, one difference with your diagram is that the cell bodies of the rods aren't stacked in the multibank array with their photoreceptive outer segments, but are all clustered together in the Outer Nuclear Layer.
Regarding the regeneration of opsin, I found that Müller cells can provide chromophores to the cones, through a separate visual cycle with a different opsin chromophore precursor. The energy for this regeneration is provided by light captured by "repurposed" opsins in the Müller cells. Source is RDH12 allows cone photoreceptors to regenerate opsin visual pigments from a chromophore precursor to escape competition with rods . So the cones being separated from the RPE by more banks of rods isn't an issue.


text:
Understanding expected mean number of breeding seasons
I've recently come across an equation for the expected mean number of breeding seasons after the first breeding season, as a function of the annual survival rate (S) and the probability of breeding,
$$
\mathbb{E}(\#\text{ of breeding seasons}) = \dfrac{1}{-\ln(S)} \times \text{breeding probability}
$$
I'm having a hard time understanding what the term $1 / -\ln(S)$ represents. Any ideas?

It's just a continuous version of the discrete calculation. The discrete version is the (infinite series) sum
$$
\sum_{i = 0}^\infty S^i \cdot bp
$$
adding up every (chance of survival to season $i$) x (breeding probability given that survival).
Making this continuous converts the equation to
$$
\begin{split}
 & \int_0^\infty bp \cdot S^i \, di \\
  = \enspace & bp \int e^{i \ln S} \, di
\end{split}
$$
integrating gives
$$
\left.bp \cdot \frac{e^{i \, \ln(S)} }{\ln(S)} \right\vert_{0}^{\infty}
$$
Evaluating gives
$$
= \frac{bp \cdot e^{-\infty} }{\ln(S)} - \frac{bp \cdot e^{0} }{\ln(S)}
$$
(remembering that $0 <= S < 1$, so $\ln(S) < 0$)
$$
= bp \cdot 0 - bp \cdot \frac{1}{\ln(S)}
= bp \cdot \left(0 - \frac{1}{\ln(S)}\right)
= bp \cdot \frac{-1}{\ln(S)}
$$

This makes sense, thanks!

@BenBolker Thank you so much for the example that LaTeX works here! I will work on completing the formatting.

I think your explanation is correct. The expected value of the exponential distribution is:
$$t \sim \text{e}^{-\lambda t} \implies \langle t \rangle = \int_0^\infty t \ \text{e}^{-\lambda t} \; \text{d}t = 1/\lambda.$$
For the exponential survival function, we have to identify the parameter $S$. Since $S$ is the number of survived individuals after one year, we derive:
$$S = \text{e}^{-\lambda} \implies \lambda = - \ln S.$$
Therefore, the life expectancy is simply:
$$\langle t \rangle = -\frac{1}{\ln S}.$$
Because the probability of a breeding to happen each year is independent, we can multiply the life expectancy by the probability that the breeding happens in a one year period. This gives us the final result:
$$\langle \# \text{ breedings} \rangle = \langle t \rangle \cdot P(\text{breeding}) = -\frac{1}{\ln S}\ P(\text{breeding}). $$

This is also a good explanation! Thanks for the help.

source: Stack Exchange

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

sort: votes


text:
Sickle cell anemia IS inherited in an autosomal recessive pattern, but sickle cell trait IS NOT inherited in an autosomal recessive pattern?
It's all about the alleles of the hemoglobin beta gene. Sickle cell anemia is inherited in an autosomal recessive pattern, which means that both copies of the gene in each cell have mutations.
Those who are heterozygous for the sickle cell allele produce both normal and abnormal hemoglobin so the inheritance pattern of the trait is considered to be codominant . Two different types of relationship between the same alleles. Why?
I think it is because in the sickle cell anemia the important thing is:
To determine whether the individual is 'HEALTHY' or 'SICK'. But in the sickle cell trait we go deeper and are concerned with the presence of 'NORMAL' or 'SICKLE' RBCs inside the body. Did I get it right?

• HbAHbA: Healthy (only normal RBCs can be seen)

• HbAHbS: Healthy (Both normal and sickle RBCs can be seen)

• HbSHbS: Sick (Only sickle RBCs can be seen)

As you can see here, the inheritance pattern for anemia is an autosomal recessive pattern, but for the trait the pattern is codominance. The question is: Why are there two different types of relationship between the same alleles?
Consider this question:

What is the type of relationship between the normal and mutant alleles (which causes sickle cell anemia) of the hemoglobin beta gene? Autosomal recessive pattern or codominance?

Can one choose one of the options? I think this question is vague. Because if the sickle cell anemia was mentioned, the answer would be autosomal recessive pattern. But if the sickle cell trait (the presence or absence of sickle RBCs) was mentioned, the answer would be codominance. Isn't it so?
Edit
With thanks to Bryan Krause, I searched a little more and saw this in Wikipedia just now.

The sickle cell trait can be used to demonstrate the concepts of co-dominance and incomplete dominance. An individual with the sickle cell trait shows incomplete dominance when the shape of the red blood cell is considered. This is because the sickling happens only at low oxygen concentrations. With regards to the actual concentration of hemoglobin in the circulating cells, the alleles demonstrate co-dominance as both 'normal' and mutant forms co-exist in the bloodstream. Thus it is an ambiguous condition showing both incomplete dominance and co-dominance.[citation needed]

Before this, I believed that only two phenotypes can be seen in HbAHbS individuals: Normal RBC and Sickle-shaped RBC
But now I doubt it. Is there one more phenotype? A red blood cell that is not normal nor sickle-shaped but rather something in between? A red blood cell that is sickled incompletely? Is this phenotype really observed, studied or defined scientifically?

Comments are not for extended discussion; this conversation has been moved to chat.

These phenotypic dominance terms you learn in school - autosomal recessive/dominant, co-dominance, incomplete dominance... these are all just descriptive terms based on phenotype that become somewhat irrelevant and outdated once you have a better molecular understanding of what exactly goes on with different alleles of a gene. If none of them apply well, that's fine, because the real world doesn't follow these basic rules.
For sickle cell anemia, the serious form of the illness, the inheritance is more or less autosomal recessive, as you say. Those with two abnormal copies of the HBB gene have symptoms; those with one copy are generally symptom-free.
However, at a cellular level, it turns out that both normal and abnormal versions of hemoglobin exist. If we define co-dominance as "contributions of both alleles are visible in the phenotype", then at an intracellular level, the phenotype is co-dominant. That said, these terms are typically used at the organismal level. After all, patterns of dominance in Mendelian inheritance far pre-date any understanding at the molecular level of these things. It's very typical for traits considered to be recessive at an organismal level to show measurable differences at a molecular level in heterozygotes, yet these differences are compensated for (such as via feedback loops in gene expression) such that the phenotype isn't observed.
If we look carefully, though, even at the whole-organism level, sickle-cell carriers (heterozygotes) don't have exactly the same phenotype as those who are homozygous for the normal HBB allele. Heterozygotes are considered as having the sickle-cell trait. They're somewhat less sensitive to malaria, but there are also some associations with cardiovascular comorbidities and signs of sickle-cell disease in adverse conditions such as dehydration, especially at high exertion in athletes. Incomplete dominance describes a heterozygous phenotype "distinct from and often intermediate to the phenotypes of the homozygous genotypes". Note in this definition the word distinct and the qualifier often intermediate. There is no stipulation that the heterozygous phenotype needs to be precisely in between the homozygous phenotypes, or even that it has to be between them at all rather than somehow orthogonal, it merely must be distinct. This seems to me like the best description for sickle-cell inheritance overall, though it may be harder to follow in a pedigree as the heterozygous phenotype may not be obvious enough to recognize in every carrier.
If you have to pick one for a multiple choice question, incomplete dominance is the most comprehensive answer, but all three of these are potential answers if you constrain the parameters of the problem. It's far less important to be able to assign these particular labels, though, than it is to understand what actually happens with a sickle cell allele.
Some more quotes from Wikipedia:

The sickle cell trait can be used to demonstrate the concepts of co-dominance and incomplete dominance. An individual with the sickle cell trait shows incomplete dominance when the shape of the red blood cell is considered. This is because the sickling happens only at low oxygen concentrations. With regards to the actual concentration of hemoglobin in the circulating cells, the alleles demonstrate co-dominance as both 'normal' and mutant forms co-exist in the bloodstream

I disagree a bit with the next sentence in Wikipedia, though:

Thus it is an ambiguous condition showing both incomplete dominance and co-dominance

I don't think it's particularly ambiguous, it's just necessary to either define what level of analysis you're making the statement about or to recognize that none of these terms are entirely sufficient to describe the complexity that exists in biology.

Defining two different titles for this (codominance and incomplete dominance) seems ironically unnecessary to me now. But it made sense back then because as you said, "Patterns of dominance in Mendelian inheritance far pre-date any understanding at the molecular level of these things."

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


text:
Help identifying a mite (?)
I live in Cambridge, UK, and found these mites (probably? not sure) in the attic. There are no bird nests at or around the dwelling, and no traces of rats or mice. There are plenty of those and not clear what they feed on. Body is about 0.7-1mm long, see photo with a ruler for scale.
Can you please help identifying these?

Welcome to Biology.SE. Can you be a bit more specific about where in the UK? This information may not be needed, but since conditions in the Shetlands and Wales (for example) are a quite different that information may help pin down your mite.

Thanks - updated (Cambridge, UK)

Great! If you don't get an answer I encourage you to check out some of the websites such as iNaturalist that specialize in identifications. If you do find an answer elsewhere it would be great if you would post an answer here that includes: discussion of key features that led to the identification, and supporting references or validated images!

In support of Acari, there doesn't seem to be any division on the scute or any elytra, so it is unlikely to be a beetle. Also no obvious separation in to head, thorax, abdomen, though you might only see this on upside-down ones.

This is a mite in the order Oribatida. Like many other oribatids, it appears to be covered with a smooth, dark, hardened, vaguely teardrop-shaped "shell", like a beetle—hence the common name "beetle mites". Its mouthparts and legs, visible at the narrower front end, are flanked by thin, flat plate-like structures called pteromorphs ("wing-shaped"), which you can also see in this photo and this SEM image. It is also the right size for an oribatid (visible to the naked eye, under 2mm).
David E. Walter notes in his key that there are similar heavily armoured mites in other groups. Most of the characteristics that are only found in oribatids, like long sensory hairs just behind their "head", can only be seen with much higher magnification. But I am reasonably confident this one is an oribatid and not a mesostigmatid/prostigmatid mite because of the combination of smooth, shiny hard shell, leg and mouthpart placement, and pteromorphs.
These tiny, harmless mites live in soil, under rocks, etc. Further identification usually requires an expert with a microscope. If you are on Twitter, the British Arachnological Society may be able to hook you up with a mite expert.

Observations from your area on iNaturalist
A checklist of UK oribatids (paywalled)

Please update your answer to explain/describe why these are Orbitid mites. How can you tell? What evidence do you have? Thanks

Amazing, thank you!


text:
Relation between respiration and concentration of citric acid

A and B are 2 reactions.
If there is an excess availability of citrate, then which of the above reactions will prevail?
I know that citric acid is formed when oxaloacetic acid reacts with acetyl coA. But how does concentration of citric acid influence the above reactions

This image is a bit misleading since both ways seem to be the reversion of each other, but in fact they are not (although the same metabolites are used).
Reaction A takes only place in gluconeogenesis which makes glucose from other metabolites (coming from the metabolism of fatty acids for example) and this pathway is only active when there is an abundance of energy present in the cell. Citrate activates the Fructose-1,6-bisphosphatase. The gluconeogenesis takes only place in liver and kidney.
Reaction B takes place in glycolysis and is the rate limiting for the whole pathway. It takes place when glucose is taken up and then used for the production of energy. The Phosphofructokinase (PFK) is inhibited by signals of excess energy as ATP (which is an allosteric inhibitor of PFK) as well as citrate and NADH/H+. While citrate is a weak allosteric inhibitor on its own, it acts as a strong inhibitor together with ATP. This makes sense since both molecules are indicators of free energy metabolites in the cell.
See these two publications for details:

"Allosteric regulatory properties of muscle phosphofructokinase."
Effect of citrate on the activities of 6-phosphofructokinase from
nervous and muscle tissues from different animals and its
relationships to the regulation of glycolysis.

If there is an excess of AMP/ADP then the enzyme is activated and phosphorylates Fructose-1-phosphate.

Although it is true that citrate can act as an inhibitor of PFK, I see to recall that the relevance of this in vivo is questionable. The key effect, not mentioned in the answer here, is that citrate is an activator of fructose 1,6 bisphosphatase, the enzyme for reaction A. Also worth mentioning that gluconeogenesis only takes place in liver and kidney.

@AlanBoyd It has both effects - and since they are adverse, this makes sense. PFK is activated by AMP/ADP which inhibits the Fructose-1,6-bisphosphatase. Thanks for mentioning.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Why does histamine release in Type I hypersensitivity help in case of parasites?
The IgE system exists because the same events which lead to often-life threatening complications of allergy, in presence of parasites are helpful in their elimination.
The tissue injury mediated via this hypersensitivity (type I) occurs due to the mediators released by mast cell degranulation due to IgE being synthesised in atopic individuals towards normal environmental particles. The effects are also due to further immune cells being recruited by the mediators. In case of parasites, this IgE is supposed to help in their elimination and not cause tissue injury, justifying its evolution as a defence mechanism.
How does this happen? If release of the mediators is a part of the pathway, even if the degranulation is localised in the vicinity of the
 parasite, the mediators will spread systemically or atleast in the
 nearby tissues with the same consequences as in the case of
 non-parasite activation of these events.
What then is the ultimate cause beneath there being tissue injury if the stimulation is unintended but there being none when the stimulation is directed and intended? Or is there some injury in the latter case also, in which case the classification of this response in absence of a parasite into hypersensitivity i only because there is no positive effect in this case, while there was some benefit accompanying the deleterious effects in the former case? Is the presence of a parasite and possible localised degranulation the only difference between these cases?

I think it does help in case of the intestinal parasites. By purging them out. I am not too sure about it though.

IgEs are generated by B-cells as a result of activation and antigen presentation. They associate with Fc receptors of mast cells and it is only when IgE is bound to antigen that the degranulation can occur . In the case of parasites, the antigen on the parasite would have generated those specific IgEs. It is the specific binding of the IgE to the surface of the parasite that causes the Mast cell to degranulate directly onto the parasite. There may be some diffusion, but most will find its target. In allergy, IgEs are produced against harmless compounds and mast cells respond in appropriately.

Also is your BlockQuote a direct quote, in which case, can you provide the citation, or is it to highlight your question, it which case you should probably just use Bold Text?

@AMR Can you elaborate on "Find its target". Is not the effect of these mediators on vasculature and musculature the part of their anti-parasite effect?

To answer the title: Histamine has a host of beneficial effects that assist the body in inhibiting and expelling parasites. Consider a parasite that's been ingested: (1) Histamine increases gastric H+ production, (2) promotes peristalsis, mucus production and vasodilation in the intestine. This causes bowel movements, diarrhea, and the mucus is a defense from the parasite. Of course, things tend to go overboard and mass degranulation does cause a lot of damage, but objectively the parasite is removed. The injury is largely unintended, or collateral damage.

it is just in terms of the fact that the Fab region of IgE's will attach to its epitope on the surface of the parasite while the Fc region associates with receptors on the surface of the mast cell, so the distance between the two will simply be the size of the complex. Degranulation will occur in that space and for the most part not much should diffuse away. This doesn't guarantee inappropriate response however. It is different when than when the IgE epitope is a soluble molecule that can trigger degranulation into the interstitial fluid where the target then becomes the hosts own cells.

@Kendall So, what you say is, this kind of degranulation injury is there also in case of parasite-removal, but then the condition is not considered hypersensitivity, since the damage is only a collateral of a positive effect. In case of wrongful stimulation, it is called hypersensitivity, since the deleterious effect is unnecessary? According to AMR, the anti parasite effect is due to histamine acting on the parasite and not on the somatic cells. Also, can you add a reference. Thanks anyways.

Hypersensitivity in itself is confounding of normal immune mechanisms. IgE and the like are extremely beneficial and specific when combatting helminthic infections (i.e. the Th2 immune response). What's weird is that some allergens have homology to helminthic proteins, and unlike helminths (broadly), allergens can be soluble and systemic (interesting read), hence allergic hypersensitivity. Against a helminth infection, we wouldn't consider it hypersensitivity as long as everything is responding normally.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Will Saliva make food go bad
My mom was telling me that if I put the unfinished bowl of milk and cereal back to the fridge, the saliva that has been stuck to the spoon gets passed to the milk. The saliva in milk will make milk go bad faster than if there were no saliva inside. Is that true? If so, how comes? It would be great if there are scientific evidences or references to back it up.
I have found a Quora post having some people saying that it will make the food go bad faster. I was not able to find any other references

It is the bacteria in the saliva , not the saliva itself.

What research have you done on your own to try to answer your question? Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Our goal is not to simply be an answer site, but rather a site that promotes self-learning with some expert help along the way.


text:
Numbering amino acid residues
While reading about primary structures of protein, I came across the following image.
What do the numberings $n-1, n, n+1$ in the below image refer to?
I thought about it : The amino acid residues are numbered from 1 to n starting from the N-terminus to the C-terminus .
But the image below shows only a part of the protein.. so why is the last residue numbered $n+1$ instead of $n$ also, why is this shown as termination?

I looked out few papers.. but they seem to be very technical and beyond the scope of my understanding.

Could you add the resource where you find the image?

@Hachiloni Actually, it is in the Grade 11 Biology Textbook (NCERT-India) (Old-edition) You can visit this link https://ncert.nic.in/ncerts/l/kebo109.pdf (Page-9)

This is a question of general scientific semantics. As you say, the image shows an internal region of a protein and is concerned with a tyrosine residue there. It is of no interest to know the absolute position of the tyrosine, but apparently necessary to refer to neighbouring residues. To do this one refers to the tyrosine residue as n so that one can refer to those on its N-terminal side by a minus designation with respect to it, and those on its C-terminal side by a plus designation. The termination (as you call it) is NOT shown. The C-terminus (noun) would end in COOH or COO–.

The image and the text accompanying it are rather confusing, especially to someone in high school biology. I think what it's trying to show is that amino acid (AA) residue numbering starts at the N-terminus (position #1) and continues to the C-terminus. If you are referring to a particular AA, you use its position - Tyr103, for example, and if you want to refer to a residue that's two positions toward the N-terminus, you would subtract 2. If you're going toward the C-terminus, you would add 2.

@David, Actually I interpreted 'n' as the last numbering and thus thought it as termination. It's clear now. Thanks Sir!

@MattDMO, Got it! Thank you Sir!

I don't understand why the question is downvoted! :(

This question is a bit hard to answer for me without more context.
However, it is clear that the n refers to the tyrosine which is highlighted in the figure as well (especially the interaction of its phenol). The other positions (n+1, n-1) are shown relative to the tyrosine.
I'm unsure about the role of tyrosine in the primary structure of proteins, but maybe this is more clearly explained where you found the figure. I'm also unsure if the glutamic acid is terminal.

Thanks! But even the textbook doesn't provide any explanation for this :( . One question, is it like we can show the positions of other residues w.r.t to a particular one? If that is so, this will suffice me.

Yes we can. The same is true for nucleotide sequences. (This is done in the fugure, too.)

Okay! Thanks for the input.

The textbook uses this as an example of the primary structure (amino acid sequence) of a peptide, but it doesn't say why.  The reason is that for many protein-protein interactions, the overall shape of the protein (secondary and tertiary structure) plays a very clear role ... but for post-translational modification of tyrosine, serine, and threonine residues, the sequence of amino acids immediately surrounding the amino acid to be modified has a particularly important role.  When tyrosine is to be modified, the relevant enzymes are tyrosine kinases, which attach phosphate at the -OH of tyrosine, and tyrosine phosphatases, which reverse this.
For consideration of the specificity of such enzymes it is quite common to align the substrate peptide sites with "n" or "0" being the position to be modified, and "n-1" or "-1" being the amino acid before it, and so on.  You can see an example for E. coli here .. not the most common place to look for this phenomenon, but interesting.  In humans there are 90-100 enzymes of each type, making these changes to any well-exposed part of a protein consistent with the specificity of that protein, with regulatory effects on the actions of many proteins that include causing them to interact with many other proteins, which contain SH2 domains, which also are targeted largely by the primary sequence around the tyrosine.  So these modifications are changing protein activity and associations in a complex network.  I think of it as a biochemical protein counterpart of the nervous system, due to the complexity of interactions that can be produced.  Note also that these phosphotyrosine sites are very easy to evolve by mutation of very few amino acids, allowing them to be introduced into new proteins to create new regulatory networks as needed, even in organisms with a long time between generations.  (They are an example of how "evolving evolvability" has been crucial to permit the evolution of large, complex, long-lived organisms)
For biologists, the most accessible piece of information is looking at the primary sequence surrounding each phosphorylation site, so this does make a relevant example of the concept ... but it would be too hard to explain it at that stage of instruction.

Thank you Sir! I get a fair (clear :P) idea of that now. +1 for your effort!


text:
What will happen if one keeps the photosynthesis plant active 24x7?
While reading this article online something said on it made me wonder.

Also, there have been suggestions and a Dawn / Dusk type of ramp up and down to simulate the slow changes in the sun have value, but we have not seen solid universal data in this regard to date...

It made me wonder if we are simulating the sun in a dark room for growing the plants with the help of red, blue, and a little bit of far-red light, what will happen to the plants if we keep the ideal conditions for which the plants carry out photosynthesis whole day? Does it affect its yield or the plants die out quick?
I am an engineering student working on indoor farming, my knowledge of botany is the same as a high school student. So if I am wrong please tell me.

Do plants 'stay awake' or fall asleep?

During the night they are mostly inactive.

Welcome to Biology SE! I'm afraid that your question as currently posed is a bit confusing. Can you please try to explain more of the context of your question and what you understand about the mechanisms at play?

@Gurkirat perhaps edit your question to say 'active' (and maybe specify what kind of activity), since plants don't go asleep or stay awake.

You might read about gardening/farming in Alaska, or other areas in the north, where even if you don't get actual midnight sun, there's no actual darkness, just a period of twilight.

this depends a lot on the plant, look at CAM plants for instance.

@John they have different metabolism, but I am talking about normal phosinthesis. If you keep the conditions ideal (maintain proper LED wavelengths throughout the day), and pump CO2 to the environment (the place you are using for indoor farming), and water, etc. Is there any possibility that the health of the plant can be hindered or they are overworked? Is such thing (overwork, health, hindrance, etc.) present in botany?

I don't know the "correct" answer (I don't think one answer covers all plants) but I have lost plants under lights when I have forgotten to cycle (on/off). They had water, food and fresh air, but some need darkness to perform optimally. Certainly blooming is often day-length related; some plants need short days, some need long.

@anongoodnurse  your answer certainly add more to my knowledge, but now I wonder what is the point of using LED if you have to maintain a cycle. Sure we can manipulate many variables now, but I always thought that this advancement would reduce the growth period by half.

This question depends on the plant. The have varied hormonal responses to light to program their lifecycle. For many plants, you can keep the light on 24/7, they will grow faster. For plants that interpret it as a sign of midsummer aridity, they may flower and seed as a response.

Ideal conditions for photosynthesis
You mention ideal conditions to carry out photosynthesis, I would just like to point out that this includes carbondioxide levels, temperature, and nutrients as well as light.
Flowering
As anongoodnurse mentions performance might be measured by blooming which, in most flowering plants, has a day-light related component. However, for general growth increasing daylight over the 'natural' day length can often increase yield.
Daylight Cycles
The important point to note is that plants do 'ramp up' at dawn getting ready to start photosynthesizing (for some plants with temporal photosynthesis mechanisms (see CAM photosynthesis) this can be even more important). The reason plants do this is because plants can suffer from 'photobleaching' which can be considered similar to sunburn in humans, if they are not ready for sunlight. Getting 'ready' can involve lots of things including opening stomata (pores) to let CO2 in, changing which metabolic pathways are active,  and moving about chloroplasts inside cells. Plants 'figure out' how and when to ramp up based on circadian rhythms which work well on 24 hour clocks and slight changes over time. Thus 12 hrs to 16 hrs can be a big change, particularly if the change happens by lights coming on earlier. Additionally, the 24 hour 'clock' means that plants will do better with 18hr light then 6hrs dark cycles than 36hrs light 6 hrs dark, because the total cycle length should be about 24hrs.
Photosynthesis Side Effects
Finally, constant photosynthesis does take its toll on plants as photorespiration accompanies photosynthesis. In C3 plants (most crops) this can reduce photosynthetic output by 25% whilst creating ammonia as a byproduct. The ammonia needs to be detoxified as a build up in the cell can cause cell death. Thus plants need enough 'respite' from photosynthesis to deal with photorespiration byproducts or they will suffer.

Thanks a lot, I was looking for an answer like this

Adding my thanks, too. +1. (Only had a vague idea of the need for darkness, but not the consequence of its absence.)


text:
difference between proximal and distal mechanisms of aging in biogerontology?
In his book Biology of Aging, Roger McDonald describes the difference between causes and mechanisms of aging; and states that the cause of aging is essentially thermodynamic (entropy) and that mechanisms can be divided in distal and proximal.

The scientific and lay literature describing biological aging can be confusing due to the misuse of the words cause and mechanism. Often these two terms are used interchangeably, although they have different meanings in the context of aging

The cause of aging refers to the thermodynamic forces that act continually on the organism throughout its life span. There exists only one cause of aging: increasing entropy.

Alterations in the biomolecules that lead to loss of function are the mechanisms of aging. There exist an infinite number of mechanisms that can be observed [...]
We also distinguish between two types of aging mechanisms: distal and proximal

then defines distal mechanism of aging as

A mechanisms of aging that underlies and is remote from the more obvious direct cause for a time-dependent functional loss. For example, obesity is the distal cause of abnormally high blood glucose concentration. Abnormally high blood glucose concentration results in the time-dependent functional loss of connective tissue due to advanced glycation end products

and proximal mechanism of aging as

A time-dependent alteration to a tissue, cell, or molecular process that lead to a loss in function

personally this seems something that he believes and in that sense not very precise academically or scientifically, because I can't find any reference regarding the subject
my question regards the following, is this information something that he believes in or does it has a foundation in biogerontology? and if the latter, can somebody kindly reference the subject with an article?

Thanks for replacing with text; it seems like if your question is about "proximal/distal" mechanisms, that you've included a bunch of unrelated text about "cause vs mechanism" and then stopped quoting where the section about "distal and proximal" is to begin.

my fundamental question is in fact about proximal/distal mechanisms but the cause/mechanism distinction also worries me, because it is the first time i'm reading it and i have no reference that proves that this is true or unanimous among biogerontologists.. however my priority is the distal/proximal mechanism

It's not uncommon to see an author provide some working definitions to keep readers from getting confused, because biologists don't typically sit everyone down to formally agree on universal definitions for every term in a given field of study. While the first point about cause vs. mechanism is a bit reductive and pedantic (imho), the fact that he even points it out suggests that it's not universally accepted in the literature. The proximal/distal distinction is probably just a useful framework for thinking about mechanisms that he will likely refer back to throughout the text.

thank you all for your contribution in this question; yes, it is likely that i'll choose that path, regarding this subject as a useful framework than a dogmatic definition.. i had the opportunity to read Ernst Mayr’s ‘‘Cause and Effect in Biology’’ where he presents the duality proximate/ultimate which is the most similar i can find in biology, beyond that i can only find related topics with sociology precisely about proximal/distal causes.. and that is another thing they say proximal/distal causes not mechanisms. thank you all again; @MikeyC feel free to write and answer if you'd like


text:
How to restrict a BLAST search to include only a few protein sequences?
I am performing a BLAST search and I need to filter the output to a certain family of proteins.
Specifically, I need to get matches within the CYP152 family of the Cytochrome P450 proteins. I can parse the results to just P450 proteins fairly easily as the "hit def" field in the output will contain "Cytochrome P450" somewhere in there if it is in fact a P450 protein sequence, but the same is not true for CYP152.
Is there some way to do this? I am using ExPASy BLAST:
http://web.expasy.org/blast/
Thanks in advance

Do you have a list of protein names in the family?

Can't you just use taxonomy filter?, but I'm sure @terdon can help you out :)

@terdon I do not, that would make my life much easier. And Rick Beeloo the taxonomy filter is not that specific, at least as far as I have found.

You're basically doing it backwards. You should start by getting the sequences of the proteins in the family and then blast your query against them. Are you looking for hits against any species? Only some? Do you have access to a Linux or Unix (OSX will do) machine?

I run Ubuntu on my laptop. And okay, are there any good sources of information that you can recommend to me? I have been searching around and can find lots of info on the P450s but not much on the CYP152 subfamily. What I have is a sequence from one protein in the CYP152 subfamily (called OleT JE) and I am trying to compare it with all CYP152 proteins.

The gene identifiers that you get in BLAST output depends on the identifiers used during the BLAST database construction. So you may not find the exact identifier you are looking for.
For restricting the BLAST results to a smaller set of proteins/nucleic acid you can choose either of the two:

Make a database with the fasta sequences of the proteins/nucleic acids that you want. You have to install BLAST and run it from the commandline. Use makeblastdb to make the database. Now you align your queries against this database. Note that now your e-values would not be the same as what you would obtain from a search against the bigger database.
As you said in the question, you can parse the results later. You would have to know what identifiers were used in the blast database that you searched against. ExPASy-BLAST would most probably use the UniProt IDs (there is an ID convertor in the UniProt website to map UniProt IDs to other IDs). If you use NCBI-BLAST (nr database) then you would need to know the GenBank IDs.


text:
Do disaccharidases require a cofactor or coenzyme to function?
I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly appreciated.

Most enzymes (especially ones catalyzing simply reactions like this) do not require cofactors or co-enzymes.

It seems that beta-glucosidases do not require co-factors but some alpha-glucosidases are co-factor dependent.
Some bacterial alpha-glucosidases (GH4 family) require NAD+ to function (Hall et al., 2009). Thermotoga maritama alpha-glucosidase (GH4 family) requires Mn2+, in addition to NAD+ to function (Lodge et al., 2003). Ferroplasma acidophilum alpha-glucosidase seems to contain iron but its role as a co-factor is not known (Ferrer et al., 2005).
For more information on alpha-glucosidases see BRENDA.

+1 I missed that (although there is a crystal structure with NAD+ that I couldn't find when I was writing It's here. Wierd thing is that apparently the NAD isn't being used as an oxidizing cofactor as it is  reported to be unchanged in the reaction.

Apparently not for lactase and β-galactosidase, as one might expect for this sort of hydrolytic reaction. There are also Wikipedia entries for maltase, sucrase and trehalase with references you can follow up to check yourself.


text:
Why does uncompetitive inhibition decrease the Michaelis constant?
I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though).
More specifically, why does uncompetitive inhibition decrease the Michaelis constant?
From wikipedia:

This reduction in the effective concentration of the E-S complex increases the enzyme's apparent affinity for the substrate through Le Chatelier's principle (Km is lowered) and decreases the maximum enzyme activity (Vmax), as it takes longer for the substrate or product to leave the active site. Uncompetitive inhibition works best when substrate concentration is high. An uncompetitive inhibitor need not resemble the substrate of the reaction it is inhibiting.

The Lineweaver-Burk Plot:

By TimVickers - Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=4549560

The uncompetetive inhibitor essentially "locks" the substrate in the enzyme thereby preventing the enzyme from catalyzing the substrate which would then decrease the amount of free enzyme. That should not, however, alter the value of $K_m$ because any copies of the enzyme that are still active ("not locked") maintain the same affinity for the substrate. I applied that same logic to noncompetitive inhibition (no change in $K_m$), hence the confusion.

First off, the difference between the types of inhibition:

competitive inhibition: The inhibitor only binds to the substrate-free form of the enzyme. (Not necessarily at the active site!)
uncompetitive inhibition: The inhibitor only binds to the substrate-bound form of the enzyme.
noncompetitive inhibition: The inhibitor binds equally well to both the substrate-bound and substrate-free forms of the enzyme. (Some people feel this is just a non-special special case of mixed inhibition.)
mixed inhibition: The inhibitor binds to both the substrate-free and substrate bound forms of the enzyme. (But not necessarily with the same affinity.)

Secondly, you need to separate out the concept of binding affinity of the substrate from the concept of $K_m$. The binding affinity of the enzyme towards the substrate is just what you think it is: the equilibrium constant between the bound and unbound forms of the enzyme, in the absence of catalysis and inhibitor.
The $K_m$, on the other hand, is an overall parameter of the rate equation, and doesn't necessarily have a direct relation to substrate binding. The confusion between the two arises from the fact that in simple enzymatic systems, under the simplified conditions we normally study them in, $K_m$ is a pretty decent approximation of the substrate binding affinity. Thus you'll have introductory textbooks saying that "$K_m$ is a measure of substrate affinity". -- a gross oversimplification. They're certainly related, but they're not exactly identical - especially when you get to more complex reaction schemes. Confusing the two leads to problems.
The enzyme inhibition cases are an example of this. Enzyme inhibitors (even competitive ones ones) don't change the intrinsic binding affinity of the free enzyme to substrate. Instead, they draw off some of the enzyme from the productive pathway. Because they change the concentration of particular enzyme species, they change the observed rate equation. How they change the rate equation depends on which enzyme species they change the concentration of.
For a full accounting, you really should look at the derivations of the rate equations, and how the extra equilibria of the inhibitor binding changes things. (e.g. here or here) But for something of an intuitive explanation:
pure noncompetitive inhibition reduces the concentrations of substrate-bound and substrate-free forms equally. (The concentration of product-bound forms being negligible in the standard initial rate equations.) This is basically the same as reducing the total amount of enzyme, i.e. reducing $V_{max}$ or apparent $k_{cat}$.
competitive At saturating substrate concentration, the amount of free enzyme (and thus the effect of inhibition) is negligible. The rate at saturating substrate (i.e. $k_{cat}$) is thus the same. Therefore, it's the apparent $K_m$ that changes. (NOTE! The actual affinity to the substrate isn't changed by the inhibitor. Instead, the inhibitor specifically reduces the amount of free enzyme available, in a way that can be compensated for by higher substrate concentrations. This just so happens to change the rate equation in the same way changing the $K_m$ does.)
uncompetitive At negligible substrate concentrations, the amount of substrate bound enzyme (and the effect of inhibition) is negligible. Thus the rate should be the same with and without the inhibitor. If you recall, the enzymatic reaction rate at negligible substrate is parameterized by $k_{cat}/K_m$. For uncompetitive inhibition, this needs to stay the same. Thus both $k_{cat}$ and $K_m$ need to change in the rate equation, to the same proportion.
mixed - A mixture of the above effects, depending on the relative affinities to the substrate bound/unbound forms of the enzyme.


text:
Material recommendation: molecular biology for mathematicians and computer scientists
I am wondering if there are some introductory learning resources on molecular biology designed specifically for scientists with heavily math-oriented curricula (math/physics/computer science).
They should be capable of conveying the main ideas in a concise way; if they could represent some concepts in a mathematical language, that would be a big plus.
Additional details
As it was pointed out in the comment, molecular biology is a very broad field so I should be more specific - although it is difficult for me. Personally, I would like to acquire some basic knowledge to interpret NGS data and go in the direction of system biology.

If it's a concise overview you're after, I'd recommend anything from the instant notes series.

from wiki, quantitative research is the systematic empirical investigation of observable phenomena via statistical, mathematical or computational techniques.This definition applies to any empirical science (which excludes math). So I am not quite sure what you mean by "quantitative scientists"

Molecular biology is a big field. Are you sure you don't want to narrow it down to any subfield of molecular biology? If you are rather interested in system biology, in molecular biophysics, in molecular genetics, in biochemistry or in molecular population genetics for examples you might want to specify.

@Remi.b ok, I have just edited to be more specific

@Remi.b So I guess molecular genetics and cell biology are the most relevant ones for NGS data analysis and system biology, but I am very ignorant so your feedback would be appreciated.

I have also come from purely non-Bio background (I am a Software/Electrical engineer who didn't study Bio even in his high-school).
As others have pointed out in comments above that Molecular Biology is a vast field. But if you want resources covering all the basics of Genetics/Molecular Genetics, then I can easily recommend the following to anyone (which are both easy to understand and very authentic ones):

Nature Scitable
Genetics by PS Verma, Agarwal, S Chand.

There are other books like this one but they all are on bioinformatics/advanced and expect some knowledge of Molecular Biology. My recommendation (proved one) are above two. Best of luck!!

I haven't started it yet, but practical computing for biologists by Haddock and Dunn might be a good place to start. Its what I will use for my Bioinformatics class. This course looks at large sets of genomic data and seeks to use analytical programs to parse out the data into codons, genes, single nucleotide polymorphisms, and mutations. If you can write a code to identify it you can sequence the genome of whatever your interested in an let the program do its thing. You just have to know the language and get comfortable with some beefy programs.

I like this book and strongly recommend it. However,  not for the OP. The book is for biologists needing to learn programming whereas the OP is a computer scientists needing to learn biology.


text:
Can DNA base pairs go through each other?
Consider the simplified version of the motion one DNA base pair held together by a hydrogen bond:

Use u and v to denote the displacements of the bases from their equilibrium position along the direction of the hydrogen bond that connects them,
Define y = u-v to measure the stretching distance between the bases in a pair of bases.
So, y = 0. u=v. No stretching. When y > 0. Stretching. When y < 0. Compression. u

I would like to say, that physically, it is not possible for u to go through v or vice versa. Meaning that the stretching distance measured by y has a lower bound. In other words and my question, does it make physical sense for two base pairs to go through each other?

What do you mean by going through? Is there any terminology for this?

I do not have any terminology for this. I am trying to visualize what the model implies. I am assuming that if that we have 1 dimensional motion (1 degree of freedom) and if I, say, fix u and let v move towards u (compression), then eventually it will have to go through u if the motion of both bases is along the hydrogen bond.

I'm voting to close this question as off-topic because this is Physics.

Covalent chemical bonds between atoms like C-N, C=N, C-C, C=C etc are actually maintained by electron orbits. It is hard to disturb these orbits. When they are disturbed, the bonds would break, which means some chemical reaction occurs. Then you get different chemicals--they are not u and v anymore. That is what I think. This seems more chemical thing rather than biology.

@243 I think OP is describing a situation where you have 2 bases in a plane, and push 1 towards the other, still in the plane. As the bases moved closer the atoms would begin to repel. We can think of it in terms of Leonard-Jones Potential, where the repulsive force is inversely proportional to the distance to the 12th power. This means that the repulsion gets really high really fast. Since the bases are magically locked in the plane, you'd probably push them close together and stop. In reality, one would pop above or to side of other.

The base pair you are describing is only stable if each base is part of a macromolecular polymer, a polynucleotide. Specifically the DNA strands need to be oriented in an anti parallel alignment, and there will be a chain, or string, of base pairs (imagine the rungs of a ladder).
Remember, individual hydrogen, or H-bonds, are one of the weakest molecular interactions that we can detect. So the scenario you propose, where one single base forms a Watson-Crick base pair with its complementary base, free in solution, is so unstable as to be undetectable.
Once the base pairs are formed in a DNA double helix (think of a flexible ladder where one end is fixed and the other end has been twisted through several clockwise revolutions) then there are many other energetic contributions that stabilize the base pairs. For example, the electrostatic repulsion of the anionic phosphates in the sugar-phosphate backbone drives the two strands apart.  The hydrophobic stacking interactions of the pi bonds of adjacent bases also makes a major contribution to the stability of the helix, and permits the H-bonds to be more stable in this context.
Finally, the fact that base pairs are only stable in polynucleotides means that if you melt a single base pair, the sugar phosphate backbones will topologically prevent any other melted base pair from "passing through" the first one.


text:
Is a nucleus more dense than the rest of the cell?
On the one hand, it seems like there's a higher density of 'stuff' in a nucleus, so it should be more dense. On the other hand, if it was more dense, I'd imagine that nuclei would 'settle' to the bottom of a cell, which would be rather surprising.
Update:
http://www.eng.umd.edu/~nsw/ench485/lab10.htm reports nucleic density of 1.4 g/cm3.
https://books.google.com/books?id=t4ZQRWvr510C&pg=PA85&lpg=PA85&dq=cytoplasm%20density%20g%2Fcm3&source=bl&ots=rEkcu0HzZE&sig=Bs4MVad_pbS7vWY2pRv6ALWf-bc&hl=en&sa=X&ved=0ahUKEwj2rLXVnLbJAhVSlogKHUjAAS8Q6AEIMTAD#v=onepage&q=cytoplasm%20density%20g%2Fcm3&f=false
reports a density of 1.03 - 1.1 g/cm3 for cytoplasm, so less dense.
do nuclei sink then? or is ICF too viscous / there too much disturbance through movement for nucleus to sink?

When you search images of cells by electron microscopy(EM), some nuclei are denser than cytosol, but others are not. You could also find partial dense area in nuclei. EM is telling how crowd with atoms the areas are. https://www.google.com/search?q=electron+microscope+cells&safe=off&client=safari&rls=en&biw=1318&bih=542&tbm=isch&tbo=u&source=univ&sa=X&ved=0ahUKEwjhrZe_h7XJAhWMOiYKHY4QCMEQsAQIHA#imgrc=_

When you hang up your shirt does it fall to the bottom of your closet?
The nucleus is a dense fibrillar network of DNA, RNA, and proteins, yes, but the subject you should take a look at is the cytoskeleton of the cell. It will will answer all your unanswered questions on the intracellular network that stabilizes, supports, and aligns the organelles within the cell.

If the shirt isn't hung up correctly. :D That makes sense, thanks for the explanation and amusing analogy.


text:
What is the efficacy of an Ebola antibody response
There is contradictory (~?) evidence in the literature that antibody responses against Ebola are effective in clearing the virus and protecting the patient. Some time ago, I wrote a bit about the literature on this in my blog (which you can find here) that one of the primary problems faced in developing an effective antibody response against Ebola is that antibodies may actually be hijacked by the virus in order to mediate entry (Takada et al).
My question is, has this observation been supported? And, if so, how do more recent vaccines address / avoid this problem?

As far as I can see the link you reference does not support the idea that antibodies mediate Ebola entry.  There was some speculation that this might happen, but I don't think there was ever much (if any) support for it (other than analogy with viruses like Dengue).  In general, lab animal vaccine trials have shown that Ebola antibodies are pretty effective.

OK, I'm ready to be embarassed - I need to check on this and see if I may have referenced the wrong article ... or, I don't know... maybe I dreamed it. I'll look into it and repost later.

iayork - I'm sorry, I cited the wrong article. The appropriate article is Takada et al - correction made with link in text above.

Although there are a handful of papers suggesting that antibodies can enhance Ebola infection, in practice Ebola vaccines seem to be highly effective both in animal models (e.g. Aerosolized Ebola vaccine protects primates and elicits lung-resident T cell responses, VSV-EBOV rapidly protects macaques against infection with the 2014/15 Ebola virus outbreak strain, Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus) and, probably, in humans (Efficacy and effectiveness of an rVSV-vectored vaccine expressing Ebola surface glycoprotein: interim results from the Guinea ring vaccination cluster-randomised trial).
If antibodies can enhance infection, how could vaccines protect?  That's not as contradictory as it sounds.  In general, antibody-mediated enhancement of infection only works under specific conditions.  Even with Dengue, the poster child for ADE, it only occurs during a specific window of antibody titers and affinities.  Ebola is probably much less adapted to needing ADE than Dengue, so it's likely that you'd only get ADE in a very narrow range of antibody titers, affinities, and perhaps targets.  So if vaccines induce high titers, high affinities, and/or a particular set of antigenic targets, ADE may never kick in -- it may be a lab curiosity that isn't relevant in the real world.
(Alternatively, it may be an issue down the road, say if vaccine-induced immunity fades in a specific way that allows it. I don't know of any evidence suggesting this would happen, but I'm not an Ebola researcher.)

--it may be a lab curiosity that isn't relevant in the real world.                        This is exactly what I have thought as well since reading the original article that brought it up, but with all the fervor to develop new vaccines, I thought it was both something to keep in mind when fast-tracking a drug as well as a question that newly published data might answer.   Ultimately, these are the kind of data that make me pay attention because something novel might show up.


text:
Evolution of Aging according to Weismann
Several authors agree to the fact that August Weismann was the first to propose an explanation to biological aging (Kirkwood and Cremer, 1982; Gems and Partridge, 2013).
A lot of hallmarks (and some contradictory) are pointed out about Weismann along his life, which I am reflecting only in these

When he suggested that group selection was the answer of aging;

August Weismann and Alfred Russel Wallace proposed that aging has evolved to remove worn-out older individuals, thereby reducing competition for scarce resources and resulting in benefits for the species. However, such an evolutionary mechanism would require group selection of a sort that makes this an untenable scenario. (Gems and Partridge, 2013)

the reason suggested by Weismann for the evolution of ageing was an adaptive one, namely that ageing is beneficial in ridding a species of old and decrepit individuals which would otherwise compete for resources with younger ones. Thus, by natural selection the somatic cells of the organism would have come to lose their capacity for unlimited survival, and ageing of the organism as a whole would have appeared. (Kirkwood and Cremer, 1982)

I don't understand how any of those arguments can justify the evolution of aging

they claim that group selection was responsible for the evolution of aging but it doesn't explain how older individuals get old.. they are just removed from the population because they got old, it doesn't  seem to explain the evolution of ageing.

When he developed the concept of panmixia to reshape his nonadaptive theory (or neutral) of biological aging.

The central component of Weismann's non-adaptive theory of ageing was the principle of panmixia which he developed [...] In brief, this principle states that as soon as any character becomes useless to an organism, natural selection ceases to operate upon it and it begins to disappear. (Kirkwood and Cremer, 1982)

How the concept of panmixia is related to the evolution of aging?

is that because since post-reproductive period does not contribute to the evolution of the species, the potential of immortality of somatic cells desapear? It doesn't make much sense..

References

Gems, D. and Partridge, L. (2013) ‘Genetics of longevity in model organisms: Debates and paradigm shifts’, Annual Review of Physiology, 75, pp. 621–644. doi: 10.1146/annurev-physiol-030212-183712
Kirkwood, T. B. L., & Cremer, T. (1982). Cytogerontology since 1881: A reappraisal of August Weismann and a review of modern progress. Human Genetics, 60(2), pp. 101–121. https://doi.org/10.1007/BF00569695

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

think I got it..
if I may I would like to answer this question since it could be helpful to anyone who's interested in this field of research.

Regarding the first question: " how any of those arguments can justify the evolution of aging "
Weismann presented a notion of group selection as a possible answer to biological aging, proposing that such mechanism becomes advantageous for the species by removing the most geriatric individuals.
how those arguments can justify the evolution of aging:  on the hypothesis that if all individuals were immortal, they would be competing with the younger ones for the available resources.

if individuals did not die they would soon multiply inordinately and would interfere with each other's healthy existence. (Weismann, 1891)

Thus, by natural selection the somatic cells of the organism would have come to lose their capacity for unlimited survival, and ageing of the organism as a whole would have appeared. (Kirkwood and Cremer, 1982)

Regarding the second question: " How the concept of panmixia is related to the evolution of aging? "
essentially it is used to justify the aforementioned concerning somatic immortality, that is, the cause of cellular aging.
when applying this concept of panmixia to the post-reproductive period, aging can arise, as this is a period that does not contribute to the evolution of the species. Thus it can be considered as an inert physiological interval, such that the potential of somatic immortality starts to disappear.

[Weismann speaking about reproduction] As soon as the individual has performed it’s share in this work of compensation, it ceases to be of any value to the species, it has fulfilled its duty and may die.
(Weismann, 1891; p. 10)

As soon as natural selection ceases to operate upon any character, structural or functional, it begins to disappear. As soon, therefore, as the immortality of somatic cells became useless they would begin to lose this attribute.
(Weismann, 1891; p. 141)

it's also important to mention, as a side note, that for Weismann, natural death arises due to the absence of cell renewal, which causes the wear of the histological tissue and thus the concept of panmixia justifies the limited number of cell division.

References
Kirkwood, T. B. L., & Cremer, T. (1982). Cytogerontology since 1881: A reappraisal of August Weismann and a review of modern progress. Human Genetics, 60(2), pp. 101–121. https://doi.org/10.1007/BF00569695
Weismann, A. (1891). Essays upon heredity and kindred biological problems. Volume I. Oxford: Clarendon Press.


text:
What happens to the cut-out introns from a pre-mRNA?
Once the spliceosome has cut out the introns from a pre-mRNA they are said to be degraded. What does that mean and is that happening in the cytosol? Can the nucleotides be used for something else within the cell?

Yes. Ribonucleases (RNAses) break down the spliced RNA strands back into mononucleotides, and these building blocks can be reused.
They will be broken down into nucleotide monophosphates, so they will have to be re-phosphorylated to triphosphates before they can be reused for transcription.
Here are a couple of reasonable reviews of the mechanisms:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177198
Note: this one also mentions that sometimes introns are not fully degraded to single nucleotides, but instead can serve as signaling molecules.
http://www.sciencedirect.com/science/article/pii/S0092867409000671

Not just signalling, some are ribozymes. Group I ans II introns are good examples.

Another use for a spliced out intronic piece of RNA is as noncoding RNA. Here's an example which include pre-mRNA also transcribing microRNAs.
http://www.nature.com/nrm/journal/v10/n2/fig_tab/nrm2632_F1.html?foxtrotcallback=true


text:
Aquaporin and the exclusion of $H^+$
As I read in my textbook, aquaporins exclude $H^+$ when absorbing water, but where does this $H^+$ come from? Additionally, is $H_3O^+$ a liquid that looks like regular water?

$\ce{H_3O^+}$ is just representation of acidic water. You'd get much better answers about this on chemistry.SE

It doesn't matter where the $H^+$ comes from in the context of this information. The textbook is just saying that the aquaporin is permeable to $H_2O$ but not to $H_3O^+$ (nor, presumably, to $OH^-$).
In any aqueous solution, especially in the presence of acids, some of the molecules will be $H_3O^+$. The pH tells you how many. It doesn't really make sense to think about what a solution of $H_3O^+$ would look like.


text:
What do you call mRNAs that translate to the same protein?
For example AUAACC and AUCACG in distinct mRNAs may both be translated to the same dipeptide Ile-Thr.


text:
Have we ever observed fertile offspring with a different number of chromosomes than the parents?
Chimpanzees are supposedly the closest relative of humans from a DNA perspective, they are both diploid, and they both undergo meiosis. However, chimpanzees have 24 chromosome pairs while humans have 23.
Have we ever observed a situation where the offspring of meiosis has a different number of chromosome pairs than the parents, the offspring lived, and the offspring was not sterile? How does evolution explain the shifting of chromosome pair counts?

Welcome to the site! That's a good question, and although I don't have time to write a full answer at the moment there's actually a good explanation of this here that you might find helpful: http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/

This is possibly a duplicate of https://biology.stackexchange.com/questions/16533/evolution-of-chromosome-numbers or https://biology.stackexchange.com/questions/16625/how-are-new-chromosomes-replicated-into-the-next-generation-via-sexual-reproduct, but the accepted answer for the latter is basically an edited version of the blogpost I linked above.

I actually attended a seminar by Mike Barker (http://eeb.arizona.edu/people/dr-michael-barker) on this yesterday; he mainly studies plant systems but has also looked at other groups (such as insects).

Thanks. I will look into the articles you post which I have not already read. I am familiar with aberrant euploidy and chromosome duplication. I am tring to understand if we have just theorized this or if it has been observed. The literature I have read at NCBI stated that no offspring of different chromosome pair counts ever survive. Not a polyploidy transfer error, but where the parent had 24 chromosome pairs and the child had 23 chromosome pairs.

In the title you are asking for "different number of chromosomes", while the final paragraph is about "different number of chromosome pairs". Could you please clarify, which is the actual question?

It is actually quite common in plant breeding (Google gets about 460K hits on "plant breeding chromosome duplication") to try to induce chromosome doubling/ltripling by exposure to such things as colchicine, which generally (at least in my understanding: I'm not an expert) produces stronger plants, larger flowers, &c.

[..] have we ever observed a situation where the offspring of meiosis has a different number of chromosome pairs than the parents, the offspring lived, and the offspring was not sterile?

Yes!
While it may seem a detail, the difficulty is to know what exactly you mean by observation. Chromosomal abnormalities, gene duplication, chromosomal duplication, robertsonian translocations, whole genome duplication are not super common but common enough to be seen repeatedly. We see them happen again and again in different lineages, we can even investigate how our environment affect such chromosomal abnormalities (Merkatz et al. 1984). So below, I am citing a few papers that I more or less randomly selected among the decently large amount of work on the subject.
Chromosomal rearrangements are sometimes involve in speciation (Rieseberg 2001).
There are many genetic disease in humans that are related to such chromosomal duplication (e.g. Down Syndrome) and de novo mutations for these mutations, while rare, are not so rare that we can witness them only on geological time scale (Veltman and Brunner, 2012)
There are soo many articles on the question that I don't really know what to cite. Of course, there are reviews that can be of interest to you (such as Zhang 2003). I tried to find a video showing a meiosis leading to chromosomal duplication but unfortunately, I have failed to find that.
The mechanisms of these mutations leading to chromosomal rearrangements are pretty well understood. You should probably start with wikipedia > gene duplication # Mechanisms of duplication for an intro.
As you talk about the difference between the number of chromosomes in chimpanzee and humans, you might want to have a look at the post Evolutionarily speaking, why do humans have 46 chromosomes where it is explains (with plenty of citations) how did the change in chromosome number occurred in our lineage.

I have read a lot about the idea of evolution

I do not want to seem pedantic but given that the vocabulary that you are using (change in kind,  concepts of transfer errors, concept of gradual change) it really suggests that all you read comes from the creationist propaganda and not from the evolution literature. Indeed nobody use these terms in the research. Those terms are mainly used as straw man from the creationist propaganda.
There are many free intro courses to evolutionary biology. You might want to have a look at Understanding Evolution by UC Berkeley.

This does not answer the question.

@Will Why not? Could you please leave a comment on what you think is missing?

@Marzipanherz :  I was looking for "yes" or "no", with examples.

The entire text is a series of examples and the first paragraph make it clear that it is a 'yes'. But just to highlight it, I will write a big 'yes' directly after me quoting the question.

Down syndrome is an example of fertile offspring with a different chromosomal number than the parents.  Persons with Down syndrome have an extra copy of chromosome 21, and so have 47 chromosomes instead of the normal 46.  Fertility is lower in persons with Down syndrome but they are not invariably infertile.  Wikipedia gives fertility for women at 50%.  Some of the children of these women also have Down syndrome.
Another example is Turner's syndrome.  Affected women lack an X chromosome and so have 45 chromosomes.  Fertility is lower in these women but some can get pregnant and bear children.
Bernard V et al. Spontaneous fertility and pregnancy outcomes amongst 480 women with Turner syndrome. Hum Reprod. 2016 Apr;31(4):782-8.
It may be that some of these persons who have different chromosomal numbers in sampled cell populations (usually blood) but are still fertile are actually [mosaics](https://en.wikipedia.org/wiki/Mosaic_(genetics).  These individuals have different populations of cells comprising them.  Perhaps the mutation leading to trisomy or monosomy occurred in one cell after the embryo was already comprised of several cells.  Cells from that lineage will show the phenotype associated with the mutation but if the germ cells are descended from cells which did not have that mutation, they would be normal and so be associated with normal fertility.

This only answers the question regarding different number of chromosomes, but not regarding a different number of chromosome pairs.

Plants are particularly well know n for this, polyploidy (duplicate sets of chromosomes) are rampart across plants and is often exploited by humans to increase fruit yields. Strawberries for instance vary from 14 to 56 chromosomes and remain cross fertile. In plants they can still be cross fertile however in animals this is has never been seen and all known polyploid animals are believed to be the result of multiple individuals having the same duplication.
Sturgeons, show various degrees of Aneuploidy (different numbers not due to duplication), and it has been studied by crossing sturgeons with different numbers of chromosomes, many of the offspring are fertile.
chromosome fusion has be observed in horses, cows, sheep, lab mice, and fruit flies, and there varying degrees of fertility. Basically the animals that we pay very close attention to the genes of have shown it, meaning it should be relatively common. The university of indiana provides a more complete list.
Insects, many insects are haplodiploidy which means males anf females have vastly different numbers of chromosomes.
Indian Muntjac (see picture) actually have different numbers of chromosomes between males and females, 7 and 6 respectively. they share this trait with wallaby and echidna.

crossbreeding of scarlet macaw with different numbers of chromosomes to reintroduce genetic diversity has been shown to be successful.
The blue butterfly is the all time winner however as the chromosome count varies wildly, without polyploidy no less. They have so many chromosomes 448-452 that the loss or fusion of some just has little effect.
A 44 chromosome human exists, who appears normal, this number is due to chromosome fusion, since he has not bred we don't know about his fertility.
As has been mentioned humans can have different numbers of chromosomes and while most or lethal some are not and those with them can remain fertile. changes in chromosomes in particular seem to be the most tolerable biologically.


text:
How come large herbivores have such thin legs?
Edit:
This question is very similar to this and related to this one (though the latter focuses on homology instead of scaling laws). However, the answer to this question is far more comprehensive, in particular it offers a plausible explanation why horse legs evolved as they did (vs human or even rhino legs).
Large grazing mammals such as horses, moose, and cows tend to have relatively thin legs despite being up to ~1000kg. For example, this rider's and her horse's legs appear to have about the same cross-sectional area both for below and above the "knee":

If this horse is 500 kg (a mid-range mass for horses), each leg would have to support 125 kg, compared to only 37.5 kg for a 75 kg adult. Why don't we see a corresponding difference in cross-section?

Possible duplicate of What is the anatomical term for a two jointed leg?

Possible duplicate of Comparative leg sizes

On that photo, the horse's shoulder is easily twice as broad as the woman's gluteal region whereas the horse's gluteal region is over 4 times as broad. That translates to 4 times and 16 times more cross-sectional area (mostly equal to strength). The calf is admittedly slimmer, but you should note that on the horse it's about 90-95% bone whereas on the human it's more like... 8-10% bone, the rest being muscle (... which a horse doesn't need due to its anatomy...).

Elephants? Just saying.

Elephant, rhinoceros, &c all have much thicker legs in proportion.  The answer, I think, lies in the fact that the animals you mention all evolved as cursorial animals (that is, they run to escape predators).  Less mass in the lower leg means it swings easier, so the animal can run faster.
There are two things you're apparently not noticing in that picture.  First, the the horse's lower leg is almost entirely bone (and some tendon), and it's bone that does the supporting.  The propulsive power comes from the large muscles of the hip, thighs, and shoulders.
Second, the lower part of the leg (with the white wrappings) is not anatomically equivalent to the human's lower leg, but to the bones of the hand and foot.  You can see this if you look closely at the rear leg in that picture.  The femur, equivalent to the human's thigh, ends at the knee just above the belly line.  Then the tibia extends about halfway down, ending at another joint which you might think is the knee, but which is called the 'hock' in horse-speak.  The white-wrapped part is a metatarsal, equivalent to human foot bones, then there pastern bones equivalent to human toe bones, ending in the hoof/toenail.
So consider that you can, if reasonably fit, walk around on tiptoe without crushing your foot and toe bones, then imagine the end result of your ancestors having done this for the last several tens of millions of years :-)
PS: With horses, there is some effect from human selection, too.  Racing & show breeds tend to have thin lower legs, draft horses & working breeds have proportionately thicker ones.  My first horse, a thorobred/arab mix, had legs about as thick as my wrists (granted, I'm a fairly muscular guy); my current mustang, about the same height & weight, has legs about twice as thick.

May I suggest you add (Or can I do this?) a picture of the horses leg structure? As you say a lot of people don't know the lower part of a horses' leg is more equivalent to the bones of a human hand or foot.

@JaneDoe1337: It would indeed be a help, but I have no idea how to do it (since SE insists on using its own arcane methods for such things).  Feel free to do so yourself.

@jamesqf there's a little button that appears when you are writing an answer and that lets you upload images or link to them from other places in the web. See the "Images" section at the bottom of this page. That doesn't seem too arcane, really.

@terdon: Maybe the little image appears in your browser.  It doesn't seem to in mine.  Also, I'm dysiconic: unless a button has actual words spelling out its function, I am highly unlikely to be able to "intuit" its function.

This is a mistake in comparative anatomy which is somewhat common. When looking at four-legged animals, people often mistakenly map the parts of the hind legs.
Here is an image that shows the different morphology of the same bones in horses and humans:

What people often think of as the thigh of a four legged creature is really our calf and shin bone! And what is often mistaken for the calf is actually our foot.
Horses evolved to run on what is actually our toenail. You can see a similar pattern when humans sprint, our fastest running pace — we pull our heels up, and land on and launch off of the balls of our feet and our toes. That foot-strike is actually how animals such as the cat and dog walk habitually.
There's an urban myth that "dog's knees bend backwards", but by looking at this graphic, you can see that what appears to be the dog's knee is actually its ankle. And both the dog's ankle and knee bend the same way ours do.

Habitually landing on our heels in a normal walking pace makes us plantigrades, alongside raccoons and kangaroos. Dogs and cats walking on their toes is called digitigrade, while swift grazers such as deer and horses we classify as unguligrade, which means walking on their toenails.
So, other answers are correct, and flesh out the full information. I just wanted to give a visual indication to correct this common error.

Can you source the first image, I want to see if I can use that.

That image of the skeletal dog standing upright is both amusing and alarming, and I will never be able to look at a dog again without imagining it wandering around like that while people aren't looking.

@WayneWerner https://www.youtube.com/watch?v=7f1ovurzU2s

@John sorry, I grabbed it off of Google image search. If you do a search for "human horse comparative anatomy" you can find many copies of it, but I don't recall which one I originally got it from.

How come large herbivores have such thin legs?
They don't. The following book does an extensive comparison of the bones of humans with other animals:
Adams BJ, Crabtree PJ. 2008. Human vs Horse. In: Comparative Skeletal Anatomy. Humana Press.
Here are some images of human bones (left) next to horse bones (right):
Radius/Ulna (fused in horses)

Humerus

Femur

From these images, the bones of horses are clearly larger than their homologous counterparts in humans. Another answer gives a good picture of where these bones lie. Even if you were to consider the horse hock as its knee/elbow and compare, you would find that:

the horse radius/ulna is ~1.9 times larger than the human humerus at the smallest diameter
the horse tibia is ~2.3 times larger then the human femur at the smallest diameter
the horse metacarpal is ~1.3 times larger than the sum of the human radius and ulna at the smallest diameter

This is a homological comparison, but we should compare the part of the leg that is visible for both animals and "forget" that the horses knee is really it's ankle; it's more relevant for scaling laws. In that case horses do have human-sized but bonier legs. Though the femur difference is still illustrative of the more robust skeleton in horses.

@KevinKostlan I've updated the answer to address this. I understand your point though, and I think even with the rough measurements I made the horse bones are still supporting more weight. I just wanted to provide some data to show that the horse bones are not that small.

@Kevin Kostlan: The important part of the like-part comparison is, I think, that the muscles remain much the same.  The hip and thigh have the largest muscles, the fingers/toes have little, even though the corresponding bones are greatly elongated in the horse.  So when you grasp something with your hand, the power is coming from muscles in the forearm - you can see the tendons moving in the wrist.

You're assuming that horses and cows are still subject to Darwinian evolution.  In fact breeding of domestic animals has mostly been controlled rather carefully by humans, to breed for characteristics which we feel are favourable, even if those characteristics are detrimental to the animal's survival in the wild.
This became most obvious in the Agricultural Revolution, with selective breeding work pioneered by Robert Bakewell and others, where animal size increased dramatically.  African cows today give you an idea of how big cows would have been before this breeding effort, but even they are the product of thousands of years of fairly selective breeding.
Horses are a similar case.  Genghis Khan's Mongol warriors used ponies of around 12hh, and these would have been relatively wild animals.
Fragility of limbs is just one way modern animals are rendered less fit in the wild, of course.  Many breeds of domesticated animals have problems giving birth without assistance, or have genetic defects which can cause the animal distress or reduce its lifespan.  These issues are usually tolerated or managed somehow, because humans prioritise the desirable features of the breed.

Your answer is evidently overstating the importance of artificial selection if you consider that wild animals, such as zebras and deer, also display this characteristic.

Wild equines are not really morphologically distinct from domesticated ones. This isn't a phenotype that's emerged in the last 6,000 years since horses were domesticated. Humans have absolutely nothing to do with why horses have thin legs.

@NuclearWang Look at different horse breeds, though. Draught horses (speed isn't important) have a lot thicker legs than racing horses (speed is of prime importance). The differences between various domesticated breeds and wild horses are many (and don't confuse wild horses with domesticated-horses-gone-wild). But there's no need to reiterate James' answer, which is a lot closer to the mark.

"You're assuming that horses and cows are still subject to Darwinian evolution." They still are. It's just that most of their evolutionary pressures are human driven, and humans are a part of nature. This is just another case of one species exerting evolutionary pressure on another.

Evidence suggests that horses may have been domesticated as early as 3500 BCE, strong evidence exists at 2000 BCE. Khan's horses would have been bred for at least 3000 years. They were hardly "relatively wild". https://en.wikipedia.org/wiki/Domestication_of_the_horse


text:
Temperature-dependence of circadian rythms
A circadian rhythm is a chemical clock. In the absence of light or other stimuli to entrain it, its speed depends on reaction rates.
As a rule of thumb reaction rates double every 10C as long as the enzymes don't denature. The "rule of thumb" predicts that a mild 0.5C temperature change would alter the 24 hour cycle by almost an hour/day, which is quite noticeable. Does (non-hazardous) heat/cold exposure advance/delay the circadian rhythm? If so, is it in line with the "rule of thumb"?

What do you mean by “entrain”? And presumably the verb, whatever it is supposed to mean, has on object. And circadian rhythms are generally referred to as “biological” clocks. In any case, the idea that  the length of circadian rhythms are limited by the rate (speed) of a chemical reaction or reactions seems to me absurd, given their length. Before twiddling your rules of thumb you need to identify the reactions that you think are limiting in a specific instance.

this question is fully answered in the wikipedia article.


text:
Is there any kind of antibiotic effective against fungi?
I know that antibiotics usually have properties affecting specifically bacterial cells, like by inhibiting peptidoglycan synthesis. but do any antibiotics exist affecting eukaryotic cells, like yeast or other fungi? I read in a text that "most" eukaryotic cells are resistant against antibiotics and that confused me.
Regardless of whether it can be used against bacteria or not, is there any kind of antibiotic effective against fungi, or any kind of eukaryotic cell?

Please be more clear. Are you asking if there's any antibiotic usually used against bacteria who's effective also for eucaryotic cells?

No, regardless of whether it is/can be used against bacteria or not. I know that the antibiotics usually have properties affecting specifically bacterial cells like by inhibiting peptidoglycan synthesis. but do any antibiotics exist affecting eukaryotic cells? like yeast? or fungi? I read in a text that "most" eukaryotic cells are resistant against antibiotics. that confused me

The term antibiotic typically refers to chemicals effective against bacteria. There are antimicrobial chemicals effective against fungi, and they are rather aptly called antifungals.
In general, for every organism, there will be a chemical that is toxic to it.

Good answer, but just one suggestion. Wikipedia's definition doesn't match the use of these terms in infectious disease medicine and pharmacology. Antibiotic (like antimicrobial) is a general term (see Goodman and Gilman Chapter 48, General Principles of Antimicrobial therapy). We have more antibacterial antibiotics, in general, since these pathogens are easier to selectively target, so most antibiotics are antibacterial antibiotics. For that reason, yes, it typically refers to chemicals effective against bacteria, but that's just because there are more of them.

Wikipedia can be a good source, but it is particularly weak for infectious disease principles.

@DeNovo Wikipedia was not my source, I just included those links for further reading. In my field, antibiotic and antibacterial are used synonymously. The WHO and ECDC seem to agree on this. That said, I'm not a medical doctor nor a pharmacist. I don't disagree with your points and you're welcome to edit my answer as you see fit, or post your own.

Yes. The antibiotic (general microorganism “targeter”) you’re looking for is an antifungal. There are fewer ways to target fungi as opposed to bacteria, but we can target them nonetheless.
The fungal cell membrane has ergosterol to regulate its permeability whereas the mammalian cell relies on cholesterol. Fungi have cell walls which are not present in mammalian cells and are different in chemical composition to bacterial cell walls. A fungal cell wall is made of chitin whereas, as you mentioned before, a bacterial cell wall is made up of peptidoglycan.
We rely on these differences to target fungi. Some antifungals bind to ergosterol (e.g. Polyenes like Amphotericin-B) whereas other agents inhibit ergosterol synthesis altogether (e.g. Azoles like Triazole). Other antifungal agents target the fungal cell wall by inhibiting the synthesis of chitin (e.g. Echinocandins like Caspofungin).
There are more ways to target fungi, like introducing nucleotide analogues (“look alikes” that don’t work) to disrupt their nucleic acid synthesis (e.g. Fluorocytosine 5-FC). Another method is to disrupt the fungal microtubule’s aggregation during mitosis (e.g. Griseofulvin), thus “arresting” the fungal cells in metaphase.
Recommended Textbooks:

Hugo & Russell’s Pharmaceutical Microbiology 8th edition, Wiley- Blackwell. Edited by S.P. Denyer et al.
ISBN 9781444330632
Essential Microbiology for Pharmacy and Pharmaceutical Science, Wiley- Blackwell. By Geoffrey Hanlon and Norman Hodges
ISBN 978-0-470-66534-3 (pbk.)

Yes, there is. The Azole class of drugs, for example, are used to treat (eukaryotic) fungal infections. One such drug is clotrimazole which targets cytochrome p450 which is responsible for the synthesis of ergosterol (a mimetic of cholesterol; not found in humans), ultimately leading to excessive fluidity in fungal membranes and their lysis.
https://www.ncbi.nlm.nih.gov/pubmed/3288361
Its not that eukaryotes are inherently resistant to antibiotics; rather, its often difficult to treat serious eukaryotic infections because humans are also eukaryotes and share similar biochemistries. See below.
The problem with clotrimazole is that, although ergosterol is not found in human, the cytochrome p450 is (i.e. in the ETC) and it serves other functions which may be affected.


text:
What does "operationally soluble" mean, re. Tax10 enzyme?
I am trying to work out whether the enzyme Tax10 is soluble or insoluble. I need to know if some buffers won't work with Tax10. I am trying to confirm Tax10 activity, having confirmed protein expression and having purified it.
Any help would be much appreciated! Thanks :)

Context:
Walker K, Long R, Croteau R. 2002. The final acylation step in taxol biosynthesis: cloning of the taxoid C13-side-chain N-benzoyltransferase from Taxus. Proc Natl Acad Sci USA 99(14):9166-9171.

The TAX10 gene overexpressed from pSBET yielded a ≈50-kDa protein (determined by SDS/PAGE), consistent with the size of the encoded enzyme, and this operationally soluble recombinant enzyme from preparative bacterial cultures was partially purified by anion exchange (DE-52) and ceramic hydroxyapatite chromatography.

(p.9169, below Figure 3)

I think all they mean is that the protein was found in the soluble fraction rather than in inclusions.

Fantastic. I thought that's what they meant. Thanks :)


text:
Is there any evidence that supports glycolysis in mitochondria or chloroplasts?
Glycolysis is known to be a part of cellular metabolism undergone by both eukaryotic and prokaryotic cells, whether under aerobic or anaerobic conditions. As the endosymbiotic theory states that mitochondria and chloroplasts were once bacteria that lived apart from eukaryotic cells, do they have any enzymes or compounds suggesting that they once did glycolysis?

On aspect of the endosymbiontic theory is that genes were transferred from the endosymbiont/new organelle to the nucleus of the host cell. Does your question include such transferred genes or only the ones remaining on the mitochondrial/plastid genomes?

A search of UniProt returns no reviewed, mitochondrially encoded genes involved in glycolysis. There are some unreviewed entries, but a brief perusal of the associated publications suggests to me that these have all been incorrectly annotated (as one may expect from unreviewed entries).
Interestingly, Rickettsia prowazekii, an obligate intracellular parasite and the modern species thought to be most closely related to mitochondria, also has no glycolytic enzymes:

Genome sequences of organisms enjoying an endosymbiotic lifestyle are at risk. The activities of homologous nuclear genes may render genes of the endosymbiont expendable and as a consequence they become vulnerable to obliteration by mutation. Good candidates for such purged genes in Rickettsia and mitochondria are genes required for amino-acid biosynthesis, nucleoside biosynthesis and anaerobic glycolyis. These and other genes would have been deleted when an ancestral genome first lived in a nucleated cell. Once genes essential to a free-living mode are lost, the endosymbiont becomes an obligate resident of its host.

Andersson SGE, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Alsmark UCM, Podowski RM, Näslund AK, Eriksson A-S, Winkler HH, Kurland CG. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.