text:
What is the longest-lasting protein in a human body?
Protein life times are, on average, not particularly long, on a human life timescale.
I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/minutes/days passed from the moment that given protein was translated. I am not sure is the same thing as asking which human protein has the longest half-life, as I think there might be "tricks" the cell uses to elongate a given protein's half-life under specific conditions.
I am pretty sure there are several ways in which a cell can preserve its proteins from degradation/denaturation if it wanted to but to what extent? I accept that a given protein post-translationally modified still is the same protein, even if cut, added to a complex, etc. etc.
And also, as correlated questions: does the answer depend on the age of the given human (starting from birth and accepting as valid proteins translated during pregnancy or even donated by the mother)? What is the oldest protein in a baby's body and what is in a elderly's body? How does the oldest protein lifetime does in comparison with the oldest nucleic acid/cell/molecule/whatever in our body?

Maternally contributed antibodies? They could be older than you if there are any that persist life-long.

Half-Baked suggestion: consider changing the title to ask for the "longest-lasting" protein in the human body.  When I first read the title, I wasn't sure if it was asking for the longest-lasting protein, or the protein that has been around the longest in evolutionary terms.

would there be a protein that is taken from the environment and cannot be produced inside the body? Like vitamins?

@Armatus Antibodies do not and cannot persist lifelong. They're actually destroyed at a rather rapid rate.

Crystallin proteins are found in the eye lens (where their main job is probably to define the refractive index of the medium); they are commonly considered to be non-regenerated. So, your crystallins are as old as you are!
Because of this absence of regeneration, the accumulate damage over time, including proteolysis, cross-linkings etc., which is one of the main reasons why visual acuity decays after a certain age: that is where cataracts come from. The cloudy lens is the result of years of degradation events in a limited pool of non-renewed proteins.
Edit: A few references:
This article shows that one can use 14C radiodating to determine the date of synthesis of lens proteins, because of their exceptionally low turnover: Lynnerup, "Radiocarbon Dating of the Human Eye Lens Crystallines Reveal Proteins without Carbon Turnover throughout Life", PLoS One (2008) 3:e1529
This excellent review suggested by iayork (thanks!) lists long-lived proteins (including crystallins) and how they were identified as such:
Toyama & Hetzer, "Protein homeostasis: live long, won’t prosper" Nat Rev Mol Cell Biol. (2013) 14:55–61

To back this up: Crystallin proteins were used to determine the age of Greenland sharks. Source

I agree it is almost certainly in the eye, but why Crystallin specifically?

Supported by Identification of long-lived proteins reveals exceptional stability of essential cellular structures and Protein homeostasis: live long, won’t prosper; in particular see Table 1 in the latter

I like Mowgli's answer, because it is a non-obvious example. However I would also point out that there are many, many protein-based structural components in the body that we know do not regenerate due to associated pathologies; so presumably these structural proteins are as old as from when they first arose in developemnt. Take the stereocilia on hair cells in the cochlea, for instance. The stereocilia structure is actin-filament based, so is a structural protein. Hearing loss occurs due to damage to these structures, which is not repaired. In fact, birds suffer only temporary hearing loss not because they regenerate these structures, but because they grow replacement hair cells.
Once you start thinking about this then, it is pretty clear that many structural proteins will be conserved throughout life (if the cell they are attached to or within remains a part of the body). And many cells of the body remain in the body throughout life, so any proteins that join the cells together, say connexin proteins that form gap junctions between cells, would also presumably be conserved. I say this because I think the energetic cost of degrading a protein that spans two membranes would be too great for it to occur. I have not heard of gap junctions being eliminated, but I may be wrong.
Mowgli's answer is nice because it involves globular rather than fibrous proteins- though Wikipedia still classifies them as structural proteins. I was interested and read this article about them. Interesting stuff! Thank you Mowgli!
I would be interested to know if there are any conserved biochemically active proteins. I would think that extracellular proteins would probably be turned over, and the best chance of finding such a conserved protein would be within a cell that remains for life post differentiation. Perhaps a proteasome complex itself (these are the protein complexes that are involved in protein degradation)?

Thank you for expanding Mowgli's answer! I personally work with actin in vitro and I never considered the fact that there could be years-old actin in our body (we usually frow away our stocks after a week :D )

I would be very surprised if ribosomes were not degraded. And proteosomes do get degraded.

A very interesting example are the cohesin molecules holding sister chromatids together in the oocytes (so only applicable to females, sorry!). Cohesion is established in utero, and these molecules are not recycled throughout life (AFAIK only shown directly for mice, not humans - https://www.ncbi.nlm.nih.gov/pubmed/20971813, https://www.ncbi.nlm.nih.gov/pubmed/26898469, but presumably same is true for us). This is considered to be a major contributor to the maternal age effect (https://en.wikipedia.org/wiki/Age_and_female_fertility) through low level loss of cohesion throughout life (since levels of cohesin can't be restored) until chromosomes start losing association between sisters which causes high chances of their missegregation (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536066/)

In terms of the common/abundant proteins, the answer would have to be elastin.
The turnover is extremely slow, with a half-life of 74 years (https://www.elastagen.com/media/The_Science_of_Elastin.pdf) or "decades" according to other sources. In any case it is very slow - slow enough that most of it lasts a lifetime.
Elastin is a major constituent of the extracellular matrix but the rate of synthesis (and breakdown) is much slower than collagen (the other major structural protein). While breakdown is extremely slow, synthesis is even slower and may not be sufficient to replace the lost elastin, resulting in decreased levels with age. This is one of the primary contributions to the aged look of older humans


text:
Is there any evidence of causation for breathing rate to affect blood pressure in a human?
I did some research and trials, and with 5 trials for a normal heart rate and 5 done 45 seconds into breath holding, the results came back showing that my heart rate of 116/65 mmHg increased to 138/90 mmHg. I was interested in the cause of this, but couldn’t seem to find any evidence online to explain why this happens, exepct for some simple studies that showed that their is a correlation.
So my question is: has there’s been any studies that hypothesize or found a reason for breath holding to affect blood pressure?

My first thoughts are this has to do with some kind of j-receptor pathway like the one mentioned in this abstract - https://www.ncbi.nlm.nih.gov/pubmed/4698499

Interesting question, it has been studied because sleep apnea is associated with hypertension in humans.
It's not my field of research, so I read a few sources to give you an answer.
There is a open-access review here (https://doi.org/10.1152/jappl.2001.90.4.1600) on the topic of episodic hypoxia, which is similar to the experiment you conducted. Two studies in dogs (https://doi.org/10.1152/jappl.1996.80.3.773 and https://www.jci.org/articles/view/119120) showed that neural reflexes, but also arousal, explain a part of the acute increase in blood pressure but here caution has to be used, as acutely holding breath may have different mechanisms on blood pressure elevation than the chronic hypoxia induced by sleep apnea.
Finally, a review (https://doi.org/10.1038/ajh.2009.43) in 2009 summarizes the evidence between sleep apnea and hypertension.
Overall, there seems to be multiple mechanisms. First, there is a sympathetic discharge during asphyxia, releasing catecholamines which can induce elevation in blood pressure by activating the baroreflex.  These are supported by studies of denervation in multiple organs. Secondly, there is activation of the renin-angiotensin-aldosterone system, a central player in blood pressure regulation. Thirdly, the animals studies show that arousal is an important factor in the acute blood pressure elevation ; in other words, being conscient of holding your breath itself induces blood pressure elevation. I cannot find the exact mechanism linking arousal to blood pressure elevation, though.

Good answer, thank you. In my research I hadn’t considered sleep apnea, that was a strong angle to use for this topic.

source: Stack Exchange

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

sort: votes


text:
What characteristic(s) of inverse agonists allow for inhibitory effects?
I know that inverse agonists have similar structure to its complement agonist; and, as a result, they have the ability to bind to the same receptor, causing an inhibition of the pathway considered.
My question is, if the agonist and inverse agonist have the same structure (and possibly/extremely likely the same energy levels, steric effects, etc.), how is it that the receptor molecule reacts differently?

Suggested edits (since I have too many pending): add Pharmacology and Chemistry tags.

The short answer is that an inverse agonist binds preferentially to the inactive state of the receptor, so it reduces the receptor's intrinsic, basal activity. The agonist was only raising the activity, not switching it on.
The most basic model of receptor pharmacology is that the receptor, $\ce{R}$, and the agonist, $\ce{A}$, are in a chemical equilibrium: $\ce{A}+\ce{R}\rightleftharpoons\ce{AR}$. In this model, the agonist bound receptor, $\ce{AR}$, generates the biological response. But in truth, this isn't a very accurate model since nothing's actually happened to the receptor. Why should $\ce{R}$ generate a biological response when it's bound but not when it's unbound? This model also wouldn't explain inverse agonists.
The del Castillo Katz model rectifies this problem by suggesting that there are two equilibria. The first is for agonist binding. And the second is for a conformational change in the receptor to an activated state, $\ce{R}^*$, that causes the biological response. Hence, $\ce{A}+\ce{R}\rightleftharpoons \ce{AR} \rightleftharpoons \ce{AR^*}$. This activated state is a different shape of the receptor, which allows a biological response. Depending on the receptor type, it could be an opened ion channel, a 7TM protein which destabilises the binding of a G-protein or more.
For many receptors (such as the GABAA receptor), the receptor can go into the active, $\ce{R^*}$, state without an agonist being bound. Hence we have the equilibrium $\ce{R}\rightleftharpoons \ce{R^*}$. This is called constitutive activity - the receptor generates some level of biological response by itself. So this shows us the chemical properties of inverse agonists. An inverse agonist binds with a higher affinity to the $\ce{R}$ form of the receptor than the $\ce{R^*}$ form. So the equilibrium shifts to the left and the receptor has reduced constitutive activity. So the drug reduces the biological effect by pulling it below the basal level. See the figure below: figure 3-1 from (Blumenthal and Garrison, 2011). NB: they opt for $\ce{R_i}$/$\ce{R_a}$ instead of $\ce{R}$/$\ce{R^*}$ and $\ce{L}$ for a generic ligand.

An agonist and inverse agonist definitely don't have the same structure otherwise they'd be the exact same molecule. They might have the same pharmacophore but they necessarily have some chemical difference that makes the inverse agonist prefer binding to $\ce{R^*}$ but not the agonist. To be honest, I'm not convinced that they even need the same pharmacophore. Although as far as I know in most cases, they do. It's not too difficult to imagine a situation where the conformational change from $\ce{R}$ to $\ce{R^*}$ moves residues in a binding pocket and prevents (sterically/electronically) the inverse agonist from binding as easily. I'm not so sure how the energy levels would work here so you'll have to get back to me on that or ask the chem/phys stackexchanges.
My crude figure below has a 7TM protein (Green) with a G protein (brown) attached. The receptor can undergo a conformational change to the $\ce{R^*}$ form (horizontally flipped) which causes the G protein to dissociate and cause some biological effect. The agonist (red star) can bind into the pocket but fits with a much higher affinity for the $\ce{R^*}$ form since the conformational change gives it a nice binding pocket. Since it fits better in the $\ce{R^*}$ state, the equilibrium shifts to the right so the G protein prefers to dissociate and the agonist introduces a biological effect.

On the other hand, the inverse agonist may fit better into the $\ce{R}$ binding pocket than the $\ce{R^*}$ binding pocket. Hence, it shifts the equilibrium to the $\ce{R}$ state, so the G protein prefers not dissociate and the biological effect is reduced.

Further reading: (Blumenthal, D. K. and Garrison, J. C. (2011). 'Pharmacodynamics: Molecular Mechanisms of Drug Action' in Goodman and Gilman. 12th ed. The Pharmacological Basis of Therapeutics) and ( Rang and Dale. (2015). 'How drugs act: general principles' in Pharmacology. 8th ed.)

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


text:
How efficiently does the human body convert the energy stored in fat into kinetic energy?
I read that one gram fat contains 9 kcal energy. There are many tables around claiming that x type of exercise for t duration burns roughly E kcal energy. I'd like to estimate how much weight one will lose by following a certain training plan based on these two values. I don't know whether I need to calculate with the heat loss too, or not. Most of these tables don't tell anything about the method they used to estimate the E values. I could workaround this problem by ignoring efficiency, but I can do that only if it is relative close to 100%. As far as I know fat goes through beta-oxidation and the citric acid cycle. After that ATP is used to move the muscles. It is hard to find anything about how efficient this process is.

this depends on largely how you define it, what we normally measure is efficiency including how much energy is used on metabolic upkeep and heating the body in addition to muscle output. we use oxygen consumption to know exactly how many calories we have "burned" when doing this.  In this study we get between 18-26% efficiency, thats calories ingested to work done. Most of the loss is in converting to ATP (~60% loss) and how much ATP we "waste" heating the body. Note efficiency drops quite a lot when you switch to anaerobic exercise.
keep in mind however the body will not start out burning fat, it has glycogen reserves it will start using first.

"keep in mind however the body will not start out burning fat, it has glycogen reserves it will start using first. " - Actually that is not true. It starts with glycogen and intramuscular fat...

@inf3rno do you have a source for that, its not that I don't believe you but it is the first I have heard of that but it does make sense physiologically.

You can use google to find some. For example this is a good starting point: https://journals.lww.com/acsm-essr/Fulltext/2005/10000/Intramuscular_Triacylglycerol_in_Energy_Metabolism.6.aspx

There was this fat burning myth, that you start "burning fat" only after 20-30 mins of aerobic exercise. That is partially true. You start with IMTG until the triglicerides arrive from the fat cells through the circulation. Without that people on ketogenic diet would not be able to do exercise...

the paper you linked states thew fat in question does not start getting utilized until 60min of exercise.

Yes, there was debate about whether it is 20-30-60 mins to mobilize fatty acids from adipose tissue. I read different values in different articles. It does not really matter though, because the muscles use IMTG until that is done. And they fill the IMTG storages with the fat from adipose tissue after the exercise is done.


text:
Fertilization of the human egg- where does our centrosome come from?
Is there a centrosome in a human egg cell? Is the reason why the egg cell remains paused before meiosis 2 because there isn't a centrosome, and it only divides when the sperm fertilizes it thus it can have a centrosome? If this is so, then how did oogenesis happen? ?

To answer the first part of your question. The sperm actually introduces two centrosomes. The centrosome then nucleates the new microtubule assembly to form the sperm aster — a step essential for successful fertilization. You can visit these sites Simerly, et al as well as Paweltz, et al

Could you provide a more recent reference? (The ones you provided are from 1995 and 1987). I ask because From Zero to Many: Control of Centriole Number in Development and Disease (2009) says: "Notably, oocytes and spermatozoa lose parts of the centrosome in a complementary manner. Centrioles, but not centrosome proteins, are lost in the oocyte. On the other hand, in sperm, the PCM material is lost, but not the centriole/basal body, which is necessary for flagella formation.  ...

...  Fertilization brings together the basal body from the sperm, which becomes a centriole within the zygote, and the PCM from the egg."


text:
Does the male and female always split evenly the genetic material given to their offspring?
Are there animals known to have a different percentage of splitting of genetic material, like the male give 75% and the female just 25%. I know that drone bees have only genetic material from their mothers, I would like to know if there are also instances in larger animals (mammals and reptiles).
If the answer is no, then do we know why it is always evenly split.


text:
Less oxygen in winter?
Since Oxygen is produced by photosynthesis, would there be less oxygen in the air in winter, where the trees shed their leaves and the sun generally shines a lot less? If yes, would that be a noticable difference?

Pretty interesting question: The short answer to it is: Yes, the seasonal O2 levels vary with the season and this can be measured.
The paper in reference 1 says that this is connected to two phenomena: Production of O2 by photosynthesis and also the uptake and release of O2 in the oceans due to higher temperatures (warmer water dissolves less gases).
The paper in reference 2 says that the northern and the southern hemisphere are basically decoupled from each other. The northern hemisphere reaches its peak of maximum O2 concentration in June/July while the southern reaches its peak around January due to the slow mixing in the athmosphere. They also say that due to more ocean area on the southern hemisphere the uptake/release processes in the ocean play a much more important role there.
The graph from paper 3 also shows that the CO2 concentration is inverse compared to O2, since during the photosynthetic period of the year CO2 is consumed.

The following figure is taken from the website of "2° Institute" and is interactive, so can actually check, when the concentration is at which level. The general O2 concentration is getting lower, it is assumed that this happens due to the human CO2 production, the source can be found here.

References (please let me know in the comments, if you can't access the articles):

Seasonal and interannual variations in atmospheric oxygen and
implications for the global carbon cycle
Seasonal variations in the atmospheric O2/N2 ratio in relation to the  kinetics of air-sea gas exchange
Seasonal and short-term variations in atmospheric potential oxygen
at Ny- Ålesund, Svalbard


text:
Offspring of parents with different number of chromosomes
Many papers report that dog-whelks (Nucella lapillus) show a distinct chromosomal polymorphism between populations of 2n = 24 up to 2n = 36. Could somebody please tell me how many chromosomes the F1 generation of parents with (male) 2n = 24 and (female) 2n = 27 would have? What would happen to the three unmatched chromosomes?


text:
Are cell biology and cytology the same science?
According to Wikipedia, the terms can be used interchangeably, but according to my college professors, cytology is exclusively the study of chromosomes and identification of their abnormalities.

Your professors are probably using cytology to refer to cytopathology which isn't strictly incorrect, but is a bit confusing since cytology also has a broader meaning.
Overall, the distinction isn't scientifically that important. Biology is so interconnected that you can't really stick strictly within any one "type" of science, they are only soft distinctions. If you need to learn a term for a course, there isn't much point to argue with your professors. Literally, the word "cytology" should refer to the study of cells, so in my opinion the narrow definition doesn't make sense, but like other words it is important to interpret it in context.
In my personal experience, I have usually heard "cell biology" used rather than "cytology" to broadly mean study of cells. If you are at an institution that calls their cytopathology labs "cytology" it doesn't much matter if there are other meanings for the word.

Another reason why the Wikipedia definition, along with other sources, confused me is the fact that I heard "cell biology" everywhere, but people rarely said "cytology". Perhaps that's why I thought that cytology was a specialized science.

Study of chromosomes is called cytogenetics.


text:
What is trans-complementation?
Is trans-complementation a complementation of transgenes?

The crystal structure reveals a trans-complementation mechanism whereby an incomplete immunoglobulin-like domain assimilates an isoform-specific myomesin interdomain sequence.
https://www.ncbi.nlm.nih.gov/pubmed/27989621

The term complementation refers to the recover of a phenotype or characteristic ("or function of a protein") that was altered due to mutations. The complementation can be a cis, a mutation in the same gene that restores function, or trans mutation on a secondary gene that restore the function.
An example from wikipedia:

For a simple example of a complementation test, suppose a geneticist is interested in studying two strains of white-eyed flies of the species Drosophila melanogaster, more commonly known as the common fruit fly. In this species, wild type flies have red eyes and eye color is known to be related to two genes, A and B. Each one of these genes has two alleles, a dominant one that codes for a working protein (A and B respectively) and a recessive one that codes for a malfunctioning protein (a and b respectively). Since both proteins are necessary for the synthesis of red pigmentation in the eyes, if a given fly is homozygous for either a or b, it will have white eyes.
  Knowing this, the geneticist may perform a complementation test on two separately obtained strains of pure-breeding white-eyed flies. The test is performed by crossing two flies, one from each strain. If the resulting progeny have red eyes, the two strains are said to complement; if the progeny have white eyes, they do not.
  If the strains complement, we imagine that one strain must have a genotype aa BB and the other AA bb, which when crossed yield the genotype AaBb. In other words, each strain is homozygous for a different deficiency that produces the same phenotype. If the strains do not complement, they both must have genotypes aa BB, AA bb, or aa bb. In other words, they are both homozygous for the same deficiency, which obviously will produce the same phenotype.

So, my first guess was wrong and trans-complementation term stands for complementation of genes arranged in trans-configuration?

@user619271 indeed.


text:
How does Ran GDP get from the cytoplasm back to the nucleus following nuclear import and export?
I understand that in Ran-dependent nuclear import Ran GTP binds importin in the nucleus, and after diffusing through the nuclear pore complex Ran GTP is hydrolyzed to Ran GDP and releases importin. How does the hydrolyzed Ran GDP get from the cytoplasm back through the nuclear pore complex to the nucleus? The same question applies to nuclear export after Ran GTP is hydrolyzed following export of the Ran GTP-exportin-cargo complex. Does Ran GTP freely diffuse through the nuclear pore complex? Is it actively transported?


text:
How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?
Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and a better than average (for a layman) understanding of how DNA works.
I understand the process of Amino Acid being coded for by specific DNA nucleotides and the chains of Amino Acid forming specific proteins - however, I am unable to find information on the topic of how actual shape is determined / coded for by DNA (again, not Hox genes and body segments).
Here is an example of what I am asking about - please note that this is just an example and I'm not specifically asking about how eyes evolved. I'm asking how changes in shape/size/structure of any part of a body happens from changes in DNA.
It's generally held that eyes evolved (in very basic terms) from a layer of photosensitive cells on the skin, which slowly formed into a cup that could detect direction, then the cup eventually closing in to form a smaller hole, and then a lens, and so on.
So my question (based on that example), would be, how does DNA (or a change in DNA) code for "create an indentation on the surface of the skin at this location". Or, "Deepen the indentation repeatedly until it is a cup". And so on.
More basic examples are "make the hind legs on a mammal slightly longer" or "make the cranium on an ape slightly larger". The question is not dependent on body part or animal type but is specifically about how DNA, in general, operates.
Hopefully the question is clearly stated and not too long - I welcome any suggestions on how to clarify the question.
Thank you!
--added--
canadianer's comment gave excellent information regarding some general principles that are involved, but I'm still hoping to find (if it's possible) a more precise and detailed answer to this.

Are you asking how eye morphogenesis evolved or how it occurs in extant organisms? Either question is interesting, but the answers may take the form of a text book. You might start with this review for the latter question.

@canadianer The eye was just an example out of many possible examples - I'm not specifically looking for information on eye development. Rather, my question is how DNA codes for shape and shape changes (as opposed to how it codes for amino acids which form proteins). Other examples include how the shape of an ear is encoded in DNA and expressed, how DNA codes for the formation of fingerprints (place a ridge here, no ridge here, etc), and any other non-body segmant "shape" on an organism.

Each example you listed would be different in the specifics, obviously, and incredibly complex. I understand you want a general answer, in which case you might be interested in and simultaneously disappointed by this post. This is just one example of tissue patterning in the developing embryo. Perhaps not as exciting as eyes or ears, but the underlying mechanism is the same: patterning is controlled by gene expression, expression is controlled by transcription factors, and transcription factors can be influenced by intercellular signalling.

You can check out this post for my recommendation on a developmental biology text book.

Thank you @canadianer ! What I'm interested is the underlying mechanism and not how any one part of the body is formed. Your links are a great start as well as the keywords "patterning", "gene expression", "transcription factors", and "intercellular signalling" which will give me a place to start searching and reading. :) I'm not afraid to do the work and take the time to actually learn the information, I just had no idea where to start and everything I tried was a dead end.

@canadianer Any other information you can provide (even a semi-detailed but simplified step-by-step of the underlying mechanism) would be great and very appreciated! Thank you.

I think adding the bounty was misguided; canadianer's comment is the best concise answer you're going to get without a textbook.

Thank you for the response Bryan. I appreciate any feedback at all on this because I've been trying to figure it out for quite a while and have not gotten far. If the consensus is that canadianer's response is as good as can be provided without a textbook then that's good to know - but I'm still (at least for now) hoping to find an explanation that doesn't require going back to college...


text:
Is identifying the genus of a fungus (mushroom specifically) enough?
Does the genus of a mushroom have enough information about it, without the species?
Let's say I wanted to identify a mushroom (when picking) to see if I can safely pick and later eat it. Let's say I successfully identified the mushroom's genus (using an identification key guide book such as this one). Is this enough to determine whether or not the mushroom is edible? Is it enough to determine other general information about it? Furthermore, is it enough to determine whether it is good-to-eat (as in not bitter)? For example, I know that some edible mushrooms have other mushrooms very similar to them that are not edible or that are bitter and difficult to cook.
In other words, are there any genuses of mushrooms that generally are recognized as edible but in reality contain both edible and inedible species of mushrooms in them?

It almost looks like you are asking as to the truth of a book. You  have not published the claims of that book here. This is opinion based and should be put on hold until the question can be rephrased.

I asked specific questions. This is not opinion based. It is about knowing whether the mushroom is poisonous or not. It is not based on that book; it is based on scientific classification and fact. I will edit.

Understood. I'm a fan of mushroom soup and don't like to take too many chances - so I'll be paying close attention.

If the answer from @theforestecologist does not answer your question, then I don't know what answer you are looking for. In other words, I find your question unclear.

Again, I would say: no, genus is not enough.
Another example: boletes (specifically, genus Boletus).
According to Wilderness College:

One of the most common and well-known groups of edible wild mushrooms are the boletes or boletus species (Boletaceae) ...

But

Many species in this group are edible, with only a handful being poisonous. The poisonous boletus species have red or deep orange pores. Outside of the few toxic species, some species of boletus are bitter or inedible.

For example, see here for a list of edible boletus mushrooms (e.g., B. edulis), while some examples of Boletus species to avoid include: B. huronensis and B. satanas
An additional issue to classifying all species in a genus as "safe to eat," is that our classifications are not always reflective of real taxonomic associations. In other words, some groups are not monophyletic and their evolutionary (and therefore physiological/nutritional) characteristics should not be assumed to originate from the same common ancestor .
This is apparently true of the boletes. From Wikipedia:

Boletus has been found to be massively polyphyletic, with only a small percentage of the over 300 species that have been assigned to Boletus actually belonging there and necessitating the description and resurrection of many more genera

See for example: Nuhn et al. (2013)1

1: Nuhn, M.E., Binder, M., Taylor, A.F., Halling, R.E. and Hibbett, D.S., 2013. Phylogenetic overview of the Boletineae. Fungal Biology, 117(7-8), pp.479-511.

It seems like the simple version of your question is: can anyone come up with even one example of 2 fungi species in the same genus in which one is edible and the other is not?
Here's one example:
The genus Amanita.
This genus contains about 600 species and contains some very toxic species -- in fact, it's often considered one of the most deadly genera of mushrooms in the world. The reason? Two "species" alone account for a large majority of mushroom-related deaths world-wide each year: the death cap (A. phalloides) and numerous species each colloquially named destroying angels (e.g., A. virosa, A. bisporigera, A. ocreata and A. verna) in their own geographic regions.
However, A. caesarea, commonly called Caesar's mushroom, is edible despite it being in this "deadly" genus. From Wikipedia:

Amanita caesarea, commonly known as Caesar's mushroom, is a highly regarded edible mushroom in the genus Amanita, native to southern Europe and North Africa. This mushroom can also be found in La Esperanza, Honduras, where a festival is celebrated annually in its honor. While it was first described by Giovanni Antonio Scopoli in 1772, this mushroom was a known favorite of early rulers of the Roman Empire.[1]

See here for further discussion and details.

Thanks for the example. This is not exactly the answer I am looking for; I will clarify the question.

A small comment about A. caesarea and A. phalloides: I've been told that both species are easy to differentiate in Italy, but not so much in Switzerland. This has caused some cases of poisonings in Italian people in Switzerland.


text:
What does "genus VI" mean in mycology?
This Guidebook is called "How to identify mushrooms to genus VI". Some other editions/versions of it say "Genus III" or "Genus I". What does this mean?

This is a multi-part series of books, with each volume numbered with roman numerals I, II, III, IV, etc meaning 1, 2, 3, 4, etc, followed by a subtitle, in this case the subtitle is "Modern Genera."
There is no meaning to "Genus VI", the title of the book series is "How to Identify Mushrooms to Genus" which indicates it will help you identify mushroom genus but will probably not bother with differentiating species of the same genus (even that is quite a lofty goal).
The authors could have instead called this book "How to Identify Mushrooms to Genus; Volume 6: Modern Genera" to convey the same meaning.


text:
Do all animal cells have lysosomes?
I know that white blood cells have lysosomes but what about other body cells? I mean, any other cell such as cells in the respiratory system.

Well not red blood cells but that's cheating

You are probably referring to the process of phagocytosis, where macrophages engulf a pathogen by trapping it inside a vesicle called "phagosome", which then fuses with a lysosome, resulting in the digestion and disposal of the pathogen.
But in fact all eukaryotic cells have lysosomes. This is of course biology we are talking about, so there are many subclasses, different names, specializations and exceptions to the rule.
In plant and fungal cells, we find vacuoles, which serve a similar function as lysosomes in animal cells. There are also "lysosome-related organelles" with specialized functions in specific cell types (Marks et al. 2014).
The main role of lysosomes has been described in the recycling of macromolecular material. Their lumen has a low pH level (below 5) and contains a lot of enzymes specialized in degradation of e.g. proteins, nucleic acids etc. They can digest cellular waste products and material taken up by endocytosis. Nutrients can be reabsorbed into the cytoplasm.
Furthermore, research has proposed additional roles in nutrient sensing and metabolic homeostasis (Perera and Zoncu 2016).
That lysosomes play a crucial role in many cell types can also be seen in lysosomal diseases, which often result in severe effects in multiple organs (Ballabio and Gieselmann 2009, Saftig and Klumpermann 2009). In these diseases, lysosomes fail to degrade their targets, which impairs their ability to clean out cellular waste.
Here is a summary from the book "The Cell".


text:
Real embryo pictures: How different zones(speeman organizer, marginal zones...) are known?
In many textbook, figures of embryo are drawn,but in reality how biologist know which zone is this one of  an embryo in gastrulation stade? Except the dorsal lip here i can't localize other thing.


text:
How old is the action of sneezing?
Is there an estimate for when the ability of sneezing evolved? A little bit of research, and some critical review of my memories tell me that:

Many, if not maybe all mammals sneeze.
Some reptiles sneeze, like turtles and iguanas.
According to this answer, I see some consider also some fish and even sponges to be capable of sneezing. However, I'd be curious to know if this is the actual same concept of sneezing, and not a stretch of definition, given that fish and sponges don't have lungs!

If it's common among mammals, I infer that it is very likely that this ability exists since at least 200 million years. I'd in fact suspect to be very unlikely that all mammals developed it independently after branching out from common ancestors. I am confident the sneezing of turtles is really comparable to ours  and that although more explosive, also iguanas'. These reptiles (according to my superficial and inexperience Google research) are known to exist since more than 215 and 190 million years respectively.
However, I don't know how old a common ancestors of turtles, iguanas, and mammals can be dated. Or how likely it is that they independently developed this skill.
I'd be very curious to know if any expert ever dated this ability.

I went and read the article indicating sponges sneeze here https://www.cell.com/current-biology/fulltext/S0960-9822(07)02261-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982207022610%3Fshowall%3Dtrue . The authors appear to define sneezing as any method of expelling unwanted or potentially harmful material, which imo makes sense for fish as well. Sponges use a much more basic intracellular communication system to identify unwanted material and trigger its expulsion, but the concept is the same.

@Astrolamb thanks for the information. For what concerns my question however I'd say that's stretching the concept. I'm curious to know about our specific way of sneezing, which is still found in many other animals.
According to that large definition arguably also urinating, spitting, crying, and sweating could find a fit. Not sure how our sneezing can be defined in biology though.

@Astrolamb Throwing up and coughing also fits that definition.

@raggot Sneezing (and ejaculation!) is a kind of cramp. That rules out several of the behaviours on your list.


text:
Does pepsin enzyme digest other enzymes like other pepsin molecules
Pepsin digests proteins, as we know, but can it digest other enzymes that are actually made up of proteins, like digesting other pepsin molecules?

Pepsin does cleave itself (Ingram, 1951) - this is termed autolysis. Pepsin (and other proteases) act on proteins with the right amino acid sequences. Pepsin prefers to cleave at phenylalanine, tryptophan or tyrosine residues (Lehninger, A. Principles of Biochemistry).
* Pepsin can also cleave inactive 'zymogen' enzymes to activate them. One of these zymogens is pepsinogen (an inactive form of pepsin itself). So you could argue that pepsin is cleaving itself here but I personally wouldn't, since pepsinogen isn't really pepsin.

Confusingly, pepsin does cleave itself - or, rather pepsinogen does to make pepsin (autocatalysis). Hmm, it also does autolysis, so I'm not sure your answer is correct ...

@gilleain I've added a note about it. I was initially going to talk about zymogens but I felt that it would be muddying the answer. Personally I'd say pepsin and pepsinogen are different things, plus (to my mind) the question is asking whether a solution of purified pepsin will eventually eat itself.

Jam, indeed - that's autolysis! Apparently, you should store pepsin at a low temperature to stop it eating itself

@gilleain Well I'll be! Never realised it did eat itself! Thanks for letting me know

Regarding your note on terminology: (1) digestion is common parlance for proteases and nucleases. (2) not all enzymes are proteins.

@canadianer Thanks for the notes - my mistake on both parts.


text:
Why is there Turner syndrome if one of the X chrosomes is inactivated anyway?
In females one of the two X chromosomes will condensate and turn into Barr bodies. So chromosome abnormality-free women will only have a single transcriptionally-active chromosome. Then why can abnormalities like Turner's syndrome still occur in the  presence of a single active X chromosome?

Pseudoautosomal region in mammals
On sexual chromosomes, we have a so-called PseudoAutosomal Region (PAR). The PAR is the region which still recombine with the Y chromosome (in males only) and is though to be important to allow separation of chromosomes during meiosis.
Pseudoautosomal region and dosage compensation
Because the PAR is diploid in males too, there is no need for a mechanism of dosage compensation and hence, in females, the PAR of the inactivated X-chromosome remain active.
Turner Syndrome
Turner syndrome is caused by an issue of dosage of functional elements found in the PAR. In people having Turner syndrome the PAR is haploid, while it remains diploid in both healthy males and healthy females.
Here is a small review paragraph from Sybert and McCauley (2004) that report the evidences suggesting that Down syndrome is caused by haploidy in the PAR. Please see the linked paper directly for further references.

Loss of interstitial or terminal long-arm material of the X chromosome (Xq) can result in short stature and primary or secondary ovarian failure.15 Deletions distal to Xq21 appear to have no effect on stature. In general, loss of the short arm (Xp) results in the full phenotype. Very distal Xp deletions are compatible with, but do not ensure, normal ovarian function. Loss of this region usually confers short stature and the typical skeletal changes, in part as a result of haploinsufficiency of the short stature–homeobox (SHOX) gene, located in the pseudoautosomal region of Y and Xp. The SHOX gene is probably not the only gene responsible for the skeletal features. Aneuploidy itself may contribute to growth failure. Loss of a region at Xp22.3 appears to be associated with the neurocognitive problems in Turner's syndrome. Loss of the testis-determining factor (SRY) gene locus on the short arm of the Y chromosome (e.g., 46,X,del(Yp)) also leads to the phenotype of Turner's syndrome, even without a 45,X cell population. A region on Xp11.4 has been proposed as critical for the development of lymphedema.

In addition, 35% of the genes in the inactivated X chrosomes are "escapees", which means that they remain active. The rest is mostly repressed by the expression of gene Xist.

@Jagoe I did not know that +1 Do you happen to know what fraction of these 35% are from the PAR? If you happen to have a reference, I would happily add that to the answer. Thanks

I've found a reference that tells of a similar figure (12-20% for humans, 3-7% for mice) for genes escaping "XCI" (X-chromosome inactivation) [https://www.cell.com/trends/genetics/pdf/S0168-9525(16)30002-6.pdf]. So yeah, the original percentage I wrote might not be accurate. I heard it from a genetics professor at college. Regarding PAR, well, I just heard it existed.

@Jagoe Ok. Note that your link is broken

https://www.cell.com/trends/genetics/pdf/S0168-9525(16)30002-6.pdf


text:
Why are the bodies of the Risso's dolphin covered in scratches?
Risso's dolphin in wild population seem to obtain scratches with aging. What is causing them and what do they mean?

[ From Jefferson et al. 2015, Marine Mammals of the World, 2nd edition, p 212: "At sea, the best identification characteristic is the coloration and scarring. Adult Risso's dolphins range from dark gray to nearly white, but are typically covered with white scratches, spots, and blotches. Many of these are thought to result from the beacks and suckers of squid, their major prey, but others may be caused by the teeth of other Risso's dolphins. If fact, this species is the most heavily-scarred of all the dolphins." ]

Hi and welcome to Bio.SE. Thanks for posting. However, please provide support for your claims. Unsupported posts come across as opinions and are best reserved for comments. We have high expectations of good answers on this site to help avoid the spread of misinformation. Please consider revising your answer to provide some sort of support to attract more positive attention and to better (and more accurately) inform our future visitors. Thanks!

Although little is known about these animals, they seem to obtain these scars from scratching in fights with their prey, giant squid, and from the teeth of other Risso's dolphin.
https://uk.whales.org/species-guide/rissos-dolphin

Most of the linear scars are thought to be caused by intraspecific interactions, e.g. scratches from each others teeth, though some more circular or oval scars are thought to come from squid.  Cookie cutter scars are not commonly described for Risso's dolphins though they are common in other whales and dolphins.
Encyclopedia of Marine Mammals.  2002. W.F. Perrin, B. Wursig, J.G.M Thewissin.  Academic Press: New York.

Hi and welcome to Bio.SE. Thanks for posting. However, please provide support for your claims. Unsupported posts come across as opinions and are best reserved for comments. We have high expectations of good answers on this site to help avoid the spread of misinformation. Please consider revising your answer to provide some sort of support to attract more positive attention and to better (and more accurately) inform our future visitors. Thanks!

As others have said, most of these marks come from intraspecies interactions. However, what makes Risso's different is that they more or less keep their marks for a long period of time.
For example, here is a blog from Morigenos (Slovenian Marine Mammal society) explaining how they use rake marks to help them identify different bottlenose dolphins from year to year. That the marks can fade or change as new marks are added.  Noting these scars is a common tactic when using photo-identification to mark individuals when studying a dolphin population. However, because rake marks and other scaring can fade, it is far more common to use the back edge of the dorsal fin to identify different individuals (Clabby, American Scientist).
Risso's dolphins, however, loose pigmentation in their skin while their wounds are healing (MacLeod, 1998), meaning that their scars last for a longer time period. So much so, that individuals within a population can be recognized up to 3 years based on their scars alone (Mariani et al.,2016).
Why is this? Likely due to male on male competition. Younger Risso's have a faster scar recovery rate, indicating that the more scars you have, the beefier you are and the more combats you have survived, making you a better mate. However, the skin pigmentation alteration is present in both females and males.
The Mariani paper really does a great job of summarizing what is known about Risso's dolphin marks, and how long they last.  It's freely available online, so it is 100% worth the read.
Monica Mariani, Angelo Miragliuolo, Barbara Mussi, Giovanni F. Russo, Giandomenico Ardizzone, Daniela S. Pace, Analysis of the natural markings of Risso’s dolphins (Grampus griseus) in the central Mediterranean Sea, Journal of Mammalogy, Volume 97, Issue 6, 5 December 2016, Pages 1512–1524, https://doi.org/10.1093/jmammal/gyw109


text:
Why is the glomerular filtrate isotonic to the blood in the capillaries?
How can the osmolarity of the filtrate be the same as the blood in the peritubular capillary when there is no red blood cells filtered?


text:
Do these large spiders in Taiwan belong to different species?
I see both of these spiders (and others) frequently on hiking trips outside of Taipei. Their large webs are often high overhead between trees but can be right across a hiking trail that hasn't been used in a few days, which can make for some excitement.
The two individuals shown in the photos were quite large; both had a body length of about 5 cm not counting legs.
They have similar body shapes but very different color. I don't know if they are completely different species, or different sex or different age.
I mostly see "Spider #2", and usually they are around 3-4 cm in body length. I see  "Spider #1" much less frequently, and I don't think I have ever spotted a smaller individual, but that could just be due to lower frequency.

Spider 1:
I spotted this on on this plant, but once disturbed he started climbing up a vertical thread back into the threes.

Spare photos: 1, 2
Spider 2:
I see these more often than Spider #1.

Adjusted brightness, contrast, sharpness to make the structure of the web more visible:

Spare photos: 1

Bottom is definitively Nephila pilipes -- see here for example. Wikipedia mentions multiple subspecies that you might want to look into for more definitive ID of top specimen. Both of your specimens are females based on the extreme sexual dimorphism (specifically, female gigantism and male dwarfism) common in this group.

@theforestecologist that's why I put Spider #1 first, I see it less frequently than the brightly-colored Spider #2.

a 5 min search on my end didn't turn up anything that looked or was described quite like your top specimen. Definitely looks related, but not sure to what degree. Again, I'd start researching the subspecies to see if you find any leads...

The following is from Biogeography and Speciation Patterns of the Golden Orb Spider Genus Nephila (Araneae: Nephilidae) in Asia, Yong-Chao Su, Yung-Hau Chang, Deborah Smith, Ming-Sheng Zhu, Matjaž Kuntner and I-Min Tso, Zoological Science, 28(1):47-55. 2011., DOI: 10.2108/zsj.28.47 http://www.bioone.org/doi/full/10.2108/zsj.28.47
Spider 1 seems a good match for C in the images below, and Spider 2 matches A and B. So I propose that both spiders are Nephila pilipes but with different color patterns.

Fig. 1. Nephila diversity in Asia and Australia and its extreme sexual size dimorphism: (A–E), N. pilipes; (A–B), female of the common color pattern, Taiwan; (C–D), female of the darker color pattern, Taiwan; (E), male (arrow) in copulatory pose on female, Singapore; (F–G), female N. antipodiana, Singapore; (H), female N. plumipes, Australia; (I–J), female N. clavata, Taiwan. Images by M. Kuntner (www.nephilidae.com).

Both of those are variations of the Giant Golden Orb Spider, just of a different age. They might be large but they are not very dangerous. Their scientific name is Nephila pilipes if you want to do more research
Both of the spiders you have shown are females of the same species. As these spiders grow they molt and spider #1 should eventually develop the same pattern as spider #2 once it matures.

Nephila pilipes (northern golden orb weaver or giant golden orb weaver) is a species of golden orb-web spider. It can be found in Japan, China, Vietnam, Cambodia, Taiwan, Malaysia, Singapore, Myanmar, Indonesia, Thailand, Laos, Philippines, Sri Lanka, India, Nepal, Papua New Guinea, and Australia. It is commonly found in primary and secondary forests and gardens. Females are large and grow to a body size of 30–50 mm (overall size up to 20 cm), with males growing to 5–6 mm. It is the largest of the orb-weaving spiders apart from the recently discovered Nephila komaci, and one of the biggest spiders in the world.

Just an interesting fact, in some regions people will eat these spiders once they are fully grown.

Thanks! At first glance I thought your comment said that in some regions these spiders eat fully grown people!

No they aren't that giant, but they can grow to be the size of someone's hand and eat birds or bats.

I may have some photos of a very tiny spider on the same web in proximity to one of these. If I find it I will ask about it separately and notify you here.

if they are red a few mm big and several of them hang around the big spider then they are most likely the males. In this particular species the males are the smaller of the sexes.

Sounds familliar; will take some time to dig those photos up.

Hi Joseph. Welcome to Bio.SE! We ask that answers (especially) those to species ID provide ample support. Thank you for taking the time to link-to and quote from the Wikipedia article, but your claim that both specimens are the same species comes across as an opinion ("I believe...") without having any formal support provided. Since the relation between the 2 specimen's in the OP's post is the main question being asked, I ask that you provide additional support/detail to back up your opinion. Thank you.

Have a look at Female, Cairns Botanic Gardens December 2010 here: http://www.arachne.org.au/01_cms/details.asp?ID=1627


text:
Does blood carry metallic nanoparticles?
I find this particular chart about constituents of blood very informative and interesting. Looking through the different components, I see metals such as copper, zinc, etc. Are these only carried as ions or conjugated to proteins, or does blood carry nanoparticles of these elements as well?

It is very unlikely to have metallic nanoparticles in blood under normal circumstances.
Reasoning:

There are specific proteins that strongly bind metal ions: transferrin and ferritin for iron,  zinc transporters (Zrt) for zinc, metallothioneins as a catch all for most heavy metal ions etc.  These tend to be intracellular so most of the metal would be bound inside cells.  Any particles would be endocytosed and oxidized to the ionic form (probably in peroxisomes), then the metal would be bound to proteins.
Metal nanoparticles as well as free ions (of metals with more than one oxidation state) have considerable catalytic activity which is non-specific (and therefore quite toxic).  They can serve as a redox catalyst as well as generate ROS from oxygen.  That's probably why metal-binding proteins have evolved.
Lastly, iron in particular is a limiting nutrient for many pathogens.  Extracellular iron is very tightly controlled as part of non-specific pathogen defenses.  There is only exactly as little iron in blood plasma (bound to transferrin) as absolutely necessary to move it to the cells that take it up.  It's unlikely there would be any free iron, because there wouldn't be any fast, specific way to take it up the way the transferrin receptor does.

'll ask a follow up question: What happens when metallo-proteins get denatured(say by thermal degradation), do they drop their metal payloads as elemental metals? Or as ions that are then taken up by other constituents?

@user1155386 Eventually, I suppose they must drop they payload at some stage of being recycled, but simple denaturation may not do it for many metalloproteins.  At least one reference I checked (Campbell PG, Metal Ions in Life Sciences. 2009 Jan 19;5:239-77) says that heavy metals don't leak out of the denatured protein fraction of cells. Most of them would drop as ions if they do drop (the exceptions being metal in heme and in iron-sulfur clusters)


text:
Organ and Bone Marrow Transplantation?
In organ transplantation the transplant is rejected by the body's immune system , but is it possible if along with organ transplant if bone marrow transplantation is carried out from the same donor , then will the Cell Mediated immunity still reject the graft ?

As Mowgli pointed out, a bone marrow transplant involves destroying the patient's own immune system with radiation and, essentially, replacing it with a new one from the bone marrow donor. If you did a double kidney/bone marrow transplant from Alice into Bob, then Bob's new immune system (which is the same as Alice's) would recognize the new kidney from Alice as self (because it is) and not attack it. Yay!
The problem is that, to the new immune system, all the rest of Bob appears to be non-self and will get attacked. This is called Graft-versus-host disease and is at least as serious a problem as organ rejection.

"The problem is that, to the new immune system, all the rest of Bob appears to be non-self and will get attacked. This is called Graft-versus-host disease and is at least as serious a problem as organ rejection": What do you think of this https://biology.stackexchange.com/questions/79881/could-bone-marrow-transplants-be-used-to-prevent-tissue-rejection-of-trans-speci as a fix for that, introduce both patient & body donors cells to the pig fetus then transplant it's bone marrow?

Bone marrow transplant requires to first destroy the pre-existing immune system with chemotherapy and/or radiations. So essentially you would not have the first immune system and my guess is that yes, in theory, it would work.
However, double-grafting an artificially immunocompromised patient (who clearly suffers from another severe pathology, if they need an organ graft in the first place) would be extremely risky as it would exponentially increase the risk and mangnitude of post-operation complications, and I think no surgeon in their right mind would ever take such risk.


text:
Will DNA nanostructures be useful for medical applications?
There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA.  I have heard researchers motivate this research with claims that it could have biomedical applications.  My question is, how likely is this to be true?  In particular, a few potential problems bother me:
(1) What is the risk that the foreign DNA strands used to build nanomechanical devices will be accidentally incorporated into the host genome?  Are there plausible strategies for avoiding this?
(2) Will it be effective in the presence of an immune system?  If the foreign DNA is not incorporated into the host genome, it seems likely to instead be destroyed by the host immune system.  Is there research addressing this issue?

"My question is how likely is this to be true." Which defines the question as a request for subjective opinions of the type that are off topic — see here.

@David If you look at the rest of the question, you see that I then clarify two particular questions.  I am not a biologist, and am asking (1) what biological mechanisms (if any) pose might accidentally incorporate foreign DNA floating around and are there any known possible strategies for avoiding this? and (2) Does the human immune system attack foreign DNA floating around inside the body?  Are there ways to prevent this?  I apologize if these seem to be subjective questions to an expert, but to me (a beginner), they are as specific as I know how to make them.  Thanks

I think biomedical applications are not an absurd perspective. More specifically, regarding your concerns:
(1) Unless the DNA is first internalized by cells, and then somehow enters the nucleus (both are not very likely, especially considering the small concentrations we're talking about here after dilution in a human body), you would still need the DNA structure to disassemble to become "available", and the strands to be long enough to be incorporated, which is usually not the case. And, of course, you would need some DNA integration mechanism to be at work, such as a recombination with genome sequences that happen to be very similar to the ones used to build the DNA nanostructure (which can be avoided during the design step). In other words, no, it's quite unlikely.
(2) Immune responses might actually be a bigger issue; in particular, some Toll-like receptors (TLR), that activate the innate immune system, can respond to DNA and RNA fragments. But immune responses may not be so problematic if the DNA nanostructures are used for short-term mission, like 1-shot delivery to a specific organ, in which case they do not need to stay around for very long. Additionally, this can be a useful feature; immune recognition can be used to direct the trafficking of nanoparticles to lymph nodes for example, where the efficieny of their payload (e.g. an immune modulator) could be maximized.


text:
How Would I Isolate and Amplify a Viral Enzyme?
what procedures would I use to isolate and amplify integrase? If I am trying to study the integrase enzyme which is found in HIV how would I
1) destroy the viral capsule to release its contents.
2) separate Integrase from other enzymes and the viral DNA.
3) make copies of the enzyme for testing.
Any help would be greatly appreciated!!

This sounds rather like a homework question. Please see the site's policy on such questions and in particular the requirement to show you have attempted to answer yourself.

Each virus would contain extremely low amounts of enzyme (probably a few individual molecules, at best); collecting and concentrating enough viruses to extract a significant amount of enzyme would be long and difficult, if at all possible.
The usual strategy in research laboratories is to clone the nucleic acid sequence coding for this protein (either by direct amplification from an HIV-infected cell, or by synthesizing a piece of DNA in vitro) and integrate it in an expression vector, that is, a larger piece of DNA, usually circular, suitable for integration in a host cell (human, or even bacterial) and carrying the sequences necessary for persistence and gene expression. This way you can produce thousands of copies of the enzyme you are interested in in each cell, and you can then purify a significant amount of integrase to study it.
To make purification easier, it is common practice to add to the gene a sequence coding for a "purification tag", that is, a few extra amino acids that have special properties that make the final protein easier to purify. Stretches of 6-8 histidine residues are very commonly used. The assumption is that the protein carrying this tag will have an activity similar to the natural enzyme, after purification.


text:
Why we see black colour when we close our eyes
Why is it neccessary that if there is no light then everythimg is black and when we close our eyes we see everthing black usually when we are in black room??

Is your question: "why does the absence of light (from the physically shielding of our pupils from taking in light) appear black?" or "why do we perceive darkness as the color black? (vs., say, all white?)?" ?

Am I unusual?  Because when I close my eyes in a dark room, I don't see complete black, but darkness with some random "light shows" going on, for instance random dots of a slightly orange-tinted grey.

The mechanism of sight is as follows (ref. 1). This was shown in the 1100s by Ibn al-Haytham (ref. 2), except the 4th step which may have been proposed by Galen in the 100s (ref. 3).

Light comes from a light source
The light then hits an object
The light then bounces off the object into your eye
Your eye sends a signal to your brain. Your brain then figures out what you're seeing

So in order for us to see, you need light getting into your eye (step 3). If you're in a dark room you have no light source, so no sight (no step 1). If you shut your eyes, you're stopping light from getting into your eye (no step 3). When there's no light getting to your eye, the eye tells this to your brain. So your brain just sees black (the absence of light).

References

Duree, G. (2011). Optics for Dummies. p. 67.

Adamson, Peter. (7 July 2016). Philosophy in the Islamic World: A History of Philosophy Without Any Gaps. p. 77.

Reeves, C. and Taylor, D. (2004). A history of the optic nerve and its diseases. p. 1097.


text:
What spider species is this?

I saw this spider yesterday and it was the first time I saw one. It had a log slender body and an almost tail like end. It also can apparently jump. Just wanted to know what species this is. Location (Cavite, Philippines)

Please provide your location and the approximate size of the spider. It'll ensure you get an accurate answer. Thank you.

Definitely a pike slinder jumper. Location and size will help with species ID.

It's one of the more unusual Jumping Spiders - similar, as Charles said above, to the North American spider Marpissa pikei, the Slender Jumping Spider (see second link below).  Yours is even thinner and more stretched out, but still clearly a Jumping Spider, from the long, heavy front legs and the big eyes on the front of its head.
Your species appears to be a spider called Mantisatta logicauda (first link below)

http://www.peckhamia.com/salticidae/diagnost/mantisat/longi-ph.htm
http://bugeric.blogspot.com/2012/07/spider-sunday-pike-slender-jumper.html


text:
Are redundant codons used in translation?
I am learning about redundancy in genetics and I came across this statement in my textbook:

more than one codon for an amino acid means that some codons are redundant - the process of protein synthesis could function without them.

I understand that codons are used to make specific amino acids. Does the statement from my textbook mean that if there are two codons which code for the same amino acid that only one of the codons code for an amino acid and not both? I know the term reduntant means that in some cases - more than one codon can code for the same amino acid - but does it also mean that some codons are not used because another codon codes for the same amino acid?
Thanks

The textbook is asserting that translation could function without redundant codons, not that it does. In reality, all possible codons are used.
See this answer on the interchangeability of codons.

The term ‘redundant’ is not ideal in this respect, as that implies a redundancy in reality rather than theory, as @canadianer points out.
Redundancy and Degeneracy
However I would mention that there is another term more usually applied to the fact that certain amino acids are encoded by more than one codon — degeneracy.
There is a Wikipedia entry on Codon Degeneracy:

Degeneracy of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations.

Although this definition may appear circular in that it refers to redundancy, I am fairly sure that historically degeneracy was one of the attributes listed for the genetic code (e.g. by Crick):
specific
non-overlapping
comma-less
degenerate
universal (no longer true)
I perceive the traces of this  in the Nature Scitable entry for the genetic code.
Synonymous Codon Usage
Codons that code for the same amino acid are termed ‘synonymous’. An obvious follow-up to the question and answer in this post is on the lines of “Does it matter which synonymous codon is used? Are all used equally and is it the same in all organisms and genes?”. The answer is that synonymous codon usage is non-random in various different circumstances. This is a broad area, but the Wikipedia entry on Codon Usage Bias is one place to start. There is also a question on this topic on this list.
“Does it also mean that some codons are not used?”
Answering this specific question here (documented in the references above) even where there is extreme bias in the codon usage in a genome, generally all possible codons are employed. This may be for regulatory reasons (if the tRNAs for these codons are rare, and hence this would be a way of slowing down translation for proteins only needed in small quantities), structural reasons (to allow a particular secondary structure for the mRNA) or some other less obvious reason.


text:
What would "N" and "V" stand for in DNA barcoding?
I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:
...CCGATCTNNxxxTTT...TTTVN

where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.
As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.
So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?

It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here


text:
Why would pedophilia exist?
From an evolutionary perspective, why would anyone ever be sexually exited by small children who could not possibly have started puberty?
Is it a confusion between some combination of sexual and non-sexual systems?
Is it a evolutionary imperfection?
Or is Darwinian thinking not necessarily applicable to human behaviour?

There are a lot of societal influences in our behaviour and also there is a lot of room, in our complex society, for developing behaviour that are side-consequence of other behavioural features that have been selected. It does not mean that "Darwinian thinking" (whatever that means) is not applicable to human behaviour but only that seeing everything as a result of selection is very misleading (and Darwin never made this mistake, hence why the term "Darwinian thinking" is misleading), maybe esp. when it comes to human behaviour.

Can someone provide data on just how heritable pedophilia is? Establishing a high heredity is necessary before applying Darwinian logic.

I can't imagine this is at all genetically linked, but rather a learned behavior or result of some traumatic experience in the person's own past.

I am guessing on this one, and there may be some good research on it, but I do know that there can be combinations of genes acting on different behaviors, such that if you have a certain combination of 5 genes, you are a nurturing parent (which would be selected for), but when you accumulate more of these tangentially related genes past some threshold, you end up with non-selected behavior. For example, for homosexuality, which has been shown to be genetically heritable, it may be that 5 genes in a suite make you super attractive to women (thus these genes stick around), while 10 genes combine to make you gay. (Note, I am NOT equating homosexuality with pedophilia in ANY sense. Homosexuality if a healthy normal trait for humans. I am just saying that this is a theory about how suites of genes can be individually selected for while some combination of them is non-selective. Similarly, heterozygous sickle-cell genotype produces resistance to malaria, which is adaptive enough to keep the gene around, which is non-adaptive in the homozygous condition.)
In answer to the other parts of your question, humans are absolutely subject to natural selection. Darwin was dead-on correct about virtually everything he said, to the point where it is frustrating for evolutionary biologists today to work in his shadow, because he pretty much got it all right in 1859. "Theory" is the strongest conclusion that science can ever come to, and people have been trying to tear down Darwin's theory for 160 years without being able to put a single dent in it.

The Darwin-praising last paragraph was completely over-the-top. Darwin got heredity wrong (wikipedia.org/wiki/Pangenesis), as gametes don't form by gluing together heredity-containing particles ("gemmules") secreted from somatic cells. Francis Galton refuted it by showing that tranfusing blood (which supposedly contained the granules) between different rabbit breeds didn't alter the characteristics of their offspring.

Darwin didn't get heredity "wrong". It was not understood at the time by anybody but Medel. The fact that the theory fit Mendel PERFECTLY, even before it was understood (which was the point of the modern synthesis...look it up if you need to) is how science, when you get it right, is predictive.

Sorry for my choice of words. More accurately, Darwin got an aspect of heredity wrong (pangenesis). I didn't meant that he got all of heredity wrong. But anyway, whether pangenesis was accurate or not would not affect Mendelian inheritance, provided that organisms didn't exchange tissues. Pangenesis dealt with gamete formation, not about character dominance-recessivity.


text:
How does the cardiac cycle and electrical activity all relate to blood pressure in the heart?
I know how the cardiac cycle works and understand the electrical activity in the heart such as the AV nodes, SA nodes and Bundles, but how do they work together in relation to blood pressure?

Blood pressure is determined by cardiac output and the total peripheral resistance, where, from Ohm's Law (Q= P/R):
Mean Arterial Pressure (MAP)= Blood flow (Q) x Total Peripheral Resistance (R)
The cardiac cycle and heart activity will essentially control the cardiac output through the FORCE and the FREQUENCY of contraction.
Cardiac output is determined by the stroke volume, and the heart rate:
CO= Stroke volume x HR
Changes in HR is linked to changes to the SAN and is controlled by sympathetic and parasympathetic inputs. An increase in HR, will cause cardiac output to increase, causing an increasing in blood pressure (simply put, other physiological changes can also influence blood pressure, such as vasoconstriction and vasodilation).
With regards to the AVN, SAN and bundles of His, this allows electrical conductance which causes the contraction of the heart. The contraction of the heart leads to blood being ejected (i.e. blood flow, which is linked to cardia output). This, together with the peripheral resistance of blood vessels will be linked to blood pressure.


text:
Why don't the heads of phospholipid bilayers repel hydrophobic molecules?
What I Think I Know: Hydrophilic and hydrophobic things repel each other. Since the cell membrane contains hydrophobic tails, it is difficult for hydrophilic molecules to pass through the cell membrane.
Question: Why don't the heads of phospholipid bilayers repel hydrophobic molecules? In other words, if the phospholipid membrane has both hydrophilic and hydrophobic portions, why do only the hydrophobic portions act as repellents?
Stipulation: I need a quotation from a textbook, university, or other credible source.
Evidence of Prior Research:
Why lipophilic molecules can pass phospholipid bilayer, in spite of 2 hydrophilic layers?: This question has a comment that links a graph from a textbook. I can't understand the graph by itself. There are no other references.
Understanding what passes through and doesn't pass through the plasma membrane: All references discuss the topic, but none answer the question.
I understand that this topic is addressed quite frequently, but the question I'm asking is never answered. Texts tend to say something like, "Ions can't get through the core because of their charge" and completely gloss over the concept of lipids getting through the heads. Please don't dismiss this as a homework question that I didn't take the time to research. This is my second try asking this question (on this site); I have spent hours trying to find an answer.

Taylor, you've done an excellent job updating your question and providing evidence of additional research effort. Thanks very much for making the extra effort. I don't foresee this question getting marked/closed as homework now, and I hope you get a good answer! Good luck! :).

@Taylor Do you mean chemicals in the intra/extracellular fluid or chemicals embedded in the plasma membrane?

@Jam I'm talking about molecules/chemicals that pass from the intracellular fluid to the extracellular fluid, or vice versa.

Your question is rooted in a misundertsanding of the hydrophobic effect. Hydrophillic and hydrophobic molecules do not repel but, rather, attract one another through van der Waals interactions. The tendency of hydrophobic molecules to aggregate in aqueous solution (ie the hydrophobic effect) is, instead of some repulsive force, actually driven entropically. I don’t think I will go into this in detail since it has been explained well in many places. That said, it is also explained very poorly in many places (which I suspect you have encountered). I recommend this website to learn about it and other intermolecular interactions.
Once you have a firm grasp on that, consider that in order for a hydrophobic molecule to reach a plasma membrane, it must already be solvated by water. The transfer of a hydrophobe from one hydrophillic environment (water) to another (head groups of the phospholipids in the plasma membrane) should be energetically negligible. The limiting step for passive diffusion across a membrane is transfer from the hydrophillic environment of the phospholipid head groups to the hydrophobic environment of their tails. In fact, the rate of diffusion across a plasma membrane increases with hydrophobicity.


text:
How do the chemicals in our skin react with stainless steel?
What acid/chemical in human skin can react with stainless steel to leave a black mark on the skin? Why is it secreted/produced in larger quantities by some people and not by others?


text:
How does the new discovery that mitochondrial dna is inherited from both parents change population genetics and other dates?
This new study seem to have pretty much proven that mtDNA is inherited from both parents. I assume that this would lead to most age estimates of ancient human populations that heavily depending on mtDNA, being discarded. Is this right?
What other things would be affected by this discovery?

What you refer to is just a (non-peer reviewed) vulgarization of an original (peer-reviewed) article. This original article is Luo et al. (2018). I only read their abstract and wants to highlight this sentence: [..] there are some exceptional cases where paternal mtDNA could be passed to the offspring. I will need to read more (I currently don't have access to it due to a paywall) to have an opinion as to whether that might affect our molecular clock estimates.

The authors also write the following: Clearly, these results will need to be brought in agreement with the fact that maternal inheritance remains absolutely dominant on an evolutionary timescale and that occasional paternal transmission events seem to have left no detectable mark on the human genetic record, indicating the opposite of your assumption.

@Astrolamb Exactly. It has been known at least from some years, that paternal inheritance of mtDNA can occur (https://en.wikipedia.org/wiki/Paternal_mtDNA_transmission). However, this is not without consequences, as there was a case of a patient whose mtDNA was 90% paternal and suffered a debilitating intolerance to exercise (https://www.nejm.org/doi/full/10.1056/NEJMoa020350).

It is also worth noting that according to Wikipedia the case described above is the only one known in humans with such a high paternal percentage. In my opinion, people with that condition would have died in the past, hence stopping the process of paternal mtDNA inheritance (assuming that they all suffer similar effects).

@Astrolamb How is it figured out that "occasional paternal transmission events seem to have left no detectable mark on the human genetic record" independently of whether mtDNA is inherited or not?

@Daud I don't have access to the entire article, so I don't know the author's reasoning. However, considering that so far only 17 individuals in 3 families have been identified who have paternal mtDNA, statistically speaking the impact of a very few compared with the billions on the planet is insignificant.

I should also add that due to decades of study on mtDNA, the vast majority of which followed expected maternal inheritance, we have a pretty decent understanding of what is expected with maternal inheritance, and almost all cases follow those predictions, so unless it were more widespread, paternal inheritance hasn't had a big enough impact to be noticeable.


text:
Why does solute potential go up as temperatures go down?
So the closer a solution's solute potential is to zero, the more water potential said solution would eventually have. The solute potential equation is -iCRT. If the temperature is 0, -iCRT would be equal to zero, and because temperature is measured in Kelvin, this would mean the solution is at absolute zero. Things can't move at absolute zero. How is it that that water has the most potential to move at absolute zero?
Same with the opposite.
If the temperature is high, wouldn't that mean water potential would be at its highest because water molecules are at high energy, jumping around everywhere?

Welcome to Biology Stackexchange. It sounds to me like your question isn't actually about biology, so I've voted that it should be moved to Chemistry Stackexchange instead. https://chemistry.stackexchange.com/

this is where I got my water potential information: https://goo.gl/t6LgvX

@user1136 — Water potential may be of concern to workers in many areas of science, just as may pH and ionization, chemical bonding, electricity etc. That does not make any of these appropriate for a SE site dedicated to questions in biology when there are SE sites specifically dedicated to chemistry and physics. It also makes sense to ask chemistry questions on SE Chemistry because they are more likely to get authoratitive answers (which will show up when a scientist from any discipline makes an internet search) there.


text:
In Study from Blue Brain they say position of synapses doesn't change even if they modify neurons, only when they change shape of neuron it changes?
https://medicalxpress.com/news/2012-09-blue-brain-accurately-neurons.html

We could vary density, position, orientation, and none of that changed
  the distribution of positions of the synapses.....
They went on to discover that the synapses positions are only robust
  as long as the morphology of each neuron is slightly different from
  each other, explaining another mystery in the brain – why neurons are
  not all identical in shape

My question is why, and how come? Am I understanding it wrong?

I'm not understanding which part you are confused by, can you try to explain the issue you have?

Ok sorry. If neurons are placed randomly, then their branches would spread differently and where interactions would happen would be different. Yet it says position of synapses / interactions is the same more or less no matter how much they change few factors... just not with shape. changing shape does change positions of interactions

It helps to go to the original article for more guidance:
Hill, S. L., Wang, Y., Riachi, I., Schürmann, F., & Markram, H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences, 109(42), E2885-E2894.
The point of this paper is that they are looking at the statistics at which neurons make connections with each other in neocortex. Neocortex is a layered structure, and cells of a particular type are identified by the location of their soma as well as the structure of their dendrites and axons. A layer 2/3 pyramidal cell, for example, has basal dendrites that spread a lot in layer 2/3 and creep into layer 4, and an apical dendrite that extends and branches in layer 1. Therefore, it can potentially receive inputs from any cell that has axons in layers 1 -> 4.
One hypothesis is that the primary determinant of which cell types are connected to which is simply the morphology of each cell type. If one cell Type A has a bunch of dendrites in a given layer, let's say layer 3, and another cell Type B has a bunch of axons in layer 3, they will have a lot of opportunities to contact and make synapses.
A second hypothesis is that cells connect with specialized guidance cues. For example, dendrites of Cell Type A release a peptide BALover that is detected by Cell Type B, and causes Cell Type B's axons to grow toward dendrites of Cell Type A. In this system, you could still get lots of dendrites of Cell A in one layer and lots of axons of Cell B in the same layer, but caused by the specific guidance cues from A->B.
In the second situation, however, we would expect the arrangement of axons and dendrites within that layer to be non-random. That is, we would find processes of B in greatest density nearest to processes of A.
If you labeled a bunch of Cell Type A from one animal, and a bunch of Cell Type B from another animal, and overlay them, they should have just as many contacts as if you labeled Cell Type A and B in the same animal if the connections are random due to morphology. If, however, there are specific guidance cues involved, you would find fewer.
Hill et al. 2012 shows evidence in favor of the first hypothesis: they get about as many contacts if they take cells from two individuals and overlay them. This is what they mean by "random placement": not completely random in all dimensions but rather random within a layer in cortex, as if the cells are taken from two different animals. Certainly guidance cues are still used and are still important for setting up the structure of cortex, but it seems like individual cells are mostly just programmed to take up a certain shape, and that shape determines their rough probability of connections. This is a good thing for the Blue Brain project, because it means that they can use composite data from many animals to establish connectivity patterns.

I completely missed the layers part. Thanks so much.


text:
How it is possible that blood group shows that a person is not the son or daughter of their parents?
I see a family in which it has only one daughter. The blood group of the mother is AB positive and the father is B positive, but the blood group of the daughter is O negative.
When she was young, they apply to shift abroad permanently. When the Embassy test their blood group, the doctor said "She is not your daughter because of her blood group".
How is it possible? Why is she not the daughter of their parents?

Have you tried reading from wikipedia > ABO blood group system? If yes, was there anything specific that was unclear to you?

yes because it is not clear for me thats why i ask this question i am confuse that how it is possible that a girl is not a daughter of her parents .why?

Your comment make it unclear what is unclear to you. The girl is the daughter of her biological parents (by definition). However, the people she calls parents might not be her biological parents. Genetics (in this example, ABO groups) can help to figure whether the supposed parents might be the biological parents.

@Jj Mmmm: How is it possible?  Obviously, either she was adopted, or the mother got pregnant by someone other than the supposed father.  See e.g. Homer and "It's a wise child that knows its own father".

@jamesqf: The mother is AB, so based on our normal understanding of blood types (without exceptions mentioned in my answer), she cannot be the biological mother of a child with blood type O.

Each person has two alleles for the blood type. The two A and B alleles are dominant. So, you don't need A/A to end up with blood type A, it could also be A/O. Having both A and B results in blood type AB. Having none of these, results in blood type O.
Following these rules, from parents being AB and B (genetically either B/B or B/O) you would expect these possible blood types for their children:
- A/B
- A/O
- B/B
- B/O
The Rh factor (positive or negative) is inherited similarly. The positive allele is dominant, so genetically +/+ or +/- would be positive, only -/- is negative.
There is a rare case of a "cis AB" mutation, where the A and B antigens are in just one allele (wiki, paper). Then the genetic alleles of an AB type could be AB (in one allele) and O.
The children of the couple could then be
- AB/B
- AB/O
- B/O
- O/O
So, there would be two possibilities for the case you describe.

The parents are not the biological parents of the child.
The mother is cisAB/O +/- and the father B/O -/-

edit: or a third way would be of course some de novo mutation in the child, resulting in the loss of A/B from the mother
edit2: maybe to answer your actual question "How can a child not be the child of its parents?".. adoption, in-vitro fertilization with donated eggs and/or sperm from other people, mix-up in the hospital..


text:
Univocal identifying of a plant cell
We yesterday got our biology-exams back and there's one exercise where I don't agree with my teacher. However, since he is the expert and not me, I need the support of external sources, i.e. experts in order to justify my statement.

Now in the exercise, we first had to identify the parts of a cell (which was shown in form of an image) and then in part b) reason whether it was an animal or plant cell.

I had identified a chloroplast and a vacuole and stated that the only cell with this organelles was the plant cell. My teacher answered that I had missed the fact, that the cell had also a cell wall (which is indeed a difference between plant and animal cells).
My question is

Is the fact that the cell had a cell wall necessary in my argumentation, i.e. are there other cells having chloroplasts and a vacuole without being a plant cell?

Could you provide a source which supports, or doesn't support my statement so that I can show it to my teacher?
Thanks in advance

Your teacher is right, chloroplasts and vacuoles are not sufficient to define a plant cell.
Amoeba have both chloroplasts (McFadden et al, PNAS, 1994) and vacuoles (Day, J. Morphology, 1927) but they are not plants - and they do not have a cell wall.
Sea slugs eat algae and can "steal" their plastids and keep them working for weeks/months, effectively becoming photosynthetic animals for a while. This is called kleptoplastidy (Pillet, Mob. Genet. Elements, 2013).


text:
What is this insect flying in my Los Angeles bathroom?
We live in the Los Angeles area. This insect has been very common in our bathrooms recently:

They're about 1/4" long, and can often be found resting on our towels. In the months leading up to December, we've been seeing them more and more.

Do they cause any harm?
Could they be responsible for the holes I've
been finding in my shirts?
Even if they're just a nuisance, how can
we get rid of them?

Looks like the common clothes moth (Tineola bisselliella). And, yes, the larvae (caterpillars) are likely the source of the holes in your shirts. You can purchase traps online or from hardware stores, or you can go the pesticide route if necessary (e.g., Delta Dust is available from online retailers).
See this site for further info, or search the web for more info on this species. https://en.wikipedia.org/wiki/Tineola_bisselliella

I thought about moths, but I read that the larva only attack clothes in airtight storage. My shirts are in a closet where I rarely close the door, and I wear them frequently. Was I wrong?