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If a trait does not appear to be advantageous to organism, why does the organism have it?
Why do organisms have some traits that do not appear to have any evolutionary advantage?

Also, let me know if this question should be merged should be merged with this thread: http://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved. They are fairly similar.

You could have answered there itself.

@WYSIWYG Fair enough, the reason I didn't is because I figured the question "Why didn't X trait evolve if it would be advantageous" and "Why did X trait evolve if it isn't advantageous" are different enough to warrant two separate questions.

There are many reasons why an organism might have a trait that does not appear to be beneficial.

The trait is actually advantageous even if it does not appear to be.
The trait is a byproduct of another trait, which is beneficial. Not all traits are the product of direct selection; traits that are byproducts of other traits are known as "spandrels", a trait coined by Stephen J. Gould and Richard Lewontin
The trait was fixed by some process other than natural selection, such as genetic drift. Genetic drift can fix traits that are neutral or even evolutionarily disadvantageous.

Also, the trait may have been beneficial at some point but no longer is. See: http://biology.stackexchange.com/questions/34466/is-there-a-name-for-the-evolutionary-loss-of-vestigial-structures


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What is the distribution of the expected number of lineages in a birth-death tree after time T?
I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death process where you only have information about lineages that currently exist today.
I am interested in this equation for the likelihood of observing N lineages after time T:

What I want is the distribution of the expected number of lineages N after time T given per-lineage birth and death rates lambda and mu. I've looked around and haven't found anything providing such an equation.

You are actually asking the explanation of the entire paper. There are 20 equations that precede this one. Have you understood them all?

@CactusWoman I reread your post and got confused. What do you mean by distribution of the expected number? Distribution over what parameter(s)? Expected value of which distribution?

Maybe it is more strategic to direct your question more in reaction to the content of the paper. Pick a particular step you don't understand and ask what it means.

@Remi.b I was beginning to write an answer but figured out that even the first equation relies on many assumptions which are not really defined in this paper. The equation in the question follows equation(3)  which is from a 1948 paper by Kendall. That's why I asked the OP if they have understood the previous equations.

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How is DNA testing used to differentiate between different species?
How is DNA testing used to determine that specimens belong to different species, rather than being subspecies, or members of the same species?
Usually the definition of species is about the ability to produce fertile offspring under natural conditions. How are markers chosen that indicate individuals are different species?
Or does this process occur the other way around? Are species identified as being different, then DNA used to identify which members are which?

Statistics of divergence
You can compute various statistics of group divergence. Typically you could consider the pairwise number of differences between any pair of individuals. For example the following two sequences
ATATATCCTGTGTCA
AAATATCTTGTGTCA
has 2 differences.
Obvious or obscure grouping
Often, individuals really group together quite naturally (if you perform a principle component analysis you will see clearly defined groups) but sometimes the groups are quite blurry.
The definition of species is arbitrary
Whether the grouping is blurry or not, it is often quite arbitrary how much two groups need to be different in order to classify them in different populations, different subspecies or different species, different genera, etc...
The problem here is more a problem of definition than a technical problem. You should have a look at this post to understand the issue behind the definition of species.

My attempt at a high school level explanation
Explain what a phylogenetic tree is
First draw a phylogenetic tree. Explain what they mean:

A node is an common ancestor
A leaf is a extant species (if the leaf gets to the top of the tree)
All species are related but some are more related than others..
Introduce the concept of sister clade
Explain that every species in a sister clade is equally related to the all the species in the other sister clade by highlighting their common ancestor.
Explain that no extant species is the ancestor of another species as the ancestors are the nodes.

You can get a short introduction to phylogenetic trees here on Biology.SE or here on Understanding Evolution.
Methods to reconstruct a phylogenetic tree
Let them wonder how we could get to know what the true phylogenetic tree is.
Suggest using phenotypic data and make them realize and if you put all the yellow flowers together, or the flying organisms (insects, birds, bats, squirrels) it won't work very well. So phenotypic data can sometimes be misleading. So explain that we can use genetic data by counting the number of pairwise differences. Let's consider the three different sequences
species A: ATCTCTG
species B: ATCTCTT
species C: AGGCATT
It sounds like the first two sequences are more closely related than any of them are to the third sequence. You can draw the tree for these three species.
Molecular clock (optional)
Knowing the rate at which mutations occur, one can date since when two lineages diverged based on genetic data. You will probably have to learn a bit more about molecular clock for yourself. You may ask a for high school explanation in another post.
Within population diversity (optional)
Recognizing the existence of genetic diversity within population is key to all evolutionary processes so it is good to let them understand the existence of such diversity early on.
Of course there is genetic diversity within a species that renders everything a little bit more complicated. For example, some of you have blue eyes while others have brown eyes (assuming there is variation for eye color among your students), this is due to the fact that the DNA sequence within each of you is a little different. Not as different as it is between humans and chimpanzee but a little bit different.
Genetic data to group populations into species
Then, you can say that genetic data can allow us to tell groups apart. You can show a PCA type of plot (without really explaining what a PCA really is) with colors. Each color correspond to a population (insiste on term population and not species). Something like

and then argue informally that light-yellow, green and red populations are probably different species while all the other populations seem to belong to the same species.
Problem with the species definition
If you really want to bring the question of the how to use genetic data to tell species apart, then you will first have to destroy their concept of species! For that, you should first have a look at this post. You will have to

Introduce the biological concept of species
Explain why this concept does not work for asexual species (hopefully they know that many species are asexual).
Give an example of another issue such as the classical (yet rarely observed) example of ring species (see here on Biology.SE or here on wikipedia)

Then, get back to the PCA and ask, how different two populations must be for them to be called different species? And make them realize that this is rather arbitrary. We can tell they are different lineages but it is up to everyone to decide what we want to call a species. However, very often vague intuition about how different a species should be is good enough.

So the description in the media, and in high school science of the use of DNA testing to identify new species from closely related groups is a gross over-simplification? I'm asking as a science teacher grappling with this content having recently been added to the curriculum.
If a student were to ask for clarification, I'd be trying to explain how DNA testing showed the samples were different enough to be considered different species, but have no way of (in appropriate level language) explaining what 'different enough' is and how it is determined. Can you simplify for high school audience?

@Jakra Answer edited. Let me know if my edit helps! It is good to see a high school teacher that bother to teach well and right.

That's really helpful! PCA is fine, its part of the curriculum anyway, it was the statistical analysis that I wouldn't have been able to explain. Your graph and explanation are going to be very helpful.

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Can a relationship exist that is mutualistic/parasitic/etc. but not considered symbiotic?
Wikipedia definition of symbiosis: "Symbiosis (from Greek σύν "together" and βίωσις "living")[2] is close and often long-term interaction between two or more different biological species."
Wikipedia definition of mutualism: "Mutualism is the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other."
In intro biology class, I (and many other people, I'm sure) was taught that mutualism is a type of symbiosis. However, now that I think more about it, it seems like some relationships that are mutualistic don't appear to fit the definition of symbiotic. Some relationships are clearly mutualistic and symbiotic (humans and gut flora, for example) but other relationships (like bees pollinating flowers) are mutualistic but don't appear to fit the definition of "close and often long-term interaction". The same of course goes for parasitic, ammensalistic, etc. relationships as well.
Thoughts, anyone?

please, rephrase your question in more succinct forma than "Thoughts, anyone?"

TL;DR: mutualistic/parasitic relationships are members of symbiotic relationships class
So, first of all, there is a way to look it up.
Secondly, the very same article in wiki has subsection on parasitism. Reading it would be useful:

This is also known as antagonistic or antipathetic symbiosis.

Also, brief search through Google Scholar will show how these words are used in context. papers include such as:

Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader?
Mutualism and parasitism: the yin and yang of plant symbioses
Mutualism or parasitism? The variable outcome of cleaning symbioses
Enhanced growth as a manifestation of parasitism and shell deposition in parasitized mollusks. Aspects of the biology of symbiosis.

Thanks for the answer. Now that I think more about it, it seems to me that all parasitisms do involve that close and long-term interaction, but I'm still not sold that all mutualisms fit the given definition of symbioses. What I'm asking about is whether an interaction that is mutually beneficial (like bees pollinating flowers) but doesn't actually involve "a close (physically) interaction" should really be considered a symbiosis. Perhaps that definition of symbiosis is incomplete? Or maybe the brief interaction between the bees and the flowers is enough for it to qualify as "close"?

what do you mean by "brief"? they won't live without each other, that is close enough for my taste. Again, these is how terms are used in specific field. Only reason to redefine them is discovery of a counter-example.

Brief as in the amount of time the bee is in physical contact with the flower is a short amount of time, compared to the lifespan of the bee and the flower, in contrast to gut flora, where the bacteria and the human are in physical contact for the entire duration of both organism's lives. It is, I suppose, not close enough for my taste, which is why I wanted to ask for some other opinions. I'll admit it's not the most exciting of questions.


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What are phenetic analyses used for?
Phenetics (grouping of organisms based on similarity) used to be claimed to be an alternative to cladistics, but now it is widely accepted that phenetic analyses cannot be used to infer evolutionary relationships. However, phenetic methods like neighbor-joining trees are still being developed today.
Are phenetic analyses still valid today for purposes other than determining evolutionary relationships, or are they completely obsolete? Does anyone have an example of a recent paper that uses phenetic analyses in a valid way?

The phenetics reference  in Wikipedia describes several places to look for phenetic analyses.

As usual, a rant from Joe Felsenstein's webpage seems relevant. Specifically, this:
"There is no consensus, even among systematists, as to what the word "cladistics" means."
Everyone seems to have agreed that phenetics--which is to say the blind faith in the results of clustering algorithms such as neighbor-joining etc.--is on its own not very useful, compared to a principled dedication to placing organisms taxonomically into monophyletic groups.
However, the hard-line cladistics point of view (e.g. Willi Hennig society) is that no method of inference other than maximum parsimony (in one of its various flavors) is acceptable, for obscure philosophical reasons that no one cares about. Frankly, for any realistic purpose, cladistically unacceptable methods such as Bayesian inference and likelihood methods perform the best. From cladistics wiki:

Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the parsimony criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified.

In other words, cladistics is more of a philosophical point of view than a group of methods. There are "soft" versions that everyone pretty much agrees on, namely the principle that monophyletic groups are preferable to paraphyletic groups. But methodologically, it's just a lot easier and more workable to use non-cladistic or even phenetic techniques rather than the (computationally frequently more onerous and not necessarily more accurate) parsimony techniques of cladistics.
For a (fairly) recent apologia specific to neighbor-joining, see here.
In short, given the highly heuristic nature of most science, most workers aren't really paying attention to these debates, and just use the tool that works for the problem they're working on. And in many cases those methods are phenetic, even if cladists claimed a victory of principle.

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Which mammals cannot synthesize taurine?
It is fairly common knowledge that domesticated cats cannot synthesize the compound taurine. Other mammals seem to be able to synthesize taurine from cysteine [source]. Are there other mammals that lack the ability to synthesize taurine?

Apparently cats can synthesize taurine from cysteine by the action of cysteine dioxygenase type 1 (CDO1) and glutamate decarboxylase 1 like (GADL1)/GAD2 enzymes. You can find out which organisms cannot synthesize taurine from cysteine from here. I don't know how to parse this data at this moment and I don't have the patience to manually check.

@WYSIWYG The Kegg map for taurine metabolism is here but if you compare felis catus with canis familiaris you find no differences in the enzymes supposedly present. If correct, this is consistent with Gwen's post.

@David Yes. Possibly the enzymes exist but are deficient.

It is a misconception that cats cannot synthesize taurine.
Cats can synthesize taurine, just like other mammals, but not enough of it to make up for an entirely taurine-deficient diet. Cats (and other mammalian carnivores) would have consumed a taurine-rich diet in the ancestral environment. It is only when they are fed vegetable/fruit/grain-derived foods that they show symptoms of taurine deficiency--because those foods have low quantities of taurine and other taurine precursors.
Other domesticated or captive carnivorous mammal species are at risk of taurine-deficiency if they are fed vegetable-derived foods, though members of the cat family (Felidae) are particularly susceptible.

Primary reference: This 2003 paper about taurine concentrations in animal feed, especially the 'Discussion' section.

Taurine  is  an  essential nutrient of cats because the rate of taurine synthesis from its dietary sulphur amino acid precursors, cysteine and methionine, is much less than the extent of loss through faecal bile
  acids  and  urine  (Knopf et al.,  1978).  From  an  evolutionary  standpoint,  taurine  was plentiful  in  the  diet  of  a  true  carnivore,  as  high  concentrations  of  taurine  are  found  in muscle  tissue. However,  as  most  domesticated  felines  normally  do  not  consume  living
  prey, they are at risk to become taurine-deficient if not adequately supplied in the diet.

This would be consistent with the Kegg entries for enzymes of taurine metabolism for dog and cat, as I mention in my comment on the question.

Perhaps you can give an example of a mammal that can actually not synthesize taurine i.e. it lacks the enzymes.

@WYSIWYG I am not aware of any.


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Would an h1 Full Agonist Prevent Sleep
According to Wikipedia the h1 receptors stop firing to effectively manage sleep.  Assuming I understand how blocking and non blocking receptors work would a full agonist on the h1 receptors effectively prevent sleep instead of create it.

The histaminergic neurons of the tuberomammillary nucleus become active during the 'wake' cycle, firing at approximately 2 Hz; during slow wave sleep, this firing rate drops to approximately 0.5 Hz. Finally, during REM sleep, histaminergic neurons stop firing altogether. It has been reported that histaminergic neurons have the most wake-selective firing pattern of all known neuronal types.

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Lower affinity drugs longer time for pathways to rebound?
Do lower affinity drugs take a longer time for pathways to rebound?
Affinity has to with strength of activating a receptor others options.
Do those with stronger affinities result in more likelihood to rebound?

This article is a good starting point for this question.
It states:
"The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not."
The dissociation constant is explained fairly well by Wikipedia.
So, the higher the affinity of a drug with it's target, the stronger it binds.
I'm assuming that by "rebound" you mean that the pathway will regain its ability to function normally.
When someone takes a quantity of a drug, it disperses throughout the body. At any given time, at any given point in the body there is some concentration of the drug. If the affinity of the drug to it's target is very high, lots of molecules will bind to the target, whereas with a low affinity drug, fewer molecules will bind.
As time goes on, the body will filter out some of the molecules, and the remaining drug molecules will diffuse to fill the space where the filtered molecules were located. As this process continues, the concentration of the drug will decrease, lowering the dissociation constant of the drug-target equation, which means that fewer of the molecules will bind, and some of the bound molecules will be released to maintain equilibrium. The longer this process continues, the closer to "normal" the pathway will become, until the concentration of the drug is negligible.
Keep in mind that all of this is dependent on the rate at which the body eliminates the drug (and how quickly the drug degrades on it's own). See here for equations and such. While concentration of the drug is a large factor in it's effects, the half-life of the drug may be a better indicator of how long it takes for a pathway to rebound than affinity of the drug. For that matter, affinity is probably a factor in the length of a drug's half-life.

Another way of stating what my question is asking is withdrawal time for these drugs although I am more interested in simply the rebound of the pathways and not the actual withdrawal effects.  There is no doubt this occurs considering if you stop taking benzos you can experience insomnia on and off for weeks and months.  You answer didn't really answer this question.

In that case could you try to phrase your question differently; it doesn't seem to ask the question effectively. Go in to more detail about what you're looking for. Even your above comment isn't particularly helpful; are you asking if withdrawal time of a drug is dependent on affinity? Additionally, please define "rebound".

Another user gave me the rebound pathway term so it seems to me there is discrepancy on what people agree on.  Yes I am essentially trying to determine withdrawal time based on affinity although withdrawal effects can be caused from a host of issues and not simply how long for a brain receptors to start functioning how they were prior to taking the drug.

Ok, that clears up a lot. Now are you asking how to predict withdrawal time mathematically based on affinity, or if there is a relationship between the two at all?

yes.  I have read time taken might effect it also assuming there might be some universal formula or something.

I don't suppose you remember where you read that?

Robert Whitaker's book talks briefly about the dopamine receptors.  It suggests it takes 3 times longer for the receptors to rebound then actually taking the drug.  It isn't a very authoritative source.

"Over time, Chouinard and Jones noted, the dopaminergic pathways tended to become permanently dysfunctional. They became irreversibly stuck in a hyperactive state,  and soon the patient's tongue was slipping rhythmically in and out of his mouth (tardive dyskinesia) and psychotic symptoms were worsening (tardive psychosis). Doctors would then need to prescribe higher doses of antipsychotics to tamp down those tardive symptoms. The most efficacious treatment is the causative agent itself, the neuroleptic"

Considering the uncertainty involved in drug-brain interaction, and how little we know about the brain, I'm not sure that I can give a good answer. If the drug in question only effected one pathway it would be simpler, but there's 3 pathways involved here. I suspect it may be dependent on the individual drug and pathway being studied. I've been unable so far to find any solid conclusions.


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Biosphere that simulates sun and moon shifts
Is there an enclosed biosphere that artificially simulates the movement of the sun and moon at increased intervals?
It is known that the sun and moon alter plant movements therefore I was wondering how far experimentation has gone.  Ideally I am wondering if they have experimented with different speeds of the moon and sun rotation and how it effects plant(and possibly other animal behavior ideas) growth.

You think about research with different day/night length and the effects on plant/animals?

@Chris Yes.  Should I give a further explanation?  The moon effects fish migration through the altering of water currents and tides.  In addition the moon alters wolf pack hunting and feeding schedules.  The sun is fairly more obvious and straightforward altering temperatures and altering bird feeding schedules and flight patterns.  There have been a couple studies down on this, but nothing I have seen that demonstrates if the abilities are instinct or learned.

Sun and moon-faking devices exist. Not sure about 'biosphere'. I have personally observed one for honeybees, but that one was fairly crude(bees are dumb). It was just a big room with a hive stand in the middle and a series of fluorescent lights on the ceiling that turned on one after the other. The goal was to mess with bee circadian rhythms and see which genes became more or less expressed in their brains.
There's a slightly more sophisticated thing called a 'grow cabinet'. It has expensive lights to produce sun-spectrum light at direct sunlight intensity and humidity and temperature controls. Scientists use them for crop research when the weather is too random and unpredictable and absolute control is required.
I believe advanced versions simulate moonlight and angle of insolation, but that sort of thing is expensive.
I don't know of any full-sized biodomes with fake celestial objects. The cost of such a biodome would be prohibitive, and the experiments it enabled might be easier(certainly cheaper) to do in a smaller container.


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Essential amino acid codons
Essential amino acids also have codons.Still they are needed by humans through diet?Will those codons do synthesize amino acids for some other purposes in humans or not?If so, what is the purpose?e.g?

Codons are like 'put green ink here'. The amino acids themselves are like green ink. Humans can write things in green ink, we just need to go and get some first, because we cannot make the ink. Does that make sense?

You are mixing things. First: Codons have nothing to do with the synthesis of amino acids.
A codon is the sequence of nucleotides on the DNA (or RNA) which code for a certain amino acid. For example UGU and UGC code for the amino acid Cysteine and given these codons it will appear in the protein being synthesized. The codons are basically a way to code the sequence of a protein with the smallest amount of information (simply by the sequence of the four nucleotides in DNA/RNA). For further information have a look at the Wikipedia page on Codons.
This look like this (image from the Wikipedia):

Okay thanks.My question is codons also code for essential amino acids right?Could you please give me an example of an enzyme or any other protein produced by DNA sequence(mRNA--triplet codons--essential amino acid) with essential amino acids in it?

They are the code for this amino acid on DNA/RNA, not more. Their synthesis is done by special enzymes (which are not all present in human, hence we have some essential amino acids) and "only" needs the right precursors.

Try http://www.uniprot.org/uniprot/P02452 for the sequence of Collagen I alpha precursor. Scroll down(pretty far) for amino acid sequence. K stands for lysine, an essential amino acid.

Answer to the comment

Could you please give me an example of an enzyme or any other protein produced by DNA sequence(mRNA--triplet codons--essential amino acid) with essential amino acids in it?

Partial Amino acid sequence of alpha amylase in Homo sapiens:
MKLFWLLFTIGF

Nucleotide sequence:
ATG AAG CTC TTT TGG TTG CTT TTC ACC ATT GGG TTC

Below s the amino acid single letter representation table that can be referred to understand the amino acid sequence

Make sure you follow the reading frame scheme to read the nucleotide sequence. Each time frame should have a triplet codon without including the previous nucleotide. I've represented it for the first few codons. You can observe essential amino acids in this protein. All the amino acids in this partial sequence are essential except glycine. Hope this helps :)

Can you shorten the example sequences? Just show something like 10 codons/aa. It just occupies more space and does not add to more information.

Perhaps worth adding that since most (all?) human initiation codons are AUG, most (all?) proteins contain an essential amino acid right there.


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Nucleotide sequence for STRING protein sequence
I have protein sequences from STRING database:
The amino acid sequence files are like this:

4932.Q0010 (Saccharomyces cerevisiae)
  MYYIMFLYNMLLIIILIFYSIVGVPIIIFNNNYYWDPDIFLFIIYYFIKFIIIFNLYLYYMINYIVYTPSGSPPGRGTYI
  LLYNMLYSYNMFIDYVMKFITCVTYMYLMFWLLSPTPSPYYVSEVPVS

I want the corresponding nucleotide sequence for the same protein ID.

4932.Q0010

I tried emboss http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/
But emboss is based on codon usage and backtranslate and it doesn't give me the original nucleotide sequence.
Then I tried DDBJ http://getentry.ddbj.nig.ac.jp/top-e.html
But DDBJ gives only amino acid sequences for corresponding Uniprot ID.
How do i get the original nucleotide sequence for the STRING protein sequences using STRING id or UniProt ID?
Any help in this regard is highly appreciated.

This should effectively clear your question http://www.uniprot.org/help/canonical_nucleotide

What is meant by canonical UniProtKB sequence?

@Raghavakrishna As it says, although most proteins derive from DNA translation, there isn't only a single way in which you can back translate the protein into nucleotide sequences.

@VivekRai But emboss can be used to backtranslate? http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/

Google is not a bad resource for such a question.
In this case I find that the Yeast Genome site has a button which returns the nucleotide sequence. You can select the genomic sequence for the locus or the coding (CDS) sequence.
http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=Q0010
They also give a link to NCBI at the bottom of the page.  I think the reason you were having such a hard time is that UniProt extracted the protein sequence from the mitochondrial genome record.  Like many genome ORF predictions, Q0010 does not seem to have a distinct nucleotide record assigned yet.
Summary:
In general  you can do a web search for the uniprot id to start.  In many cases, like this one you will find that the nucleotide seq is only a chromosomal sequence record.   Biodatabases are a bit of a maze - there are scores of them out there, you may find that someone has clipped the nucleotide sequence of the gene out, which is helpful if there are introns!

OK for yeast,This is good.But for other organisms what is the way out?

i added a note to the post...


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How large are the inner ear hairs?
I was always under the impression that the auditory hairs located deep within the ear, past the ear drum, are microscopic.
After taking a shower today, I was softly padding my outer ear with some tissue paper to dry any moisture, when some wax just got attached to it. What was unusual was that there were some hairs on it (3-5 perhaps, overlapping) that were about half a centimeter in length.
Are these just regular hairs that grow in the inner/outer ear? Or are they the ones that actually aid in hearing (the ones I thought were microscopic).
My question is to verify whether or not these hair shafts I observed are used in auditory perception. Either way, are these supposed to fall off?

Those are just ordinary hairs growing in your ear, like the kind you find in your nose and, if you are fortunate, on the top of your head. The "hair cells" of the inner ear aren't really "hairs" at all, they are totally different, and you would never find them falling out of your ear.
Hairs like on your head are protein filaments produced by follicles in the skin.
Hair cells in the inner ear, on the other hand, are sensory epithelial cells with stereocilia, which are protrusions of the cell membrane. Those membrane protrusions have mechanically gated channels which are coupled to nearby protrusions; when the whole cell is pushed one way or the other, that influences the mechanical stress on those channels and they open and close, which produces an electrical signal that can be sensed by the auditory nerve.
These special 'hair cells' are way way deep in your ear, past your ear drum, past three little bones that conduct sound into your cochlea. If you are touching those, you are in bad shape indeed - this is very very unlikely under normal circumstances.


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Do floating plants on a quiet body of water significantly affect the evaporation?
A situation such as a pond where a plant like duck weed covers essentially all visible surface water  : Is evaporation slowed or stopped ?

To what degree are you or are you not interested in including the plants' evapotranspiration rate into the evaporation rate of the pond water? In other words, are you more interested in the net change of water level or in the specific mechanism of surface evaporation from the pond surface?

Actually I am interested in heat loss . I cover the pond with Styrofoam panels in cold ( air below 50 F) weather. The Koi don't care but I have tropicals in it; Danios .They have tolerated water temp. down to 50 F  . I want to avoid putting on the panels for an occasional cold night.


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What makes boric acid so toxic to roaches and not so much to any other insect?
When I look up boric acid on the net there are various ads for it to kill roaches but no explanation of why it is effective on roaches. I am in East TX , roach central. When my house was built I put pounds of boric acid in between the studs before drywall went up . For 25 years  I don't think I saw a dozen roaches in the house. But starting this spring ,I have killed a few roaches every night . As if they became immune to the boric acid ( as much as I put in ,it could not be gone). We have pets so I am reluctant to use insecticide in the house.

boric acid plus sugar is a common ant control home remedy as well. The belief is that it crystalizes inside the insect and blocks their digestive tract


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Why does fresh zinc oxide cause chills but "old oxide" does not?
Inhalation of fresh zinc oxide causes chills; aka- zinc chills, brass founders ague, oxide shakes, etc. But if the oxide is a few hours old it will not cause chills. I had them once long ago, an old experience person explained the situation which I had never heard of. Pollution controls and modern safety practice have made it very rare in the US today. It can occur if one inadvertently causes a "zinc boil" by overheating a brass melt or oxy-acetylene cutting galvanized steel, etc.

Can you include a reference to something besides your personal experience? It seems very unlikely to me that anything here is involving the "fresh"ness of anything; it sounds like you're talking about a situation where there are inhalable metal oxides present compared to a situation where there are not inhalable metal oxides present. In that case the "why" is a bit boringly obvious, is it not? Can you clarify your question to make it more clear where the uncertainty lies?

I'd wager that your "old zinc oxide" is nothing more than rough-powdered whereas the irritant stuff from welding is nanometre-sized and finely dispersed in air (from experience and observation).

this is possibly because fresh zinc in the air is not fully oxidized and the old zinc in the air are.maybe you can ask a related question over at https://chemistry.stackexchange.com/ and link to this one.

Is what you're describing the same as metal fume fever?  This article describes it and says the particle size should be under 1 micron for acute systemic effects, and also says that aggregation of these particles occurs.  Do you know whether the old oxide you describe clumps up into larger particles?

Note the reference states "freshly formed" zinc oxide. Also, Zinc oxide is produced by mixing hot zinc vapor ( very small particles) with air. Wikipedia article not accurate ; i am looking for the book reference.


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Relation between OD with different microbial growth
Equal volumes of cell suspensions of Escherichia coli, Saccharomyces cerevisiae, Streptococcus lactis and Mycoplasma pneumoniae, all have the same OD600nm = 0.50. Which cell suspension would have the minimum and maximum number of cells, respectively?

Welcome to Bio.SE! What efforts did you make to answer this homework assignment? If you can't provide them, I'm afraid your question will be downvoted and closed. (see https://biology.stackexchange.com/help/homework)

Difficult to say with the information you have given. Here is a paper on the subject if you are interested. The relationship between OD and cell count depends on morphology and size, which in turn depend on culture condition, strain, etc...

Based on size, and if this is a homework question, you might expect yeast to be the largest and Mycoplasma to be the smallest.


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We know archea and eukarya are more closely related but endosymbiotic theory says eukarya have evolved from prokaryotes, justify the statements?
I am confused if eukaryotes have evolved from prokaryotes then how are they more closely related to archea?

I'm voting to close this question as off-topic because it is based on a false premise.


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How were genes located before the development of bioinformatics?
I would like to know the detailed procedure of how scientists in earlier time were able to locate genes like how we were able to locate Huntington gene in 1983?

Could you clarify what you mean by  earlier time, are you asking how the Huntington's was located or before it was located, and in what organism? And what precisely do you think bioinformatics has to do with it? What research have you done yourself to find the answer, and why don't you start your title with a capital letter like almost everyone else and run a spelling check if English is not your first language.

The detailed procedure of how scientists located the huntingtin gene spans at least a decade and includes multiple papers, and so your question seems rather broad. It was mapped to chromosome 4 in 1983 but the full ORF, with CAG repeats, wasn't identified until 1993.

Your question is also broad in that different techniques were often used for different genes. See this answer for a very brief summary of how the insulin gene was discovered.

The earliest genome maps were constructed from Escherichia coli by abusing conjugation of special Hfr-mutants. I'm assuming you are somewhat familiar with bacterial conjugation - the process of transferring genetic material between bacterial cells.
Usually, only mobile plasmids are transferred. They carry the necessary tra-genes for the construction of the sex-pilus, replication and transfer system. They also need the oriT-site (origin of transfer), at which transfer is initiated. A famous mobile plasmid is the F-plasmid.
Some mutant cells integrated the F-plasmid into their main chromosome via recombination. Thus, they are able to transfer their whole genome to a recipient cell. These strains are called Hfr-strains (high frequency of recombination) and they were used intensely in early genome mapping.
They discovered, that it takes roughly 100 minutes for a Hfr strain to transfer its entire genome to another cell. By interrupting conjugation (e.g. by vigorous shaking) the transfer was interruped and the genome could be divided into sections by transfer time (10min, 20min, 30min and so on).
The function of the genes (or genome sections) was revealed by mating Hfr strains with defective mutants. If the mutant was unable to grow on saccharose for example, several conjugation experiments with different mating times were conducted. When a mutant was able to grow on saccharose again after mating, the transfer time was checked. If the strain was able to grow again after 30 minutes of conjugation, but not after 20, they knew the genes necessary for saccharose growth lay in the 20 - 30 min region.
It took a painstaking amount of experiments with a wide range of mutants to construct the first map of E. coli genes, but it was achieved before even the nucleotide sequences were known.

Just to complement Pythagyros.
Sequencing and bioinformatics were already around in 1983, actually Frederick Sanger and colleagues published their automated method of sequencing (Sanger sequencing) in 1977. They published the complete sequence of the bacteriophage φX174.
Other methods of DNA sequencing had been around since the first one in 1970 established by Ray Wu.


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DNA code and codon
I work as a highschool teacher and I believe that in most highschool textbooks in my country there is a lost-in-translation problem involving some molecular biology basics. It has spread to the point one starts to doubt his basic knowledge, so here it goes:
For example, let's say that a triplet in mRNA is:
5' AUG 3'
That triplet is named CODON. (no problem there)
The DNA that corresponds to it has two strand.
One is coding or sense strand and contains the corresponding triplet 5' ATG 3'
The other is non-coding or antisense strand and contains the triplet 3' TAC 5'
Highschool textbooks in my country say that the triplet 3' TAC 5' , therefore the non-coding strand, is the CODE.
It makes no sense to me whatsoever, but I'd like to check it out since in English literature the term code is rarely used anyway and genetic code is usually presented as codons. Sometimes, when the list of DNA triplets is given (and it's always in 5'->3' direction since the information is read that way) it says "DNA codons".
So, to sum it up - is the DNA CODE equal to triplets in the coding or the non-coding strand?
Thanx in advance!

I wonder why you put in parenthesis: "(and it's always in 5'->3' direction since the information is read that way)". Do you mean: even if might as well be the other direction that wouldn't answer the question?

The non-coding strand is indeed not the coding strand as the name suggests. It is the template strand. The template strand serves as the strand from where the mRNA is constructed upon. The mRNA contains the complement of the template strand, and is ,in fact, the actual codon. This is also the reason why the other strand is called the coding strand, it's the complement of the template strand, which makes it essentially the same as the mRNA, except uracil is replaced by thymine.
DNA Strand section:
5'---A-T-G---3' => coding strand
     : : :
3'---T-A-C---5' => template strand

mRNA formation:
5'---A-U-G---3' => mRNA strand
     : : :
3'---T-A-C---5' => template strand

are the coding strand and template strand synonyms?

@BenHughes Nope, but they are complementary to each other. It's both of those strands that make up DNA. During transcription, the two strands split and the mRNA strand forms taking one of them as a template (hence it's name template strand). The other one doesn't do anything, but has the same base pairs (T replacing U) as the mRNA, hence called the coding strand.

In the English literature, a sequence like your 3' TAC 5' (when considered as the complement to a 5' ATG 3' or 5' AUG 3' codon) is typically called an anticodon.  Most often this is in the context of a tRNA having an anticodon to a codon on an mRNA.  See, for example, this page from Molecular Biology of the Cell or, similarly, this page from Berg's Biochemistry
Generally, code is used in molecular biology to refer to the conceptual mapping from a codon sequence to an amino acid (or meta function like STOP), or collectively to the whole set of such mappings.  The latter kind of reference is more likely to use the longer name the genetic code.

Very helpful you "bring up" anticodon. Are you sure that this term is not exclusively used in mentioned context of transfer-(t)-RNA? The question seems to be on coding/negative "strand" relating/corresponding to "template"/transcribing(cp. related answer by David) "strand". In that sense, the anti-codon of a t-RNA doesn't appear to be a "strand".

@PeterBernhard, I disagree with you about what the question is asking, which is exactly why I added my answer after Twisted Genes' answer, which does a fine job of explaining strands. The OP mentions strands only as a point of reference for the actual question, which occurs in the last large paragraph.  I believe he is asking about the names for triplets, and in English they are 'codon' and 'anticodon', and not about strands.  (I also discuss the usage of 'code' which is another aspect of the question.)  'Anticodon' is not used much, and probably does appear primarily in the context of tRNA.

Maybe "Anti-" ought to be (trying some irony) opposed to the wording of the question "...the non-coding strand, is the CODE. " As I found with David quoted above, it's very well a matter of linguistics, too. As you  say in your second part of your answer, "Crick's CODE" refers to that eminent fact that the proteins of life are made from amino acids which there is THE code for, hence - to my mind - "coding" for what IS the code, and not for that template fabricating. Your second part is the answer, question not on difference codon/anticodon (you made me emphasize). Will read all your reference.

Would you agree with  "anticodon" in a wider sense being in use for any sequence that complements what has been defined as codon? -  One more example I suggest is "interfering" RNA that matches m-RNA which may be named "non-coding anti-codon"? -  Is non-coding, i.e. are anti-codons always read from `3 to '5, even when, as genes, are found on the 5' to 3' -codon strand? Thank you.

Albert, The cell you quote, says, defining: "anticodon - Sequence of three nucleotides in a transfer RNA molecule that is complementary to a three-nucleotide codon in a messenger RNA molecule". In fact, the term seems to be restricted to the context of tRNA.


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when does osmosis stop
I have a question about osmosis that goes a bit deeper than most basic textbooks so I cannot find the answer.Here's the problem:
Imagine an animal cell, say a red blood cell, in a slightly hypotonic solution.
The water starts to flow in osmotically.
The concentration of solute in the cell decreases.
The cell slowly starts to swell but does not burst.
The question is:
Does this water entering increases the pressure on the membrane (similar to turgor in plant cells only less, because the cell can increase in volume - comparable to elastic energy that must be overcome when blowing a baloon...) and does this cause osmosis to stop BEFORE the concentrations come to equilibrum (meaning that cytoplasm still has a bit more solute concentration than outside of cell) or do the concentrations perfectly match?
Thanx in advance.

It doesn't
As long as liquid water is present osmosis will never stop, the closest you can get is a point at which it happens at equal rates in both directions, called equilibrium.
Plant cells will help you understand as osmosis will create immense internal pressure as water enters the cell even though the cell cannot expand thanks to the cell wall. the amount of water inside the cell will keep rising until it reaches equilibrium, this also makes the cell more rigid.

I found this, which I think proves my point, but I cannot say I really understand all the math behind it.
https://i.sstatic.net/GgO01.jpg
http://www.princeton.edu/~akosmrlj/MAE545_S2017/lecture13-14_slides.pdf

If animal cells are incubated in pure (or v. Low solute conc.) water, they will swell until they burst.
So in that respect, I think osmosis doesn't stop for animal cells. At least not until either equilibrium has been reached, or the cell has burst.

Equilibrium must be reached for osmosis to stop, but what equilibrium? Look at this example: http://canacopegdl.com/images/osmosis/osmosis-14.jpg    Here, as water level rises in one side and falls in the other, hydrostatic pressure builds up. When hydrostatic pressure equals osmotic, net water flow into the STILL HYPERTONIC solution stops from the STILL HYPOTONIC one. My assumption is that something similar (just to a lesser extent) exists in the case of animal cell swelling so osmosis stops when the pressure buildup in the cell equals osmotic pressure.

Hydrostatic pressure won't effect cells in the same way as that scenario. As the cells are surrounded by the solution, the pressure against the cell wall can lead to the cell bursting, if the osmotic potential of the solution is off. For mammalian cells, it's typically around 300 milliosmolar. Similar to tissue fluid.

Anyway, not really. Either the cell will swell and burst, or shrivel and die. In both scenarios the membrane disintegrates, so the cells contents mix with the solution. Now for an artificial membrane that cannot burst. That's a different question.


text:
is this an insect?

The creature is about 1 1/2 inches long and about 1/4 inch at its thickest point. It appears to have six leg. It also appears to be covered in fur. It seems to have four eyes, two facing forwards and one at either side of its head. The head is snake like in appearance. The tail is able to wrap itself around things; it was hanging by it from a leaf. The creature was found in a garden in the North East of England.

Looks like you have a caterpillar.


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Why does plasma protein saturation of a drug increase its volume of distribution and clearance rate?
I need help understanding this statement from Goodman and Gilman's "The Pharmacological Basis of Therapeutics:"

For a drug that is metabolized
  by the liver with a low intrinsic clearance-extraction ratio, saturation
  of plasma-protein binding will cause both V (distribution volume) and CL (clearance rate) to increase as drug concentrations increase.

This is how the textbook defines distribution volume and clearance.
$$\text {distribution}\ \text{volume} = \frac{\text{amount of drug in the body}}{\text{concentration in plasma or blood}}$$
$$\text{clearance rate} = \text{bioavailability} \ \cdot \frac{\text{dosing rate}}{\text{concentration at steady state}}$$
I think I get the grasp of it somewhat, but I would like to verify if my reasoning is correct.
The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug. As a result, the amount of drug in the body increases while the concentration in plasma or blood stays the same.  Hence, the increase in distribution volume.
As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.
However, I am not sure why the fact that plasma proteins are saturated matters.
For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered. For clearance rate to increase, however, unbound drug in plasma needs to be able to increase when more drug is administered. What am I understanding wrong?

First a couple of clarifications:

You wrote:

For the distribution volume to increase, unbound drug concentration in plasma should stay constant while tissue drug concentration has to increase when more drug is administered.
Actually, it is the total drug concentration in plasma (bound plus unbound) which matters while calculating distribution volume.

Clearance is better defined as $ \frac{\text{Rate of elimination}}{\text{Plasma concentration}}$. The equation you mentioned above is a derived formula for calculation of dosing rates.

Now for the answer. The basic principle is: when plasma proteins get saturated, increasing drug concentration increases both tissue concentration and unbound drug concentration in plasma, because the drug has "nowhere else to go".
Thus your reasoning is correct when you say this:
The reason why volume of distribution increases is because the drug is distributed to tissues other than blood once the plasma proteins are saturated with the drug.
Of course, our understanding here is that the increase in total plasma concentration is marginal as compared to the increase in tissue concentration.
However, the following does not seem to be correct:
As for clearance rate, it increases because the zeroth order reaction is always faster than the first order reaction in Michaelis-Menten kinetics.
(Perhaps you are confusing plasma proteins with drug metabolising enzymes?)
The answer to the clearance part can be obtained when you recall that we are talking of a drug with low hepatic extraction ratio. Thus, clearance is proportional to unbound drug concentration. As already mentioned above, unbound drug concentration increases on increasing drug concentration.
Hope that answers your queries.
Reference:
Buxton ILO. Pharmacokinetics: the dynamics of drug absorption, distribution, metabolism, and elimination. In: Brunton LL, Hilal-Dandan R, Knollmann BC (editors). Goodman & Gilman's the pharmacological basis of therapeutics. 13th ed. New York: McGraw-Hill Professional; 2017. pp 13–29.

Welcome to Biology.SE! This looks like a good answer, but answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. This is a good example of how to format references. ——— Thank you for taking the [tour], but you may also want to consult the help pages for additional advice on [Answer] effectively on this site. Thank you!


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Is slow growth a virulence factor?
Many slow-growth pathogens (e.g. Mycobacterium tuberculosis, lentivirus, Rhabdovirus, Leptospira spp) are difficult to treat. In addition, a review of 61 pathogens found that

slower growing pathogens are significantly more virulent than faster growing pathogens

I was wondering why this may be the case. Is slow growth a virulence factor? How does slow growth benefit a pathogen?


text:
What is the average membrane potential for a neuron?
I'm familiar with the resting membrane potential and other relevant values, but I wondered if there was any research done on the average subthreshold potential of a neuronal membrane over time.

The average subthreshold potential varies greatly with the type of neuron as well as with brain state. In some states, like slow wave sleep in cortex, the membrane potential oscillates between a hyperpolarized (~rest) and depolarized (~threshold) membrane potential. It's far too broad to come up with an "average" value here.


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What is intercalary mitosis in bacteria?
According to Wikipedia, in vegetative reproduction fragmentation takes place, and Spirogyra simply undergoes intercalary mitosis to form new filaments.
How is 'intercalary' defined in a bacterial context, does have to do anything blank or dead cells of Spirogyra?

To define, intercalary differentiation or mitosis applies to any cytogenesis through mitosis which arises between different specialised tissues or cells. Spirogyra may undertake either sexual reproduction, should conditions prove to be adverse, or asexual. The latter involves an 'intercalary mitosis'. This entails a fragmentation in the original filament in order to produce additional filaments.
Within bacteria, a good analogy may be the 'Blue-Green algae', a deceptive misnomer for phototrophic cyanobacteria. Thus, in the context of filamentous bacterial colonies, you may consider intercalary binary fission, cell division within the filament.
More information available from: http://bioweb.uwlax.edu/bio203/2010/fenske_megh/reproduction.htm


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What is the role of triton in buffer for western blot assay?
What is the role of triton in buffer for western blot assay?
I understand it has to do with preventing non-specific binding of the antibody.

That's exactly it. Triton is a detergent and incorporating it just makes it a little more difficult for everything to bind. Here's how I imagine blocking buffer working:
PBS/TBS: buffering pH
milk/BSA: uniformly interacting with the entirety of the blot. The idea is that these will a) adsorb to the parts of the blot that don't already have much sample in them (since "empty" areas of the blot would otherwise adsorb the detection antibody/ies (this is a source of nonspecific binding).
Triton (or, more commonly, Tween-20): OK, now think about what's on your blot. Your antibody will have weak interactions with just about anything there. A detergent interacts with everything it touches (antibody and adsorbed proteins on the blot) to reduce binding affinity in lots of these interactions (although, some interesting counterexamples can be found here), thereby making the less-favorable binding even less favorable, decreasing the chances of your detection antibody retaining these weaker (off-target) interactions. The preceding article also suggests that the use of nonionic detergents lowers the signal intensity of the Western (and to a different degree across proteins).

Low concentrations of nonionic detergents can help to solubilize a complex mixture of proteins.  In other words, some of the antibodies in the serum might precipitate, which would effectively lower their concentration in solution.  If some of the primary antibody precipitates and binds to the filter then it could lead to a higher background signal when it is recognized by the secondary antibody, prior to the detection step.


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Are Richard Lynn's estimates of African IQ inherently innacurate on the basis that most Africans aren't mentally retarded?
I've been looking at Richard Lynn's studies on average African IQ, and he seems to estimate really low IQs in the 60s range (e.g. http://www.sciencedirect.com/science/article/pii/S0160289609001275?via%3Dihub).
However, is this inherently wrong, as somebody who would score that low in a Western country would no doubt be mentally retarded (and this isn't the case for most African people)?

The study has been heavily criticized e.g.
Wicherts and his colleagues examined over 100 published studies, concluding that there is no evidence to back up Lynn's claims. Amongst other flaws, Lynn used selective data by systematically ignoring Africans with high IQ scores (Controversial study of African IQ levels is 'deeply flawed')
Lynn replied to the criticism but not at all convincingly. No one seems to have taken him very seriously outside of racist hacks looking to support their bigotry

I am not sure this really is a biology question. Sounds more like a question of social demography.

IQ is just a measure of how good you are at taking IQ tests, that's it. Those tests are usually culturally biased towards middle income first world citizens (among other things). Think of it this way, questions about mortgages, supermarkets, airplanes, or such thing presuppose the person being questions knows a reasonable amount about those things, this is not a reasonable assumption in many places around the world.
The classic "a train leave chicago at 10:00..." is a perfect example since the reader needs to know what a trains is, that chicago is a place, and what 10:00 means additionally they need to be familiar with reading exact measures of time and velocity, that they have already been taught basic math, are familiar with abstract questions, and that they are experienced readers, these are all fine assumptions for the New York suburbs but pretty bad ones for sub saharan subsistence farmers.
People who try to write the questions for said cultures often run into the reverse problem, we think of travels as a steady rate but to people who travel by boat know allowances need to be given for things like the speed the stream is moving, or the paddler taking breaks for lunch, information the writer may wrongfully assume or not understand. I recall a question about two people traveling along the same road that was consistently wrong because people in that culture thought is was proper for the faster person to slow down to match the slower for the safety of both (the norm in said society) so they constantly calculated their speed as the same, something the writers never anticipated.
There are millions of these differences across cultures and these cultural differences quickly snowball in to large differences when taking identical tests. So you are not seeing a real difference in intelligence just an artifact of culturally biased testing.

+1 That and when the metric becomes the goal, it's no longer a good metric.

Yeah, it's like trying to judge my intelligence by asking questions about TV shows or popular music - to which my answers would be a universal "Duh?" :-)

How do you define being "mentally retarded"? In order to minimize the difference in measured IQ that might be due to people growing up under different circumstances in different cultures you could try to measure how people with different ethnic backgrounds achieve in a multicultural society. Citation from a paper regarding school results in Florida, USA:

The number of ill-prepared students in Florida remains troubling, as
  do the differences by race and ethnicity: 38 percent of black students
  currently read at grade level. That compares with 53 percent of
  Hispanics, 69 percent of whites and 76 percent of Asians.

http://www.maswired.com/florida-lowers-standards-for-latino-black-students/
Obviously being able to read at some level does not have to correlate with IQ in a simple fashion and people in Florida who are reported to be "white" or "black" might have a mixed ethic background. I do not know if any large scale investigations trying to link IQ with ethnic background in countries such as the USA are done, as the subject might be deemed as controversial. If there are differences in school results, SAT-scores etc. that might at least give you a hint of how large the differences between different ethnic groups might be.


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How diverse are the sperm cells of an individual male due to random mutations?
Due to the sheer number of sperm cells in an individual and the rate of mutations, are they likely to be incredibly diverse and encompass most of what we see across our species?  For instance would it be likely to find sperm cells that could result in extreme height, intelligence, different skin colour,etc even if the father didn't have any of those genes in their DNA, but a sperm cell did due to mutations?

A pre-print study was recently published regarding sperm cell mutations. Contrary, to what you might expect the ratio of paternal to maternal mutations was quite stable from puberty and onward. See Gao, ..., Przeworski: Overlooked roles of DNA damage and maternal age in generating human germline mutations. They conclude that spermatogenesis does not underlie the male bias in human mutation.


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Is there any difference between fascia and skin ?Are both the different names of the same thing?
Skin is the outermost layer of the body ,and it consists of two layers; epidermis and the second layer the dermis .There is another layer the (third layer) beneath the dermis called superficial fascia or subcutaneous tissue. I want to know that is superficial facia  a part of skin.?Can we say that fascia is another name of skin?

The superficial fascia is the lowermost layer of the skin found in nearly all parts of the body and it usually blends with the reticular region of the dermis. But that doesn't mean it's a part of the dermis. The subcutaneous tissue/hypodermis/superficial fascia is NOT part of the skin but lies beneath the  dermis of the skin. Therefore, it can't be used as an alternative name for the skin.

Fascia is made up of sheets of connective tissue located below the cutaneous layer. These fibrous tissues attach, stabilize & separate muscles, maintain vessel patency, and enclose different organs.
Fascia can be classified as superficial, deep, visceral, or parietal.
Superficial: Superficial fascia is found directly under the skin and superficial adipose tissue layers. It can sometimes include muscle fibers; for example: platysma muscle in the neck, the external anal sphincter, and the dartos fascia in the scrotum.
Deep: This one surrounds bones, muscles, nerves, and blood vessels. It is commonly has a more fibrous consistency and rich in hyaluronan as compared to the other subtypes. Deep fascia tends to be highly vascularized and contains well developed lymphatics. It is further divided into 2 subtypes:

Aponeurotic fascia
It forms into sheets of pearly-white fibrous tissue to attach muscles needing a wide area of attachment. Aponeurosis can thin into a tendon and become a point of origin or insertion for other muscles. Some examples of aponeurotic fascia include the fascia of the face, limbs, thoracolumbar fascia, and rectus sheath.
Epimysial fascia
Also known as the epimysium, this is the connective tissue sheath surrounding skeletal muscle and can, in some cases, connect directly to the periosteum of bones.

Visceral: Visceral fascia surrounds organs in cavities like the abdomen, lung (pleura), and heart (pericardium).
Parietal: Parietal fascia is a general term for tissues that line the wall of a body cavity just outside of the parietal layer of serosa. The most commonly known parietal fascia is found in the pelvis.


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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


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Michaelis-Menten equation; how to find the constants from enzyme activity experimental results?
I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat?
I did an experiment on catalase and its breakdown of hydrogen peroxide. I used a gas pressure sensor to track how much O2 was produced from the reaction over time. The following is an example raw plot of what I found. Point 0 is when I put the substrate and the reaction started (so I think I can call this the "maximum amount of substrate concentration" - in the Michaelis-Menten plot, it should be on the far right side.)

To find the speed of the reaction at each point, I thought of finding the slopes between each point, which basically equates to finding the derivative. Since the raw plot I found looks like a logarithm function, so I would predict that the derivative would look like a hyperbola (with x > 0). Indeed, this is the (crude) graph of the "derivative" of the previous plot, which looks like a hyperbola:

I believe that Kmax is the y-value of the first point in this graph - the initial velocity when the substrate is mixed with the enzyme. The substrate concentration is at highest at time 0, and the substrate concentration decreases as time increases.
So I thought, to make the Michaelis-Menten graph, I should flip the x-axis so that the substrate concentration is increasing along the x-axis. Yet, my problem was that if I do this, then the graph ends up not looking like the Michaelis curve...

What I would have wanted to find is the Michaelis-Menten curve, so that I can also derive the Km and Kcat values. Does anyone know how to do this? Or am I doing my steps wrong? Thank you very much for helping me!
Michaelis-Menten Curve:

Have you got data for different concentrations of hydrogen peroxode?
If so you should choose a time point that falls on the linear part of your time graph. And plot the rate at that time point for each substrate concentration.
That will give you a MM curve where you can calculate the values you desire. You cannot calculate them with just your time data that you have provided.

No, unfortunately I do not. That is why I was wondering whether I could do any MM calculations from what data I have. I guess I cannot then (unless I assume that substrate concentration decreases linearly across time - the only thing I know is how much H2O2 I put in at the beginning). Thank you very much for your reply anyway!

@lia the point is that you need to run this experiment multiple times, with multiple different starting concentrations of $H_2O_2$, find the initial (linear) rate for each, and then plot the rate vs. starting concentration. That's what this answer is trying to tell you.


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Why does alum work on blisters in the mouth/cold sores?
Alum used to be an age old tradition to treat sores in the mouth and it worked beautifully.Foes anyone know why Alum works on sores in the mouth ?

Welcome to SE Biology. Please take the guided tour and then read about how to ask a good question. You will see that you are expected to "Search and Research" before posting. Have you done this? If the articles you have found don't answer your question, reference them, say what they do say and why that is insufficient. Otherwise I am afraid your question is likely to be removed.

Alum has been shown to be effective in treating aphthous stomatitis (canker sores) and it is believed to be due to the compound's significant drying effect. Alum is known as an astringent - a chemical compound that tends to shrink or constrict body tissues. More information on alum's astringent properties are reported in this paper. As the infected tissue shrinks there is a decrease in pressure due to swelling and this less pressure around the nerves in the affected area. The exact mechanism is still under question.


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Why doesn't ovulation occur in both ovaries simultaneously?
I know that in human body ovulation takes place at only 1 ovary every month. But development of a follicle depends on FSH levels in the blood, and since both the ovaries are exposed to the same blood supply, how does it make sense for development of follicle to be seen only in one ovary? Aren't both ovaries exposed to same FSH levels every month?
I am not able to figure out the solution to this anomaly and would appreciate some answers.

I don't know the answer to this but it could simply be that once an ovary has ovulated it enters some sort of refractory period so that it ends up skipping a cycle.

@AlanBoyd - Ovulation isn't democratic. Each ovary has an equal chance of ovulating every cycle. I don't know why that is, but it is.

@anongoodnurse I had got the idea that they alternated.


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Around what time did dark skin disappear from Europe?
As Europeans gradually became lighter skinned, there would have been people that still had dark skin. Around what time period did Europeans become completely light skinned?

This should be relevant: How europeans evolved white skin) (http://www.sciencemag.org/news/ 2015).


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Are there any techniques for manufacturing exosomes in the lab?
I'm interested in the idea of using exosomes as an alternative transfection agent / delivery mechanism for gene editing applications (CRISPR/cas9, etc).
Information on the matter is sparse.. Does anyone know of any practical techniques for manufacturing exosomes in the lab?

Information on the matter is sparse You can search for any paper that studies exosomes and they'll describe how they obtained them. Is there something specific you cannot find?

"Manufacturing" in the sense of isolation for research or as a clinical product? Current production methods involve multiple ultracentrifugation, filtration and wash steps followed by detection by immunoassay with culture supernatants as a starting material. In other words, you need an ultracentrifuge. There are small-scale kits for exosome isolation but there's a lot of contaminants often times. Try this publication if you can. Wolters-Kluwer/Ovid are hard to access IMO.

@canadianer isolation is not easy for exosomes of certain cell types like cardiomyocytes, where you'd need direct access to a heart. And many cells often only accept exosomes that are specific to those cell types. In light of this problem, it would be desirable to have a way to manufacture or synthesize exosomes tailor made to certain cell types. That's really what I'm looking for. Techniques for synthesis rather than isolation.


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Are exosomes useful as a transfection or delivery mechanism in gene editing?
The use of viruses as transfection or delivery agents for gene editing (CRISPR/cas9, etc) is well known. However, one problem with using viruses to deliver DNA into cells is the possibility of triggering an adverse immune response.
Cells already use exosomes to transport various cargo in and out of cells. Does this characteristic make exosomes ideal candidates for delivering gene editing cargo as well?
Also, are there any known examples or studies involving repurposing exosomes for gene editing? Specifically for CRISPER/cas9 applications?


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How can carnitine enter the mitochondrial matrix without OCTN2?
Some people have defects on the gene SLC22A5, giving them problems with their OCTN2 transport protein (Organic cation transport).
OCTN2 transports carnitine into the mitochondial matrix where it can be used to create cellular energy.

Treatment indications for individuals with the defect on SLC22A5 includes oral or intravenous carnitine supplementation.
But one piece is missing...
If their OCTN2 is defective, then how does supplementing carnitine solve the problem? If they are deficient or lacking in OCTN2, how does carnitine even enter the mitochondrial matrix? (with no functional OCTN2 to transport it through?)
But the condition of these patients often improves with supplementation. So the carnitine is getting in there somehow.
Is there another route via which carnitine enters into the mitochondrial matrix?

Where is the picture from? As far as I can tell SLC22A5 (OCTN2) is annotated as a plasma membrane protein, and the disorder is related to defective uptake into the cell, not into mitochondria. The protein labeled OCTN2 in your picture rather looks like the carnitine-acylcarnitine translocase, SLC25A20.

The image is from here: http://www.kanazawa-u.ac.jp/research_bulletin/feature201309F003.html (Dr. Tamai actually responded to me that he thinks it's a mistake and that the person who created the image might have misunderstood the paper it was based on). I will update the answer according to his response.

Short answer -- looks like the image in my question might be flawed, and OCTN2 probably isn't even involved in inner mitochondrial transport. Lesson: don't believe everything you find on google image search!
Longer answer - So I went back to the page where I originally found the image and saw that Dr. Ikumi Tamai was featured as one of the researchers who originally described OCTN2 back in the late 90s.
So I contacted Dr. Tamai via email-- and he responded to me a few hours later!
In his response, Dr. Tamai stated that while OCTN2 is expressed in various places in the body -- it is mostly active in the kidney -- and works there to conserve blood carnitine by re-capturing it from urine and returning it to the blood.
He added that jvm mice (which have defects in OCTN2 that cause carnitine deficiency) respond favorably to carnitine supplementation because the defect mostly just lowers blood carnitine levels, and simply raising those levels improves the condition of the mice.
This seems to suggest that OCTN2 does NOT play any role in transporting carnitine within the mitochondria.
Dr. Tamai noted that the image, which seems to depict OCTN2 sitting on the inner mitochondrial membrane, might have been designed by someone who did not fully understand the science of OCTN2, and that different transporters are likely responsible for the transporting of carnitine into and out of cellular and mitochondrial membranes (not OCTN2!).
In short -- it seems like that little pink blob in the image above should NOT be OCTN2 (even though it is labeled as such) and should probably be another transporter altogether.

Nice way to get the answer! The protein in the image is carnitine-acylcarnitine translocase.

@canadianer thanks! And more thanks for filling in another piece of the 'puzzle' for me regarding carnitine-acylcarnitine translocase.


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Phylogenetic method to detect shift in mean of continuous variable
I am currently working on a project where I study the change of a continuous morphological variable with body size (measured as body weight) across diverse taxa (insects, spiders, lizards, frogs). In order to account for the non-independence of the data, I built an approximate tree based on published phylogenies. I have a reasonable branching pattern down to family or genus level for most taxa, but lack statistically supported branch length.
I find a strong change of the scaling coefficient when using phylogenetic least squares (with a covariance matrix based on my tree) vs a non-corrected least-squares approach, suggesting that most of the change observed in my continuous variable is explained by evolutionary history, rather than by body mass as such. I would now like to investigate how early on in the tree these shifts occur.
Intuitively, I could start collapsing my tree into polytomies down to arbitrary taxonomic levels, eg genus, family, order etc, and re-do my phylogenetic least squares. I would expect a stepwise approximation of the pgls to the uncorrected result (in the extreme case, I would end up with a star phylogeny, which should give an identical result to my uncorrected regression). Such an approach may allow to say something about whether most of the change occurs between genera, families etc, but it requires the use of somewhat arbitrary (and controversial) taxonomic levels. I would be grateful if someone would have an alternative suggestions on how to perform such an analysis, with arbitrary branch length and non-ultrametric trees.
Thanks
Thriceguy

Quick question - do you have fossils for your trait and group?

I have no fossils. The non-contemptuous tree tips (I assume your question relates to them?) arise because different parts of the tree are resolved to different levels, and I set all branch length to 1 in my analysis. I suppose I should be able to ultrametrize the tree, however, if this would be helpful/better/required.

In case anyone encounters a similar problem, this blog entry: http://blog.phytools.org/2012/11/code-for-contmap-new-minor-phytools.html, and, in more detail, this paper http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12066/full may provide a solution. In short, one can estimate ancestral states of continuous or discrete variables and plot them on an existing tree. In case of scaling studies, phylogenetic residuals from a regression of the trait against mass may be the most meaningful parameter, clearly visualising the contribution of common history independent of size.

Do you want to test this formally or just evaluate whether the variance seems to lie closer to the root of the tips of the tree? To me, your basic idea to test "how early on in the tree these shifts occur" seems to imply a model with different rates of evolution (e.g. stasis-shift-stasis). If that is the case, I think you need to fit evolutionary models with different assumptions (bursts, brownian motions etc) to your dataset, to see which one fits best. See e.g. Uyeda et al (2011) for inspiration. Or am I misunderstanding you?


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Independent contrasts with non-homologous traits
I have morphometric measurements for a trait across various animal taxa, and would like to study the relationship between the size of this trait, and the animals' body size. In theory, I can account for the non-independence of the data with phylogenetic methods, such as independent contrasts. However, I have very different groups in my tree (for example insects and lizards), and even within more closely related groups, the structures are often not homologous. Does this present a problem for independent contrasts/phylogenetic least squares? For example, the structure is not homologous between ants and flies, yet every (sensible?) tree would treat a fly as more similar to an ant than to any lizard. Is this justified if structures are analogous? If not, are there any ways to deal with this problem?

When you calculate the PICs of a trait, you are making a statement about how that trait evolved. The purpose of PICs is to account for phylogenetic non-independence. However, when you are comparing two analogous traits, those two traits are in fact phylogenetically independent of each other; they do not share a common origin. Thus, I think it would be an error to perform PICs on analogous traits because those traits do not share an evolutionary origin.
How to deal with this problem would depend on the specific question you are asking. One thing to do would be to perform PICs on each trait independently on just the portion of the tree that that trait occurs so you are not comparing analogous traits.
You've probably already read this, but I recommend that anyone who hasn't check out Felsenstein's 1985 paper describing the PIC method.

Thanks, that makes sense! I think your suggestion is similar to one of the ideas I had: Essentially, I could build groups within which the trait in question is homologous, and connect all these groups to the tree root. As a consequence, the shared branch length between groups across which the trait is analogous would be zero, and thus the data would be treated as effectively independent in a PIC or phylogenetic least-squares, or am I missing something?

@David I'll admit that I'm not entirely sure about this, but I think you should not set the branch lengths between the groups to zero because that would imply that the groups are highly related. On the contrary, setting the branch lengths to be very large would imply that they are effectively unrelated. However, if it were me, I would perform separate analyses on each group and not try to get them to fit into a phylogenetic analysis together

Sorry for being not very clear: I was talking about the branch length shared between groups were the trait is non-homologous being equal to zero, so that there are effectively independent, or unrelated. Does this make more sense to you?


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DIY storing family DNAs' samples for future uses (eg medical)
I have a question I could not get an understandable reply from Google and I am no expert in the matter, so my plead to you is if you could give me practical and relatively easy to follow advice.
With the view of the breakthroughs in DNA research and all the anticipated applications to medicine in the near-future, I am willing to build a storage of the DNAs in my family (eg 20-30 people, some at a very old age). The use may not be for cloning :) but rather, for eg to map and trace specific hereditary genes when such services become more available to the wide public; and thus, probably help with a personalized medicine for someone, or find genome problems, and probably be able to 'turn them off' at some point.
Is there a way I can extract cells (ie from inside the cheek, or hairs), and store them for a few decades while preserving the DNA (eg put them in a freezer at -18C or in some solution)?
I have only common knowledge in this area so apologies if the examples are silly, but I assume you can understand my point.
I would be grateful if you provide practical instructions as: "you buy 500ml of the chemical xx"; or "mix 150ml of xx and 200ml of zz", so me and anyone who finds the idea appealing, can follow.
Ps-the lower the costs of the procedures, the better (I found some personal "dna vaults" costing several '000$).
Thank you for your consideration!

If you have access to a laboratory (or at the very least a centrifuge and pipettes) and some laboratory experience you can extract the DNA from the cells which would be much easier to store. There are a number of commercial DNA extraction kits available that are easy to find on google and order online. I don't want to promote any particular brand but I've mostly used DNEasy made by Qiagen (really just because that's what I'm used to). All the step-by-step instructions are in the kit and all the reagents are also in the kit with the exception of 100% ethanol which should be easy to obtain.
If you have significant molecular biology experience and access to a full lab with a fumehood and appropriate safety installations you can try a manual extraction using trizol or phenol-chloroform. This would be slightly cheaper however given the toxicity of these agents I wouldn't recommend this for you. It really doesn't sound like you have these resources available to you.
Once you have the DNA extracted you can dilute it in Tris-EDTA or the elution buffer that comes in the kit. You can store extracted DNA in a regular fridge (4C) for several years. If you're looking to store for decades you may want to rent space in a -80C freezer but this would be more expensive. A fridge may be just right to suit your needs. You should be careful that this fridge has a backup power supply.
I should be clear that although extracting DNA is the easiest way to do this for somebody with experience, you should not try if you don't know what you're doing. Some of these reagents are dangerous and you are likely to ruin the samples you've taken from your family members and end up with no DNA at all. Good luck!

You could store DNA diluted in water at -20C for a very long time. The only problem with at home storage would be the type of freezer most households have. These come standard with defrosting feature, which thaws up the freezer to remove the ice accumulation... This would affect the stability of the DNA at long term scale. Having a styrofoam box to protect the samples could however dampen the elevation of temperature around your DNA.
As for the DIY extraction, most extraction methods use either chloroform or chaotropic salts... those are very toxic and dangerous. A "dirty" extraction would be the best approach. You would still need a centrifuge, NaOH, EDTA, and Tris Base for a very simple approach (1). The referenced protocol is prescribed for rodent tissue, but could be applied to small skin snips or buccal frottis (not that I recommend ripping skin from your relatives...).
For the various reagents, Sigma-Aldrich sells pure chemicals, but I have no idea if particulars can buy on their website.
(1) http://jaxmice.jax.org/support/genotyping/dna-isolation-protocols.html

At page 12 of this pdf there is an easy protocol for DNA extraction from saliva. You just need soap and salt to do it (it works even without Chelex, but you get better DNA quality if you use it). A microcentrifuge is requested for this protocol, you can find them on eBay for less than 100 dollars. If the max speed is not high enough you can always spin for a longer time at lower speed. I tried it and it works.
Once you have the DNA, you can store it in a normal freezer (-20) for decades, just avoid to defrost it a refreeze it multiple time or it will deteriorate.

So cryopreservation would be the long-term mode of storage, and you'd do something like store your sample in a cryonic freezer supplied w/ liquid nitrogen at -196C. Cellgro provides some recommendations for cryopreservation here. Keep in mind, cryonic freezers are typically pricey, but broady, the idea is you need to keep your cells at the right temperature, in the right media. The source I gave you provides suggestions for media, DMSO as a cryoprotectant, and a protein source to protect the cells during the process. Also, keep in mind there are recovery issues with cryopreservation. There's some data to suggest reactive oxygen species, and apoptosis mechanisms damage/fragment the DNA in cells that have undergone that sort of freezing(1, 2, 3). These articles mainly refer to sperm storage.

I don't think OP is asking about storing live cells, but rather DNA. You certainly don't need liquid nitrogen for that, once you've purified it.

Thank you for the idea, surely it is an option one can choose. I assume the costs would be for a space in such a freezer, shippings and to hire some pro. to do the procedures you bookmarked. As MattDMo added, cryopreservation seems to be a way used mostly to preserve cells alive (we did that with our child's embryo-cord, as many parents do). I have a feeling there are even some simpler ways to preserve ONLY dna which can be analyzed after a while; I think of biologists being able to evaluate dna extracted from the remains of species long been extinct, or early humans.

Basically agree with the other answers, but a bit of clarification. The bottom line here is that DNA is actually a really stable molecule - after all, it's evolved to be! So assuming your principal goal is 'keep enough DNA that you can read genomes and/or epigenomes'*, the main requirements for storage are low and steady temperatures. For instance ancient DNA studies regularly collect partial DNA, and even whole genomes, from organisms including humans that are thousands of years old. The key here is temperature stability.
So with that in mind:
1) I'd keep two samples, a DNA extraction** and some whole tissue. This might mean cheek swab, some blood, something like that. There's lots of material out there. Teeth are pretty good, if any of those come your way!
2) 'Cryo' stuff (at least in the UK) would be taken to mean 'very cold, something to do with cryonics, and generally aimed at preserving whole life etc'. This is way out of scope for the OP even if you agree the (contentious) claims those practitioners make.
3) Can't emphasise enough that domestic freezers won't cut it. In general you can DIYbio / hack lots of lab kit that's overpriced (water baths, gels, even PCR machines can be bodged to a degree) but as mentioned above, domestic kit will defrost periodically (even assuming you have a UPS to guard against power outages) and those temperature fluctuations will shred your DNA.
4) One final thought, bearing in mind 100yr-old DNA at -4 is probably going to be in better shape than 20yr-old DNA at -80 with periodic warming: You don't, by any chance, happen to live near any glaciers, do you? Because if so you might as well make a bio-time capsule: the ultimate backup! ;)
Either way - good luck.

*Mind you, the simplest thing to do is sequence your relatives' genomes now? Or are you waiting for costs to fall?
**The reason to keep a whole tissue sample as well as extracted DNA is this: While extracted DNA is likely to be more stable over very long periods of time, current DNA extractions have been optimised to work well with current DNA sequencing techniques but may inhibit future ones. For example, some of the well-established Tris-EDTA step https://biology.stackexchange.com/users/15594/jack mentions are contraindicated for Oxford Nanopore (MinION/PromethION) sequencing preps IIRC.


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Is it necessary for spiders to both wrap the prey in silk, and inject them with venom?
I stumbled upon the following paragraph on the Wiki page about Argiope bruennichi:

When a prey item is first caught in the web, Argiope bruennichi will
  quickly immobilise its prey by wrapping it in silk. The prey is then
  bitten and then injected with a paralysing venom and a
  protein-dissolving enzyme.

On hindsight, it seems a bit redundant to do both those things. If prey is caught in the web, which is rather sticky and therefore restricts its movement, isn't it possible for the spider to go right ahead and inject venom?
Or on the other hand, if it wraps and immobilises the prey in silk, wouldn't it be more logical to then leave it to die, from some sort of evolutionary standpoint of wanting to saving energy and resources?

Nice question!
Based on some previous observations on other web spiders, I belive that these "redundant" behaviors are selected to avoid prey scapes, and are not trully redundant if we remenber that some preys are able to evade even if wraped. Some beetles can find a way out from the web, moving their strong legs with projections, eventually some silk lines are cut. Also beetles are more protected against bites then are other bugs, since many are under their natural armor.
Other possible explanation** :some bees, ants and wasps produces chemical signals when in trouble, attracting their sisters. From the spider point of view, this could be a way to get more food. But too many of these insects could possibly destroy the web, only because their are numerous. Obviously these are speculations.
Also, some wasps prey on web spiders. If the wasp eventually touches the web and entangles itself, now the wrap/bite strategy turns in defensive way, maybe with the "danger turns dinner" bonus.
 I did not search too much, but probably someone has alread tested some of these possibilities. Also, I read once that some spiders can treat distinct preys in distinct ways, even releasing some undesirable bugs from the web.
** This bee-wasp-ants-hypothesis is not based on observation, only on knowlodge about insects and spiders.