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How may the age of a child be estimated when required to do so, in video-graphic evidence?
How may it be possible to roughly conclude that a subject in a select piece of video-graphic evidence presented, is in fact a child, i.e. without the subject being, physically examined?
Is it possible that biological/developmental/theoretical evidence can be salvaged from the superficial appearance of the child in a video, to estimate age? Providing that the source is of High quality.
My reasoning as to why I query this, is due to there being few superficial-biological-visual-markers, that can be used as solid evidence to come to a conclusion in situations where this might be necessary (for example, in law enforcement cases that relate to the aforementioned). Particularly so, as the rate of maturity, in terms of physical appearance is not constant. For example, it's not improbable that a 25 year-old woman may be mistaken for a 16 year-old girl, due to specific physical characteristics.

In short, without direct physical evidence (forensic or medical examination), testimony, or documentation to act as proof, you are left up to the discretion of the court to determine whether evidence is admissible and up to a jury to decide if it is reasonable to presume that a person depicted is of a certain age if no other evidence to the contrary is provided. This is beyond the objective nature of science.
Please be aware, that as you are making this question specifically about criminal evidence, I am addressing that aspect of your question. There are ways of dealing with and presenting evidence that may preclude the need for any scientific proof of age, as it is up to the determination of reasonableness by the jury that is the overriding factor. If the jury does not reasonably feel that the person depicted is a minor as may be the case if the actual identity of the victim cannot be established, or if the accused could not have reasonably known that the person was a minor, unable of providing legal consent, then they can vote to acquit the accused.
Video’s Role in the Criminal Justice Process: DRC to ICC

Since documentary and forensic evidence could not prove age, the Prosecutor relied, in part, on a series of video clips showing: i) Lubanga at the military training camps speaking to children; and ii) children serving as his bodyguards. A sample of the footage from the opening argument can be watched here and below.

You will also see if you follow this link that the normal clinical determinant of age, examination of growth plates is not relevant as that data was generated on American and European populations and is likely different for African children, as their access to nutrition and the childhood illnesses that they face likely have much more to do with the changes in bone plates that can be used to determine age forensically.
While this example is related to an international court of law hearing a war crimes tribunal, the charge given to most juries would be that they are the judges of the facts and if a reasonable person would arrive at a certain conclusion.
From the Connecticut Supreme Court Jury Instructions. Most US States will have similar statutes and guidelines.
1.2-6 Evidence

You will decide what the facts are from the evidence that will be presented in this courtroom. That evidence will consist of the testimony of witnesses, documents and other material admitted into evidence as exhibits, and any facts on which the lawyers agree or that I may instruct you to accept.
The following are not evidence and you must not consider them as evidence in deciding the facts of this case:
statements and arguments by the attorneys,
  questions and objections of the attorneys, and
  testimony that I instruct you to disregard.
  There are two kinds of evidence: direct and circumstantial. Direct evidence is testimony by a witness about what that witness personally saw or heard or did. Circumstantial evidence is indirect evidence; that is, it is evidence from which you can infer another fact. As an example: if you wake up in the morning and see that the sidewalk is wet, you may infer that it rained during the night. The wet sidewalk is circumstantial evidence that it rained. Other evidence, however, may provide another explanation for the water on the sidewalk, such as a garden hose that was left on overnight. Therefore, before you decide that a fact has been proved by circumstantial evidence, you must consider all the evidence in the light of reason, experience and common sense.
In deciding this case, you may consider both direct and circumstantial evidence. The law permits you to give equal weight to both, but it is for you to decide how much weight to give to any evidence.
Some evidence may be admitted for a limited purpose only. When I instruct you that a piece of evidence has been admitted for a limited purpose, you must consider it only for that purpose and for no other.

2.2-3  Reasonable Doubt

The meaning of reasonable doubt can be arrived at by emphasizing the word reasonable.  It is not a surmise, a guess or mere conjecture.1  It is not a doubt raised by anyone simply for the sake of raising a doubt.  It is such a doubt as, in serious affairs that concern you, you would heed; that is, such a doubt as would cause reasonable men and women to hesitate to act upon it in matters of importance.2  It is not hesitation springing from any feelings of pity or sympathy for the accused or any other person who might be affected by your decision.  It is, in other words, a real doubt, an honest doubt, a doubt that has its foundation in the evidence or lack of evidence.3  It is doubt that is honestly entertained and is reasonable in light of the evidence after a fair comparison and careful examination of the entire evidence.4

EDIT: Due to a moderator edit of the question, the following section is no longer valid to the question and has been stricken
As you can see from this statute 7.4-3  Obscenity as to Minors -- § 53a-196 it is up to the discretion of the jury to determine whether or not the person depicted in the video was a minor and that the person accused of the crime knew that the person was a minor.

Conclusion
In summary, the state must prove beyond a reasonable doubt that 1) the (material / performance) was obscene as to minors, 2) the defendant promoted the (materials / performance) to another person, knowing of its character and contents, and 3) knew that the other person was a minor.
If you unanimously find that the state has proved beyond a reasonable doubt each of the elements of the crime of obscenity as to minors, then you shall find the defendant guilty.  On the other hand, if you unanimously find that the state has failed to prove beyond a reasonable doubt any of the elements, you shall then find the defendant not guilty.

As a result, even if the prosecutor can prove that the person depicted is a minor, it may still rely on whether or not the state can prove that the accused knew the age of the person they are accused of exploiting.
Part 7 subsection 7 is related to how the State of Connecticut instructs juries related to Child Pornography
So, from a legal perspective, it is highly subjective, and even from a clinical perspective, it is likely that there are different metrics related to different populations and how children's developmental conditions affects their bone structure, onset of puberty, and display of secondary sexual characteristics.

+1 Good answer! You added more than I sought for in terms of Law, it lacked Biological context though (which is understandable as it was a very specific theory question). It would be nice if you could possibly add a bit more towards the biological aspects of the question. Anyhow, you managed to get more up-votes than i did on the actual question haha. Chopped logic. Thank you!

One thing missing here: In some jurisdictions, child porn is more defined by how the actor/actress looks than what their actual age is. In these cases, science is pretty much irrelevant to the courts.


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Hydrophobic proteins in the body?
I know that we can get hydrophobic amino acids, but are there any proteins in the body whose surface is hydrophobic? If so what is their typical function and where can they typically be found and if not why not?

Are there any proteins in the body whose surface is hydrophobic?

Sure. Although you are right in thinking that most proteins have hydrophilic surfaces, some are very hydrophobic. My favorite example is Elastin, it is the main component of the skin which grants it elasticity. In fact, the hydrophobic nature of elastin is what confers it its function. The idea, briefly said, is that a insoluble/hydrophobic structure will tend to minimize it's surface area with water, so if you stretch such a substance (i.e. increase the surface area), it will pull back to the minimum surface area state.
Reference: Li, Daggett. Molecular basis for the extensibility of elastin. Journal of Muscle Research & Cell Motility (2002).

Also many membrane proteins, as being hydrophobic is what allows them to sit in the membrane.

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Chronic-stress of predation risk in vertebrate prey
Prey must be vigilant when their predators are around.
Predators may affect mortality (and morbidity, i.e. loss of quality of life) through these mechanisms:

Direct attacks, including injuries sustained if the prey manages to escape.

Changes in the prey's foraging/hunting behavior which may restrict access to high-quality food sources.

A chronic stress response, which in humans has been documented to increase mortality.

Have the health effects of chronic stress in wild prey populations been documented? Can the strength of effect (3) be comparable to (1) or (2)?

How would one do that, given that: the animals are wild, thus not under our supervision; our supervision (including observation, and capturing for bloodwork) would be stressful in itself; which animals are more stressed and which are less stressed? How to prove correlation/causation? There are some experiments or studies one can do with wild animals. This doesn't seem to be one of them. However, is there a reason to think, knowing this happens from humans and animal studies, to think it doesn't in wild animals?

@anongoodnurse: The best way, besides some sort of implanted real-time monitoring system, is to use "sluggish" biochemical markers (similar to how A1C is a three-month moving average of sugar levels). Most likely such a study would "piggyback" on other studies which need to take samples.
One hypothesis is that novel predatory risks cause more chronic stress than the predators a prey is "used to". Similar to humans not being adapted to the different type of stress we face in modern society. Selection pressure hasn't had the time to weed out the harmful long-term stress effects on the body.

Do you know of any such markers? how would one know what caused the stress? Your desired info is very specific.

Not specific to this, but somewhat similar studies of baboons by Sapolsky did look at chronic stress (related to social status).

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Human defenses to toxoplasmosis
Toxoplasmosis modifies the rat's brain to make them love (and be eaten by) cats. It also infects ~30% of humans, and modifies traits in several bad ways (i.e. schizophrenia and increased reaction time). However, humans are thought to be a "dead end" for the parasite. Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance. If so, why are so many people infected?

Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance.

Well, I think in this case "Significant" isn't qualified. Significant selective pressure can come in many forms, but as you mention about 30% of humans are infected with Toxopolasma, and the vast majority remain capable and functional. Remember that selective pressure applies to the ability to take advantage of resources and reproduce. People with toxoplasmosis are almost always capable of surviving and reproducing, so I doubt the pressure is all that much.
There is also significant incentive for Toxoplasma to develop the ability to adapt to humans, as it would open up a whole new resource for them to take advantage of. How fast the parasite is capable of adapting, or even if it's possible to eventually include humans in their life cycle, is something that would take some studying.
Our immune systems, in turn, try to kill the parasite regardless of whether we're being taken advantage of or not. You might be interested in reading up on the Red Queen Hypothesis - a theory that delineates how the immune system is at constant war with its environment and potential new threats.
As for your last question...

... why are so many people infected?

That's easy. :-)
Cats have become a popular pet, and most of the time the parasite doesn't significantly affect us. If either of those changes, you'll see a change in infection rates.

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Hive building animals
Many species of animals build nests to live in. However, a beehive is a structure built by Homo sapians that houses Apis mellifera (or a related bee species). Are there other species of animals that build hives, i.e. that build structures designed to house a species different than their own.

Not specifically to nest other species, but I know there are ant species who colonies the nests of other species of ants e.g. Dino ants in Brazil.

Probably not in the spirit of the question, but there are species of ants that farm fungi.

What you're referring to is called metabiosis:

a mode of living in which one organism is dependent on another for
preparation of an environment in which it can live.

Examples:
The Goby and the Pistol shrimp. youtube video
The video shows these housemates cooperating, the goby, with its capable vision keeping watch, the shrimp, pushing sand and detritus from the shared burrow. This extends to keeping watch whilst the goby feeds - waggling and snapping it's claws as a warning if a potential predator shows, the goby bringing back food to the burrow, the shrimp eating the leftovers. In times of hardship the shrimp will eat the bodily waste of the fish.
Hermit crabs:
Their non-calcified abdomen makes their adoption of a marine snail-shell obligatory. As time goes by, with growth, they will seek-out a bigger or more suitable home, competing and combatting (rather carefully not to expose their vulnerable parts) until a compromise is found - usually on the terms set by the largest or fiercest crab present (youtube video BBC).
The dresser crab (decorator crab) (But this is stretching the definition a little):

newscientist.com 2015 Fair usage
These decapods show discretion, camouflaging their appearance with whatever is around, sea anemones, weed, a sea urchin as above or increasingly, human made detritus (youtube video). Using their spikey shell to immobilise their covering. Though in this case there is no strict dependance, the anemone is thought to benefit by food particles being stirred-up by the crab during feeding and passage.

The goby+shrimp is the best example. The snails unwittingly give their shells up to the hermit crabs when they die, so it is not an "intentional" act on the part of the snails.


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Multicellular organisms as DNA banks
Animal -> bacterial gene transfer seems easier than bacteria -> animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).
Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although "seeing" this would be difficult)? Is this effect "significant" for evolution in microbes?

This sea slug is one example of prokaryotic genes ending up in an animal. The slug ingests chloroplasts from algae and incorporates them into its own cytoplasm. It has also acquired, presumably through horizontal gene transfer, some or all of those genes necessary to maintain the chloroplast. While this is not a gene transfer from a free-living prokaryote, chloroplasts are essentially cyanobacteria.
For the paper (PDF), see here.
Also see a more general review here (free full text).

If we're allowing gene transfer from endosymbionts to their host, then human cells are an example. Almost all of the mitochondrial proteins are coded for in the nucleus.

This isn't your typical case though. Also see second review.

This paper seems relevant. I just found it and don't have access, so I haven't read it. It does seem to suggest that there is evidence for eukaryotic genes being taken up by a prokaryote.
I would imagine this is rare, though. Eukaryotic cells don't tend to just spew their genetic material everywhere. Most death pathways involve breaking down any genetic material in the cell, I believe.

But prokaryotic cells infect Eukaryotes and then can leave and go on. During the infection DNA can be transferred.

Maybe, but this is the only example I found searching the literature. If you find more evidence, feel free to link.


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Mammalian advantage at filling large-animal niches after the KT extinction?
Larger animals are more prone to extinction due in part to smaller numbers. The asteroid that impacted 65 million years ago killed off the larger mammals and dinosaurs but spared some of the smaller ones. The smaller niches were refilled by both mammals and Theropods (as birds), but there is a paucity of large bird species. Is there a reason mammals were better at refilling these large-animal niches?

Just a guess, but most birds fly.  Evolving a large size means they can no longer fly, so there's a complex evolutionary path, probably first becoming a small flightless bird (as e.g. the kiwi), then increasing in size.  Mammals just had to become bigger.

Also, there is an additional evolutionary barrier in that birds wings might need a lot of evolution to become limbs again - so the mammals have a head start on being quadrepeds.

@Polypipe Wrangler: Quadrupeds, yes, but we have a number of examples of large flightles birds that are bipedal, with vestigal wings - the ostrich, emu, rhea, and the extinct phorusrhacids (AKA "terror birds"): https://en.wikipedia.org/wiki/Phorusrhacidae

Birds have to feed and guard there eggs for 30-40 days, against the elements and against predators, whereas mammals can bear larger offspring in exposed environments. That's especially an advantage for swimming mammal megafauna, because the birds can't lay eggs in water, and also for predator-intensive environments and for forests.
Birds lack hands and teeth and four sets of claws for manipulating leaves and prey and defense. Birds can only have a hooked bill to peel up prey, and less sophisticated molars for herbivory. The sheer range of mammal teeth shapes appears to be an advantage compared to beaks.
Quadrupeds have some advantage for running and turning without falling over, whereas birds mostly have long necks which are a bit of an easy target for horns and claws and teeth.
It's interesting to think about a pack of wolves attacking an ostritch, and a pack of predator ostritches attacking a springbok... The wolves and the springbok have a wider range of attacks and defenses to use for survival.


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Animals with very high bite pressures
When media, such as this site wants to explain just how dangerous large animals are, they often quote bite-forces as pounds per square inch (psi).
However, it appears that they mixed up the units, as the numbers they give are the total force in pounds.
But what animals have the strongest bite force per unit area? There is no obvious scaling law here: scale up an animal 2 fold and the cross-sections of both the muscles and the teeth and jaws both quadruple. This puts tiny insect mandibles are on a level playing field with our largest beasts.
Instead, bite-pressure will be niche-dependent as well as the details of the animal's anatomy (such as mechanics of the jaws). It may be somewhat hard to define contact area given the complex shape of teeth and mouthparts in general; maybe one could measure the indented area in a tough material that the animal chomps down on.
Given that our strongest biomaterial found yet is microscopic teeth and that microscopic materials tend to be stronger than bulk materials, it seems likely to be a small animal. Is there any data to support this?

I think the correlation between strength of materials and highest bite pressure may be misguided. You don't need an even stronger exotic material or construction if maximum bite pressures can be supported by the more mundane materials and constructions that everything else with lower bite forces already uses. Kind of like assuming strength of materials in eating utencils correlates with the weight of  food being eaten...steel is already so strong food weight is not even part of the equation.

They are not confusing total force and PSI they are giving you the force per unit area. (although the megalodon is achieved with poor methods) A T-rex is putting 10,000 pounds of pressure on a square inch of tooth surface. Muscle strength is based on cross section, larger muscles have larger cross sections producing drastically more force.

@DKNguyen: Material strength is important well beyond maximum bite pressure. Accidental ingestion of rocks or bone, eccentric loading, fatigue, etc mean you want a high "safety margin". Human teeth do break after all.

@John: Don't larger mouths have larger teeth as well, so there is more tooth area to distribute the force on?

@KevinKostlan no more tooth area means a larger total force for the calculations given. Keep in mind we are given the PSI. If you were calculating from the total force then yes more area would mean less PSI. Teeth in general is a way to increase the PSI of a bite, pointed teeth spread force across a smaller area.


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Dragonfly Identification
I have been clearing brush by a lake in northwest Missouri and seen a lot of dragonflies. It's hard to get decent pictures because my phone camera sucks and they fly away before I get close. But here is one I managed to get:

I got one other picture of another species, but it's much lower quality.

The first one is a blue dasher (Pachydiplax longipennis).
Sorry, I couldn't identify the second one but it is more probably the same.

Did you want to edit this further? I was reluctant to accept it right away, but I think you're correct on the first one. The second one is probably too blurry to tell much.

@user137: Thanks. I completely forgot about this one. I still think they both are the same. source:  http://www.insectidentification.org/insect-description.asp?identification=Blue-Dasher

The overall body shape of the second dragonfly looks like a Libellula (Skimmer), due to its broad flat abdomen. It also seems to have distinct bands on all four wings, dark patches where the wings connect and a light blue abdomen, which would indicate e.g. a male Plathemis/Libellula lydia (Common whitetail). The picture is blurry though, and there might be other similar species that it can be mistaken for (the wiki page mentions a couple of similar species).

(picture from wikipedia)

It looks right to me. I probably should have split this into 2 questions so I could have two answers.

@user137 Well, its difficult to know in advance whether you've seen one or two species.


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Why would you mix polymerases in PCR?
I was reading a manual for kit that requires you to amplify DNA by PCR before analyzing it in the kit. The manual suggests mixing proofreading and non-proofreading polymerases:

For
  PCR
  products
  >2500
  bp
  in
  length,
  use
  a
  DNA
  polymerase
  blend
  containing
  Taq
  DNA
  polymerase
  supplemented
  with
  a
  proofreading
  DNA
  polymerase

How would this improve the amplification of long products? It suggests using only a proofreading polymerase for fragments below 2500 bases. Does the addition of a non-proofreading polymerase improve speed? I have TAQ and PFU Ultra, but both instructions say to use an extension time of 1 minute per kb.

The Taq polymerase is a rather fast enzyme (the synthesis rate is around 1 kb/min), but the backdraw is that it has no 3'- 5'exonuclease activity which would enable to proofread the newly synthesized DNA. This leads to the introduction of errors and the chance of getting these is higher the longer the DNA you want to synthesize is.
Polymerases which are able to proofread (which have the exonuclease activity) like Pfu have a much lower error rate, but are on the other hand also much slower, typically around 0,5 kb/min. Pfu is also more expensive than the Taq polymerase. See table 1 from reference 1 below:

To combine the advantages of both polymerases, you typically use a blend of Taq and Pfu. Then you get the high processivity of the Taq combined with the proofreading capacity of the Pfu and get good yields of DNA with a low amount of mutations. See also reference 2 for details on this system.
References:

Error Rate Comparison during Polymerase Chain Reaction by DNA
Polymerase
Effective amplification of long targets from cloned inserts and
human genomic DNA.

To add to the answer, the reason this works is because Taq will stall and fall off the DNA after a misincorporation. (Taq isn't particularly progressive.) If Taq just continued on after misincorporation, Pfu wouldn't have a chance to edit it. By falling off, Taq gives the slower Pfu time to bind to the DNA, edit out the misincorporation, and continue on. When there's no Pfu, Taq does eventually continue on past the misincorporation. But that process tends to be slower than that for Pfu binding and editing, so when Pfu is present the error correcting path is preferred.

So I've been having trouble with another project, which requires I use PCR to amplify a 4400 base gene, or an entire plasmid. I've been using PFU ultra alone, and the reaction takes 5 - 6 hours. How much Taq polymerase should I add to improve the reaction speed?


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Transfect Mammalian Cells with Single Stranded DNA?
Agrobacteria can deliver parts of their DNA to plant cells as T-DNA, transfer DNA. This DNA is delivered as a single strand and can be integrated into the plant genome or can be converted to a double stranded molecule by priming the T-DNA to make it a substrate for a DNA polymerase. This article describes the process, but Nature makes getting to the article hard, sorry.
What I'm interested in is delivery of DNA to mammalian cells. I tried to find articles that used single stranded DNA in mammalian cells, but couldn't find much. Maybe I didn't spend enough time searching. I saw some suggestions that single stranded DNA could trigger apoptosis, or that single stranded DNA could be used to manipulate DNA repair mechanisms to cause integration into the genome.
However, is there any way to deliver a single stranded DNA, and have it converted to a double stranded plasmid in situ? Would probably need an RNA or DNA primer, but I don't see why you couldn't pre-bind the primer and deliver the whole complex.

http://www.pnas.org/content/96/7/3729.full.pdf
Let me know if that's anything like you're looking for and I'll keep looking into it.

@Kendall Thanks for that paper. While it's interesting, it seems to focus on nuclear entry of single stranded DNA with agrobacteria proteins, and does not test if the delivered DNA can produce protein.

Not sure any of them are what you want, but have you gone through all the references from https://en.wikipedia.org/wiki/Transfection#Methods ? :-)


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Origin of the 260/280 ratio?
This is not a duplicate of all the other 260/280 ratio questions, I already know that DNA is supposed to be 1.8 and RNA is supposed to be 2.0. However, this might be more appropriate for chemistry, and will move it if I have to.
My question has to do with the Poly A tails on mRNA. I've been doing in vitro transcription and tailing for a while now and have noticed that the untailed RNA has a 260/280 of about 2.0, like you'd expect, but successful tailing results in ratios from 2.15 to 2.45, with higher ratios correlating to better band shifts on agarose gels, implying a longer tail. I suspect the reason for this is because the adenine has a much higher 260/280 than the other bases, so if you add a lot of adenines to the 3' end of the RNA you add much more 260 absorbance than 280 absorbance.
After seeing this I tried to come up with a mathematical method to estimate tail length based on 260/280, since gels are annoying, while I can get the ratio directly from the nanodrop.
I started by using the 260/280 for each nucleotide, A: 4.50, G: 1.15, C: 1.51, U: 4.00, T: 1.47 source here: 1. I then took the sequence for the Luciferase gene I'm using for mRNA and counted the nucleotides, 449 A, 566 C, 470 G, 374 U. I tried to get the weighted average of the 260/280 for my RNA.
A: 449 x 4.50 = 2020.50
C: 566 x 1.51 =  854.60
G: 470 x 1.15 =  540.50
U: 374 x 4.00 = 1496.00
Sum:            4911.60

Nucleotides: 449 + 566 + 470 + 374 = 1859
Sum / Nucleotides : 4911.60 / 1859 = 2.64

2.64 is clearly not 2.0. Even accounting for the potential effect of pH and ionic strength on RNA 260/280 ( acidic solutions have lower ratios ) I can't explain why the calculated ratio is so high. Even if we assumed an RNA with 25% of each base, the weighted average is still (1.15 + 4.50 + 1.51 + 4.00)/4 = 2.79, even higher than for my real sequence.
Doing the same calculation for DNA, (1.15 + 4.50 + 1.51 + 1.47)/4 = 2.16.
So why don't my calculated ratios for RNA and DNA 260/280 match the "ideal" ratios of 2.0 and 1.8?

I bet it has something to do with base stacking interactions.

Here's one explanation: It's not the base composition that determines UV absorbance (260 nm), but whether the nucleic acid is in a single- or double stranded state.
Promega cites Griffiths biochemical methods that claims that double-stranded DNA absorbs UV less strongly than denatured DNA due to the stacking interactions between the bases.
I think your calculations must be wrong, since you can not expect a polymer to have the same spectrometric behaviour as the sum of all monomers. The absorbance of a molecule depends on its surroundings (like solvent, or nearby chemical groups). Bases within a DNA strand have much less contact to the solvent (H2O) when compared to a single nucleotide. In general, bases in ssRNA (single stranded RNA) and dsDNA interact with each other via aromatic pi-stacking. This affects the energies of the electrons that are responsible for light absorbance.
Most importantly, each base inside a dsDNA strand is engaged with a hydrogen bond from the other strand, which (I presume) significantly shifts electron energies and hence also its absorbance behavior. This might also be the reason why low pH decreases UV absorption of RNA (260 nm), since hydrogen acceptors are protonated just like in the double stranded state.

Seems reasonable in general, but polyA would surely be single-stranded and, hence, unstacked, which would give a higher value than obtained. I just wonder how one gets enough mRNA to do an accurate 260/280.

Pi stacking happens in any single stranded nucleic acid. I presume that user137 somehow accumulated luciferase mRNA using e.g. in vitro transcription.


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Why don't phagocytes eliminate mutualistic foreign organisms residing in our body?
Many organisms residing in our body and have a symbiotic mutualistic relationship with our body e.g. organisms in our small intestines. How come our body does not activate an immune response against them? Is it that the organisms have self antigens, or do the immune cells have no antibodies for these organisms? Also, how come our immune system is able to respond to these same organisms if they cause an infection in our body? E.g. Entamoeba histolytica causing amoebic dysentery.

Molecular context is important here. E.coli in your colon is OK with the body, it is taken up by phagocytes as part of normal "surveillance". Your immune system will learn and gain "tolerence" to these mutualistic bacteria as long as they are in the correct environment.
If that same E.coli is a pathogenic strain or finds a way into the blood stream (sepsis), your body will recognize that it does not belong and mount a immune response. There are different classes of antibodies with different properties including where they are predominantly found. For instance IgE is found in mucosa but not in serum.
On top of that there are the 'Danger/Pathogen associated molecular patterns' (DAMPs or PAMPs). Cells can 'sense' general molecular patterns such as LPS, unmethylated CpG DNA, double stranded RNA through a class of molecules called Toll-like receptors (TLRs). Different TLRs are found in different cells or cell surfaces and they are the 'first line' response against inappropriate bacteria or viruses.
Once the TLRs are activated the cells will produce 'Danger Signals' called cytokines which initiates an immune response. In the absence of 'Danger Signals' present in the microenvironment, our immune system won't really begin mounting an immune response but just 'surveys'.
In this 'danger' context, you get robust phagocytic response.
If you'd like to learn more about this Mucosal Immunology is what the topic is called. All in all, the vast majority of our immune system is mucosal, it's just less studied relative to humoral immunity since it's harder to study.

So does this mean that there are certain LPS along with double stranded RNA and unmethylated CpG DNA that are displayed by bacteria (or other flora in the body) when they become pathogenic? These molecules are recognised by immune cells which results in an immune response. Is this what you mean to say?

@Tamur No, these are very broad molecular patterns, almost all bacteria will have them as normal molecules, so both pathogenic and non-pathogenic. What they do do is detect when bacteria is in an inappropriate place in the body, like the blood, muscle tissues, lymphatic system etc... TLRs are expressed in many cells, the most important being epithelial (skin) cells. So the skin is an immune organ. TLRs are not restricted to blood immune cells.


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Do self-exciting neurons exist?
I have two questions concerning self-exciting neurons in the brain.

Have directly self-exciting neurons been oberved, i.e. neurons with an axon terminal building a synapse with one of its own dendrites.
Does self-excitation work?

I guess that self-excitation can only work when the following time constants fit to each other:

refactory period of the neuron's membrane voltage (approx 1 milliseconds)
run time of the signal along the axon
refactory period of the synapse (approx 5-6 milliseconds)

I tried to estimate a typical run time by taking a not untypical axon length of 1cm = 0.01m and dividing it by a typical nerve propagation speed of 10 m/sec, getting 0.001 sec = 1 millisecond. Direct self-excitation would not work because the synapse would not be ready when the self-exciting signal arrives.
The other way around: Only when the run time is longer than the two refactory periods direct self-excitation might work.
Once again: Are there known examples of direct self-excitation in the human brain or nervous system?

Short Answer
Yes, autapses exist, though the role of excitatory autapses in particular is unclear.
Long Answer
A lot of your assumptions are wrong for biological neurons (I'm suspecting you have a background in artificial neural networks but that might be inaccurate). These don't directly impact your question of whether these connections exist, but I think they are important for understanding how they could function, which is just as important if not more so.

The 'refractory period' refers to a period in which a cell cannot or is less likely to fire an action potential. Cells can receive inputs freely during their refractory period.
Neurons are not single compartments. Action potentials are generated near the soma, and although they can propagate into the dendrites, synapses out on the dendrites can be fairly electrically isolated from the soma, and synaptic potentials in dendrites can take some time, easily a ms or two, to affect the soma, and they also last for several ms. They can also affect the potency of other nearby synapses.
Although axons can be cms or more in length, dendrites are rarely found and further than 1 mm from a soma in the CNS (there can be exceptions, of course; I am mostly thinking of neocortex), and most dendrites are within 100-200 um from the soma. So travel distances are much shorter than your estimate. However, synaptic transmission itself is somewhat slow, so you can add another .5 ms, and your estimate for speed is quite fast for the brain; the link you gave applies to peripheral fibers and spinal cord to brain transmission only (note they are talking about "nerves"), so your overall estimate of 1 ms from spike to autapse turns out to be reasonable, but for different reasons.
It isn't meaningful to talk about refractory periods for most synapses. Synapses can display short-term depression and/or facilitation but that isn't the same as a refractory period. Only at particular synapses containing a single release site does it make any sense to talk about refractory periods.
Cells are not activated by an individual synapse, with a few exceptions in very specialized brain areas. So just because a cell has been made to fire tells you nothing about whether a particular synapse was activated. In fact, unless that cell has fired previously very recently, you can be confident that an autapse would not have contributed to that particular firing event.

Evidence for excitatory autapses
You specifically asked about self-excitation, but it's important to know that inhibitory self-synapses also exist, and they are much more common between GABAergic inhibitory cells than between excitatory cells (Bekkers, 1998). Inhibitory autapses make a lot of functional sense because they serve as direct negative feedback.
However, excitatory autapses do exist and they may have function significance(Bekkers, 2009), rather than just being rare "accidents" that do little. In Aplysia, for example, there are autapses that cause an excitatory plateau potential during feeding behavior, maintaining activity for a long duration (Saada et al., 2009).
In mammalian neocortex, excitatory autapses have been observed but their function is unclear. Their properties can be a bit different from other synapses (Liu et al., 2013). Spike-timing dependent plasticity would suggest that autapses should shrink and go away, but they don't, which suggests they might have some functional utility, though it isn't understood yet. There are many computational attempts to find some function, which I won't list here but you can easily find by searching a reference like Google Scholar for recent articles about "autapses."
Experimentally, the role of autapses in vivo is difficult to study because there is no specific way to selectively suppress autapses outside of a computational environment, or a reduced prep where individual cells can be activated without activity in the rest of the network.

References
Bekkers, J. M. (1998). Neurophysiology: Are autapses prodigal synapses?. Current biology, 8(2), R52-R55.
Bekkers, J. M. (2009). Synaptic transmission: excitatory autapses find a function?. Current Biology, 19(7), R296-R298.
Saada, R., Miller, N., Hurwitz, I., & Susswein, A. J. (2009). Autaptic excitation elicits persistent activity and a plateau potential in a neuron of known behavioral function. Current Biology, 19(6), 479-484.
Liu, H., Chapman, E. R., & Dean, C. (2013). “Self” versus “non-self” connectivity dictates properties of synaptic transmission and plasticity. PloS one, 8(4), e62414.

Thank you so much, Bryan! But how would you call the period of time that a synapse needs to "reset", e.g. absorbing and/or reproducing the transmitter molecules?

@HansStricker That period of time doesn't exist in a meaningful way, nothing is waiting for that to happen. You can ask another question on that if you'd like (it's a good question) and I'll happily answer, only reason I'm demurring is it's frowned upon to ask/answer new questions in comments because they won't be indexed in any way.

My assumption on refraction times of synapses was from here: http://www.snl.salk.edu/~zador/PDF/1309.pdf:
"[...]  the synaptic refractory period - a brief 5–6 ms period [...] during which the synapse is incapable of transmission [...]"

@HansStricker Can you give a full citation and quote from one of those references? I very briefly looked at three of the papers I think you are referencing and they don't have anything to do with a synaptic refractory period. Again, this all would be better in a new question rather than a conversation in the comments.

Got it, thank you, that's better. They are talking here about very specific low-vesicle-count synapses that contain essentially a single release site. It has nothing to do with the time to clear neurotransmitter out of the cleft or refill vesicles, but just because it takes some time for a new vesicle to get into place at the synapse. I wouldn't generalize that to all synapses. I'll edit my answer to allow some nuance.

It's also important to recognize that connections between two cells rarely involve a single synapse; for a given axon contacting a given cell's dendrites, any one action potential might only cause release at 10-20% of the possible release sites. All of the others remain potentially able to release at the next action potential with no delay; in fact, the probability can be increased due to short-term facilitation.

I agree that this topic is worth an own question. May I contact you before I post it? This is my email adress: stricker@syspedia.de

Let us continue this discussion in chat.

"100-200 um" do you mean micrometer?

@Mockingbird Yes. um is a fairly common shorthand for micron/micrometer in informal contexts due to the similarity of "u" and the appearance of the Greek letter "mu" which is the more formal shorthand.

'plateau potential'?  Do you mean some potential remaining constant over time?

@Mockingbird Yeah, essentially a potential that keeps the cell more depolarized than it would be at rest, but relatively constant (not perfectly constant). It is a common phenomenon in motor systems, for example see wikipedia here: https://en.wikipedia.org/wiki/Plateau_potentials

Also see https://scholar.google.com/scholar?hl=en&q=plateau+potential

Self excitation can also be realized via leaky ion channels causing a constant rate of depolarization. This is for example the case for the generation of the heart beat by pacemaker cells
If you are more broadly interested in examples of self-generated activity, you might also want to look at circadian clocks, which are essentially biochemical oscillators that ultimately modulate firing rates of neurons.

Aside from autapses and pacemaking cells, there are also some kinds of sensory neurons that exhibit a spontaneous resting (constantly depolarizing) activity that helps with encoding stimuli. The benefit of having constant activity is that stimuli can further excite or inhibit this activity, and this can be valuable information.
Sensory neurons such as olfactory receptor neurons - whose function is to detect and relay information about airborne chemicals - also exhibit spontaneous activity. The exact rate probably depends on the olfactory receptors found on the dendritic region of the neurons, which are, as mentioned, leaky. Many other sensory neurons share this property with olfactory sensory neurons.
Example reading on olfactory receptor neurons.


text:
The almost extinct dinosaurs
Dinosaurs split into "lizard-hipped" and "bird-hipped" dinosaurs. Of these two groups, only the "lizard-hipped" (Saurischia) survived (these names are backwards).
Of Saurischia, only Theropoda survived. The diverse Sauropodomorpha clade died out fully.
Of Theropoda, only Tetanurae survived.
Of Tetanurae only Coelurosauria survived. And so on. By the time we got to Aves (birds) we are (according to wikipedia) 46 levels deep (if I counted correctly) with most levels unnamed. Aves is defined as the smallest clade that includes all living birds. In addition, we can go several levels outward to Avemetatarsalia and still have birds the only living group thereof (why we don't consider everything in Avemetatarsalia a "dinosaur" is unclear to me).
In contrast, the evolution of mammals does not follow such extreme pruning, starting from Synapsida (the sister clade to Reptila), there are 17 steps to take us to Mammalia according to wikipedia. Of course, there are probably many more branches along the lineage of birds and mammals than is known form the fossil record, but a 2.5:1 ratio in known branches is still intriguing.

Is it true that the tree leading to birds had more "pruning" extinctions than most other clades such as mammals?
If so, why would this be?

Note that "steps" or "levels" in the phylogeny have no biological reality. They will vary depending on the level of details humans get access to and care to describe. Comparing the shapes of different branches of the tree of life is a legitimate question, but relying on such steps or levels might be a problem. That said, I don't have a better proposal.

@bli: That is what my first question gets at, is the difference in depth "real" or just because humans happen to have more details about the evolution of birds than of mammals?

keep in mind dinosaurs were successful for a LOT longer than mammals so it is not surprising there was a lot more diversification. T-rex is closer to the present day than it is to the first dinosaur by a large margin. we also have a LOT more dinosaur fossils than early mammals. also think about how severe the KT extinction was, 75% of all species, that alone is responsible for most of the pruning.


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When DNA is at its uncondensed form, what can it do?
I think it can do two things:

The cell may be duplicating the genome during S phase.
The cell may be transcribing the DNA into mRNA.

Question: Can the two activities occur at the same time or one at a time? In other words, are cells efficient multi-taskers?

At least in bacteria they can. In optimal conditions, E. coli divides itself about once every 20-30 minutes. Wich is more important, the replication time of its genome is about 40-50 minutes. That means that, in exponential phase, E. coli has at least two active replication bubbles. Since the density of ribosomes must be more or less constant, aswell that the new cells needs to synthetise peptidoglycan and other cell components, that means that replication and transcription occurs simultanously. If not, ribosomes, enzimes, tRNAs and mRNAs would be diluded in every replication event.
In eukarya I see no reason of why that shouldn't be possible. The formation of chromatin is not a random event and some specific proteins are required during short periods of time during some steps of mitosis, so it's logic to assume that some specific parts are not compacted or that transcriptional activity can occur even in chromatin.
The specific region that is duplicating itself in a given time will probably be unable to transcribe, because the polymerase complex is pretty big and they need to open the double helix, and that. But this is somehow like children playing in the train tracks. Once the train aproaches, the children stay apart, and they continue again when the train has gone.


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Why don't neurons die during a stent procedure in the brain?
Stents are used to provide scaffolding to the blood vessels. When they are used in arteries or arterioles in brain, won't neurons die because of lack of oxygen during procedure?

I am assuming you are asking because of occlusion during balloon angioplasty. If not, please clarify.
Ischemic stroke occurs when a blood vessel to the brain is occuluded by a clot or some other emboli or poor perfusion due to atherosclerosis (a type of narrowing of the vascular lumen). Given enough time, ischemia can produce tissue death, called infarction. It is possible to suffer an ischemic stroke (or ischemia to any tissue) without substantial infarction if reperfusion occurs quickly enough.
Time to tissue death
For stroke, the catchphrase "time is brain" is often used to indicate the importance of occulsion time in stroke. Cell death is not instant upon loss of oxygen, but rather occurs throughout any extended reduction in blood flow as well as during reperfusion.
The brain is more sensitive to ischemia than other tissues like the heart, but there is still a window in which little to no damage is done. By 5 minutes, however, neuron death can begin.
Balloon Angioplasty
When using balloon angioplasty (including during balloon delivery of stents), a single vessel is occluded for ~30-180 seconds. It is also possible for multiple individual inflations. Importantly, this time range is normally kept less than the ~5 minute range for damage to occur.
Embolic protection
One of the dangers during balloon angioplasty is the release of particles from the vascular wall that is being opened up. Those particles can cause distal embolisms. In other organs like the heart, this problem is fairly minor, because only small amounts of myocardial tissue are expected to be impacted which will not have a major impact on heart function. However, loss of small regions of brain could have significant impacts on patient recovery. Therefore, embolic protection strategies are sometimes employed which include devices to block distal flow or capture emboli. The use of these devices is very case-dependent, because if there is already a significant blockage it may not be possible to use particular devices for a particular case.
In any case, pharmacological protection with drugs like aspirin and clopidogrel are standard for interventional angioplasty procedures.
Balloon alternatives
Balloon-mounted stents are standard for coronary procedures, but in the periphery, including carotid and neurovascular implants, there are other stent types, such as nitinol, a shape-metal alloy of nickel and titanium. These are also known as self-expanding stents. They are deployed by removing a protective sheath and they open up on their own. Thus, there is no total occlusion during a nitinol stent deployment. However, balloons can still be used with nitinol stents to open up the original blockage, because the nitinol stents themselves don't "push" nearly as hard against the walls.
In my opinion, the major benefit to nitinol stents is not that occlusion isn't necessary for their deployment, but rather that they are not sensitive to crushing. With a regular stainless steel stent, external pressure would permanently deform the stent. In the heart that isn't a problem, because if someone is poking you in your myocardium you have bigger problems. However, the carotid arteries are fairly exposed in the neck, and a regular metal stent in the neck could be compressed and deformed. Instead, nitinol will snap back into position, like the underlying tissue.
Neurovascular circulation redundancy through collaterals
Although any ischemic tissue can eventually develop collateral circulation pathways to bypass the occlusion (assuming partial and not total occlusion, sufficient to keep the tissue alive in the meantime), the neurovascular system is unique for the high degree of redundancy present even in normal individuals with no blockages. Therefore, occlusion of a single vessel even permanently may not cause substantial symptoms. Of course this will vary from patient to patient and depends on the patency of collaterals, overall vascular health, and specific anatomy at the site of treatment.
Caveats
Of course there are risks in any surgical procedure. It is unlikely that there is zero neuronal death during any neurovascular procedure. Rather, these procedures are used when there is already significant risk or imminent damage without intervention; the intent is to create as little damage as possible while either solving an acute problem that is much worse, or reducing the likelihood of future infarction events.
References
Kulik, T., Kusano, Y., Aronhime, S., Sandler, A. L., & Winn, H. R. (2008). Regulation of cerebral vasculature in normal and ischemic brain. Neuropharmacology, 55(3), 281-288.
Lee, J. M., Grabb, M. C., Zipfel, G. J., & Choi, D. W. (2000). Brain tissue responses to ischemia. The Journal of clinical investigation, 106(6), 723-731.
Mousa, A. Y., Campbell, J. E., AbuRahma, A. F., & Bates, M. C. (2012). Current update of cerebral embolic protection devices. Journal of vascular surgery, 56(5), 1429-1437.
Pan, Jie, et al. "Reperfusion injury following cerebral ischemia: pathophysiology, MR imaging, and potential therapies." Neuroradiology 49.2 (2007): 93-102.
Saver, J. L. (2006). Time is brain—quantified. Stroke, 37(1), 263-266.
(disclaimer: I worked for a major manufacturer of intravascular catheters and stents for about 4 years. I was last employed by that company ~8 years ago and no longer have any financial relationship with that company. Everything in this post represents my own personal views. I am not a medical doctor; this information should not be taken as medical advice. Only your doctors/interventionalist can give appropriate medical advice according to your specific case)


text:
What is this insect in Southeast Idaho?
This thing ran out of the wall of my dorm hallway. It had a lot of what look like antennae, and it's very fast.

(click to enlarge)

related post: Is this silverfish? My apartment very dry

That is a silverfish, order Zygentoma (also known as Thysanura). Likely genus Lepisma (family Lepismatidae). Zygentoma are insects, and are the sister taxon to Pterygota (winged insects)

I should have added that these are harmless.

Admittedly, that was one of my main concerns

They're harmless to people, but they feed on stuff like paper. Usually the presence of these creatures (not the insect itself) is considered to be related to hygiene issues.

@wie5Ooma Very loosely related. Not like cockroaches. Many clean homes have silverfish. And they don't generally cause much damage to anything.


text:
Terminology for inefficacy of selection on recessive alleles
I am wondering is there some proper terminology which is used to say that deleterious recessive alleles might be able to hide, reducing the the efficacy of selection, in diploid organisms/chromosomes.
I was thinking about Y chromosome linked mutation and their inability to hide from purging by selection behind other alleles by being recessive... perhaps something like recessive sheltering? e.g. "In the Y chromosome mutations are more easily purged because recessive sheltering does not occur" ?

I don't think you require a special term. In this context recessive implicitly connotes hidden, as in the genotype is hidden  because the phenotype is masked (a.k.a. known as wild-type).

I think "penetrance" (http://en.wikipedia.org/wiki/Penetrance) might be the term you're seeking

No, penetrance is the fraction of homozygous mutants that display the loss of function phenotype--for recessive alleles.

I think recessive refuge is the term you are looking for (this is the best link I could find, sorry: https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/)

Masked allele is a term that is sometimes used for recessive alleles, and it should be suitable to the situation you describe. A common phrasing could be; "The wild type allele is masking the expression of the deleterious allele X.".
For your particular example you could use:

Deleterious mutations on the Y chromosome are more easily purged since they cannot be masked by alleles on a homologous chromosome.

An example can also be found in the abstract to Otto & Goldstein (1992):

With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases ("alternation of generations").


text:
How do sex biased genes evolve?
I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes).
I understand that gene duplication can lead to two sex-limited genes, the derived being expressed in one sex and the ancestral being expressed in the other.
Can the sex determining cascade cause sex-biased expression of a single locus? My thinking is that upstream differences between males and females might bring about regulatory opportunity to loci under sexually antagonistic selection over expression level. For example, if males favour upregulation in a locus, males who evolve some kind of transcription factor affecting that locus which responds to male-specific isoforms of DSX (in Drosophila), which could then cause the antagonistically selected locus to be more highly expressed in males without producing a negatively selected correlated response in females.
Is this correct? Are there other ways?
(Note: I'm looking for a clear explanation of the mechanics behind sex biased gene expression. Drosophila examples would be of particular worth)


text:
Is cell senescence in culture comparable to that in vivo?
A cell is 'senescent' when is has permanently left the cell-cycle. This can be caused by stresses, or by reaching the 'Hayflick limit' (the cell has reached its replicative lifespan, as defined by its telomeres).
Cells cultured in vitro can be used as models to study senescence (or sometimes 'ageing', although the distinction there is not necessarily within scope of this question) by growing the same population of cells for a long time (many passages). A common method to identify a senescent cell population is to use beta-galactosidase staining.
I was wondering to what degree senescent cells in culture (identified by beta-gal staining) are actually comparable to those you might expect in vivo. I ask because it seems to me that a terminally senescent cell may not actually survive long in an organism, so what we refer to as senescent cells in vivo are actually pre-senescent cells? I haven't got any basis for this, just a feeling. (Very scientific I know).

maybe the term you are looking for is 'apoptosis'?

Senescence does not equal cell death, but is simply an arrested state in which the cell still remains viable (1). It has been shown throughout the literature that this state corresponds with an altered cell cycle profile different from contact inhibition or damage-induced arrest (2). This corresponds with an enlarged cell size, altered gene expression (3, 4), and the pH-dependent expression of β-galactosidase (5). This has been shown both in cultured cells and in animal models (6, 7).

Goldstein, S. (1990) Science 249, 1129-1133.
Sherwood, S. W. et al. (1988) Proc. Natl. Acad. Sci. , USA 85, 9086-9090.
Cristofalo, V. J. et al. (1998) Crit. Rev. Eukaryot Gene Expr. 8, 43-80.
Linskens, M. H. et al. (1995) Nucleic Acid Res. 23, 3244-3251.
Dimri, G. et al. (1995) Proc. Natl. Acad. Sci., USA 92, 9363-9367.
Swarbrick, A. et al. (2008) Proc. Natl. Acad. Sci., USA 105, 5402-7.
Efeyan, A. et al. (2009) PLoS One 4, e5475.

Hi - thanks for the info on senescent cells. So you are saying that cells senesced in culture are comparable to those in vivo? Or you are saying that they are not comparable, because senescent cells in vivo are not necessarily replicatively senesced cells?

Cells in culture are necessarily different than those in vivo, as they are (generally) lacking the 3D structure, extra-cellular matrix, and heterogeneity found in tissues, but fundamentally senescence is the same across all cells, regardless of where they happen to be living at the moment. It is characterized by the phenotypes I mentioned above, including cell cycle arrest and replication inhibition. "Replicatively senesced" is redundant :)

I wouldn't have said redundant, simply because that is what our in vivo experiment was designed to emulate - we have aged a culture of cells (human primary cell lines) by repeated passage until growth arrest (confirmed by β-galactosidase, morphological changes, and drastic slowing of doubling time). We are now using these as models of senescence in vitro. If I understand you correctly then this is a reasonable model because senescent cells tend to display quite a homogenous phenotype? So even though senescent cells in vitro may have arrived by a different route, this is still a good model?

I can't judge your model as a whole (appropriateness of cell lines used, method of culture, etc.), but this sounds pretty good. The senescent cell phenotype is fairly homogeneous, allowing for the fact that different cell types and different cell lines can have vastly different overall phenotypes in terms of gene expression, morphology, etc., and these may be affected by the route by which senescence was arrived. The model sounds good, but keep in mind it's only a model, and you need to judge your assumptions carefully when looking at your results.

Many thanks indeed for your input, and the links.

No problem at all. If you like the answer, would you mind marking it as such? Thanks!


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How low potassium can potatoes have due to low potassium in soil?
According to Wikipedia 100 grams of potatoes has 2005 milligrams of potassium.
But if there is low potassium in the soil where it grows, it may not be able to acquire so much potassium.
How little of potassium can a healthy-looking potato have?

Do you have any reference that suggests potato potassium concentration is appreciably affected at all by soil potassium? My naive expectation would be that low potassium in the soil would primarily stunt growth, as this is what generally happens with plants more generally.

@BryanKrause no, i do not have references. i think some molecules are acquired if they are present, not if they are not. i think, potatoes have relatively much of potassium, so they may gather it in amounts much more than it is required for their growth.


text:
Why can't humans digest dietary fiber when we can digest starch?
So, I can see that there's a couple of questions touching on this subject already, but none of them answer the aspect that I'm curious about:
Dietary fiber is a polymer composed of multiple starch molecules chained together, and starch molecules are polymers composed of multiple sugar molecules chained together, right?
So, why are our bodies are able to digest starches and not dietary fiber, when the process for digesting starches involves breaking up the starch polymers into sugar molecules? Why can't the same enzymes used to break down starches break dietary fiber down into its component starch molecules, or break individual sugar molecules off of the ends of them?
Is it simply a matter of time, and we simply pass put the partially-digested remains of the dietary fiber because it doesn't remain in our gut long enough to properly digest? I know that cows have multiple stomachs to facilitate the digestion of grass, but I also know that they've got symbiotic bacteria helping them out as well.

You are mistaken about dietary fiber — please read the linked wikipedia page and [edit] or delete your post according to whether you still have a question.

@tyersome Huh, it looks like there's more than one kind of dietary fiber. TIL. I think I'm asking about cellulose specifically, then.

Then I suggest you read up on what cellulose is — it is not starch (the bonds between glucose units are different).

@tyersome If the correct answer is something like "starches are held together with A bonds, dietary fibers are held together with B bonds, and the enzymes only work to break A bonds for X reason", I'd be happy to accept that answer.

How much organic chemistry do you know? This is ultimately a question about glycosidic bonds ... and since dietary fiber isn't one thing so there is no general answer, which means you need to focus your question.

@tyersome "How much organic chemistry do you know?" I've watched some cooking videos on Youtube by people like Ann Reardon and Adam Ragusea, and I know the general sort of high-school stuff about cells.

Did the nice answer from @MattDMo help you? If so please accept it — if not, please leave a comment explaining why. In addition, your post needs to be edited to fit this answer. ——— I suspect you will need to learn the basics of organic chemistry to really appreciate his answer. If so, there are many resources available online, but I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy can be very helpful.

@tyersome I was waiting 24 hours so that people in other time zones could post their answers, then I forgot. Answer accepted.

"starches are held together with A bonds, dietary fibers are held together with B bonds, and the enzymes only work to break A bonds for X reason"

What you wrote here is correct. A is primarily an α(1,4)-glycosidic bond and B in cellulose is primarily a β(1,4)-glycosidic bond.

From Chemistry of Life at abpischools.org.uk
Maltose is one of the disaccharides produced when starches are broken down, while cellobiose is a disaccharide from cellulose.
Alpha bonds are broken during digestion of starches by the enzyme known as α-amylase, in particular one that specializes in breaking α-(1,4) bonds (there are other alpha bonds, like α-(1,2), as well). Humans express a number of α-amylases. However, β-(1,4)-amylase is only expressed in bacteria, fungi, and plants. Even cows and other grass-eating animals can't digest cellulose on their own – they have massive colonies of bacteria in their digestive systems to do it for them.
The reason α-amylases can't break β bonds is that the two different molecules have rather different chemical "shapes", even though the structures look very similar in the flat drawing above. You may have heard that enzymes work by a sort of "lock and key" model. The substrate (the thing being chemically altered by the enzyme) fits into a specifically-shaped binding pocket surrounding the active site on the enzyme, just like a key fitting into a lock. If the key is the wrong shape, sometimes even by just a little bit, it won't fit properly and won't open the lock. In the same way, if a potential substrate doesn't have the correct chemical "shape", it won't fit into the binding pocket of the enzyme and be acted upon.


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How to construct a sgRNA library with multiple samples?
I was wondering if anyone has already experience with constructing sgRNA libraries. We are interested in doing a knock-out experiment (loss-of-function) with 5 different conditions.
I have found this protocol from Joung et al.
In the protocol they have 10 different Fwd primer with no unique barcodes, only the eight Rev primers contains unique barcodes for different samples in KO.
Do I understand it correctly, that I can pool together only eight samples in one sequencing run with this protocol?
I would like to better understand the protocol of constructing an ngs library for sgRNA samples. If someone can point me to the right link/page?
Are there more complex library preparation kits out there which can deal with more samples?


text:
rRNA colony PCR amplification not working
We used some universal primers to amplify rDNA in a certain isolated bacterial specie. The problem is that rDNA PCR is not amplifying.
Primers were working well in other strains of same bacterial specie.
Do you know what could be happening? Maybe strain-specific PCR inhibitors? This strain was successfully amplified using ERIC PCR.


text:
Do sweat pores change diameter?
In Cholinergic Urticaria, some people believe that the itching which is generally more in winters might be because that the diameter of sweat pores is less due to less activity(less sweat production) and in summers the diameter is usually more due to high activity (more sweat production).
Question: Hence the question in general, Do sweat pores change diameter?

Personal medical questions are off-topic here at SE.Biology. This question is legit and well written but please remove any link to yourself. Thank you.

I edited your question so that it might not get closed. Please revert of modify my changes as you like.

gud one @cagliari2005

what is your question? Why it happens more in winter than in summer? Or what the causes are?

I think I included the causes as far as researchers know today in my question,but if you wanna go more into detail into causes then fine.... @AliceD plz make sure its focus is on my question in bold.

Pores don't change size; that is, the diameter of pore does not increase or decrease in hot or cold environments. Your skin, where pores are located, is not muscle but an organ so the pores don't contract or expand.

Pores can become clogged with dirt, oil, and debris (make up). When pores are clogged, you are more inclined to notice which would cause the illusion that the pore is bigger.

It's important to know that you can't actually "shrink" your pores. They're nothing but small openings in the skin -- because they don't have muscles, they can't open or close. So although you can't physically change the structure of your pores by making them smaller, there are things that you can do to minimize their appearance$^1$.

Just learned something.

@cagliari2005 it is actually common that people think pores expand and contract. The reason is because washing with warm water loosens debris cleaning the pores. Therefore, people then think the pores expanded when it was just warm water loosen the gunk.


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Evolution and the levels of selection
Reading Okasha's "Evolution and the levels of selection" he talks about "the levels of selection problem." There is a bit of a problem with this opening chapter because, while he talks about why the levels of selection problem is a problem, he doesn't define what the levels of selection problem is.
The opening line from the book..

"The levels of selection problem is one of the most fundamental in
  evolutionary biology, for it arises directly from the underlying logic
  of Darwinism. The problem can be seen as the upshot of three
  factors..."

I think what he means by the "levels of selection problem" is that selection acts on many levels, and what is adaptive at one level may be maladaptive at another. Therefore we can not define selection as acting at one single level, and studying it as such is likely to lead to incorrect conclusions - studying selection is not a simple process. Can anyone provide a firm definition of what Okasha, and the general community on the matter, mean by the "levels of selection problem"?
(Note: The factors are the abstract nature of the principles of selection, the hierarchical nature of biological organisation, and the process of adaptation via natural selection).

Reeve and Keller in the first chapter of Levels of Selection in Evolution (Princeton Univ. Press,1999) seem to address this question in the second item in the following paragraph.

The purpose of this volume is to sample current theoretical and empirical research on (1) how natural selection among lower-level biological units (e.g., organisms) creates higher-level units (e.g., societies), and (2) given that multiple levels exist, how natural selection at one biological level affects selection at lower or higher levels [boldface added]. These two problems together constitute what Leigh (chap. 2) calls the "fundamental problem of ethology." Indeed, as Leigh further suggests, they could be viewed jointly as the "fundamental problem of biology," when genes and organisms are also included as adjacent levels in the biological hierarchy. This generalization has the desirable property of immediately removing the long-standing conceptual chasm between organismal and molecular biologists.

The authors suggest definitions of fitness that account for hierarchical relationships (the level of selection problem) by considering the effect of a trait (nepotism among social insects) on "adjacent" biological levels, such as individual and colony.
By measuring what they call 'absolute fitness force' they propose to eclipse what they see as spurious debate over the fundamental level of selection (genes vs. individuals, say).
A somewhat surprising aspect of their discussion emerges here:
"It is still embarrassingly common to read inaccurate statements...that frogs have to produce many eggs to ensure the survival of the species because tadpoles suffer extremely high rates of predation, or that wolves have evolved ritualized displays to establish dominance hierarchies because physical combats would be too disadvantageous for the species. These naive statements betray a widespread and persistent misunderstanding of the level at which natural selection most commonly operates."
Their point is that such statements focus on the wrong level of selection (group), and that stronger selection may occur at the individual level; their overall argument being that both levels should be factored in.
I cannot present this as a 'community definition' but it may be a representative example.

So I am pretty close with my understanding already then? Including selection at all levels is essential to understanding how traits and populations of the units of selection will evolve.

I think there is a debate with 'DNA fundamentalists' claiming that there really can only be one mediator of selection (there is no level of selection problem!) and the multilevel folks claiming that there are forces beyond kin selection that influence evolution.  You might be just representing one pov here. The debate has been published in Science/Nature recently so I think its fair to say that it is not resolved.

@shigeta: Yes, the answer really only deals with the definition. Your comment is a good caveat or if you think it's preferable I can add a note to the answer. Thanks.


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How many cells does the hermaphrodite version of Caenorhabditis elegans have?
Wikipedia states:

The male C. elegans, for example, has 1031 cells

How many cells does the female version have?

Homework questions and trivial questions about basic biological concepts are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. https://www.google.com/#q=how+many+cells+in+female+c+elegans

959 Somatic Cells according to WormBase and The WormBook.


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Proof of mechanisms and causal relationships in biology
Statistical methods in biology are strongly encouraged: they are quantifiable, unbiased, and usually the only ones that are accepted as evidence.
However, it doesn't seem like the whole picture.
Say, someone wants to prove the hypothesis that wings are used for flight. He (or she) conducts an experiment: takes two groups of birds, ties up wings of all birds in one of the groups, then throws them out of a window and gets statistically significant data that birds with tied wings do not fly.
However, strictly speaking, he didn't prove that birds use wings to fly: only that birds with tied up wings didn't fly when thrown out of window. Or, as they say, correlation does not imply causation.
To tie the hypothesis to the results, he might include a paragraph in the discussion that "wings have large area, there are muscles that can flap them etc" - in other words, explain how wings could be used to fly. However, this explanation isn't statistical, or quantifiable: he just wrote a "story", perhaps used some common sense - but last time I checked, it's not evidence.
And that's pretty much what happens in every paper on biology: when they try to prove some mechanism, they include an experiment results and stats for a single aspect that is related to the mechanism (which, obviously, cannot explain the mechanism on its own), but then, when it comes to discussion, they just drop all the numbers and start explaining the phenomenon "logically" and eventually come to the conclusion. To be honest, they could've done no experiment at all and just went to explanation straightaway.
So what I wanted to ask:

Is there such a method of proof in biology as "proof by explanation", or something like that - when the author just explains the causual effects from, say, physics perspective and comes to a conclusion? Perhaps, even something similar to mathematical proof? Does this constitute valid evidence?
Are there any formal requirements for such proof? Perhaps, some way to quantify it or reduce to a "formula" of some sort?
Say, I wanted to publish a paper about some new protein that affects testosterone production. If I did no stats at all, or experiments like trying to remove the gene for the protein from some individuals and seeing what happens in comparison to control group, but instead just extracted and described the structure of the protein, identified the binding sites to some testosterone precursor, and explained how it can affect the testosterone production chemically, would it be a valid paper?

Your hypothetical paper on a novel protein that describes the structure and binding sites for a testosterone precursor would be an excellent paper. It just wouldn't be about the effect of the protein. There is more to biology than causal relationships.

The right policy is to exactly state what is observed and not make any far fetched conclusions. It is a matter of academic practice and therefore your question is not really on-topic here. [academia.se] may be a better place for your question.

You are missing a much simpler and more common method. film birds in flight, then demonstrate mathematically that the wings as used are providing the lift that is enabling flight. That is direct evidence for your hypothesis. You can further test it by clipping the wings or putting the birds in a vacuum, or a hundred other strange experiments. You may want to look into biomechanics, the types of studies you are looking for are far more common. How a limb works is not really a statistical question but more of a dynamics one.
Statistics is a secondary way of testing, used when more direct methods are not possible or terribly impractical. to use your last example yes that would be a perfectly valid way to determine a proteins function, there are limitations reasons we don't usually determine protein functions this way, not just becasue often we discover the function before isolating the protein), but even when it is you also want to test it in other ways that is true of anything in science.  This one reason science prefers multiple lines of evidence since one line can compensate for the flaws in a different line.
"Proof by explanation" has specific connotations in biology that may not be what you are really asking about*. Often it refers to unverifiable narrative explanation which is not acceptable in science. Also you never prove anything in science, (even more so with statistics) we shy away from the term proof because it brings to mind absolute proof which cannot exist. In science you can demonstrate something or show it is the most likely known explanation but you do not "prove" it. Research is not one off events but cumulative and constructive, the more lines of evidence the firmer a concepts standing.

What I thinks you are really asking is something much more fundamental to how science works and what empiricism and verification is. You may have better luck with this on a philosophy of science discussion, than a specific field of science since you seem more confused about how science operates. science has both experimental and descriptive research each with its own value.

"Often it refers to unverifiable narrative explanation which is not acceptable in science"
Well I understand that - but how does one make "unverifiable" narrative a verifiable narrative? Stats allow making verifiable, formal evidence out of unverifiable counting. But there seem to be no formal procedure to "proof by explanation/description".
"you never prove anything in science"
Well I understand that, I just don't know how to call it properly.- no-one ever talks about this method.

A narrative is just a description of a sequence of connected events, Anything from plate tectonics,  to a description of how a beaver builds a dam can be a narrative, the important thing is that the narrative be testable. Does it make predictions, for the bird example the hypothesis birds use their wings to fly makes several predictions including wings generate lift, birds without wings will not fly, and  the simplest that birds fly. Is model of the universe presented by the narrative empirically distinct from one in which it does not occur, AKA invisible dragon test.


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How are behaviors genetically coded in animals?
I am curious as to how complex behavior is passed down genetically? For example, how is the building of a web genetically coded in a spider? And how is the complex behavior of constricting prey coded into a boa? As these critters do not get raised by their parents, and hence cannot learn to copy these behaviors, it has to be genetically imprinted. How?

Some will probably be genetic, yes, but many will be learned. Just like you learned from your parents and will teach your children. What makes you think that any learned behaviors are passed down genetically? They might be, perhaps through some form of epigenetic modification, but it's unlikely to be very common.

user1894167 - I edited your post as it contained inconsistencies as rightly pointed out by @terdon. If, however, this edited version no longer reflects your original question, please feel more than free to roll back. However, in that case additional edits are recommended, as your original question was confusing.

There can be whole books written on this topic and we wont still have answered this question. How instincts are genetically coded is still under research. For some there is an answer. Therefore I ask you to narrow down to a specific case.

@WYSIWYG - I must say I find this question highly intriguing. How could it be narrowed down? Perhaps focus on a single well-investigated species with a known, reproducible complex behavior such as a web-weaving spider? If I wasn't rep farming I would be bountying this question heavily.

@AliceD primitive instincts like fear can be explained based on epinephrine signaling. But web-spinning and all are much more complex and you very well know that we don't know the answer to these complex instincts and these are actively being researched upon. This is one of those unanswerable questions :P

thanks for the edit Alice. I think you phrased it better.

WYSYWIG could you point me towards the examples where there is an answer. I can only access free links, Or even just to links on active research not solved questions.

I will focus my answer on the evolution of orb web spiders (Fig. 1), because arachnids, like insects, are relatively non-complex creatures with an obvious systematic behavior (the weaving of highly symmetric, repeating structures). Hence I reasoned this would be a good approach of investigating the answer to this question.
The orb-weavers (Orbiculariae, an informal name for the taxon containing the superfamilies Deinopoidea and Araneoidea) are among the most diverse lineages of spiders (Hormiga & Griswold, 2014).

Fig. 1. Orb web. Source: Encyclopedia Britannica
Bond et al. (2014) report that according to various estimations the date of the origin of the orb web was somewhere around the Lower Jurassic 201 million years ago and 52 million years ago, and the authors support the view of a monophyletic origin of the orb web.
Despite this excellent opportunity to elucidate the (monophyletic) genetic underpinnings of the evolution, and hence the passing down of orb weaving, are largely unknown. Not only is the evolution of orb weaving unknown, even the evolution of the intricate physical properties of the silk are largely unknown. For example, how the sticky glue araneoid orb web evolved is a mystery. This complex multicharacter trait is hypothesized as a key innovation to explain the increase in diversity of araneoidea. For example, araneoid orbs contain viscous adhesives and they have low UV-reflectance and are hence less visible to insects. There exists one proposed evolutionary pathway from the dry, cribellate orb web of deinopoids to the sticky glue orb web of araneoids, but that's about it (Hormiga & Griswold, 2014).
In all, physical properties of silks contained in webs are hardly explained in evolutionary terms, let alone the behavioral profiles necessary to make a web out of it.
References
- Bond et al., Curr Biol (2014); 24(15): 1765–71
- Hormiga & Griswold, Annu Rev Entomol (2014); 59:487–512

I think http://www.thenakedscientists.com/forum/index.php?topic=26203.0 is claiming to answer the part of the question re spiders.

@user1894167 - that link describes arachnid behavior

well the first post does seem to be claiming a genetic explanation that leads to structured web building in spiders. I'm not saying I believe it since it doesnt cite any sources but just thought I would post an alternative explanation.


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Medical Uses of toxic venom
One interesting thing I recently learned is that venom has medical uses that can actually save lives! But from what I see so far this either applies to venoms from creatures that are not fatal to humans or that only proteins or enzymes from these venoms are what is being used medically.
Are these proteins or enzymes themselves fatal to humans or is this just a misrepresentation of the fact that venoms can save human lives?
EDIT: To clarfiy, while I realize venom is harmless in lower doses, I also read the following :
Enzymes from cobra venom may be instrumental to finding cures for Parkinson's disease and Alzheimer's disease.
An enzyme derived from copperhead venom could be used to treatment for breast cancer.
What I was not sure of was whether the enzyme by itself was toxic or they were just extracting a non-lethal element of the venom to use medically. Can this enzyme alone of venom administered in large enough doses be fatal?

Can you specify to which venoms you're referring? Can they not do both under different circumstances? I hardly think anyone is trying to misrepresent anything.

Maybe I am understanding your question wrong, but venom is only deadly when given in a certain amount. From that point of view, everything can be lethal, even water. This makes the first part of your question shaky. For example, digitalis extracts can save live-threatening heart failure, but in large amounts it can kill. Further, proteins in snake venom are the chief toxins as far as I know. So the second part of your question is unclear. In all, I think the question needs to be specified before it can be answered.

You should narrow it down. For example just talk about cobra venom. Different venoms act differently; some are enzymes others are not.


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What are the most important factors influencing a person’s gut microbes?

You are your bacteria! The probiotics and the antibiotics...

There has been on going discussions about how our gut bacteria is important for a healthy lifestyle.

Figure 1: Schematic diagram illustrating potential or known mechanisms
  whereby probiotic bacteria might impact on the microbiota. These
  mechanisms include (1) competition for dietary ingredients as growth
  substrates, (2) bioconversion of, for example, sugars into
  fermentation products with inhibitory properties, (3) production of
  growth substrates, for example, EPS or vitamins, for other bacteria,
  (4) direct antagonism by bacteriocins, (5) competitive exclusion for
  binding sites, (6) improved barrier function, (7) reduction of
  inflammation, thus altering intestinal properties for colonization and
  persistence within, and (8) stimulation of innate immune response (by
  unknown mechanisms). IEC: epithelial cells, DC: dendritic cells,
  T:T-cells. For further details, see main text.

Also, an online search provides numerous articles about diet aspect that alters our gut bacteria.
e.g.
1.A New Diet Quickly Alters Gut Bacteria-(not sure about the credibility and relevance to humans as the study is on mice)
2.Artificial Sweeteners Change How Our Gut Bacteria Work, Paving The Way To Diabetes And Obesity
3.Changing gut bacteria through diet affects brain function
As far as the GIT is concerned, health, lifestyle, eating habits and the environment a person is living may be at large influence and affect one's gut microbes.
Are there day to day encounters, in-depth examples and references that can prove the factors which influence our gut microbes the most?

There was an interesting paper that showed fecal transplants actual can switch a skinny mouse to an obese mouse and visa versa!

@GoodGravy mice are cute, but I am keen on human. Nonetheless please share the paper if you have. ;)

I'll look it up. It is basically showing that gut bacteria are far more influential on us that previously thought, to the point where maybe (big asterisk/disclaimer) they can be applied in medicine.


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Application of Latin names for Taxonomy
The current taxonomy has family names like Canidae and Felidae. But Felidae has sub families like Felinae and Pantherinae. Roaring cats and non-roaring cats. My question is based on the fact that we can have common words for these families based in Latin: Felines, Canines, Pantherines. Can every family in the taxonomy be represented by this latter form? Is Pantherine a valid name? Is was created by dropping the a from the subfamily but caninine was created by dropping the da from the main family and replacing with in.

Is "Pantherine" a valid vernacular name for this group in English? Sure, although "panther" is much clearer ("Pantherine" in English would mean "like a panther", not "a panther"). Also, many family names are fairly obscure: even a pretty well-known group, like Apidae, would become "Apinine" in your scheme, which is less clear to me than "a family of bees".
Is it a valid family name? No. The International Code of Zoological Nomenclature (ICZN Code), which governs all scientific names for animals, says:

Article 29.2. Suffixes for family-group names. The suffix -OIDEA is used for a superfamily name, -IDAE for a family name, -INAE for a subfamily name, -INI for the name of a tribe, and -INA for the name of a subtribe. These suffixes must not be used at other family-group ranks. The suffixes of names for taxa at other ranks in the family-group are not regulated. [emphasis mine]

Family names that don't have an "-idae" suffix need to be corrected (ICZN Code Article 32.5.3.1).
Note that the ICZN Code doesn't cover other ranks in the family-group or above.

I think OP is getting at the fact that certain non-formal names are "valid" in English to refer to members of a group, hence: scarabaeid, coleopteran, neopteran, etc.

Yes I think the common English form are valid too. I would however like to know the correct forms for singular and plural in zoological and botanical names since comman names are not always obvious. I would assume all nouns there are in plural since they are talking about groups. And I assume the form is neutral. But I see words like Goniotrichum which is singular neutral so I wonder if I can change to Goniotricha ? Or is there some article I can read that would show how to convert all latin taxa names to common forms? like deuterostomia to deuterostomes.

And you say Apidae would become Apinine but in my system it would be Apeidos since wiktionary lists eidos as the singular form of idae.

Goniotrichum is a genus name, which are usually singular nouns -- a name like Homo sapiens means "[a] sapient [adjective] Human [noun]". IMO you would refer to "Goniotrichum species", rather than "Goniotrichums".


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Why do we see black when we close our eyelids?
Why do we usually see black when we close our eyelids assuming there is no strong light source outside?
I realize we never really stop seeing as long as our eyes are healthy but based on assumption I would have assumed that the back of the eyelids would be the same as the front and this could be a range of skin colors other than black.
Is it because most times not enough light is being reflected off the back to show the color?

This is easily answered by first washing your hands, then standing in front of a mirror, pulling an eyelid away from the eye, then folding it to look at the underside. Hint: it's not black.

Hah! That sounds painful and it does not answer the question the in actual text of the post which is why we see black when we close our eyelids. I will retitle the question. Sorry.

The question is actually not a question of biology but of the physics of light. Absence of light is black. Closing your eyelids prevent the light to reach your eyes, so you see black. Even if the interior of your eyelids were snow white, you would still see black.

the cone cell in the eye allows you to see different colors, and it only function in an illuminated environment, and function less in a less illuminated area.
 when your eyes is closed totally obstruct the entrance of incident ray from the outside thereby causing only the rod cell to be functioning .then the only thing you can observe is total darkness.

can you add a reference for your answer?


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Does Cas9 require a nuclear localization signal (NLS) for it to work in a Eukaryote?
I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell.   Several papers report using a viral NLS, but is it absolutely necessary?   Could Cas9 be trafficked to nucleus without addition of a NLS?

As far as I know it should be needed because it can not enter the nucleus otherwise.

Most of the Cas9 genes you buy for mammalian gene editing experiments will contain at least one copy of the SV40 NLS sequence.

Yes, it does.
In general, proteins required in the nucleus must be directed there by some mechanism. https://en.wikipedia.org/wiki/Nuclear_localization_sequence
Adding a nuclear localization sequence to the N-term of a protein is a very efficient and established way to accomplish this.
Also, as a supporting fact, you can notice that any CRISPR/Cas expression plasmids for mammalian cells on Addgene (here an example http://www.addgene.org/48138/ ) contains one or more NLS at the N-term of the Cas sequence.
Here some links for further reading:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1083765/
https://www.ncbi.nlm.nih.gov/pubmed/27126810
https://www.ncbi.nlm.nih.gov/pubmed/26173234

The transport from cytoplasm to nucleus is mediated by importin family. Importion family recognize NLS and transport proteins such as transcription factors into nucleus. So, NLS is necessary for cas9 to be transported into nucleus.

can you add some references to your answer? it always helps for others on the site to have further reading and substantiate claims.