text:
Pipetting: do human experimenters need liquid class information?
I've been working on a protocol standardization project where, among other things, we want protocols to be able to be run equivalently by both humans and robots.
Something that I've noticed in doing so is that there's a radically different amount of information typically assumed needed by a human vs. a robot when it comes to pipetting.
With a robot, it is generally recommended to understand the nature of the liquid thoroughly, specify the liquid class (which includes information on viscosity, volatility, polarity, etc), and do quite a bit of quality control to make sure than when you want to pipette 100 µL you actually get 100 µL. A typical example is shown on this page by Hamilton.
With a human experimenter, however, the protocol pretty much always just says "pipette 100 µL" and assumes that the human can figure out all of the potential issues that we have to be so careful for with robots.
Is this actually a safe assumption, or just something that we don't typically check during protocol development for humans? Is it really intuitively obvious for nearly all liquids, or should our protocols be providing more guidance for humans as well?

I have answered this question from my viewpoint as a student, but I think it could benefit from an answer(s) from someone who is on other side of the "experience" divide, and is more used to giving advice than taking it.

I don't wish to be overtly critical, but how is this a question about biology? I have already removed the incorrect tag "synthetic biology", but even as a methods question it seems to be only answerable in a subjective sense as human psychology, or in a legal sense in relation to the laws of a particular jurisdiction  relating to some form of industrial safety.

@David I'm really not sure how you're coming to that conclusion: this is a problem of biological protocol replicability.

@David I've added the lab-techniques tag as well; if you disagree with this question, then what do you find different from other lab-techniques questions on this site?

Lab techniques questions are of the form "How do I (best) do such and such?" That sort of question allows an objective answer "You can do it by..." Your question seems to be of the form whether it is necessary to write instructions to people performing a particular (common) laboratory technique. This can only be answered subjectively. I have voted to close this question on that basis, i.e. it is a matter of opinion.

@David Interesting; my own assessment, which supported my choice to ask, is that this falls solidly on the good subjective side of the bar, but of course that is, itself, a subjective judgement.

For what it's worth, I find this a particularly interesting question which already has interesting answers and a very refreshing change from most questions we get. One of the long term problems we've had here is the relative dearth of professional biologists asking professional-level questions so I am really surprised to see this already has two close votes! I would have thought this is exactly the sort of question we want to attract and support.

"the human can figure out all of the potential issues" Yes, it's one of the first things we got taught in chem lab. You could start with the information provided in those courses.

In my experience it is very rare to see a protocol for humans that describes how to pipette a certain liquid, but I don't have as many years pipetting as others do.
In general, it is left to the experimenter to observe the behavior of the liquid and act accordingly. It is quite easy to determine when a liquid is leaking (e.g. ethanol) or when it is very viscous (e.g. glycerol), and determine that a change in technique is required. In this case, I would ask someone else in the lab how to deal with the situation. This is something that robots cannot do.
However, not everyone has expert help available, and although it is fairly obvious when a technique isn't working, often the solution is not intuitive. Additionally, the advice of others in the lab could be unhelpful or even inaccurate. For example, I was told to cut the tip off a pipette in order to pipette Tween-20 more easily, however in reading for this answer have discovered that this is not recommended at all! (See eppendorf FAQ linked below).
Therefore, I would say that, unless the liquid is to be pipetted in the same way as water, it is always useful to provide information for those who are not knowledgeable or do not have easy access to expert practitioners.
For some examples of the sorts of problems that experimenters come up against, and therefore which liquids especially could use instructions in protocols, see this set of FAQs from eppendorf on handling liquids.

Wow... I think it's particularly revealing how answering this question actually ended up causing you to discover that an "oral tradition" answer was incorrect! It seems that pipetting actually has a lot of knowledge required in order to do it correctly?

As with so many things we do in the lab, we are often in a rather high local minima of 'what worked for postdoc Bob 15 years ago and has been handed down ever since'

Many don't know that pipettes are calibrated for water solutions. Organic solvents (like ethanol) have a different partial pressure and can't be measured with a water calibrated pipette.  This is crucial in some experiments.

The most finicky pipetting situations I've encountered are with regard to emulsions. The worst example I've encountered is the 10x Chromium, which asks you to dispense 95uL on a P-200 multichannel over the course of 30s to avoid breaking emulsions.  But plenty of other emulsion-based protocols (often single-cell-related) specify slow pipetting

I work on software that controls one model of robotic pipetter.  There are a few reasons why we use complex liquid class definitions:

One of the selling points of using a robot is high speed.  You can handle a wide range of viscosities if you set a conservative (slow) speed for aspiration/dispense, but for solutions that don't require this, we'd like to be able to move more quickly.  In many cases, the different liquid classes are about optimizing the time required while still maintaining the desired precision and accuracy.

Robotic pipetters will often dispense multiple times after a single aspiration of a larger volume.  To do this accurately, we compensate for a variety of effects, including the effect of the column pressure, which depends on the reagent density.  In the end, this is also largely about improving speed.

In some applications, precision is especially important and you can use settings for the robot that improve precision.  Let's say you have something that is extremely sensitive to getting the right pH.  You could pre-titrate a buffer to the correct pH and load that into the system, but if you're trying to produce an assay grid on a microplate, you'd have to make a bunch of buffers.  A well-calibrated robotic system can mix from stock buffers to produce the assay directly, since it has the necessary precision for mixing very small volumes.

Not having much personal lab experience since school, I can't speak to how precisely/accurately pipetting is done in labs by human beings.  It probably varies quite a bit from lab to lab and likely depends on the skill and tiredness level of the person doing the work.  I did it enough times to know that even basic pipetting of aqueous solutions has a bit of a knack to it and was glad when I was done with the labs that required it.  In any case, I thought it might be useful to have an idea of why the robotic control seems so much more complicated; it's mostly because robots are trying to do it faster and without the benefit of being able to observe the reagent's behavior while using it.

I appreciate you sharing your expertise about the robotics, but that's the side that I'm more familiar with as well. I'm afraid however, that as currently written this answer isn't shedding terribly much light for me on the question about whether humans need more information than they are typically given.

@jakebeal, it doesn’t quite say it explicitly, but I interpreted this answer as saying “humans don’t pipette in the quite the same way, and therefore may not need as many details.”

@MattKrause Agreed; I was hoping for a little bit more description and basis for that conclusion.

@jakebeal I'm not aware of nay research on the topic, but I would suspect that even if you give explicit instructions to human operators, they might try to apply them, but most likely they'll largely fall back on their learned muscle memory and habits from their training/practice.  In a sense, I'd say the humans already have the liquid class information in their brains, to the extent that they've encountered those types before.  Humans also have the major benefit of being able to look at the pipette tip and see if there's still fluid stuck inside and can adapt accordingly.

Just to be clear, it has been many years since I have done real lab work, so I am certainly not an expert on the specific question.   However, I have a fair amount of experience writing clear instructions to cover complex (and often bespoke) processes.
As Dan Bryant has explained, robotic systems absolutely need the additional detail in order to complete their tasks optimized for speed (and a control method without the built in feedback loops that come with a human).
My experience writing procedures for humans is that same level of detail will actually be a significant negative, at least on techniques that are considered standard knowledge.   Providing what humans consider 'unnecessary detail' tends to result in a problem where your procedure is 'skimmed' for key information, which may result in lower adherence rather than improved results.
Another consideration is your level of expertise - do you know every situation where a task specific pipette is required?  Because if you specify it once, you create an expectation that you will specify it every time, so any situation you miss may cause an error, and the probability of error is higher with operators having less experience - the primary audience for detailed procedures.
There are solutions, but they tend to depend on your documentation standards and the documentation tools in use.   The simplest is often to move the robot only detail into an appendix (or something similar, such as a collapsing box).  This means the person programming the robot will be able to drag the detail out when required, but the 'visual noise' for the humans will be reduced.

Re: specifying robot details, most vendors will ship liquid class information with the tool covering the majority of cases, so you generally only need to go through a careful calibration process on your own if you need particularly tight performance or you have an unusual fluid.  The parameters and configuration process will also vary between vendors/tools, since, among other things, there are a variety of different technologies in use that all operate slightly differently.  It's worth specifying the liquid class you used for replication, but would be hard to distill to tool-independent info.

That is a very good point about including unnecessary detail. If this information is included it should be in a subtle/optional way so that it won't distract people who don't need it.

In my experience, I've never seen more than "pipette 100 μl" or at most "caution viscous liquid". Also I've only been taught how to pipette in a general manner and never about how to do it with special liquids except for the "cut the tip off" advise so before Noah's answer I had never heard of reverse pipetting or using a multivette to accurately pipette glycerol for example as described on the eppendorf website. However, when pipetting glycerol for example I could tell that I needed to pipette it slowly and I could check visually that I had (about) the right volume using the marks on the tip. So compared to a robot I can use my eyes to adjust and it's good enough in my particular case and with a single tube it is not optimal and it may not hold true with a multichannel pipette so having good and better pipetting habits would be better for reproducibility.
Now if I can see the "cut the tip" advice and the standalone "pipette 100 μl " instruction work to some extend, "commercial" grade protocol would probably have the instruction written as "using a multivette (or using the reverse pipetting technique) pipette 100 μl".
Another thing to consider is the definition of protocol which if we take wikipedia's definition is not just a succession of steps to perform :

In addition to detailed procedures, equipment, and instruments, protocols will also contain study objectives, reasoning for experimental design, reasoning for chosen sample sizes, safety precautions, and how results were calculated and reported, including statistical analysis and any rules for predefining and documenting excluded data to avoid bias.

What we usually consider as a protocol is the "Quick protocol" with only the steps to perform where you're more likely to find the "pipette 100 μl" type instruction. But if you consider the more detailed protocol you'll find more information. I don't have an example for liquid handling but if you consider the qiagen miniprep protocol depending if you take the quick version or the full one you may not be doing the same thing. Let's take step 2 as an example :

quick protocol :

Add 250 μl Buffer P2 and mix thoroughly by inverting the tube
4–6 times until the solution becomes clear. Do not allow the lysis reaction to
proceed for more than 5 min. If using LyseBlue reagent, the solution will turn
blue.

handbook :

Add 250 μl Buffer P2 and mix thoroughly by inverting the tube 4–6 times.
Mix gently by inverting the tube. Do not vortex, because this will result in shearing of
genomic DNA and contamination of plasmid. If continue inverting the tube until the
solution becomes viscous and slightly clear. Do not allow the lysis reaction to proceed for
more than 5 min.
If LyseBlue has been added to Buffer P1, the cell suspension will turn blue after addition
of Buffer P2. Mixing should result in a homogeneously colored suspension. If the
suspension contains localized colorless regions, or if brownish cell clumps are still visible,
continue mixing the solution until a homogeneously colored suspension is achieved.

If we consider only the mix part here, "gently" is the key word. If you've been handed only the quick protocol and you're an inexperience user even just by inverting too strongly you may end up shearing the genomic DNA and thus contaminate your sample what can impact your downstream application.
So the bottom line is that "pipette 100 μl" may be enough for experience users and/or some applications on a quick protocol but you may also want to have the instruction "pipette 100 μl using a multivette (or using the reverse pipetting technique)" on a more detailed protocol for inexperience user or troubleshooting purposes.

Thank you for the information about the miniprep protocol! I'd always assumed that thoroughly meant that it didn't need to be/shouldn't be gentle. I normally shake the tube viciously for that step...


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Do strictly anaerobic organisms use metabolic reactions requiring oxygen?
When looking through genome annotations of strictly anaerobic organisms I see reactions featuring oxygen. I suspect these are likely an artifact of the annotation process. But I am wondering if it is possible for such organisms to have oxygen associated metabolism. Strict anaerobes are known to die in the presence of oxygen due to the lack oxidative stress pathways. So I cannot think of any reason for oxygen to be part of their metabolism.

Here is one of the reactions I came accross: Ferroxidase: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2H2O

source: Stack Exchange

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sort: votes


text:
Can inhibition of lymphocytes migration be a direct cause of chronic inflammation?
Here is the original slide:

I am thinking about the "cord factor" sentence in a more general case.
Assume you inhibit Leucocytes migration.
How does this lead to accumulation of macrophages in the site of infection?

Can you edit your question to be more specific, and not use "Leu" as an abbreviation ?  (Leu has other meanings).   Leukocytes come in many types - lymphocytes, macrophages and neutrophils, for example.  The effects of inhibiting their migration may vary.  What specifically do you want to know?
I'm not sure if your example with Cord Factor is a suitable basis for your question...According to this cord factor is generally pro-inflammatory and acts by preventing fusion between vesicles that may contain M.tuberculosis and lysosomes.

Can you provide a link to the original document that includes your sentence ?  That might help us.

I edited your question both to add your image of the slide and to remove your "quote", which was not at all what the slide said. Also, it should be clarified here that cord factor comes from M. tuberculosis.

The only reference I can find re cord factor inhibiting leukocyte migration is this one  . It cites reference 33 as a basis for that statement and I don't see any such finding there. Skimming the abstracts of references 32 and 34 also don't seem to suggest such a finding, either. So I think the premise of the question may be in error.  If you can find a reference for such activity, then I think we can look at any such specific activity.   Basically, I think that part of the slide is wrong.

The mechanism is likely very straightforward. Activated macrophages already in the area are releasing pro-inflammatory cytokines like TNFα, IL-1β, IL-6, IL-12, MIP-2, etc. These are not only important for granuloma formation, but they also recruit other immune cells to the area. However, since cord factor has this anti-migratory effect, once the cells get there they can't leave. This is important because activated macrophages are key antigen-presenting cells (once they kill and break down the antigen, in this case Mycobacteria), and they need to move to the spleen to assist in the upregulation of the adaptive immune response. By preventing this, mycobacteria can evade part of the immune system - part of the reason why TB is so hard to clear once acquired.

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text:
What is frank dehydration?
On Wikipedia article about Urine specific gravity we can read:

A specific gravity greater than 1.035 is consistent with frank dehydration.

What is frank dehydration? How it is different than regular dehydration?

A higher specific gravity means a higher concentration of salt. And a lower concentration of water. You can now think about reasons why the human body looses lots of water, the most likely is heat and not enough resupply of water. The Wikipedia article also states that the normal specific density is between 1.000 and 1.030, so you are beyond the normal range.

What about frank word, it's any special wording to indicate some kind of type of dehydration?

"Frank dehydration" is not really a regular medical term. You can suspect this by using Google search with "frank dehydration" in quotes and site:gov (only 3 websites showing up) and site:edu (2 websites) operators.
The term "frank dehydration" as an informal term can refer to "obvious," "actual," "test-confirmed" dehydration as opposed to feeling dehydrated or thirsty.
Tests to confirm dehydration include a combination of the body exam (dry mouth, prolonged skin turgor, decreased body weight), urine tests (dark urine, increased urine specific gravity, decreased urination frequency and 24-hour urine volume) and blood tests (increased sodium levels - hypernatremia).


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How was the cama's life expectancy computed?
A cama is a hybrid between a male dromedary camel and a female llama. The first cama was born on January 14, 1998, yet on the Wikipedia page it is said that a cama's life span is 30–40 years. How was that number determined? Is it simply the average between a camel's and a llama's life spans?

http://en.wikipedia.org/wiki/Life_expectancy#Calculating_life_expectancies

probably just an educated guess...

Since no source is given for the 30 - 40 years estimate in Wikipedia, we can't find out how the authors of the Wiki page reached that estimate, but 'someone made an educated guess' seems likely. There are a few reasonable ways that one might educatedly guess the longevity of the cama, but there are good reasons to treat those educated guesses with caution.
First, as you suggested, you could just estimate the cama's longevity from the life expectancy of camels and llamas. This is likely to fall in the right ball-park, but should be interpreted with caution: ligers (lion - tiger hybrids) are reputed to have high rates of premature death, and the same may well apply to camas.
Second, you could plug the animal's body measurements, metabolic-rate measurements, or similar measurements into a model which relates species' attributes to a measure of their longevity. Many different models of lifespan have been built (e.g. here), and if your goal is to get a rough estimate of how long a member of a particular species will live, those models are not a bad way of making a first guess. The 'this is a weird hybrid and might have issues with premature death' caveat still applies, though.


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What is the physiological difference between cortisone and cortisol?
There is only hydrogen bond different.
Cortisol is synthesized by our body, while cortisone is given to the patient.
Why you cannot give cortisol directly to the patient?
I think the reason is metabolism that cortisol will break (probably in liver) and not be useful.
Or expansive to produce.
Cortisone however can be given.
What is the physiological difference between cortisone and cortisol?

Cortisol is directly given to the patient - it is then called Hydrocortisone. I don't know why this is done but probably to avoid confusion because both names are too similar.
The difference between both forms is one hydrogen atom at the C11 position of the molecule in Cortisol (or Hydrocortison) (image from here):

Otherwise is Cortisol (or Hydrocortisone) the active version, while Cortisone isn't very active in the human body.
Both forms can enzymatically turned into the other form (from active to inactive and vice versa). Since Cortisone needs to be activated in the liver, it can only be used for oral uptake. Most of the uses which are colloquially called Cortisone in fact contain Hydrocortisone.


text:
How many chemical species are on average in a typical plant and animal cell?
I want to know what sort of range there is on the number of different chemical species in a typical plant and animal cell. Failing that, some specific examples (with sources please).
Thanks

What is a chemical for you?

anything that can diffuse in the cell

well there are about 6000 distinct proteins in a yeast cell. So I would guess in the hundreds of thousands. https://www.sciencealert.com/simple-cell-has-42-million-protein-molecules-life-universe-everything

There is no average plant cell.  However this article describes a whole plant flux balance model with 333 metabolites. This won't describe a lot of the molecules plants make.
I seem to remember a natural product analysis of garlic that had scores of sulphur containing compounds that give its distinctive smell for instance.  This model would be a simplified plant which has no special characteristics like that, which probably doesn't exist.  Its probably not less than half the number of compounds that some plants produce or use.

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Is there a DNA sequence that is true for all primates?
There are a total of 324 million known variants from sequenced human genomes. https://en.m.wikipedia.org/wiki/Human_genetic_variation
Is there an DNA sequence that is true for all primates?  Is this more acceptable on another site maybe?

It's not totally clear what you mean by the words "identifier" and "true". do you mean "is there a DNA sequence that exists in all primates?" if so, how long do you need it to be? does it need to be in a homologous location in all primate genomes? It is trivially true that the one-letter sequences A, G, C, and T exist in all primate genomes, but I doubt that is what you mean. why do you want this sequence?

Please rephrase your question. It is not clear what is meant with "324 million variants from..". Is this the total number of human genomes that have been sequences or are these the total number of alleles that have been found? Please also report your source. Please also specify what you mean with "identifier". Do you mean any sequence, that is common in all human genomes, but is expected not to occur in any other species? Then the answer - forced by stochastics- is yes, without any doubt whatsoever. Finally, what does your last sentence mean?

Ribosomal RNA sequences (rRNA) are present and highly conserved in nearly all organisms (excluding viruses) and serve as the basis for reconstructing the tree of life (archaea, bacteria and eukaryota). Such reconstruction obviously implies that there also differences between rRNA sequences, but they are smaller for a limited taxonomic groupings, such as primates. Still, even within primates there is some variation, although identical regions can be identified, see, e.g., here.

Thanks to your Wikipedia link, I was able to track what you meant with "324 M variants". These numbers refer to entries in the dbSNP (single nucleotide polymorphism database).
If you have a look at the submission guideline, it is not allowed to submit sequences over 50 nt: https://www.ncbi.nlm.nih.gov/snp/docs/submission/hts_launch_and_introductory_material/
This means your number doesn't necessarily refer to either the number of known alleles (might be longer) or the number of fully sequences humans (might give many SNPs per sequencing).
Anyways, if you compare this (incomplete) number to the size of the human genome (3.1 billion), you will see that the genome is roughly 10x bigger than the total count of known SNPs. Those heavily are enriched in SNP loci, meaning they overlap in location.
So from this data one may only say that >>90% of the genome consists of non-known SNP sites. So your question is answered with a yes, most of the genome is similar/"true", while this just reflects the current state of knowledge and most certainly, the number of known SNPs will increase over time.

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text:
Looking for source: Biologic reactions of people saying "no"
Searching for this topic is incredibly tedious because the word "no" is the main point of interest and I always end up on sites saying how "saying no is good for your health" but I am looking for the medical evidence of this claim.
I remember very faintly hearing about measurable physical effects on a person in a situation where this person says the word "no" to something.
There was an experiment where scientists (I suppose neuro-scientists?) were able to measure the effect of saying "no". Colloquially speaking the body was "closing" in a sense that the person went in some unconscious defence mode, stress levels were rising, change in muscle tone were measurable etc.
When I also remember correctly these effects were measurable even without exposing the person to a specific situation. Just saying "no" wholeheartedly triggered those effects.
Did someone hear about this one? I am looking for any clue to get more information on that.
Edit: I add to the excellent hint from Vadim: I am indeed looking for a credible source where experiments were conducted in a controlled manner and not someone sticking electrodes on people in the mall :D. And I also think this experiment would be hard to do right in the first place since you basically would have to deprive the people from any external stimuli which by itself would probably also already cause side effects.

Most of the claims that "saying no is good for one's health" are grounded in psychology. In other words, they are  not experimentally verifiable. Likewise, health here refers not only literally to physical health, but also to psychological health, which in itself is something hard to define.
Surely, in situations of high stress saying "no" can actually result in some measurable responses, in which case it can be studied within the context physiology and neuroscience. However, this would address only a small part of the situationd covered by the original claim - discarding any effects on psychological health as well as long-lasting effects on the physical health.
To summarize: for a scientific study the claim needs to be made more specific, i.e., apply to well-defined situations and responses.
Disclaimer
I feel that a clarification is needed, lest what I wrote above is interpreted as a negative view of psychology.
I am not claiming that all of the psychology is outside of the scientific method, but a big part of it is - at least outside of being possible to study in a laboratory setting. And this is by no means unimportant part, in terms of the role it plays in our society. While words not scientific often carry negative connotation, in practice any scientist should recognize that scientific method has its limitations - many phenomena (psychological, social, economic, etc.) are not sufficiently reproducible and controllable to study experimentally, yet too important to dismiss.

@user1136 I never said all/whole. I added a clarification, lest my answer is misinterpreted.

I think your claims are likely false and certainly misleading. You need to add citations to support your opinions here

@theforestecologist Could you provide a more detailed comment? The two claims that I make are a) there seems to be no proper scientific research on the subject and b) any such research should be conducted using proper scientific procedures. Your comment doesn't make much sense to me, and I would appreciate a clarification.

@Vadim sure. Overall, you make a lot of your statements sound definitive, but you don't provide much rationale nor any support for your claims. Examples: Sentence 1: you say "most" ; where is that claim coming from? Can you cite multiple studies or a review? Sentence 2: why aren't they experimentally verifiable? That seems like your opinion without any support. Sentence 3: i'd guess a lot of therapists would disagree. Etc. Also, your disclaimer is appreciated but is also narrow in scope given the immense amount of psychology research that has been done in the last 80+ years


text:
Action potential and sodium channels
In this video on electro tonic potential, the tutor says that when the potassium channels open the potential drops from +40mV to -80mV, where the sodium channels have already closed at +40mV.
Now in that case,
wouldn't the sodium channels that usually open at -55mV open up again when the potential is on its way reaching -80mV from +40mV, thereby making changes in all the potential differences that are occurring normally(according to the video)?
Thanks for the help.

The key to understanding this is to digest the fact that there are two gates blocking a normal sodium channel. These gates are called the activation gate (on the extracellular side) and the inactivation gate on the intracellular side. Both of these together, or any one of these alone, if closed, can block the sodium current from entering the cell.

In the resting state, the activation gate is closed and the inactivation gate is open. There is no influx of sodium. Owing to a neurotransmitter release, there is depolarization of the plasma membrane around the channel. As soon as the potential reaches a fixed threshold value, there is a change in the conformation of the sodium channel. The voltage is sensed by a biophysical voltage sensor, a part of the channel.
At the threshold potential, both the gates respond by reversing their state. But owing to the biophysical structure, the response of the activation gate is faster than the response of the inactivation gate. What happens is that the activation gate quickly opens allowing the influx of sodium ions, generating the action potential. The inactivation gate is closing but before it closes, the activation gate has been open for some time and the action potential is already fired due to considerable depolarization.
After some time, the inactivation gate also closes completely, blocking the sodium influx. By this time, the potential is at the peak of the action potential, the potassium channels have opened, and the re-polarisation phase begins. Here the inactivation gate is closed, thouh the activation gate is still open above the threshold potential. As the potential dips below the threshold, again the gates reverse their states but they respond with different speeds. First, the activation gate closes while the inactivation gate is still closed, and then the inactivation gate opens. In this way, during repolarisation, no sodium influx occurs since atleast one of the two gates is always closed.

I hope I answered your questions. Here are further links to understand this in greater detail.

Wikipedia
Mechanism of sodium channel inactivation
Basics of Voltage-Gated ion channels in Neuroscience
Mechanism of Voltage gated Channels in general(Detailed)

A more technical and biophysically accurate version of the diagram.


text:
What are the sites of nutrient digestion and absorption in the human GI tract?
Where does nutrient digestion and then absorption take place for different nutrients along the alimentary tract?

Hi Carlos - Welcome to BiologySE... you're question is a bit vague... especially with the use of the term "food groups" - where have you looked for the answer to this question already?

The saliva from your mouth will slowly start to digest starches.
Then the stomach specializes in digesting protein with enzymes and its highly acidic content.
The small intestine will digest proteins, starchs and carbs (with the help of the enzymes traveling from the stomach).
The liver and pancreas secretions will join in the small intestine will help break down fats and complete digestion.
The small intestin is responsible of absorbing the vast majority of digested nutrients and the water is then mostly absorbed by the colon.
Source: Your Digestive System and How It Works


text:
By what mechanism is NADP+ converted to NADPH in Photosystem I?
Here is my current understanding:
$\mathrm{NADP^{+}}$ takes 2 electrons from Ferredoxin at the end of the electron transport chain to generate $\mathrm{NADP^{-}}$.  An $\mathrm{H^{+}}$ ion in the stroma binds through the extra electron, generating $\mathrm{NADPH}$.  All of this is facilitated by Ferredoxin-$\mathrm{NADP^{+}}$ reductase.
Sources: https://en.wikipedia.org/wiki/Ferredoxin%E2%80%94NADP(%2B)_reductase
http://www.bio.davidson.edu/Courses/Bio111/NADPH.html

Exactly what is your question?

This came off to me as a mechanistic question, I edited the title. I'm unsure why this was closed, though, since some good papers exist to elucidate the FNP mechanism in photosystem I.

OVERVIEW (verbatim from the article)

Plastidic ferredoxin−NADP+ reductases (FNRs) accept electrons
  by two sequential one-electron transfer steps from two
  molecules of the one-electron donor ferredoxin to generate
  their fully reduced hydroquinone state, FNRrd, through the
  formation of an intermediate neutral semiquinone form, FNRsq.
  FNRrd then transfers both electrons as a hydride to the
  nicotinamide adenine dinucleotide phosphate (NADP+
  )
  coenzyme in a single step (Figure 1A).1,2

Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin–NADP+ Reductase and NADP+: The Role of Tyr303 (Institutional access will be required!)
Basically, FNR is a flavoprotein with a stabilized FAD prosthetic group that can alternate 3 oxidation states with 0, 1 or 2 electrons. NADP+ binds in the FNR active site, and recognition of the AMP group causes a conformational change that brings the nicotinamide portion in proximity with the isoalloxazine group of the FAD. Ferredoxin is a single-electron carrier where two molecules of ferredoxin sequentially donate electrons to the FAD group that produces a hydroquinone FADH2. The actual architecture of the charge transfer complex formed in the active site mediates the formal hydride transfer that produces NADPH*. As far as I can tell, the hydride transfer occurs while the ferredoxin is still bound due to the effect electron transfer to FAD has on the pKa and protonation of a Glu312 that stabilizes NADP+ too much in the absence of ferredoxin (source).
NADPH ends up getting released after the catalytic cycle.
*I'm still trying to find some more detailed information on the catalytic mechanism.


text:
Of people who develop Alzheimer disease, are those people genetically predisposed to it?
I have read a lot lately about microbiological pathogens that are found in blood vessels in the brain of patient's with Alzheimer disease (positive association).
So, I am confused whether there are genetic markers and testing of susceptibility to this disease, or whether there is some other type of disease process occurring here (given the microbiological pathogens association). Is that widely discussed in the popular press?

In part, there are in fact numerous polymorphic markers that detail genetic predisposition to AD. Markers can differ between the type of AD they predispose, however: familial versus sporadic, for example. To give a good example, of four isoforms the apolipoprotein ε4 isoform is known to greatly increase the chance one will develop AD.


text:
Why does depolarisation by high intracellular K+ trigger calcium channels opening?
I have learnt that in pancreatic beta cells, glucose being metabolised in the cell causes a high ATP level, which triggers ATP-dependent potassium channels to close. This means that potassium can't leave the cell anymore, which depolarises the membrane and causes voltage-gated calcium channels to open and release calcium into the cell to trigger insulin release. I don't understand why this happens, because both potassium and calcium being positively charged. Wouldn't this depolarise the membrane even more? I thought this would be unfavourable.

Ca2+ is very often the trigger to release neurotransmitter or, in this case, hormones. Ca2+ entry in the cell is important to activate the fusion of secretory vesicles with the membrane in pancreatic beta cells as shown in Fig. 1 (Thurmond, 2000). The function of Ca2+ entry is not so much related to its depolarizing actions.

Fig. 1. Ca2+-mediated insulin secretion. Glucose-stimulates insulin secretion by increasing the ATP/ADP ratio, which inhibits the ATP-sensitive KATP-channels, leading to membrane depolarization and opening of voltage-dependent calcium channels (VDCC), with a resultant major increase in cytosolic calcium, which, in turn, triggers exocytosis. SNARE proteins play a critical role in insulin granule secretion. The linking of the plasma membrane proteins syntaxin and SNAP-25 to vesicle protein VAMP-2/synaptobrevin-2 cause the docking of the vesicle, bringing insulin granules in close contact with the plasma membrane and calcium channels, after opening of calcium channels, the readily releasable pool (RRP) insulin granules located nearby are exposed to high level of Ca2+, resulting in RRP granule exocytosis. Source: Ren et al. (2007)
Ca2+ entry in the cell is potentially toxic and closely regulated. For example, internal stores are actively involved in the release and re-uptake of Ca2+ (Pian-Smith et al., 1988). Although Ca2+ influx will depolarize the cell further, it will not contribute substantially to the membrane potential compared to the effects of K+ and Na+.
References
- Pian-Smith et al., Endocrinology (1988); 123(4):1984-91
- Ren et al.,  J Transl Med (2007)
- Thurmond, Landes Bioscience (2000)

First of all, this is a complex question with no easy answer. Ion channels and electrophysiology can be a very confusing topic. Part of the challenge to understanding these processes is that you need to be able to remember that ions (e.g. sodium, potassium and calcium) are not only trying to move towards chemical equilibrium, but also electrical equilibrium as well.

In the pancreatic beta-cell insulin secretion is tightly regulated. As you state in the question, glucose enters the beta-cell and is metabolized creating an INCREASE in the ATP content of the cell. This increased ATP binds to ATP-sensitive potassium channels and CLOSES them. Remember, these channels are typically OPEN and allow potassium to normally flow OUT of the cell (because that would be potassium flowing DOWN its concentration gradient... potassium concentration is higher inside the cell than outside the cell). Note: This is the opposite for calcium, which would flow INTO the cell and down its concentration gradient (calcium outside the cell is higher than calcium inside the cell).
At the same time the ATP-sensitive channels are acting, there are Na/K ATPase pumps at work to move sodium OUT of the cell and potassium INTO to the cell (against the concentration gradients of both those ions). When the ATP-sensitive potassium channels close, it causes a build up of potassium INSIDE the cell because you have made the cell less permeable to potassium (when potassium can't flow OUT of the cell through the CLOSED ATP-sensitive channels it makes the membrane less polarized - i.e. become less negative or more positive - however you want to think about it).
When the cell reaches a threshold potential (that is, when it becomes depolarized to a certain point), it will cause opening of a type of voltage sensitive calcium channels. At this point, calcium channels open and allow calcium to flow down its concentration gradient and INTO the beta-cells. This calcium entry is required for the release of insulin vesicles through a mechanism that is outside the scope of this question, but unrelated to the calcium channels opening and closing.

The interesting thing about the calcium channels is that they INACTIVATE after a short amount of time and CLOSE on their own. Inactivation and closure is an intrinsic property of that type of calcium channel, and the channels do not REACTIVATE until the cell returns to being polarized once again. This inactivation is what limits the amount of calcium flux INTO the cell, which as mentioned in the other answer can be toxic to the cell.
So, in brief... the ATP-sensitive potassium channels CLOSE, the cell depolarizes when it reaches the threshold potential for the voltage-sensitive calcium channels. Those calcium channels open, calcium flows into the cell and works with other machinery to cause insulin secretion. In the meantime, the calcium channels quickly inactivate and close. The basal ion pumps then return the membrane potential back to its resting state. This return to a polarized resting state allows the voltage-gated calcium channels to 'reset' or reactivate, and then the entire process can occur once again.
I have simplified the explanation and left out some extraneous details - for more information about the specific types of channels see the references.
References to Read More:
(1) Review discussing ATP-sensitive potassium channels and voltage gated calcium channels in insulin secretion.
(2) Comprehensive review from the Endocrine Journal on insulin secretion, which discusses specifically both fast and slow calcium channels, inactivation and insulin secretion.
(3) Review talking about voltage gated channels in insulin secretion from the journal Diabetes.
(4) Open access article with a heavily detailed figure of the beta cell. However, has the different types of calcium channels and other ion channels to help with the understanding of this complicated topic.

As far as I know K⁺ channels remain closed unless triggered. You are saying that ATP closes the channel which means it was already open. How? What is the trigger?

@WYSIWYG the potassium channels in the beta cell are inward rectifying potassium channels (KIR) that are typically open - they are sensitive to the ATP/ADP ratio within the cell... that is, when glucose (the stimulus for insulin secretion) enters the cell it is metabolized and generates more ATP... the channels "sense" this change in ATP and CLOSE in response to that.

There's a great explanation on wikipedia on these channels as well - stated more elegantly than I can... https://en.wikipedia.org/wiki/ATP-sensitive_potassium_channel

@WYSIWYG - the picture from AliceD actually shows the ATP/ADP ratio changing and then an arrow drawn to the K-channel indicating that it closes


text:
How are ions 'pumped' across a membrane during electron transport?
A number of sites (including this one) that provide descriptions of photosynthesis state that high energy electrons 'pump' ions across a membrane. What is the actual 'pumping' mechanism? I've looked at Wikipedia and at a number of YouTube lectures/tutorials but so far have only found statements as to the where and when but not the how of this important process.

This is a good question, but the answer is likely to be very technical, and I think these mechanisms are still bein debated; see for example http://www.ncbi.nlm.nih.gov/pubmed/21545285  calling this "one of the most challenging research subjects in life science" ...

Thanks for your interest. I've had a further hunt round and found an article in Wikipedia on active transport . A little way down there's a section about secondary active transport that I think could be related to the pumping mechanism in photosynthesis - but I'm not qualified to say!

Short answer:
Electrons flow through membranes by floating through kind of channels made out of iron-sulfur clusters.
Long answer:
Let's take a look at the electron transport chain in the inner mitochodrial membrane. There is a proton gradient across the membrane building up a potential difference by pumping protons across the membrane as electeons flow through the respiratory chain. They (electrons) like to flow throught the respiratory chain because they can go from enzyme to enzyme each with a lower standart free energy. These enymes together form one big complex within the inner membrane with Fe-S clusters enabeling electrons to flow through the membrane by giving them a kind of a power stroke (see here).
This as an simplyfied answer on a example.

Thanks for your answer. I think I'm starting to understand this a little. I think what I was missing was that: "Whenever a molecule is reduced by acquiring an electron, the electron (e -) brings with it a negative charge. In many cases, this charge is rapidly neutralized by the addition of a proton (H+) from water, so that the net effect of the reduction is to transfer an entire hydrogen atom, H+ + e -". The quote is from this site that I found really helpful - though I'll need to study it a good deal more. As a layman I found 'pump' misleading.

Nice!  Still, I think it should be kept in mind that these are very recent findings; the structure of complex I was only recently resolved, and the precise mechanisms are likely to be debated for some time to come.

Moreover there are many other kinds of proton pumps that work differently.

Thanks for the additional comments @WYSIWYG: I trust that the principle  remains the same i.e. a set of redox reactions with the H+ transported across the membrane in association with the electron as it 'neutralises' the negative charge of the electron? I'm new to biology so want to make sure I've understood the basic ideas/processes correctly.


text:
Germ layer and platyhelminthes
Some introductory biology textbooks state that sometimes the body cavity is formed from pouches pinched off from the endoderm. So, I am interested in understanding  what 'pouches pinched off' actually means? Also, are platyhelminthes triploblastic or diploblastic (my professor says that they are diploblastic but books write that they are triploblastic).

Could you split this into two questions? Since the two don't seem to have a relation as platys dont have a coelom itself. I get it that they are 2 separate things you talk about but still!

@polisetty you can answer both qs: What does 'pouches pinched off' means and the other one is whether platyhelminthes are triploblastic?

planarians seem to be triploblastic. There is a reference to three germ layers in this paper https://www.researchgate.net/profile/Jose_Martin-Duran/publication/221982471_Planarian_embryology_in_the_era_of_comparative_developmental_biology/links/00b4952ea46adccee6000000.pdf skip to the embryology part. I guess the other two classes too should turn out to be triploblastic


text:
Immunity to one's own microbiome
It seems that a human bite can be very dangerous, because of the myriads of bacterial species found in saliva.  This leads to several questions that, perhaps, may have the same single answer.  But, I'll boil it down to a single question per the comment.
Is there a mechanism by which the body "tames" their own oral bacteria that could otherwise be dangerous pathogens, so that the bacteria don't cause pathology but also don't arouse a typical immune response or inflammation?
No doubt this question has been explored often, but I haven't been able to find a clear answer.

This is a good questions, but it is difficult to answer in brief.  To point toward an answer, consider that many members of the oral microbiome are considered pathobionts, meaning that they are symbiotic in their native niche but pathogenic in other contexts.

Upon reading the article to which you provided a link, it seems that the interactions between different species in the oral bacterial community may be important for keeping potentially pathogenic members of that community in check -- but the article doesn't indicate how that occurs.  I know for example that bacteria can modify the pH of a medium and thereby control bacteria or yeasts that require a specific range of pH.  But in a complex community like the mouth, a change that inhibits some pathogens might well benefit other pathogens.  Are there lots of independent factors analogous to pH?

Please limit yourself to one question per post. Take a close look at your linked reference to see if it answers any of the questions for you. That might help you narrow things down.

One way to identify mechanisms by which the body tames the microbes in the mouth is to observe what happens when those mechanisms are impaired:

Deviation from symbiosis among the bacterial community
  leads to “dysbiosis”, a state of community disturbance. Dysbiosis
  occurs due to many confounding factors that predispose a shift in the
  composition and relative abundance of microbial communities.
  (Dentistry Journal)

1) Immunity
Normal innate, cellular and humoral immunity helps to prevent oral flora from causing infections.
a) When the immunity is impaired due to a disease (HIV/AIDS, cancer...) or long-term treatment with antibiotics, steroids, immunosuppressants or chemotherapeutics, a part of normal flora, such as the yeast Candida, can overgrow and cause oral thrush.

Host defense against infections with Candida spp. depends on rapid
  activation of an acute inflammatory response by innate immunity,
  followed by an incremental stimulation of specific immune responses
  mediated by T-cells (cellular immunity) or B-cells (humoral immunity). (Immunology of oral candidiasis, J Pharm Bioallied Sci.)

Picture 1: Oral candidiasis (source: Wikipedia, creative commons license)
b) Impaired immunity can result in osteomyelitis of the mandible, caused, for example, by the Actinomyces bacteria:

Systemic factors such as diabetes mellitus, agranulocytosis, leukemia,
  severe anemia, malnutrition, or alcohol abuse affect immune
  surveillance and lead to impairing the osteomyelitis
Actinomycotic druses and filaments were detected from the sequestrum
  of the fracture site (Rapidly Progressing Osteomyelitis of the
  Mandible, Case Reports in Dentistry)

2) Saliva
Saliva helps to prevent mouth infections by flushing microbes into the gut and by the antimicrobial substances.

Among such protective factors, the flushing effect of saliva flow is
  the most important one...(Antimicrobial function of human
  saliva--how important is it for oral health?, Acta Odontol
  Scand.)
Importantly, saliva is crucial for defense against microbial species,
  as it is rich in antimicrobial compounds such as hydrogen peroxide,
  lactoferrin, and lysozymes...disruptions in saliva secretion increase the frequency of oral
  conditions such as oral candidiasis, gum disease, and tooth decay
  (caries), as well as respiratory tract infections (The power of
  saliva: Antimicrobial and beyond, PLoS)

Impaired saliva excretion due to a disease (salivary stones, Sjögren's syndrome, untreated diabetes, radiation injury) or drugs (antihypertensives, antidepressants, tranquilizers, diuretics, antihistamines...) can result in dry mouth (xerostomia), which increases the risk of oral thrush and other mouth infections.
3) Lack of substrate for microbial overgrowth
Clean healthy mouth does not contain enough food for microbial overgrowth.
On the other hand, in untreated diabetes mellitus, the abundance of glucose in the saliva promotes the overgrowth of the yeast Candida (oral thrush):

A dry mouth coupled with a higher amount of glucose in the saliva can
  also make for favourable conditions for thrush.
  (Diabetes.co.uk)

Mouth full of food debris due to poor hygiene can promote bacterial overgrowth:

Periodontitis is caused by certain bacteria (known as periodontal
  bacteria) and by the local inflammation triggered by those bacteria.
  Although these periodontal bacteria are naturally present in the
  mouth, they are only harmful when the conditions are right for them to
  increase dramatically in numbers. This happens when a layer of
  bacteria and food debris, known as plaque, builds up and is left
  undisturbed on the teeth...(What is periodontitis, European
  Federation of Periodontology)

The bacteria from normal oral flora often involved in periodontitis: Porphyromonas and Streptococcus (Lumenlearning.com).
4) pH
The normal pH in the mouth is 6.2-7.6 (Journal of Indian Society of Periodontology). When it falls under certain value known as critical pH (~5.5), acids derived from bacterial fermentation of dietary sugars start to dissolve tooth enamel and cause caries. The bacterium Streptococcus mutans is a part of normal oral flora, but is commonly involved in caries (Lumenlearning.com).
5) Low susceptibility of mouth mucosa for certain microbial toxins
Certain microbes, such as Staphyloccocus aureus, which are a part of normal mouth flora do not likely cause infections in the mouth, even when they appear in the mouth in much greater amounts, for example, in food poisoning and even if these microbes can cause severe diarrhea (Centers of Disease Control and Prevention). This is because the mouth mucosa is not susceptible for the toxins secreted by these bacteria, while the stomach or intestinal mucosa is.

This answer is definitely useful, but not quite satisfying.  #1(a) indicates that the immune system is active in manipulating the ratios of oral flora without necessarily eliminating any particular species.  #2 points out that saliva flow constrains the ratios according to the relative abilities of species to find safe niches to avoid being washed out.  #3 indicates that the ratios of different available nutrients affect the growth ratios of different species that depend on specific nutrients.  #4 mentions pH, which can be considered analogous to temperature and will affect species ratios

@S.McGrew What did you expect? There are surely more mechanisms and more specifics, but I don't think I need to cover just about everything. My intention was to show there are certain mechanisms that allow the oral flora to exist without being harmful.

according to species' preferred pH range.  #5 points out that different bacterial species have different inherent ability to break down specific tissues in the body.   All of this supports the idea that oral flora form an ecosystem in which the various member species regulate each others' growth via the usual competition, cooperation, and other such interactions, and that the body "simply" imposes constraints that tend to shape the overall microbial ecosystem.

I would like a better understanding of how and why those constraints work, and how the microflora interact, and what the modes and conditions of stability are.  Links to research on that topic would be welcome!

I personally find it impossible to say why something works when it works normally. Because it just works. For me, the only way to say how it works is to observe mechanism when they are disrupted and conclude from that how they normally work. To go into more specifics, I would need to know what goal, beyond just knowing some facts, are you trying to reach. There were interesting sub-questions in your original question, but that appeared to be broad. You may want to open some of those as separate questions.

re "What did you expect?", I think what I'm looking for is specific mechanisms by which the body regulates a whole community of hundreds of species of microbes.  Or, specific mechanisms by which the body manages to get along with a given pathogen without mounting an immune response to it.  I'm an engineer, not a biologist, and want to know how things work at a fundamental level.  Can't quite bring myself to be satisfied with "it just works" - though I understand that some things (especially in biology) are far from being figured out yet to the level I'm hoping for.

@S.McGrew, "taming" oral microbiome by lack of food for microbes, immune response (cellular and humoral) and antimicrobial agents in saliva are specific mechanisms. I believe that making a more specific answer makes sense when the question is also more specific, in which case we all know what actual goal we are solving.

It's an interesting question.
More interestingly there are a number of articles and a lot of studies are going on to prove that by manipulating oral microbiota, Caries or Periodontal diseases can be prevented.
At this I want to point out as the OP has asked about the body's way of 'taming' the flora, I will share the references of the studies in which the oral flora was manipulated not by body's own mechanism but externally. And this resulted in prevention of oral diseases commonly seen.
This answer is an add on knowledge which I will share, I know not the exact answer since how the oral cavity by itself provides immunity has been satisfactorily answered by @Jan.

Probiotic
therapy or -
bacteriotherapy’ (Rajendhran and Gunasek-
aran, 2010) has the potential to naturally cure and
prevent disease at its early stages by incorporating
beneficial bacteria that can reestablish an ecological
balance or enhance the biodiversity of a microflora. For
example, research showed that individuals with high
amounts of Capnocytophaga ochracea had lower
amounts of P. gingivalis and displayed no periodontal
disease progression. Individuals with low C. ochracea
did exhibit disease progression. In probiotic treatment, a
patient found to have elevated levels of P. gingivalis
could be given C. ochracea probiotics to reestablish a
healthy equilibrium before any periodontal disease
generates.

Here is the article


text:
How can I decrease the generation time of Drosophila melanogaster?
I have a gene deletion strain of Drosophila melanogaster made with CRIPR/Cas9, and now I have to clean the background of this strain (TM6C balancer background) by making backcrosses with wild type. Normally, it takes 12 days for the entire life cycle at 25°C.
How can I decrease the generation time of Drosophila melanogaster?

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site. Adding sources/citations and telling us where you've already looked  would help make it clear that you've satisfied this requirement. Please take the [tour] and consult the [help] starting with [ask] for details. ——— Also, which "life stage", or do you mean lifecycle? Finally, please don't use bold text in excess — it doesn't add anything.

I've edited your post to (I hope) be a bit clearer. Please make sure I've not altered your intended meaning and if you like any of the wording I used please [edit] your title accordingly. ——— Also it would be good if you could mention whether there are any known environmental sensitivities due to your deletion (and tell us what you deleted unless that is secret). If for example your strain was heat sensitive, that would rule out trying growth at increased temperature.

The Bloomington Drosophila Stock Center has a lot of information on Drosophila stock propagation. Their Working with Drosophila Stocks guide includes the following excerpt:

The frequency with which new subcultures need to be established depends on the health and fecundity of the genotype, the temperature at which it is raised, and the density of the cultures. Temperature has a large effect on the rate of Drosophila development. Generation time (from egg to adult) is approximately: 7 days at 29°C, 9 days at 25°C, 11 days at 22°C, 19 days at 18°C.

So, try keeping your flies at 29°C.

Thank you very much。 I try it.

@WiKC — If this answer addressed your problem, please consider accepting it by clicking on the check mark/tick to the left of the answer, turning it green. This marks the question as resolved to your satisfaction, and awards reputation both to you and the person who answered. Once you have >= 15 reputation points, you may also upvote the answer if you wish. There is no obligation to do either.

@tyersome thanks for the edit, I misread the question

You're welcome!


text:
What is this large, lively barnacle?
Yesterday I found this creature in a rocky cove in central California, around mid tide (+ 3 feet). It's about 3-4 inches long. At first I thought it was dead, but it closed its mouth when I removed the tiny white pebble, and rotated the operculum rapidly when I poked the bit of exposed yellowish flesh underneath. I think it's some sort of acorn barnacle, but haven't been able to identify a species with the white shell and distinctive red-and-white color and texture differences on the opercular plates. What could it be?

Update: this is a giant acorn barnacle, Balanus nubilis. Between Pacific Tides mentions that they can vary widely in coloration, and there's a picture of a similarly colored one here.
We had our ID confirmed by email by a representative of the Monterey Bay Aquarium, who added this info:

You beat me to it.  That is indeed a giant acorn barnacle (Balanus
nubilus).  Unfortunately, barnacles can’t survive long after being
detached from their rocks and they’re unable to reattach on their own.
Rocky intertidal zones are harsh environments and animals living in
these areas must deal with both water and air, rapidly changing
temperatures, exposure to sunlight, desiccation, high wave energy, and
predators from both land and sea.
The stringy threads attached to the barnacle in your photo are the
byssal threads of California mussels.  Mussels secrete these threads
to anchor themselves to rocks, each other, barnacles, etc.  It’s very
common to see mussels and barnacles clumped together in high surf
zones.

I think it's a thatched barnacle (Semibalanus cariosus). The iNaturalist app would also be a helpful tool in which to ask this question.

Welcome to the site. This is a good answer, but can you tell us why you think it is the thatched barnacle, and perhaps provide some links with information about these animals? It would really improve your answer.


text:
Single-cell subcloning of BV-2 cells?
I am trying to knock-out genes in BV-2 cell line. However, the majority of protocols require cell subcloning and expanding. I tried to subcone these cells and grow clones in DMEM+10% heat-inactivated FBS+1% PS (usual media I am using)+Insulin-Transferrin-Selenium. My cells did not grow and eventually died. Maybe there are supplements that I can add to the media to promote cell growth from one cell? I am considering using conditioned media from the same BV-2 cell culture after culturing them for a few days. Should it work?

Welcome to the Biology Stack Exchange. Please take a [tour] and visit the [help] for more information about the site and what we do here. This isn't a simple question and answer site, so things are a little different to more conventional forums.

We would need a few more details on how you go about your subcloning to troubleshoot why it isn't working.

As always, consulting reference materials is a good idea: https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/cell-culture-and-cell-culture-analysis/mammalian-cell-culture/poor-cell-growth

I am growing these cells routinely in the lab, and they grow fine with usual media (cell thawing is always successful, they are not contaminated etc.). When I do subcloning i calculate cells so there is one cell in 100ul media. And then i seed them in 96-wp. After they attach i search wells where is only one cell in the well (subclone). And the next step would be expanding the subclones. I read articles where similar things were done and did not find any specific requirements for successful subcloning.

Are your knockouts lethal?

It shouldn’t be, I am knock-outing CB1 and CB2 receptors (separately).  There are also transgenic mice without CB1 (it results in 30% mortality in mice if knockouted in whole organisms). Mouse who doesn't have CB1 receptors in microglia cells are fine as far as know.


text:
Average and lowest degrees of kinship/consanguinity among humans?
I would appreciate insight into the average, median, RMS or any similar measure of relatedness among the current world population - and perhaps something about how rapidly this may be changing. A similar question is how un-related any two humans can be: i.e., what is the lowest degree of consanguinity between the two most distantly related people. The context is an exploration of how humans have evolved tendencies toward racism and other in/outgroup distinctions, when all humans share such a large fraction of DNA with each other, very nearly as much with non-human primates, and about half even with fruit flies. Might be some helpful lessons in there!
Apologies if the question is ill-formed, or answer readily available someplace - I've browsed the Web for several years on this topic, and found nothing I could understand..
Accessible material about most recent common ancestor and identical ancestor point seems to indicate a wide range of both methodologies and results, based mainly on statistical simulations since "hard" genetic structures apparently do not persist. MRCA datings based on mitochondrial and other genetics seem to line up with human behavioral modernity, ca. 200 kya. But there seem to be extreme estimates as recent as 2.3 kya, which implies a lot of mobility and high fertility by some not-so-distant forebears (like Genghis Khan). In any case, IAP may be a better starting point for this shared-anncestry question.
I'm guessing that no human is further than about a 10th~12th cousin to any other. Can't be more that 32nd, since 2^33 is more than the number of living humans!
All thoughts, including guesses more informed than mine, will be appreciated.
~ ~ ~ ~ ~
Addendum - tried to post this as an answer, but it was deleted:
MANY thanks to Zo-Bro-23 for the time, effort and creativity to create his response. I hope it is well-indexed for future explorers to find!
In case useful or interesting to anyone,or sparks further contributions, here were/are my main motivations for this inquiry:

Though having working knowledge of physical and natural sciences, and having minored in anthropology at Uni, I have never really grasped current estimations of "most recent common ancestor" and "identical ancestors point." This is probably due to my poor understanding of populations statistics, but may also reflect the huge uncertainty in and conflict between various MRCA and IAP methodologies. So I'm always seeking a simpler, if less precise, way to understand these propositions. Time-dependent mean/max degree of consanguinity seems like such a heuristic.

The ancestor cone, as mentioned in the Quartz article linked by Zo-Bro-23: I've been using the same term for decades, so I suppose it's a natural way to describe something that isn't precisely conic or biconic. For me, the description follows naturally from the notion of the light (bi-)cone in Minkowski diagrams, extending the idea of a photon's world-line to that of a genomic cluster.

I've long wondered about both genetic and memetic (e.g. religion, language, cuisine, art, toolmaking) contingency as they result from and induce changes in the topology of the ancestor cone. There are numerous groups that for geographic, religious or other reasons have been largely independent since we all left the Great Rift Valley (or wherever humanity arose). Having studied a bit of cultural diffusion, I've wondered if genetics, linguistics or anything else might give insight into how often and effectively the occasional Marco Polo or Squanto voluntarily or involuntarily acts as emissary between cultures. Many of these exchanges have apparently had significant cultural influence, and in some cases perhaps genetic as well. It might take very few such, over hundreds or thousands of generations, to lower substantially the degree of consanguinity of all humans.

This does not even count the much larger migrations, both voluntary (e.g. Bering Strait crossings that peopled the Americas), semi-voluntary (the Irish famine that so strongly influenced US culture) or entirely unwillingly (the African slave trade). Another question concerns the influence of sex-linked characteristics in Africans on the general American population, where for several centuries, the great majority of interbreeding appears to have been between White males and (usually unwilling, one imagines) Black females. Perhaps too hot a topic for research?

Pedigree collapse is a conflating factor of special interest to me, as most of my known ancestors belonged to a relatively small ethnic group that favored in-marriage, and (due to low social standing) was not attractive for outsiders to join. So other than couplings of necessity (rape, isolated populations), our cone is probably pretty narrow down to the bottom of the historic timeline. Not directly related by mechanism but probably relevant is the Galton–Watson process, the extinction of family names when a named lineage runs out of (usually male now; perhaps less so in "primitive" matriarchal societies) descendants.

Not long ago, it was popularly believed that explosive population growth since the industrial revolution resulted in the number of living humans exceeding the number deceased. Current credible estimates seem to place the latter at slightly more than 100 bn, - a dozen ghosts standing behind each living soul. Theme for an SF movie?

There is also the question of speciation. It is widely accepted that Homo sapiens and Homo neanderthalensis interbred to a considerable degree. This would, of course, violate pre-cladistic notions of what constitutes a species. (The cited Quartz article could have been titled "Everyone on Earth is actually your cousin - including some non-humans." And if all humans are at least 15th cousins, how far are we from other living families, even phyla?) I believe that barring "lost world" scenarios, we have been alone on the planet for all of historic time, hence for the lives of most H. sapiens. But if we date humanity to behavioral modernity, and plot the ancestor cone with a logarithmic or horizontal axis (or even force it into a cylinder of constant width), the influence of some of these factors on present-day consanguinity might be seen as comparable to those of posited bottlenecks like the Toba catastrophe, climate change, pandemics etc.; and on a smaller scale, founder effects like the peopling of the Pacific islands and Australia.

It's interesting that you say you've been searching/browsing the internet and haven't seen anything (I believe you.) I wasn't even looking for this when I came across an article (a scientific paper) on genetic differences between populations based on geographical distance. I wish I could remember where I saw it, I'd post a link. I don't know just how much literature there is on the subject, but there's definitely some out there.

@cTen, sorry that I took so long to answer. Although I found an article that states the final answer of "15th cousin", I didn't understand the equation that author used, so I just derived my own equation from start. I hope my answer is correct  Please feel free to edit or comment if you think that anything is wrong or if you didn't understand something I went over.

TL;DR: Most humans would be around your 13th cousin to your 15th  cousin
Please feel free to edit the formatting of my equations to make them look better.
Deriving an equation
For simplicity's sake, we are assuming that only "blood relations" count. What I mean by this is, your mother's sister's son will count as your cousin, but your father's sister-in-law's daughter will not count as your cousin. Marriage relations will not be counted, and only birth relations will be.
Let's tackle this step by step. We are trying to find the degree of kinship when the number of relatives you have in that degree exceeds 8 billion. However, let's start by simply deriving an equation to find the number of cousins you have in a certain degree. For example, your siblings would be degree 0, first cousins would be degree 1, and so on. Let's denote this by the variable n. Now, given a person in any degree of kinship with you, you would share an ancestor with them. That is the definition of kinship. Given a person in degree n with you, your closest common ancestor will be n + 1 generations from you. That means that with your siblings (degree 0), your closest common ancestor is 1 generation from you (your parents). That is simple. Now, we want to find out how many common ancestors you have in that generation. Again, this is fairly simple. That would be 2n + 1. This can be understood by the fact that you have 2 parents, each of them have 2 parents, each of them have 2 parents, etc. The number of ancestors is getting multiplied by 2 each time. However, the number of ancestral couples you have in that generation would be 2n + 1/2 or simply 2n.
Now, let's assume that everyone has x number of children. This means that each of those 2n people would have x number of children. The number of children in the next generation would then be 2n * x. Each of those children will have x children, and so the number of children in the next generation would be 2n * x * x or 2n * x2. Hence, the formula for the number of people in your generation with whom you share this common ancestor would be 2n * xn + 1 (since the original ancestors are n + 1 generations above you).
However, we are not done yet. Of these children, some of them might be duplicates. What I mean is, you have 4 grandparents. We have assumed that each of them have x children and that each of those children have x children. So the total should be x2 children in the end. However, you count as both your father's child and your mother's child. This means that there will actually be less than x2 children. However, we only care about you, so we can just subtract the places where you are duplicated. This is essentially xn duplicates. Logically, that's because each of your ancestral generation (except the last one) are having only x children instead of 2x, which is value that we get when we count the two parents. So, the final equation is as follows:
c = (2n * xn + 1) - (xn + 1)
where c is the number of cousins you would have below a certain degree, given that x is the average number of children per person, and n is the degree.
A couple of notes on the equation

We are subtracting 1 to account for you - You are not your own cousin
This will not work for siblings - You will get one less than the actual number

Testing the equation
If everyone has 3 children, you would have 14 first cousins. Your mother will have 2 siblings, and each of them will have three children. This is a total of 6 cousins from your mother's side. You will also have 6 cousins from your father's side. Added to your 2 siblings, that is a total of 14 (6 + 6 + 2). From the equation we get:
c = (2n * xn + 1) - (xn + 1)
Since everyone has 3 children, x = 3.
Since we are looking at first cousins, n = 1.
So the equation is:
c = (2n * xn + 1) - (xn + 1)
c = (21 * 31 + 1) - (31 + 1)
c = (2 * 32) - (3 + 1)
c = (2 * 9) - (4)
c = 18 - 4
c = 14
This means that we have 14 first cousins (if everyone has three children). Since this is what we arrived logically, the equation must be correct.
Although this is not a formal proof, I did go over this in my head for many hours, and it seems to work fine. Please comment if you have any revisions for the equation, and I am more than happy to make an edit.
Some caveats
Until now, we have assumed that everyone has exactly three children. However, this is not the case. Since we only need an approximate for our final answer, we will be using the average birth rate value. This means that most people will have x number of children. Some might have none, some might have many. However, using this value should give us a fairly good approximation.
Also, according to Rutgers anthropology professor Robin Fox, 80% of all marriages in history have been between second cousins or closer. This means that there you will have a lot less cousins than predicted by the equation, since even though we are assuming everyone to have x number of children, two people together are having x number of children, and so the total number of children in a generation will be much lower than predicted. Since inbreeding is so common, there's also a chance that you could be much further from someone than predicted by the equation.
Nevertheless, let's try to do some calculation. Before that, we need to think a bit more about population genetics. In India (where I am from), there is mostly only intermarriage (Indians marrying Indians). Although this is starting to change now, it was more or less like that for a long time. Because of this, there is a very low chance that I will be related to an American. We might have a common ancestor, but we might have to go as far as the first Homo Sapien for that. Because, of this, I might be much more related to a random Indian than a random human being. I have done some calculations for you below, but try experimenting on your own:
Rearranging the equation to find the degree of kinship
We will rearrange this equation to solve for n (the degree of kinship):
c = (2n * xn + 1) - (xn + 1)
c = (2n * xn * x) - (xn + 1)
c ≈ xn (2nx - 1) - We are ignoring the 1 because it is insignificant when xn is large enough
c ≈ (2x)nx - We are ignoring the 1 again because 2n is going to be very large for these problems
log c ≈ (n log 2x) + log x
log c - log x ≈ n log 2x
n ≈ $\frac{log c - log x}{log 2x}$
Since we are making some approximations in this rearrangements, we will need to do some trial-and-error work using the original equation in order to ensure that the answer is correct.
Calculation 1 - How many degrees is an Indian away from me?
Value of x: Average birth rate in India: 2.20 births per woman
Value of c: 1.38 billion
n ≈ $\frac{log c - log x}{log 2x}$
n ≈ $\frac{log (1.38 * 10^9) - log 2.20}{log 4.40}$
n ≈ $\frac{9.1398790864 - 0.34242268082}{0.64345267648}$
n ≈ $\frac{8.79745640558}{0.64345267648}$
n ≈ 13.6722663953
Verifying our answer
Value of n = 13
c = (213 * 2.2014) - (x13 + 1)
c = (8192 * 62218.2127343) - (28281.0057883 + 1)
c = (509691598.719) - (28282.0057883)
c = 509663316.713 ≈ 510 million
Value of n = 14
c = (214 * 2.2015) - (x14 + 1)
c = (16384 * 136880.068015) - (62218.2127343 + 1)
c = (2242643034.36) - (62219.2127343)
c = 2242580815.15 ≈ 2.2 billion
This means that I have roughly 510 million 13th cousins and roughly 2.2 billion 14th cousins.
Thus, the furthest an Indian can be is my 14th cousin.
Calculation 2 - How many degrees is another human being from me?
Value of x: Average birth rate across the world: 2.3 births per woman
Value of c: 7.9 billion
n ≈ $\frac{log c - log x}{log 2x}$
n ≈ $\frac{log (7.9 * 10^9) - log 2.3}{log 4.6}$
n ≈ $\frac{9.89762709129 - 0.36172783601}{0.66275783168}$
n ≈ $\frac{9.53589925528}{0.66275783168}$
n ≈ 14.3882105944
Verifying our answer
Value of n = 14
c = (214 * 2.2015) - (x14 + 1)
c = (16384 * 136880.068015) - (62218.2127343 + 1)
c = (2242643034.36) - (62219.2127343)
c = 2242580815.15 ≈ 2.2 billion
Value of n = 15
c = (215 * 2.2016) - (x15 + 1)
c = (32768 * 301136.149634) - (136880.068015 + 1)
c = (9867629351.21) - (136881.068015)
c = 9867492470.14 ≈ 9.9 billion
This means that I have roughly 2.2 billion 14th cousins and roughly 9.9 billion 15th cousins.
Thus, the furthest that any human can be is my 15th cousin.
Evaluation of results
Although these results show that we are all very close (depending on how you evaluate the results) in terms of kinship, there is another factor to consider. Through a phenomenon known as pedigree collapse, it is estimated that we share many common ancestors. That is, our great-great-grandfather from our mother's side might be the same as our great-great-grandfather from our father's side. This means that most people will be further than calculated by this equation. For example, if two cousins had a child, that child would only have six great-grandparents, not eight. Thus, that child will have less cousins than somebody else. We have also not considered marital relationships, and have only considered birth relations. Hence, the actual answer to your question might vary significantly from the values we calculated.
To learn more about this field, I would recommend checking out this article. It is very well-written in my opinion.

One useful concept that you can use to do your estimations is "genetic distance" as is commonly measured using "fixation index".
Basically what you to is that you estimate/calculate the average number of pairwise differences if you compare chromosomes from people within one population (population A).
Then you compare the number you get with the average number of pairwise differences if you take one person from population A and another person from population B.
If the average number of pairwise differences within population A is 900 and the average number of pairwise differences between a person from population A and a person from population B is 1000 you get the genetic distance as measured with fixation index as "((1000-900)/1000)" = 0.1.
You are asking:
"what is the lowest degree of consanguinity between the two most distantly related people."
Here is a "Cavalli-Sforza" diagram showing how related different people are using the fixation index method:

I think the two most different peoples are some group of African pygmies and people on Papua New Guinea. (I can't find the link right now). One reason might be that Africans have no neanderthal admixture while people on Papua New Guinea have most of all, above 4 percent according to some estimate.
Note that as humans are "diploid", we have two copies of most chromosomes. Therefore you can in principle calculate how closely related you are to yourself using the same method.
Because of for instance "migration bottlenecks" African peoples tend to have the most variation among them.


text:
What is this fungus in my plant growth medium?
I am growing S. lycopersicum on 1x Gamborgs medium and have been getting some fungal like contamination. The media contains 0.2% sucrose and Bacto-Agar. Plants are grown at a 21 c - 20 c day, night cycle. The contamination is characterised by squiggly string like structures that penetrate the agar. Structures vary in size but are usually 1-3 millimetres.

EDIT:
Under Compound microscope:
100x

200x

400x

any chance you could pick a few out and get pictures on a slide under a compound microscope?

And an overall photo of the fungal colonies if you can get them. Also: this might be some use. They list several genera with spiral hyphae.

I will upload the compound now, it's not very clear as the structures are buried in the agar.

I have tried putting it under a slide but the stucture does not stay intact

Interesting - I don't see any cellular structures, but, as you say, this might be because of integrity and clarity issues. Could it be the track of something like a nematode or a protozoan, as it looks like a burrow?

Burrow like a leaf miner caterpillar might make inside a leaf that is. Though the regularity of the shape makes a biological structure more likely. Could you get a sample from each end and see what's there? An inverted microscope might be able to give you some depth if you are looking through the agar, but optical clarity will be a problem with the agar. Another thing to check would be to see if you can get it to replicate - take a sample onto a fresh plate (no plant) and see if it multiplies/grows.

@bob1 Sorry for the delay on this, you are correct, nematodes! We haven't verified which species, but they appear to be plant parsitic (based on presence of a needle like stylet). My guess is the nematode leaves a track of contamination, resulting in these interesting tracks.

That would make a great self-answer, especially if you get the species narrowed down. I won't be any help there, never done any nematode ID before.


text:
What percent of the population has some form of synesthesia?
Data I am trying to get my hands on:

What types of synesthesia (e.g. Grapheme-color synesthesia,  Chromesthesia, etc.) are most common across the population?
What percent of population has that type of synesthesia?

It would also be great if there's geographical (genealogical) data on what types of synesthesia are more common to what areas.
What percent of the population has what type of synesthesia?

The phenomenon
Synesthesia is a neurological phenomenon in which a stimulus in one sensory or cognitive pathway triggers an experience in another.  Some hallmarks:1

It tends to be developmental, arising early in childhood.
It is involuntary.
It is stable over time (i.e. the same stimulus leads to the same sensory experience).

Epidemiology
The best paper I found on the issue is by Simner et al, 2006.2 The authors first review prior literature on the topic and then describe their own methodology and study addressing the question of prevalence. Regarding prior research:

Estimates of the prevalence of synesthesia have diverged widely....estimates range from 1 in 4.....to 1 in 25000 - 100 000.

Not so helpful.
They point out some problems with prior studies: one group of surveys relied on self-referral and made the (conservative) assumption that all non-responders to an invitation to participate were non-synesthetes. Another set of studies avoided this problem by questioning every member of a participant pool but established the prevalence only “subjectively” (their wording, although I note that this is an inherently subjective phenomenon!).
Simner's own group used a validated survey questionnaire about specific synesthetic experiences (the specificity and prior validation of this overcoming the  "subjective" aspect in their view). They found an overall prevalence of 4.4% for any type of synesthesia. Importantly, the male: female ratio was not significantly different from 1 in this group, in contrast to many prior studies which have found a marked female predominance, ranging from 2:1 to 5:1 (references in Simner's paper for those interested).
Modalities of experience
To address your question about the types of sensory experience involved, I turn to a more recent review article1 that compiled results from multiple studies. In this report, grapheme-color type synesthesia was most common (86%). These participants see a number or letter and experience a particular color in association. This was followed by followed by time-space type (62%), a group who associates units of time with a particular space relative to their body.  The third most common was music-color type (41%), which is fairly straightforward. The majority experienced more than one type (clearly, given the percentages).
Here is a graph showing the percentage of the cohort who reported particular synesthetic experiences, grouped according to the category of inducer:

Note that the most common type mentioned above, grapheme-color, includes all three of the first categories - "digits," "letters," and  "words" on this graph. Although only the inducers are listed here, the most common associated perceptions were indeed color (97%), followed by spatial configurations (62%). In most cases the color was static (73%) but in some people it moved in a specific direction (16%).

Niccolai V1, Jennes J, Stoerig P, Van Leeuwen TM. Modality and variability of synesthetic experience. Am J Psychol. 2012 Spring;125(1):81-94.
Simner J1, Mulvenna C, Sagiv N, Tsakanikos E, Witherby SA, Fraser C, Scott K, Ward J. Synaesthesia: the prevalence of atypical cross-modal experiences. Perception. 2006;35(8):1024-33.


text:
Microtiter Dish Biofilm Formation Assay- Pseudomonas and Crystal Violet
If Pseudomonas is a gram negative bacteria, it does not retain crystal violet but why is it that so many people are using crystal violet staining in theri Microtiter Dish Biofilm Formation Assay?

Could you provide more context? A citation to a paper that uses this assay?

heres an assay citation: http://www.ncbi.nlm.nih.gov/pubmed/21307833

I think the answer is along the lines of: gram negative bacteria still use glycans externally when they form biofilms and stain with Methyl violet as a result.

So effectively, we not not actually enumerating the number of cell but instead the extend of the biofilm matrix?

Using the Gram stain for differentiation between G- and + requires the addition of alcohol, the critical step in Gram staining. Actually the first step, simple staining, goes the same for all types of bacteria. All bacteria gain the stain, but addition of alcohol makes the lipid in bacteria like Pseudomonas to lose it.


text:
Why do human females have permanently prominent breasts?
Humans seem to be the only animal whose females have breasts that permanently have a "full" appearance, ie a prominent amount of tissue even when not lactating, whereas other species' breasts seem to almost totally "deflate" when not longer lactating.
Why is that?
This feature has costs to the organism; significant biomass is dedicated and perhaps mobility is impacted. Given there are costs, for the feature to have come into existence, evolution/adaptation principles suggest there must have been some advantage.
Is there some biological advantage?
Are they vestiges of an adaptation that gave a significant advantage to some prior species or in some specific (presumably cold) prior environmental conditions?
Is there any credible research to support certain reasons?

My suspicion is that although genders can be distinguished easily enough, even from a distance, using other secondary characteristics, the answer may have an anthropological/social answer, rather than a biological one.

@Always I have changed the question to "primates", but there seem to be very few. Hand on... when not lactating aren't bovine udders "empty"? Whereas human breasts stay "full" in appearance?

@Always I've retracted the edit and gone back to a more general statement, but clarified that they more or less appear as if lactating all the time. Other species' breasts enlarge when lactating, but basically almost totally "deflate" when not lactating. This is a serious question by the way. I think it is clear enough now.

@AlwaysConfused Use comments only for requesting clarification or providing suggestions in the context of the post. Do not use comments for discussions. Some of your comments were not even directly related to the question.

there are tradeoffs and constraints in adaptive evolution, e.g. breasts swell substantially when breastfeeding, perhaps the non-lactating state represents a middle ground where it is easy to make swell when needed but keep them small at other times

You may be interested in Breast asymmetry, sexual selection, and human reproductive success.
Abstract:

Breasts of human females are large compared to those of closely related primate species,
  and they can thus be hypothesized recently or currently to have been subject to directional
  sexual selection. Here we show that (1) large breasts have higher levels of fluctuating
  asymmetry than small breasts, (2) breast fluctuating asymmetry is higher in women without
  children than in women with at least one child, (3) breast fluctuating symmetry is
  a reliable predictor of age-independent fecundity, and (4) breast fluctuating symmetry
  appears to be associated with sexual selection. These conclusions were similar in studies
  from two cultures differing in fecundity and brenstfeeding traditions (Spain; New Mexico,
  U.S.A.). Choosy males that prefer females with symmetrical breasts may experience a
  direct fitness benefit in terms of increased fecundity and an indirect benefit in terms of
  attractive or fecund daughters.

Some quotes from the text:

The size of breasts in human females is large compared to that of other primate
  species, and there has thus been a recent evolutionary change in breast size.
  Human breasts are characterized by their large size and rapid development prior
  to and during puberty, when growth of other body parts also reaches a high level.
  They can thus be considered costly structures in terms of energy use. …
  Heavy investment in breast development during puberty may seem puzzling
  because the functional significance of breasts is far from obvious. There is no
  or little relationship between breast size and production and composition of milk
  in current industrial societies (reviews in Anderson 1983; Cant 1981; Low et al.
  1987), and breasts have therefore been hypothesized to constitute a deceptive signal
  used by women to attract preferred mates (Low et al. 1987). In prehistoric
  human populations, conditions may have been different, when mother's milk
  was the sole source of nutrition for young children and when resources often
  may have been more limited than in present industrial societies. In this study
  we show that large breasts tend to be more asymmetric than small breasts. In
  prehistoric societies, where resources were likely to be less available or more unevenly
  distributed among women, breast asymmetries are likely to have been much
  larger than in present industrial societies with relatively easy access to resources. …
If the relationship between breast size and fluctuating
  asymmetry is robust, we hypothesize that a directional preference for large, symmetrical
  breasts, as apparently found in some cultures (Ellis 1954), can be maintained
  in the population because selection for large breasts will be balanced by
  selection against asymmetrical breasts
We also show that breast symmetry is a reliable predictor of age-independent
  fecundity, and that choosy males that use breast symmetry as a cue in their mate
  choice will experience an advantage in terms of reproductive success. Breast symmetry
  can thus be considered a reliable signal used in intersexual communication.

There are two theories that I find attractive regarding the prominence of the human breast. AS many have pointed out, human breast are really strange in mammals. Chimps are flat chested and have no problem nursing their young. And most of the female breast is fat tissue rather than milk glands (which grow during pregnancy and are mostly degraded after lactation stops)
theory 1
Human breast are under sexual selection. Men like big breast. So it gets selected for. There is much justification reported such as breast being a status of health (plenty of fat reserves) and estrogen levels, and thus a proxy for fertility.
However I have not seen any real data to back such an idea, such as A-B cup women being less attractive than C-D cup women. Nor data that women with small breast are less fertile than women with bigger breast.
theory 2
Anti smothering device. Human babies have no snout. So without a prominent breast to create an air space between the body of the mother and the nose of the baby, the baby would suffocate itself when nursing. And a chimp baby does have more of a snout than a human baby.
It is an intriguing idea. However it is also known that human breast does grow during pregnancy, becoming more prominent (particularly apparent for women with small breast). And such gains can be lost once lactation stops. So with that said... is there a reason why the female breast needs to be elevated all the time and not just after pregnancy. I have also not encountered any evidence that women with small breast are smothering their babies when breast feeding.
So at this moment I am leaning towards a hybrid idea...a hypothesis of my own.... that the human breast initially became more prominent for a biological reason.. perhaps a truly flat breast which chimps have really does smother babies without a snout. However once these small breast emerged, they came under the attention of men, and were sexual selected to a far larger size that we see today.

I think I remember reading once from Desmond Morris, and possibly from the Naked Ape, that (at least) one of the reasons that humans have large breasts is because they resemble to the buttocks.
It's definitely because of sexual selection, and apparently, it's also connected to the fact that lot of our body language messaging comes from our front side. (Contrary to some other apes that can have larger or swollen buttocks for sexual messaging).

Yes,  I recall many years ago some anthropologist postulating the signal of presented buttocks of a receptive female is more difficult with an upright posture, so breasts could have evolved to mimic this signal.

Even though human females' breasts appear full, they're only filled with milk after giving birth or parturition. Other times they're mostly made up of fat.
And they're full mostime probably only to signal the males that they're capable of raising a baby.

Tanvi- can you add some references to your answer? We generally appreciate references to external links/sources for all answers on this site. Thanks for your contribution!

Ya sure! Here are the links I referred: http://googleweblight.com/?lite_url=http://www.livescience.com/32745-why-do-women-have-breasts.html&ei=0AWhxY8O&lc=en-IN&s=1&m=890&host=www.google.co.in&ts=1474395463&sig=AKOVD66SUPVRn9NeVo3Cmq5drZDBoU-YGQ
https://www.quora.com/Is-there-an-evolutionary-reason-for-why-only-human-females-have-permanent-breasts-among-all-other-mammals                  Is this okay?

That does not answer why they are not annulled after menopause.