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What is sense RNA?
I heard my professor use this term.He said that it is a RNA that has the sense of synthesising the protein. But there's no authentic online source to verify it, except this one (biology-pages.info) which says:

Messenger RNA (mRNA) is single-stranded. Its sequence of nucleotides is called "sense" because it results in a gene product (protein). Normally, its unpaired nucleotides are "read" by transfer RNA anticodons as the ribosome proceeds to translate the message.

So my question , is mRNA or the pre-mRNA called the sense RNA ?

I suppose it could be, considering that things like siRNA use "anti-sense" sequences to form double-stranded RNA, targeting it to the degradation pathway, but I've never heard the term before. It's kind of like we hear the term "disgruntled" all the time, but no one is ever described as being "gruntled".

When I see this it seems logical to call every mRNA sense RNA.

Both mRNA and pre-mRNA would be considered "sense"
The term "sense" means that the strand is the direct coding strand. That is, the strand that has the proper codons to be translated into the protein of interest. This term can be applied to both DNA and RNA.
The term "anti-sense" means that the strand is Watson-Crick complementary to the "sense" strand. Likewise, the term can be applied to both DNA and RNA.
The "anti-sense" strand of DNA is used as the template to create an RNA transcript that copies the "sense" strand of DNA. Therefore, the mRNA is always "sense" regardless of its stage of maturity.


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Why do ostriches have wings?
Wings serve most birds for flying, or (as in penguins) for swimming. But ostriches, which exclusively use only their legs for locomotion, still have wings. Why?

Watch Planet Earth II - Grasslands. There is apparently a funny use for those wings :)

Related: Why don't mammals have more than 4 limbs?.

There is a common misconception that a selective process is needed to remove a feature from a population. However, the correct approach is quite the opposite: selective processes normally maintain a feature in a population: if a given feature stops promoting selective advantage, its corresponding genes start to "erode" and the feature disappears from the population (and that can happen in different rates, depending on several factors: have in mind that maladaptative features do exist).
That being said, the maintenance of wings in ostriches indicates us that there must be a reason for it.
It has been hypothesised that wings:

Improve balance when running;
Helps regulating temperature;
Serve as mating display.

(source: University of Washington)

What do you mean
"by genes start to erode"?

Imagine that the mutation rate is the same along all the DNA. We have 2 genes, one that gives advantage and one that stopped giving any selective advantage. Thinking about the population as a whole, the first gene remains almost the same: mutants are removed. But the second gene starts accumulating mutations. That's the "erosion" in my answer. It's not a common term in evolution, I borrowed it from Sean Carroll in "The making of the fittest".

this doesn't answer the question, the op is asking why they have them, not why they haven't lost them.

And that's precisely what I answered.

They are vestigial structures.
Vestigiality refers to genetically determined structures or attributes that have lost some or all of their ancestral function in a given species, but have been retained during the process of evolution.

The emergence of vestigiality occurs by normal evolutionary processes, typically by loss of function of a feature that is no longer subject to positive selection pressures when it loses its value in a changing environment. The feature may be selected against more urgently when its function becomes definitively harmful. Typical examples of both types occur in the loss of flying capability in island-dwelling species.

In the case of an ostrich,  its ancestors used wings to fly,  but the  development of  faster running abilities,  keener eyesight and a paucity of capable predators allowed the bird to  no longer receive positive selective pressure  to have " functional"   wings.
It's late.  I'll add more detail in the am.

I am not sure vestigial is the correct term in this case. Since the wings have acquired (or never lost) another function during male display. Furthermore I think they help balance while running.

@have fun : I thought about that, but really vestigiality can be used in instances in which an organism's feature has lost "SOME or all" of its "ancestral function." In this case, the ostrich has lost SOME of its wing functionality (flying). So I think vestigiality still applies.

Why not?
Since the wing on a ostrich does not harm the animal, there is no selection pressure to remove it from  the population. And male ostriches do use their wings for mating displays. So it isn't completely without use.

Or to put it a bit differently, ostriches with wings the size they are are not at a competitive disadvantage to those with smaller (or larger) wings, so when/if random size changes happen, there's no preferential selection.  At least not in the time span we can look at: it's possible that if we came back in a few million years, ostrich descendants would have smaller wings, or they might not be visible at all.  (Though the genes might be there, like the "sonic hedgehog" gene in snakes: http://news.nationalgeographic.com/2016/10/snakes-grow-legs-evolution/snakes-grow-legs-evolution/ )

source: Stack Exchange

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Molds associated with Aflatoxin?
I've been reading how some molds may be carcinogenic. In particular, molds associated with the fungus metabolite, Aflatoxin.
Are the types of mold that produce this toxin, present in buildings/showers/domestic environments, or do they only grow on food-stuffs?

I've made a few linguistic changes. Also fungus is singular, fungi plural. Correct this in answer too.

Strictly speaking the common bread mould Rhizopus sp. does not produce aflatoxin.
The fungus Aspergillus flavus which belongs to the class Ascomycetes secretes aflatoxin. It attacks cereal grains , legumes, tree nuts. The fungi are green in colour and 'mould' like in appearance.
The fungus attacks the food stuffs and storage grains. So under favourable conditions it may grow in your store room if it finds food for its growth. Also Aspergillus can grow at temperatures as high as 48°C and even at low temperatures like 5-8°C.
Edit: On being asked for sources I include some which strongly support my claim
1. For suitable conditions of growth of the fungi visit https://en.m.wikipedia.org/wiki/Aspergillus_flavus and read under the Environment heading.
2. Visit https://bioweb.uwlax.edu/bio203/s2013/ernst_ale2/habitat.htm and read from " Aspergillus flavus is omnipresent " upto " Aspergillus may also grow on or inside walls in homes, especially if the house is damp or has been damaged by flooding. "
3.https://www.moldbacteria.com/mold-types.html this site provides a list of different fungi found in our homes. Here you can find Aspergillus flavus to grow in flower pot soil. Moreover other species of Aspergillus are found in kitchens and bathrooms.

So it is impossible for it to grow on walls?

I presume it cannot grow directly on walls unless it gets nutrition and moisture for its growth. Now if there is a damp wall the fundi may find some organic matter and may grow on it.

Sorry in the third line it is fungi

Including reliable citations within your answer to back-up your claims, is essential. Please consider adding the sources of the information you used, into your answer, as soon as you're able to. Thank you :)

For suitable conditions for the growth of the fungi see https://en.m.wikipedia.org/wiki/Aspergillus_flavus and read under the Environment heading, next visit https://bioweb.uwlax.edu/bio203/s2013/ernst_ale2/habitat.htm and read from " Aspergillus flavus is omnipresent.....  " upto "Aspergillus may also grow on or inside walls in homes, especially if the house is damp or has been
                                                   damaged by flooding. "

I have included some sources, check the answer for them.

This confuses me, showers are "damp". Does it or does it not grow in showers? Assuming there is no food in the bathroom.

also the reference is a student project. Some of its references are "mold removing sites" which I dont consider unbiased. I cant find any info on where and how it grows from the references in this student project. Let me know if you find something.

I will try to include more sources as soon as I find them. Moreover you can  think about this simple logic, the metal mouthpiece if your shower can hold water for a far less time than the cracks in walls or old air conditioners can , so naturally the fungi has more chances to grow in cracks of walls than in your shower.

https://www.moldbacteria.com/mold-types.html this site provides a list of different fungi found in your home. Here you can find Aspergillus flavus to grow in flower pot soil. Moreover other species of Aspergillus are found in kitchens and bathrooms.

Thats still not a research reference. Thanks alot for looking tho! This material has been to some help, and I can keep look from these places myself aswell. Its hard to dig for stuff like this without any academic traning in biology.
Let me know if you find somthing more rigorous btw!!

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Which are the best apps and websites for insect identification?
My kids keep asking me to identify some insects they found, and I am often caught off guard, as I have very little matter knowledge.
I have found the Insect Orders app quite useful, but still quite challenging.
Is there anything else, in terms of apps or websites, which is better for insect identification?

I think many reliable websites and apps of high quality will have a relatively narrow scope both geographically and taxonomically. The exception might be some keys to the level of orders and maybe some families. I therefore think this question is rather broad and opinion-based. Where do you live and what level of taxonomic determination are you after (species, families, orders etc; what taxonomic groups)?

@fileunderwater, though I 100% agree that targeting resources that focus on specific geographic locations is best, there are a number of general sites (such as bugguide and even this site) which can lead to identification of insects from a broad range of locations. If the OP is looking for more general resources, then I think this question is valid (i.e., not too broad) and should be reopened. IMO.

However, given my last comment, @Joe_74, you could provide a more specific location, and we could try to provide some resources that are more specific to your location.

There are not many beginner-friendly apps that I am aware of. However, there are a few websites you can use.
BugGuide has a relatively nice picture-based search system. You will also gradually learn to easily identify various characteristics of an insect, thus making your search easier.
Insect identification is more beginner-friendly and more suitable to your kids.
You can also ask either here, or perhaps in the reddit community if you have trouble identifying a particular bug.
If they become interested I would recommend searching your local book store or library for a good field guide (depending on your location). Entomology can be a fun excuse to get out of your house and learn something in the process.


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Absorption of pentoses in intestine
Why pentoses are absorbed by facilitated diffusion in intestine? Wouldn't it be futile because , when the pentose concentration is lower in intestine, the pentoses would diffuse back to the intestinal lumen? So does our body looses them? If not then what is preventing this backflow?

First, pentoses aren't a major source of nutrition, at least for humans. That said, pentose absorption works the same way a lot of nutrient absorption works: the "magic" of metabolism, with respect to diffusion.
Pentoses leave the intestinal lumen, entering the intestinal cells, where their concentration is lower. From there, they again travel via facilitated diffusion into the bloodstream, again because their concentration is lower in the bloodstream.
From there, we can expect one of two outcomes: either an equilibrium will eventually be reached(i.e., lumen==intestine==blood), or the bloodstream pentoses need to be metabolized into something else. Indeed, certain pentoses (specifically D-ribose; I'm not sure if others can end up in this pathway as well but it is a very common pentose) can be metabolized in the pentose phosphate pathway for anabolic purposes. Others may end up in proteoglycans.
Regardless of the metabolic pathway, the effect on the process you are wondering about is the same: the metabolites no longer "count" in terms of concentrations for diffusion. Because membranes are not permeable to everything, if they are not permeable to the products of metabolism there is no way for those products to "diffuse backwards."


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Is sigma factor a transcription factor?
After I googled 'sigma TF' I stumbled upon two papers(only).
From a paper:

Sigma factors (sigmas) are bacterial transcription factors that bind core RNA polymerase (RNAP) and direct transcription initiation at cognate promoter sites.

and another paper had the title -

Specific binding of the transcription factor sigma-54 to promoter DNA.

However this contradicts with my book- Principle of Genetics Snustard and Simmons:

Unlike their prokaryotic counterparts, eukaryotic RNAPs cannot initiate transcription by themselves .... require the assistance of protein transcription factors to start synthesis.

Is it a TF?
Note: From what TFs are, sigma factor seems to be a TF to me.

As far as I know, a sigma factor is an initiation factor that must be connected to the RNA-Polymerase in order to bind to a specific sequence in the DNA and initiate the transcription. A TF in the other hand, is for the regulation of transcription..

Having read @loolipop’s answer, you should realize that this is a semantic question, with no right or wrong answer. If you define it in terms of the known characteristics of eukaryotic transcription factors, prokaryotic sigma factors clearly do not conform. However, if you define transcription factor as a protein that is required for transcription (by analogy to the terminology for translation factors), or even as a protein that confers specificity on the initiation of transcription, then the sigma factors can be called transcription factors.
Because of the differences between the prokaryotic and eukaryotic systems, I think it more useful to maintain the historic terminology* (check Berg et al., for example) for prokaryotic transcription and, unlike the authors you quote, just refer to the sigma proteins as ‘sigma factors’. This allows you to discuss the similarities and differences between prokaryotic sigma factors and eukaryotic transcription factors without confusion.
*Historic Terminology.
The prokaryotic transcription system was worked out in detail at a time that almost the only thing that was known about eukaryotic transcription was the existence of different RNA polymerases for mRNA and rRNA. The term transcription factor was never used for the sigma factors. The index of the 5th edition of Berg et al. (2001) contains no entry for transcription factor, and focuses on prokaryotic transcription. The index of the 11th edition of The Biochemistry of the Nucleic Acids (Adams et al.), about ten years earlier, does have entries, but almost exclusively for eukaryotes. The only entries that refer to prokaryotes actually relate to termination of transcription, and the term is used to distinguish between (rho) factor-dependent and factor-independent termination.

Prokaryotic sigma factors confer specific promoter recognition to RNAP via Sigma subunit σ1.1, which acts as a DNA 'mimic' - occupying the downstream DNA binding site. This interaction is displaced only when the promoter region is bound, hence conferring the specificity.
Note that Sigma factor on its own cannot bind DNA, as σ1.1 binds σ4 in the unbound form, preventing binding to any sequence.
Source: Section 2. Structural Organisation of σ70 and Other Group 1 σ Factors in this paper
This is in contrast to eukaryotic transcription factors, which can bind to the DNA on their own - indeed the assembly of the general transcriptional machinery in eukaryotes (read: In Yeast) is stepwise and involves first the binding of TFIID to the DNA, then TFIIA, then TFIIB, before finally the Polymerase is incorporated into the growing complex. Source: Molecular Biology of the Gene - James D. Watson, p.g.449-454
In prokaryotes, the sigma factor needs to be bound to the core enzyme (forming the holoenzyme) in order for this promoter specificity to be achieved. Your book 'Principle of Genetics - Snustard and Simmons' is referring to the core RNAP, not the holoenzyme with the Sigma factor bound.
This is why sigma factors are often not included under the umbrella term of 'transcription factor' - they achieve the same functionality as eukaryotic TFs, but are fundamentally different in terms of their binding to the polymerase.
Often authors note that eukaryotes need TFs whereas prokaryotes don't because the point they want to convey is that eukaryotes use huge multiprotein complexes bound to the Polymerase, whereas prokaryotes just use the RNAP holoenzyme, giving Sigma factors a somewhat 'special' place among the transcription factors.

Please add some references to your answer.


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Secondary/ Acquired lactose intolerance

Acquired lactose intolerance may occur due to a sudden and high intake of milk-based diets. Lactase is an inducible enzyme.

So if lactase is an inducible enzyme then why increase intake of lactose is causing negative effect? Why more lactase isn't produced in more lactose intake conditions?

Searching for the quote you included led me to the original source.
I wouldn't spend too much time worrying about this particular source, and look at some other sources for more information on acquired lactose intolerance. I think there may be some translation/language issues with this section in this particular source. I believe what the author is trying to convey is not that the intolerance is coming from the increased intake, but that the symptoms of intolerance are coming from a sudden increase in lactose intake following a period of low/no lactose intake, where "sudden" essentially means "faster than lactase induction can occur."
That said, I think this is really more an issue of poor wording in a textbook. The whole section is a bit strangely worded, particularly the part on "flatulence" which this author describes as "characterized by increased intestinal motility, cramps, and irritation" - while these issues may certainly accompany flatulence, this definition of these symptoms characterizing flatulence is not correct, as one can certainly have flatulence with normal intestinal function.

You are right about the source. Iam currently reading that book. Could you please suggest a better book?

For biochemistry in general, or for lactose intolerance in particular? For the former, I just looked quickly and found a syllabus from my current institution using this book for an upper-level undergraduate/low-level graduate biochem course. Full disclosure: the textbook authors appear to be the instructors in that course, though I have no personal connection to those instructors or their department besides sharing a university. For the latter, I would suggest a scientific review article rather than a book.


text:
Infinite site model and Watterson's Estimator
Why is it that under migration, the watterson's estimator (theta) is upward biased? What does upward bias means? And why do we have downward bias under exponential growth? Lastly, is it only the watterson's estimator whose variance would decrease with increasing recombination rate or would the tajima's estimator's variance would decrease too?


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How often do retrotransposons jump in human cells?
If I followed the life of a typical cell in my body, how many retrotransposon jumps would I observe per day? I'm only interested in a rough order-of-magnitude estimate: should I think of it as a common event that happens basically all the time in most of my cells, or is it a rare event that happens only occasionally in my body?

For just rough order-of-magnitude, try this reference. Their experimental design seems to maximize transpositions so it should be a reasonable upper bound.
There is a lot of variability, but some retrotransposons jumped in ~1000 cells per million, others only a few per million such that they were difficult to detect, after about 1 month in HeLa cells.
The same reference gives an estimate of 10,000 retrotransposon elements in a mammalian genome, though, again, their transposition frequencies vary considerably.

You should also point out that the HeLa genome is incredibly unstable, which could definitely account for some (a lot?) of the activity seen. I haven't had a chance to read the whole paper in detail, but it very well could be that some of the genetic defects in HeLas related to "protecting" the genome and mutational repair are at play here.

@MattDMo Oh absolutely - I didn't go into specifics but I did mention that their design seems to maximize the transpositions.

true, I did see that. I just didn't want the OP to think that the numbers were in any way applicable to normal cells. Good answer, though, the paper was interesting.


text:
How can I determine where meiosis occurs in the life cycle of a plant?
To fill out this diagram with the mitosis, meiosis, and ploidy , we start with the definition that spores are haploid (N).
Based on knowing that as the sperm and eggs are N, the gametophyte is also N (as only fusion can make something go from N to 2N).
Then I know that the link between spores and gametophytes is mitosis, as we go from N to N.
Similiarly, as zygotes are 2N, and spores are N, either the link between zygote to sporophytes OR the link between sporophytes to spores must be meiosis.
Can I figure out at which stage meiosis occurs with this information, or do I need to know more about the definitions of the different parts of the life cycle? How do I know that sporophyte to spores, and not zygote to sporophyte, is Meiosis?
 (Source)

I posted the information from these comments into an answer and edited the original question to try to make it more straightforward, based on what I learned about what your actual questions were. Feel free to revert or re-edit if I have mischaracterized anything; if all is well, you can delete your comments and I will as well to just clean up a bit.

All of these terms are just names for things that existed long before someone named them, and although you can figure out some of the ploidy from the diagram, you need to know the terms/definitions to complete it all.
Sporophytes are just the name for the diploid cells of a plant/algae that reproduces through a haploid life stage called a spore. You could consider the zygote almost like it is a "special sporophyte" from the perspective of ploidy: it's only special because it's the first cell assembled from two haploid cells. All of the other sporophytes are produced from mitosis from either another sporophyte or from the original zygote.
Being diploid is nice because you have two copies of every gene, which is more robust to mutations (while also maintaining genetic diversity for later generations), and, crucially, it lets one organism make a variety of haploid spawn for sexual reproduction.
Maybe you are wondering just about the terms haploid/diploid, and why "2N" vs "N"? The important thing is it isn't just the total number of chromosomes, it's the number of COPIES of each chromosome: with N you have just 1 of each, with 2N you have two of each. The important thing is that they are homologous, it doesn't matter if N is 1 or 2 or 40.


text:
What strange jelly-like thing is shown in the photo?
What is shown in the pictures below? The photo was taken at the Australia's south coast (Queenscliff). The length of the thing is no longer than 50 cm... It doesn't move and has jelly-like consistency... My guesses were either some product (egg cluster or excrement) coming out of a mollusk, a torn part of some kind of sea plant or a part of a jelly-like creature...

This is my guess, based on your location, colour and the jelly-like structure: this is an colonial tunicate from the Genus Botrylloides, probably Botrylloides leachii.

Thanks @Gerardo! Yes, they look similar, but not exactly the same. For example, the shape is not elongated as on the photos, and internal rings don't look exactly like on the photos... I tried to google all names you've written, but didn't find anything that would look the same... However, I agree, it might be a colony of some living organisms, encapsulated in a jelly substance for survival purposes...

I did some research after commenting that, and I agree with you. I never saw it on the sand (but I always go to the beach on the other side of the bay, next to Frankston).

I see, maybe this one was washed away out of the sea and I should have brought it back into water. Maybe I discovered a new species :)

Do you have additional photos? Did you happen to  manipulate it in any way?  (e.g., poke it,  break it open,  etc)?

Jost poke.. Didnt move at all

I agree with @Gerardo-Furtado's comment that what you most likely have here is a colonial tunicate (or sea squirt) from the genus Botrylloides.
According to images and information available via the Taxanomic Toolkit for Marine Life of Port Phillip Bay$^2$, it appears as though you have a specimen of Botrylloides perspicuus (aka B. perspicuum).

[Photo credit: Mark Norman / Museum Victoria]

[Photo credit: Mark Norman / Museum Victoria]
Background

See here for a good general description of colonial tunicates (using the example of a related Botrylloides species).

In general, colonial tunicates are composed of numerous zooids embedded in a firm matrix called a tunic (or test).

Description

B. perspicuus is a colonial ascidian that can persist in tropical and subtropical waters at depths ranging from 1-170 m.

From The Australian Ascidiacea$^1$ (my emphasis):

External Appearance: The colonies are always robust, but very variable. Some are large, flat, stalked or sessile lobes up to about 4cm long, while others are thick, investing colonies, sometimes growing around wees or other debris. Occasionally ,the lobes are constricted along their length, and sometimes a stalked lobe grows out from a sessile cushion.

The test is always firm, translucent and smooth....

Zooids are sometimes in circular systems, arranged in rows along the length of the colony.

As with other species in the subfamily, the colours of the living colony are very variable.... [including] orange zooids.

The Australian Ascidiacea$^1$ also provides remarks about similarities/differences between B. perspicuus and closely related B. leachi (mentioned in the question's comments):

One difference to note is that B. perspicuus has a firmer tunic, which might explain the retained shape of the OP's specimen even out of water.

Range

This species lives primarily around Australia, with specimens ID'd from waters off Western Australia, South Australia, Victoria , and New South Wales$^1$. The specimen is found in Port Phillip Bay$^2$, which is where the OP's location (Queenscliff) is located.

  [Source: Atlas of Living Australia]
Other Info

Another similar looking species is B. violaceus, but this species is typically found elsewhere in the world.

Like many tunicates, B. perspicuus has been known to invade non-native waters, including those of the eastern Pacific and the Caribbean.

Transport of adult colonies on boat hulls, sea chests and aquaculture equipment is the most likely cause of anthropogenic introduction.

Though ID'd as a different related species, photos showing specimens very similar looking to that of B. perspicuus were documented around the United States.

Citations

Kott, P. (1985). The Australian Ascidiacea part 1, Phlebobranchia and Stolidobranchia. Mem Qd Mus. 23: pp 278-279., available online at http://biostor.org/reference/109626/page/279

Patullo, B., 2011, Ascidian, Botrylloides perspicuum, in Taxonomic Toolkit for marine life of Port Phillip Bay, Museum Victoria, accessed 27 Feb 2017, http://portphillipmarinelife.net.au:8098/species/10656

Note: The remaining info is supported by the above linked websites without formal citations.

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text:
The mechanism of the evolutionary rate hypothesis
There are several hypotheses for explaining the latitudinal gradients in species diversity (link). Of which, the evolutionary rate hypothesis states that warm temperature increases the rate of speciation. I want to know why warm temperature facilitates evolution.
This is not a question, but... some other hypotheses specifically discuss how a factor influences the rate of evolution (e.g., the size hypothesis discusses how large area can promote speciation). I think temperature hypothesis is a better name for the evolutionary rate hypothesis.

Related question: Is there a hypothesis that attempts to explain patterns of species richness along all three energy-related environmental gradients?


text:
What is the role of various immune cells in demylinating neuropathy?
Is there a simple description or article of the life cycle of tcells and other immune cells and how they become programmed to attack the myelin of the nerves?
When I try to read through an article like this: http://m.neurology.org/content/56/1/74.full its pretty frustrating. I consider myself fairly technical but not versed in biological systems.

Hi I don't think there is a simple way of describing the way the immune system works. However I'll give it a rough go. The immune system can be broken into two major categories, The innate immune system which does not need to learn about what foreign bodies are and works via physical systems such as the skin and molecular structures on cells such as PAMP-receptors (Pathogen associated mollecular pattern receptors) on Phagocytic cells (such as macrophages, neutrophils, ...) which innately recognize the bad guys which have characteristic non human molecular structures.
The other half of the immune system is called the adaptive immune system in which specialized cells T-cells and B-cells, rearrange their own DNA to create new and varied receptors which are specific for foreign antibodies.
T and B cells work together to recognize different sides(epitopes) of foreign mollecules (foreign peptides) and have to agree that the mollecule is foreign. A process of clonal selection and deletion of T-cells and B-cells in the thymus and bone marrow respectively can sometimes go wrong and this leads to auto-immunity. For example some B-cells which recognize self antigens might escape clonal deletion during their maturation process, and become later (many years ?) activated by a T cell which recognizes an adjuvant (close by aggravating molecule, such as a viral surface molecule).
Once the B-cells matures they can secrete self anti bodies.
Finally the innate and adaptive immune systems work together and shouldn't be thought of as separate. For example the complement system is part of the innate immune system as a molecular cascade amplifying immune system signals and works with both the adaptive and innate systems.
It would help if you can describe the specific type of autoimmune condition that you are investigating as there may be several ways that the immune system can become directed towards self.
There is a great online course from UC IRVINE and whose videos/lectures on the immune system available on youtube, you'll need at least 27 hours of good concentration, the autoimmune lectures are towards the last ones.
https://www.youtube.com/watch?v=gVCfC8WW4eU&list=PLIHnZ4fK_IyJaH2WNHIk2cFsnR2UM4z7t
My understanding is still evolving, however I hope this helps.

Nice answer. Please add some more references for ones who'd want further reading.

Wow - thanks for your answer! I just ran across this message - dont know how I missed it - but thanks!

I should add that I am trying to understand the steps that involve B-cells and why/ what caused the system to attack peripheral nerves. The condition is CIDP which has suddenly afflicted my wife. Perfectly healthy, no strange event, no fever/ sickness or other identifiable issue! Suddenly she start loosing feeling in hand and feet, progressing up the peripherals. Diagnosed as demyelinating by several clinics.


text:
Are tergo-sternal muscles of cockroach involved in blood circulation?
Tergosternal muscles help in the blood circulation in a cockroach as well as in movement of the wings for flying. I came across a question that claims that these muscles are used in blood circulation as well. I can't seem to see a relation between blood circulation and these muscles.

Could you link to the question that you reference? Here's how!

It is not the tergo sternal muscles that are involved in blood circulation in cockroaches. Tergo sternal muscles help in breathing. It is the Alary muscles that help in blood circulation. The alary muscles are associated with all the thireen chambers of cockroach's heart on either side of it. The alternate contraction and relaxation of these muscles help to pump the blood.

Sources which support my answer:

Tergo sternal muscles are involved in respiration, Look into the book "A Dictionary of Entomology" pg 4, link
Alary muscles help in blood circulation, link

Please provide citations/links to the sources you used to help provide some credibility to your answer

@theforestecologist I have included suitable links in support of my answer please check them.


text:
Are glycoproteins and glycolipids present only on the cell surface membrane?
I haven't read this being stated explicitly, however whenever I read about proteins and glycoproteins this seems to be implied. For example, in this Wikipedia article,

Lipid and proteins on the cell membrane surface often have short carbohydrate chains protruding out from the cell surface, known as glycolipids and glycoproteins.

My question is, is this the case? And if so, why would they only be present on the cell surface/plasma membrane. Would they not be useful elsewhere in the cell for example for vesicle trafficing as receptors for targetting sequences?
One idea I have is that, to the best of my knowledge, the enzymes for glycosylation are present in the endoplasmic reticulum and Golgi lumens (oligosaccharyl transferase in ER, etc) so glycosylation would only occur on the part of the protein/lipid that is topologically outside of the cell, however this brings up more questions:

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.
Why would there not be glycosylation enzymes on the cytosolic side?

This journal article has some information on glycolipids: "Membrane lipids: where they are and how they behave.".

Since you asked three questions, I'll answer them one by one.

Are glycoproteins and glycolipids present only on the cell surface membrane?

No, glycoproteins have many functions and are certainly not restricted to cell membranes.
Some examples of glycoproteins in blood include fibrinogen, antibodies, miraculin, etc. See this:

Fibrinogen (factor I) is a glycoprotein in vertebrates that helps in the formation of blood clots.

For a more detailed list of glycoproteins, see this wikipedia article.
On the other hand, glycolipids are found only on cell membranes. See this:

Glycolipids are lipids with a carbohydrate attached by a glycosidic bond. Their role is to maintain stability of the membrane and to facilitate cellular recognition. The carbohydrates are found on the outer surface of all eukaryotic cell membranes.

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.

Glycoproteins, or any proteins, after they are completely processed , don't just float around in the cell and reach their appropriate place. Its obviously not that proteins 'know' where to go, but they are actually taken to their appropriate places. This is known as protein targeting. See this:

Protein targeting or protein sorting is the biological mechanism by which proteins are transported to the appropriate destinations in the cell or outside of it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases.

There are differences between cell membrane and organelle membrane, which makes them distinguishable for targeting factors.

Why would there not be glycosylation enzymes on the cytosolic side?

Glycosylation is a post-translational modification or proteins.

Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Only certain proteins require glycosylation, that is why they are translated by ribosomes connected to golgi apparatus or endoplasmic reticulum. If glycosylation enzymes are present everywhere in the cell, then every protein that encounters them would get modified and, possibly, non-functional. Thus, there are special compartments in the cell for such purposes.
EDIT: To answer the questions you asked in comments:

are there any glycoproteins found elsewhere inside the cell? For example in the mitochondria?

We aren't sure about that yet. There have been a couple of studies to find out whether there could be glycoproteins in mitochondria, one of which is this:

Isolated intact mitochondria selectively incorporate monosaccharides from nucleotide diphosphate monosaccharides into protein. Fucose, mannose, glucose, and galactose were incorporated by the mitochondria into glycoprotein; xylose was not. Structural integrity of the mitochondria was not necessary for the incorporation of monosaccharide into glycoprotein; mitochondria broken by homogenization also incorporated monosaccharide. The monosaccharides incorporated into glycoprotein were localized in the inner mitochondrial membranes, the same membranes which contain the protein into which leucine is incorporated by the isolated mitochondria.

If there are glycoproteins in mitochondria, they could be at many other places too inside a cell.

does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm?

Glycoproteins are not required inside cell (I, or maybe nobody, knows why). Their main function is as receptors or secreted products, thus they are not found inside a cell. However, glycosyltransferases can behave as dynamic glycoproteins and hence are found inside cells. See this:

Glycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based.

Metroplex thank you for your reply. I still have a question though; so glycoproteins can be secreted as well as being destined for the plasma membrane, but are there any glycoproteins found elsewhere inside the cell? For example in the mitochondira? I know there will be glycoproteins present inside vesicles which have just come from the plasma memebrane, and these will be returned. But what about glycorproteins being specifically targetted to regions in the cell which are not the plasma membrane and are not excreted?

Question 2: Also, I understand now why glycosylation enzymes would not be present inside of the cytoplasm, however does this not seem a bit of a shame for the cell? I mean, does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm? It seems impossible, unless they were to be transported in from the ER lumen or from outside of the cell through chennel or carrier proteins, but I have never heard of a channel, carrier big enough to achieve something like this...

I hope you find the modified answer helpful. Please add the above questions too in your main question.


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What is the standard method for measuring soil and substrate acidity
Soils and other plant substrates differ a lot in their moisture content. In dry matter a pH is not measurable without adding water, but this has the problem of the resulting value not being independent of the amount of water added. In controlled conditions pKa measurements would be used instead as they are independent of the amount of water, but would this would require information about chemical composition that is generally unobtainable.
What is the standard way of reporting acidity of soils? I would think that there is probably some kind of measurement based on mass or volume. Or, perhaps the log scale renders the amount of water negligible for most purposes?

Soil should first be processed by drying the soil to ensure a standard "dry" sample is analyzed. 55$^o$C in drying ovens for 24 hours works for most non-water-zone soils, but more time at 50 - 55 $^o$C (as long as it's consistent between samples) can be used to dry out wetter samples. One can then put the soil through sieves to remove rocks and other debris (2mm sieve is common).
To actually measure soil pH, one combines 1 part soil with 1 part water and then measure with an electrode (McLean 1982)$^1$.
By always using 1 part soil to 1 part water, you maintain a consistent relative amount of water per sample and therefore can account for different sample sizes.
The final value is reported as pH.
You can find the McLean (1982) resource here for $15 or likely for free from a nearby university library. The paper has been cited over 2800 times.
[1] McLean, E.O. 1982. Soil pH and lime requirement. In A.L. Page et al. (ed.) Methods of soil analysis, part 2. Agronomy Monogr. 9, 2nd ed. ASA and SSSA pp 199–223.
EDIT:
As @Roland pointed out in the comments, other standards do exist.
For example, the International Organization for Standardization (ISO) maintains reports describing  standard protocols for different methods (which therefore are sometimes used):

ISO 10390:2005 specifies an instrumental method for the routine determination of pH using a glass electrode in a 1:5 (volume fraction) suspension of soil in water (pH in H2O), in 1 mol/l potassium chloride solution (pH in KCl) or in 0,01 mol/l calcium chloride solution (pH in CaCl2).
ISO 10390:2005 is applicable to all types of air-dried soil samples, for example pretreated in accordance with ISO 11464.

The USDA describes several standard protocols used by their laboratory at the National Soil Survey Center to measure soil pH (Hydrogen-Ion Activity) in their Soil Survey Laboratory Methods Manual (version 5, 2014). See specifically, pages 265-281 for various soil suspension and soil extract methods.

Note: They cite repeatedly the McLean (1982) paper as a  source for determining pH using an electrode.

They also provide further notes in this technical note.

The EPA (US Environmental Protection Agency) similarly has a protocol that they use. Their electrometric approach using a digital pH meter involves the insertion of a glass electrode into a soil suspension made by mixing the soil 1:1 with a reagent solution (see referenced notes below).

EPA protocol for soil pH (Method 9045D): Revision 4 (2004) available here

References "Chapter One" of technical note SW846 (I link to Update V revision 2, July 2014), which relates back to 2-2 of EPA-600/4-79-019

Again, the overall takeaways are:

Reporting soil acidity as pH is standard
There are multiple standard methods to measure the pH; Just be sure to properly cite your approach!

At least among soil scientists, it's pretty common to use 0.01 M CaCl solution instead of pure water. The top answer there briefly explains why. See also: http://www.iso.org/iso/catalogue_detail.htm?csnumber=40879

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


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Transmembrane protein: does signal peptide always form a loop?
So I have read a few times that

b. SP probably forms loop not arrow. Loop enters channel (translocon) in membrane. SP loop is probably what opens (gates) the channel on the cytoplasmic side.

Source
And I was wondering why this would be the case? It seems much more complicated to me for the protein to loop around than fior the signal peptide to just embed itself in the translocator pore and the rest of the polypeptide chain be synthesised in the cytoplasmic side.
Then if the protein was meant to pass through the membrane again, there wold be another start-transfer signal sequence (so the two first signal sequences would be two start-transfer sequences rather than a start transfer and a stop transfer).

I think perhaps a picture might help, also see some lecture notes here, where I pulled the pictures from: in short, if you have an unbroken chain, you can't stick it through a hole except as a loop unless you start at the very end, and often you don't want to do that.
Signal sequences can be anywhere on the protein. That portion is the part of the peptide that binds to the translocator pore in the membrane. That portion has to stay bound for the process to continue: it isn't possible to just "feed through" the growing polypeptide without securing it somehow, and that's precisely what the signal sequence is doing by interacting with the translocon.

http://web.uconn.edu/mcb380/fig12-45a.GIF

http://web.uconn.edu/mcb380/fig12-45b.GIF
This process also allows for all sorts of arrangements: sending the whole protein through, or just the N- or C- end, or having multiple signal sequences to create multiple transmembrane domains. Especially in the latter case, there really isn't any other way to do it except by forming some loop someplace, unless you were to actually ligate separate polypeptides together, which would be quite messy and difficult and require additional specialized enzymes: much more complicated than a nice, tidy loop.


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What kind of hawk is in this picture?
I found this hawk(?) sitting on a fence near a small duck pond with a fountain near my workplace in Fort Smith, Arkansas, USA. There are some wooded hills (deciduous) nearby. It let me get within 3 meters or so before flying up to a tree across the pond. Based on measurements made of the fence it was sitting on, I'm guessing a height of 50 cm (20 inches) head to tail, I assume it'd have a wingspan of 60-70 cm perhaps (24-28 inches).

My best guess it either the Red-shouldered Hawk or Red-tailed Hawk. Unfortunately, I couldn't get a good picture of its back/tail. Any idea what species this is? I came across the bird during winter.

Any guess on the height or wingspan? (just for completeness sake).

@theforestecologist Thanks for the tip. I updated the photo with measurements of the fence and included my guesstimate for height/wingspan.

It looks very much like an immature red shouldered hawk.

Immature Red-shouldered Hawks can be tricky to identify. Immature Red-tails show a belly band and are less heavily marked on the upper chest than young Red-shouldered Hawks.

Red shouldered hawks are smaller and like deciduous forests, like perching on wires, branches, etc. Red tailed hawks are usually birds of open spaces. They hunt from lower down than red tails, and they're often found near water (especially rivers and swamps), as they like frogs and snakes.

Look for Red-shouldered Hawks in deciduous woodlands, often near rivers and swamps. They build stick nests in a main crotch of a large tree. During migration, Red-shouldered Hawks often move high overhead along ridges or along the coast.

Limited to a phone for a while and can't do much (I'm a dinosaur) but info and pictures here.

I'm not sure if the white eyebrows lean towards the red-shouldered more than red-tailed hawks (which appear to be that case from the guide you posted).

@Wayne Werner - I agree that the white eyebrow leans more towards a red-tailed, but if you look at a lot of pictures, some red shouldereds have white eyelines, and the size, chest markings, and habitat all point more to a red-shouldered. They aren't big. I surprised an adult red shouldered eating a snake on my driveway (in the woods). They're quite a bit smaller than red tailed hawks (who used to eat my guinea hens.)

A local outdoorsman also pointed out the possibility of it being a Sharp-shinned Hawk or Cooper’s Hawk. Not sure how good of a match those are, but thought I'd mention it.

@Jeff Bridgman - I know nothing about Sharp-shinned Hawks, but the shape is not quite right for a Cooper's Hawk.

Sharp Shins are much smaller , close to the size of a robin.

Red shoulder will hunt from a perch ( as shown). Rare for a red tail.


text:
Why doesn't cellular, replicative senescence (or the hayflick limit) constrain the normal development of an organism?
The wikipedia article on cellular senescence states:

Cellular senescence is the phenomenon by which normal diploid cells cease to divide. In culture, fibroblasts can reach a maximum of 50 cell divisions before becoming senescent. This phenomenon is known as "replicative senescence", or the Hayflick limit.

My question is, if many cells in diploid organisms (e.g. humans) have an inbuilt limit of the number of cell divisions, how is it that a human can develop from a single celled zygote to a organism comprised of many 10's of trillions of cells - if many cells can only divide 50 or 60 times?
Wouldn't the cells "use up" their available telemeres during development? or is it a simple mathematical relationship, that whilst yes, existing cells are "burning up" their telemeres as they divide during development, but because the number of cells are increasing exponentially they develop all the tissue mass the organism needs before hitting the hayflick limit?
e.g. if cell numbers are doubling during each division phase, it only takes 30 doublings to achieve a billion cells, after 40 doublings you have a trillion cells.
i.e. after 40 or 45 doublings it has developed all the tissue mass of a mature organism, and still has some telemeres left over for additional tissue generation during the organisms lifetime?

Read about telomerase - the Wikipedia article you mention talks about it specifically as a mechanism for getting around the limit - but yes, you can also get an awful lot of cells with 50 or 60 divisions; 10^18.

One cell divides into two. Each of those divides into two. Each of those divides into two... Etc. If this happened 50 times, you would get 2^50=1,125,899,906,842,620 cells. That's plenty and then some.

Yes this article expresses it as a formula: $ Nt = N_0 2^{tf} $ where Nt is number of cells at time t,
N0 number of cells initially, t is time (days), f is
frequency of cell cyces per unit time

You pretty much have answered your own question. It is a math problem. Cells are burning up their telomeres during fetal development onward but the cells are multiplying exponentially in number.
But biology is a bit messy, embryonic stem cells do have telomerase activity and their telomerase are maintain. So the clock doesn't start counting down immediately.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2360127/
Temporal wise hES cells are around 4–5 days post fertilization, at which time they consist of 50–150 cells. https://en.wikipedia.org/wiki/Embryonic_stem_cell.
So you don't quite start with an n of 1 cell. But of an n of 50-150 (in humans)... before you start to see telomere shortening. With that head start those 50 doubling can make a lot more cells. By my guestimate with excel ~1.69E17 cells ~320 tons. More than enough you to last a life time.)

Thanks,  the links you provided were useful. I also found an article on the maths behind cell division It would be interesting to come across an article which specifically addressed the "race" between tissue mass created through cell division and the hayflick limit. But I guess we need to figure that out ourselves, and then as you mention there is always the fact that biology is a bit messy :)


text:
Does the Valsalva maneuver require a completely closed airway? How do the effects compare to exhalation against partial resistance?
The Valsalva maneuver is defined as "attempted exhalation against a closed airway", "The effort to breathe out forcibly while the mouth and nose are firmly closed or the vocal cords pressed together", or, colloquially, straining as if you were trying to poop. It can "pop" the eustachian tubes open, stimulate the vagus nerve, and briefly spike blood pressure, occasionally leading to people dying from a burst aneurysm on the toilet.
Some breathing practices involve pushing air out against resistance, such as ujjayi breath in yoga. This can be done by partly closing the glottis while exhaling, or by firmly exhaling through the mouth with lips slightly open, as if one were whistling. It can also happen while forcefully exhaling through a congested nose.
This seems like it should raise eustachian and thoracic pressure in the same way as the "full" Valsalva maneuver, though to a lesser extent. Are the effects of these other breathing practices similar to the Valsalva maneuver, or are there any unique effects of the Valsalva maneuver that only occur with a fully closed airway?
As a second question, would you expect any unique effects exhaling against resistance? It seems different in that the practitioner is still breathing, and that they can continue the practice indefinitely, as opposed to a breath-holding Valsalva.

Since commercial divers that wear diving helmets cannot pinch their nose shut with their fingers, a retractable 'nose clearing device' is provided in the helmet, or similarly a block that the nose can be pressed against. The device generally does not completely occlude the nose, but enough that if the exhaled flow rate is high enough, the middle ear can be equalized.

The eustachian tubes exit into the nasal cavity superior to the glottis.  Thus restricting the glottis while exhaling cannot increase pressure in the nasal cavity / eustachians.  Only by closing the nostrils can that be achieved, and only while exhaling.  Even a technique like circular breathing cannot maintain pressure in the nasal cavity since that's necessarily the entry point for every new breath, be it mouth or nose.

Please add some references to your answer.


text:
Male Parenting from Evolution point
From evolution point of view can we explain as to why mothers care about child rearing more than fathers? Is it Social phenomenon or genetic phenomenon?
Are mothers hard wired to take care of children more or they are socially forced to do so?

Are you talking about humans only? There are many species (although not the majority) in which males parent more than females.

I think good answers would address multiple species and should also address how common male primary parenting is...

I am focusing more on humans

Because mother invest the most material and time into producing the offspring, so there is a stronger pressure on them to not waste it. Males can go impregnate other females so there is a stronger possible disadvantage for child rearing, few mates thus fewer offspring. Whereas a female can't have more offspring by finding other males while currently carrying offspring so they are forced to sink a lot of time and energy into the offspring. So evolution strongly disfavors females who waste those resources by abandoning the offspring.
Strong K strategists like human tend to override much of this becasue of how much investment the offspring need. So there is a strong pressure for the female to only accept mates that can provide a great deal of resources, including time. And males can seriously hurt the chances of their offspring surviving by abandoning them. But there is still more built in investment on the part of the female.
There is one other factor, A female knows who her offspring are, males do not, so the offspring they invest in might not be theirs, so there is a pressure to not put all their eggs in one basket so to speak, this is also why males tend to be more worried about physical infidelity (cuckolding) while females worry more about risk of abandonment (loss of support).
Now remember this is males an females in general, individual species can have different pressures. And remember that humans have very complex behavior so much of this just amounts to tendencies on average, not hard and fast rules.
More on the ethology of mating here. http://www.tandfonline.com/doi/pdf/10.1080/11250008409439461

John,  you could further strengthen your answer by providing some references.


text:
What is the role of tracrRNA in CRISPR-cas9?
From what I understand, in a CRISPR cas9 complex, gRNA is comprised of tracrRNA and crRNA.  I've read that crRNA is the part which is matched to the DNA which is targeted, but what role does tracrRNA play in the process?  That I'm not clear about.  Also, unless this should be its own question; how is gRNA prepared with cas9 protein?  Does the protein automatically bind to certain RNA strands?

Thank you for your answer.  I have read some of the articles you've given (the link for the second one didn't work).  I've also looked up some other resources; from what I understand, the tracrrna is like an RNA scaffold of sorts, which keeps the complex in active form and which recruits the crRNA to the cas9 molecule.  Based on the first paper, am I to conclude that cas9 proteins isolated from certain species each have certain tracrrna sequences that could be sued with any crRNA (like cas9 proteins from different species recognizing certain PAM sequences)?

Sorry, I have fixed the second link. You are on the right track, the tracrRNA does act like a scaffold. You are also correct that Cas9 homologs from different species appear to have tracrRNA sequences quite divergent from one another. However they must have sequence complementary to the pre-crRNA in order to form the complex so can't be used with any crRNA.

Also, the PAM site recognition does appear to be dependent on the Cas9 in use (If you are interested check out 10.1038/nature13579 and 10.1038/nature14592). This places additional constraints on the pairing of tracrRNA and crRNA.

Your two questions are related and you are correct in your supposition that the Cas9 protein associates to a specific RNA sequence. That of the tracrRNA processed with the crRNA into a gRNA. This is achieved without any other aid so could be considered to  do so automatically. How specific the tracrRNA sequence needs to be is an interesting and often overlooked question.
When comparing tracrRNA from different species it is clear that there is not a lot of sequence conservation but they are predicted to be contain similar secondary structures.
Matching tracrRNA and Cas9 from closely related species does result in in vitro DNA cleavage but this does not work with more distantly related species. Nevertheless they are remarkably versatile and this has been exploited in a number of exciting genome engineering applications where additional structures are added without compromising the binding of the RNA to the Cas9.
The tracrRNA and the crRNA together form the gRNA which targets the Cas9 protein to the location of cleavage. In the endogenous bacterial systems the gRNA takes the form of a processed RNA duplex but in the genome editing implementations this takes the form of a single chimeric RNA with the two components already fused together.
When it comes to actual cleavage of DNA it is important that the Cas9 is in the correct conformation and changes in this are known to occur when binding to the target DNA. Recent work suggests the tracrRNA plays a role in maintaining the Cas9 protein in an active form allowing it to be able to target DNA.
It likely also contributes to the overall stability (and thus efficiency) of the CRISPR-Cas9 complex.
Ultimately the tracrRNA is an essential component of the CRISPR-Cas9 system via it's role in both guiding the Cas9 protein to its target and aiding it's function.
The following references might be of interest to you:
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems
Guide RNA engineering for versatile Cas9 functionality
Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease

In short, tracrRNA keeps the CRISPR-Cas9 complex (of RNA and the Cas9 protein) catalytically active:

Image source: Figure 5 from Lim, Y. et al., 2016. Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease. Nature Communications, 7, p.13350. Available at: http://dx.doi.org/10.1038/ncomms13350.

This was shown by pre-incubating different sets of components together for 20 minutes, then adding the missing component(s) and observing the resulting amount of DNA cleavage activity. For example, in the "pink" experiment, only the Cas9 protein and tracrRNA are pre-incubated together and the crRNA is added just before the 5 minute cleavage time:

Image source: Figure 1 from Lim, Y. et al., 2016. Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease. Nature Communications, 7, p.13350. Available at: http://dx.doi.org/10.1038/ncomms13350.

The green bar represents the Cas9 protein pre-incubated for 20 minutes with both the tracrRNA and crRNA. The pink bar shows that pre-incubating with tracrRNA but without crRNA still results in the same level of activity (measured as fraction of cleaved product). However, when the tracrRNA is not included in the pre-incubation, as in the yellow and blue experiments, the activity is much reduced.


text:
What is a microsome?
This site says:

In cell biology, microsomes are vesicle-like artifacts re-formed from pieces of the endoplasmic reticulum (ER) when eukaryotic cells are broken-up in the laboratory; microsomes are not present in healthy, living cells.

Whereas this other site says:

Microsome is another name for the smooth endoplasmic reticulum (ER).

Are they both correct? Which one is correct?

Google says "microsome
ˈmʌɪkrəsəʊm/
nounBIOLOGY
a fragment of endoplasmic reticulum and attached ribosomes obtained by the centrifugation of homogenized cells."

Or see this

@Metroplex so second site must use the word fragment?

Yes it should.

The first quote is correct. 'Microsome' is more of a lab term. This is because, as said they are found (re-formed) after centrifugation and as such aren't seen in an intact cell. Differential centrifugation is a technique used to separate cellular constituents into fractions. To quote,

The microsomal fraction is the pellet produced when the postmitochondrial supernatant is centrifuged at 50,000g for 60 minutes. Microsomes are small vesicles enclosed by a biological membrane. During centrifugation, the endoplasmic reticulum is fragmented into microsomes

The microsomal fraction may also contain pieces from the plasma membranes apart from those from the ER.


text:
Why doesn't CAS9 cleave the original CRISPR sequence in the bacterial genome?
CAS9 is the RNA-guided endonuclease that cleaves DNA as specified by the RNA sequence and is used to target viruses that infect bacteria. So why doesn't this RNA+endonuclease combo also cleave the original CRISPR spacer sequences (which also have the same DNA?). Is it the same reason that the bacterial genome is methylated (and hence protects from restriction enzymes)? Does methylation also make a difference to CAS9 as it does to restriction enzymes?
This actually was a doubt asked to Eric Lander in this lecture.

It is not the methylation status. The crRNA is not only complementary to the spacer sequence within the CRISPR array but also to the repeat sequence flanking that spacer. The additional base pairing of the sgRNA with the repeat prevents a nucleolytic cleavage by Cas9. In addition, the arrays typically do not contain PAM sequences.
Here you will find a nice illustration:

The explanation regarding complementarity of the 5' handle is true for Type III CRISPR-Cas systems. In type II systems such as Cas9 a protospacer adjacent motif is required for self vs non-self recognition.
PS: If this question was asked to Eric Lander and he was obviously not able to answer (otherwise why is the question asked here?) then I am not surprised as to why his "Heroes of CRISPR" is so inaccurate and misrepresenting.

Please add some references to your answer.


text:
How early can we know the sex of a human being now?
Do we need to wait till a Zygote forms?

Before the zygote, there is no individual for which sex can be defined! However, it is possible to know the sex of the future zygote if you know the gametes that are going to fuse.
In humans, just like in all placental mammals (which excl. kangaroos and platypus), sex is defined by sexual chromosomes, where males are XY while females are XX. A mother can therefore only pass on an X (and have no influence on the sex of the offspring) while a father can pass on either an X or a Y which will determine the sex of the offspring. Knowing the paternal gamete (the spermatozoid), one can infer what the sex of the future offspring will be. Of course, in one ejaculate, there are about as many X-bearing gametes than Y-bearing gametes.
Technically speaking, could typically make a karyotype to infer whether chromosome X or Y is being transmitted.

@SanjuktaGhosh Remi said "possible to know the sex", not "know the possible sex" i.e. if you know what sex chromosome the sperm is carrying, you can tell what zygote will result.

@Remi How to know that technically for a normally combined XX or XY?

Make a karyotype (info edited in the post). Does this answer your question?

@Remi  If we do not consider ethics, once a X-Y or a X-X combine, we can find it and do karyotype?

Do you mean "fuse" (like after fecundation) by saying "combine"? What is "it" in can we find it? You can do a karyotype on any cell (whether haploid or diploid). On diploid human cells you can infer sex from karyotype. On haploid human cell, the concept of sex makes no sense but you can still infer whether the haploid cell carries an X or a Y chromosome

So after the combination of an egg and a sperm, before sex organs develop (7-12weeks), it is still possible to infer sex, right? Have human beings proved a particular egg does not tend to select an x sperm or a y sperm? (I know apparently it is in a passive mode.)

Quite early when combined with IVF.
At present there are two method that are available for use.
The first is genetic testing of preimplantation genetic screening (PGS). A single cell is taken from the embryo and tested for sex by genetic testing. Only the right sex embryo is implanted. http://www.babycenter.com/0_choosing-your-babys-sex-what-the-scientists-say_2915.bc?page=1
The second method is the Ericsson method, which is based on the fact that Y sperm swim faster than X sperm, as the Y sperm are smaller.
http://www.babycenter.com/0_choosing-your-babys-sex-what-the-scientists-say_2915.bc?page=2
At present there is also a 3rd method that is used in animals but has not gain FDA approval for human use. And that is sperm sorting using florescence activated cell sorting (FACS). In this method a flow cyctometer is used in conjunction with a non-toxic cell permeable DNA dye. the idea here is to sort sperm based on their DNA content. X sperm have more DNA than Y sperm as the X chromosome is bigger than the Y chromosome. This method is called Microsort https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256056/. Primary concerns is that the DNA might cause DNA damage.
An older method that was greatly used between 1970 to early 1980s to sort sperm by sex was density gradient centrifugation. The idea being X sperm being denser than Y sperm as the X chromosome is bigger than the Y. This method of gender sorting is still available in some IVF clinics but medical studies indicate that the method is ineffective http://www.ingender.com/gender-selection/ericsson/Percoll.aspx
More stuff to read about
http://www.reproduction-online.org/content/145/1/R15.full
http://chooseagender.com/methods-of-gender-selection.aspx.

Can you please provide a source showing that X and Y sperm can be separated via centrifuge?

The link to IVF lab in my answer states that they use centrifugation to separate X and Y sperm. Even success rate and the cost that they will charge. However if you want a scientific paper, here is one. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169681/ Or wikipedia if preferred https://en.wikipedia.org/wiki/Sperm_sorting

The Wikipedia article is about general sorting. The paragraph about centrifugation is for sorting by sperm quality, not X/Y. Flow cytometry is the one that can be used for differentiation, stating "...flow cytometry is the only currently used technique able to determine the sex of future progeny...". The second article is interesting, but I'm not sure if it actually indicates that the centrifugation is what's actually used for sorting sperm, rather than mixing and separating out additives, and it seems to indicate that the methods aren't very successful. Someone else should weigh in on that.

Hmm.. while centrifugation of sperm to separate out X and Y sperm has been done for the last 30 years, it appears that the method has fallen out of favor. I will change the answer to reflect this and thrown in more stuff I have read about on this subject.

@Jay  I mean for a normally combined XX or YY,  how do know it is XX or YY after they combine. It is different with we can control which combines with Y.

Oh. It depends on how daring you are. Using amniocentesis you can sample the amniotic fluid and obtain cells. And test those cells. Amniocentesis is typically done at 16 wk http://www.webmd.com/baby/amniocentesis-17766 But some facilities will do it as early as 11wk http://americanpregnancy.org/prenatal-testing/amniocentesis/ But the earlier you do this, the higher the risk of a spontaneous abortion. If you use ultrasound to tell the sex of the fetus, it is 16-20wk http://www.babycenter.com/404_when-and-how-can-i-find-out-my-babys-sex_10366575.bc?PageSpeed=noscript


text:
Why do some organelle (like ER and Golgi complex) cannot be seen under microscope during cell division?
I have recently read in a book that organelles like ER (endoplasmic reticulum) and Golgi Complex cannot be seen under a compound microscope during cell division. Why does this happen, and where do the organelles go during that time?

Could you cite which book you read this in?

In my textbook of 11 th grade.

By saying "disappear" I actually mean - cannot be seen under compound microscope, as under normal circumstances ER can be clearly seen.

Please include the title, year published, editors, edition, and publisher of any cited works if possible.

This is not my area of expertise at all, but here are some recent papers that might shed light on this: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117859, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719565/, http://jcb.rupress.org/content/179/5/895

A cell when undergoes the process of cell division there are structures known as spindle fibres that are required to pull the chromosomes off to the poles of the cell so that it can be segregated into the cells properly while division. These spindle fibres are made of microtubules that are protein molecules constituting the cytoskeleton of a cell. Endoplasmic reticulum and Golgi apparatus are also providing a lot of support to the cells.
Also endoplasmic reticulum and Golgi apparatus are the sites where most of protein forms. While cell division these two organelles disintegrate so as to provide protein for microtubules formation, and so as to reduce support of the cell so the division of the cell is comparatively easier.
Also, during the cell division everything divides equally between the two daughter cells, so ER and Golgi bodies disintegrate so they can be equally divided into the two daughter cells.
Also, nuclear envelope is the continuation of the endoplasmic reticulum. Hence endoplasmic reticulum disintegrates with the nuclear envelope.
Here I have provided a set of possible reasons for your question.
You can refer Raven's biology for further information.

Could you please provide citations of your claims, which would help to enrich the answer. Also I don't get the point "While cell division these two organelles disintegrate so as to provide protein for microtubules formation" which you have said, as all the proteins required to run the division phase of the cell cycle are synthesized during the G1 phase so there is no need to disintegrate some organelles to provide that.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814503/


text:
What is the theoretical maximum height of a herbaceous plant stem?
Foreword: I'm posting this here instead of, say, Worldbuilding, because while it is based in a speculative concept, this is a question purely of biology as we know it instead of speculative biology under non-real conditions. I would address that later and elsewhere. And sorry if this is actually more physics than biology, I have trouble pinning these things down.
I'm trying to determine what the maximum height of a non-woody plant stem can be (i.e. I don't want the tallest flowers). I think the primary issue at hand is load-bearing and resistance to bending. So I found this 1997 paper by Schulgasser and Witzum that sort of discusses what I'm looking for. It suggests that the plant's ability to resist shear forces is a matter of how bundles of fiber are arranged inside the stem and of the plant's internal pressure, which affects how much weight it can stably bear. But I'm no biologist, so the paper is difficult to penetrate. I'm sure there are other issues limiting the height of non-woody plants, like the maximum height above the ground that capillary pressure can raise water. Considering all factors, what is the theoretical maximum height of a herbaceous plant?
I've found this question, which concerns the tallest real herbaceous plant, while my question concerns the theoretical. But I would like to extend that question - are there any examples of fossil herbaceous plants that are larger than the modern banana plant, and do they run up against the theoretical maximum?

Unfortunately I think, despite your forward, unless you are interested in existing plants this feels a bit to speculative. Maybe you could reformulate and break up your question, e.g., ask what maximum observed root pressures are.

@BryanKrause Well, there is a difference between speculation and calculation based on established knowledge. The 1997 paper has several useful equations - I simply don't know how to use them.

I don't disagree about the relevance of calculations; I think the issue is that your question is putting together a lot of separate calculations and putting them all into a "maximum." For capillary transport of liquids, for example, a factor that is really important is the diameter of the tube. Well, one might be able to make a very small tube and go a long distance, but this introduces other issues, maybe not enough nutrient delivery to support a large enough stem for that height. Can you try to break your question down into the problems you are having with the equations in the paper?

I believe I see your point - that all the potential limits one could calculate based on various factors would be difficult to unify. Well, the larger issue is that I don't know enough about plant physiology to know what things I don't know. The paper is only one side of things. I'll try posing this question on Worldbuilding if it proves unworkable here, but I felt the chance of encountering a plant physiologist who could answer the question was a lot higher on Biology.

I'll let others decide definitively whether your question is indeed off-topic, but I think you could also reformulate a question to try to capture the things you don't know, without requiring speculation. Perhaps a question about "besides capillary limits and shear forces on stem fibers, what key factors limit plant height?" Not being a botanist myself, maybe that question is still too broad, but I think it's more in the right direction for this site. Hope that's helpful.

I think it is a legitimate question, how tall can a herbaceous (non woody) plant grow.  I am not sure what is the theoretical limit is,  but the tallest species of banana tree (Musa Ingens) is 15m tall. And the tallest bamboo species  Dendrocalamus giganteus is 25-35m tall.

A bit related: How do-trees lift water higher than 10 meters

Do you consider palms and bamboo as herbaceous, non-woody plants? They are normally not seen as woody plants since they don't produce wood in the strict sense. This makes a big difference to answers to your question.

Looks like some Cyatheaceae (Pteridophyta) can reach up to 20 meters high.

Update: I have edited the answer for a better structure and for providing reliable references.
Some of the factors that influence growth, while keeping in mind that every species has particular needs:
•   light, temperature
•   insufficient light leads to etiolation
•   water
•   amount of water and dry substances, page 185
•   water influences diameter
•   soil
•   wind
•   macronutrients
•   citokinin
•   genotype
•   heterosis
•   inbreeding
•   pinching the stem stops its growth and promotes lateral stems (I understand that you don't want to, but I list it here so that you can watch out accidents - involuntary pinching has the same effect)
•   root type
•   shelter near a fence or a wall
You might find some info as to what to consider in your calculations in this paper, although it's about trees.
Just for the purpose of knowledge, herbaceous vines like Ipomoea are also stems and they can grow longer than vertical ones. There may be more to add, but I'm only a Horticulture student, not a plant physiologist.
I strongly recommend to ask plant related questions on Gardening and Landscaping SE, a small community, but a very enthusiastic one. Also, hardly can someone become a good gardener without knowing at least the basics of plant biology and psysiology, so you have a major chance there of receiving answers in a few hours, not days.
Good luck with your project and I hope you'll return to tell us your conclusions. We will be happy to see you interdisciplinary approach.

Please add some references to your answer.

Ok, but it's going to take some time searching for them in English, as I have aquired this knowledge from various subjects and courses in almost four years in university and the references were in another language.

Its all right if it takes time. The point is that you must have a citation for your claim in an answer.


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Can the Quarternary Extinction event be linked to the spread of mankind around the world?
Evidence is presented in a variety of media by Paul S. Martin as his 'Overkill hypothesis', particularly in Twilight of the Mammoths.
The internet describes this idea as 'controversial.' Other than the works of Paul Martin, what evidence has been presented supporting this hypothesis?

Please provide more information for your question. Do you have a source that presents this hypothesis or some other reason to believe so. Please indicate some evidence of prior attempts to research/answer your own question

@theforestecologist I have read Paul Martin and generally agree with him. However, I haven't found any other semi-credible popular science books that agree with him. I asked the question in the general sense to see what other evidence was out there, preferably in readable summary forms.

Mr. Martin has forgotten one glaring problem with this hypothesis--TIMING.

extinctions rarely have a single cause however humans could very well have been a contributing factor. Intelligence makes for some destructive hunting methods like setting a grass fire to kill a herd of animals or driving half a herd off a cliff to eat only a few of them.

Mammoth much like elephants are believed to be particularly vulnerable, the breed slowly and have few natural predators, the introduction of just one new species of predator (and in humans case a very successful one) can be devastating to a species like that.

Only in islands can this hypothesis be supported.  But islands are NOT continents, and that raises problems with the hypothesis.  The most inconspicuous of which is timing.
In Australia, the gap between man setting foot on Australia and the extinction of Australia's megafauna was 17,000 years. Too long.
Man left Africa and set foot in Eurasia more or less than 50,000 years ago, yet the extinction of Eurasia's megafauna happened 10,000 years ago. Too long.
The oldest discovered American, "Eve", was discovered in a cave in Mexico's Yucatan Peninsula and dated to be 13,500 years old, 500 years older than the supposed time that man crossed Beringia. This could imply that man crossed Beringia at a far earlier date, yet the dating of the extinction of America's megafauna coincided with that in Eurasia. Too long.
There's also into consideration the Younger Dryas climate chaos phenomenon, which did coincide with the extinction of the 30 genera of Pleistocene megafauna, a handful of microfauna and plants, not to mention the Clovis culture itself.
If man was the cause of the extinction event, the gap between man setting foot in new lands and the megafaunal extinction would've been a few generations, not a few millennia.

Do you have any concrete evidence or citations to support your answer? I confess I know nothing about the hypothesis being described, so I can't judge the validity of your answer. As it stands now, the answer is completely opinion-based.

http://www.bbc.com/earth/story/20161102-what-really-happened-to-mammoths-and-other-ice-age-giants?ocid=fbert  http://www.sciencemag.org/news/2016/08/climate-change-not-humans-killed-giant-camels-and-sloths-south-america  https://en.wikipedia.org/wiki/Younger_Dryas

why only a few generations? do you think humans would instantly fill the land mass? A lag is to be expected since humans need to reach semi-isolated areas and hunting an organism to extinction is not going to happen instantaneously, it took humans many generations to cause even the uncontroversial extinctions. Then you have to consider whether humans are the final cause or just so severely weaken the population than something else can easily take them out. Saying it took too long is just misleading unless you can quantify how long it "should" take.

@John  Look no further than the damage done in the 19th and 20th centuries with modern megafauna like bison, rhinoceros and antelope.

none of which are extinct, even with firearms, so even under perfect circumstances it is not fast, unless the starting populations are tiny.

@John  What matters is the crash itself.


text:
Is inbreeding really efficient at producing homozygosity?

Inbreeding results in homozygosity.

I've come across this concept many times  and there's a question that comes to my mind every time I read it.
Let us suppose the character we are trying to establish is dominant trait controlled by a biallelic gene and the two individuals (animals) we have selected to inbreed  both have the genotypes Aa.
Aa x Aa = AA/ Aa/ aa in the ratio 1:2:1
So the possibility of having a homozygous dominant is 25% while that of heterozygous is 50%.
As the breeder has no access to technologies and find out the genotype of the F1 individuals there's a possibility that he would choose two F1 individuals with Aa genotype once again (which has the highest possibility of occurrence). And the same is repeated , production of F2 offsprings with 50% possibility of heterozygous individuals.
Edit:
So getting a homozygous dominant individual is very less likely to happen.
My question, is inbreeding really efficient at producing homozygosity?

Depends on the allele variants and their frequencies in the population. You can calculate the efficiency if you know these parameters. It also depends on the effects of the genotype on fitness.

I think this "problem" is somewhat contrived, as the modern breeder will have access to genetic technology, but even in "the old days", they would be selecting for a certain trait, whatever that may be. They then just take the offspring that exhibit that trait, backcross them, and so on and so on for as many generations as is needed (10 pops to mind for mouse knockouts/transgenics).

And the same is repeated , production of F2 offsprings with 50% possibility of heterozygous individuals.

That's not correct.
Let's start with a population with 100% of heterozygotes:
100% Aa

And, just to create a highly exaggerated model, let's suppose that these individuals perform the most drastic case of inbreeding: self-fertilization. Inbreed occurs when an individual perform sexual reproduction with a closely related organism, and no one is more closely related to someone than himself!
After the first "inbreeding" generation, we'll have:
25% AA
50% Aa
25% aa

So, 50% of heterozygotes.
If this population inbreeds again, we'll have at the second generation:
37.5% AA
25% Aa
37.5% aa

So, 75% of homozygotes versus 25% of heterozygotes.
In the third generation:
43.75% AA
12.5% Aa
43.5% aa

And in the fourth generation:
46.875% AA
6.25% Aa
46.875% aa

Thus, in only 4 generations, we have 93.75% of homozygotes versus 6.25% of heterozygotes. Mathematically, the heterozygotes never disappear. Biologically, however, if a population shows self-fertilization, heterozygotes disappear in few generations.
Now, let's get out of this overly exaggerated example with self-fertilization and back to your question, where the organisms perform cross-fertilization:
The problem with your reasoning is that (correct me if I'm wrong) you're starting with a couple (Aa) and supposing that all their descendants will mate randomly. Of course, the allele frequencies will remain the same. But that's not inbreeding. By definition, inbreed is a non-random mating system. For a real inbreed to occur, the mating individuals should be more closely related than
those drawn by chance from the population.
In conclusion, given enough time, inbreeding (and genetic drift as well) has the effect of eradicating heterozygotes from the population.


text:
Calculation of Malthusian fertility and mortality from birth and death rates
In a simple Malthusian model, the population $p$ grows according to $p = p_0e^{rt}$, where $r = \beta - \mu$, $\beta$ is the "fertility" parameter and $\mu$ the "mortality" parameter. In the case of $\beta$, the closest thing to this parameter is the Total Fertility Rate. Is there a meaningful way to convert from one to the other? An easy formula might be something along the lines of
$$
\beta \approx \frac{1}{2T}\text{TFR},
$$
where $T$ is the reproductive lifetime, but this doesn't account for gender imbalances or a more nuanced way of treating the instantaneous nature of the parameter.

If every member of the population breeds, the mean number of children born from a single individual during their whole life is $\beta$ times the duration of their life. The mean life duration is $1/\mu$. Hence the total fertility rate in the homogenous model you suggest is $$\frac\beta\mu$$ If only some proportion $p$ of the population can breed, the total fertility rate of each breeding individual is $$\frac\beta{p\mu}$$


text:
Clarify pre-column pressure vs. system pressure vs. backpressure for prepacked columns used with the äkta purification system
Background: I am using the Äkta pure system for protein purification, with prepacked columns from GE-healthcare. Just to take one example, I use the HisTrap 5 mL column (IMAC: immobilized metal affinity chromatography). I understands the effects of over-exceeding the pressure limits of a column, and therefore vigorously set the pre-column pressure to 0.5MPa everytime I use the äkta. However, I am starting to question or how I should think about the different pressure, and if 0.5MPa is correct for the different columns I am using.
I was taught to always set the pre-columns pressure, which makes sense since as far as I can tell – this is the actual pressure inside the column (pressure felt by the resin). However, If I open the documentation on the HisTrap 5 mL column from GE-healthcare, I can’t seem to find much about the pre-column pressure limit. I also find the terms max-backpressure limit in the documentation for the column, and system pressure.
Questions: How is the system pressure different from the pre-columns pressure? Should I calculate the pre-column pressure myself as an effect of the size and length of the tubing leading to the column? Is there a good article or webpage that goes through this theory at a basic level?
It seems obvious, but how can backpressure be created in a system that is not closed and goes one way (or perhaps the Äkta is creating the pressure)?

https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0ahUKEwirg8XYmZTZAhUEiSwKHTUOC_MQFggoMAA&url=http%3A%2F%2Fproteins.gelifesciences.com%2F~%2Fmedia%2Fprotein-purification-ib%2Fdocuments%2Fhandbooks%2Fakta-chromatography-systems.pdf%3Fla%3Den&usg=AOvVaw2v8INehaa7HnPDoEEtp8Dk Chapter 7 of this document may be of help.

Is there a good article or webpage that goes through this theory at a basic level?
Yes, Chapter 7 of the manual linked to by Andreas Tosstorff is a good source, and is also the source of the images below. The manuals for your ÄKTA system and the HisTrap columns discuss pressure in some detail as well.
How can backpressure be created in a system that is not closed and goes one way?
This is a physics question and, not being a physicist, I can't go into detail. However, I also use the ÄKTA system for FPLC and may be able to provide some form of an answer. Any fluid moving through tubing experiences some resistance from, for example, friction between the fluid and the tubing walls, bends in the tubing and obstructions like filters, mixers, valves, etc. Even though the system is open at one end, there is resistance to the flow of fluid through it which creates backpressure. The largest sources of backpressure in the FPLC system at low flow rates are filters, flow restrictors (if installed) and the column itself.
How is the system pressure different from the pre-columns pressure?
The system pressure for the ÄKTA is measured at the pump. This measurement in itself is not very informative. The pressures that are important as far as keeping your column safe are the pre- and post-column pressures (the pressure measured immediately before and after the column, respectively), and the difference between these two (the pressure across the column). Your column has two pressure limits:

Hardware pressure limit: this is the maximum pressure the column itself will withstand before there is a risk of failure. I know this from experience after a malfunctioning valve gave 4 times the maximum hardware pressure to my column. In my case, failure meant the top of the column blowing. The pre-column pressure should not exceed the hardware pressure limit.
Resin pressure limit: this is the maximum pressure the resin within the column can withstand before collapsing. The pressure across the column should not exceed the resin pressure limit.

Should I calculate the pre-column pressure myself as an effect of the size and length of the tubing leading to the column?
Some ÄKTA systems are capable of measuring pre- and post-column pressures directly. Mine is not, and I don't know about yours. In the case where pressure is measured at the pump, the pre-column pressure is equal to backpressure between the pump and the column (caused by the tubing/filter/etc.) subtracted from the measured system pressure. To determine this, you essentially disconnect the top of the column, run the system under your intended conditions and record the measured pressure (this is the backpressure generated before the column). The manual for my columns (HiTrap Q) explains this step by step, and yours may as well.

The manual also explains how to determine pressure across the column in a similar manner. However, in my experience, the flow path after the column is relatively unrestrictive (unless a flow restrictor is installed), and its contribution to backpressure is relatively be negligible. Thus the pressure across the column is reasonably equal to the pre-column pressure, which is also reasonably equal to the measured system pressure. Furthermore, listed in every manual I read is some statement to the effect of:

The maximum pressure over the packed bed (Δp) is an approximate limit. It is dependent on the characteristics of the chromatography medium and on sample/liquid viscosity. The measured value also includes the pressure generated by the column tubing. For many columns, the recommended flow rate is a better guideline for protecting the packed bed.

In fact, the manual for my columns doesn't even list the resin pressure limit and it took substantial digging to find out what it actually is. I always run at the recommended flow-rate and set the system pressure alarm at the resin pressure limit (0.3 mPa in my case versus 0.5 mPa hardware limit) without any of the corrections mentioned above. However, depending specifically on your system and usage, it may be necessary to make them.


text:
What is protein folding and how is it relevant to disease?
I am trying to understand what is protein folding and how it could help cure some diseases.
When reading articles about it, it looks like the goal is to find perfect folds for proteins because some diseases are due to proteins that don't fold correctly. I don't understand why do we need to find them in the first place?  Don't correctly folded proteins already exist in the body of people who aren't affected by those diseases? Why do we need to manually find those structures instead of simply "reading" the structure of the correctly folded proteins in the body of non affected people?
In the end, is the goal to find the best structure or to find the folding proecess ? Or both ?
Thank you!

Please try to make the title of your questions as specific as you can. "Questions about" should never be included. They are all questions, so this is superfluous. Your question is about protein folding, so say what it is you want to know about. I have done this for you. If it is not your question then modify it.

@David Can't understand what you meant by "If it is not your question then modify it" ?

I mean, if the title does not reflect what you want to ask, then change it so that it is. I have interpreted it from the content of your question, but it is your question so you should improve the title if you are not happy with it.

@David Oh ok ! Thank you for the edit ! Yes I should pay more attention to that.

Protein folding is a complex thing. There are huge computer algorithms and huge mainframes which are trying to predict the final 3D structure of a protein.
Knowing the tertiary and the quaternary structure of a protein, allows us to understand why diseases happen. In many cases a mutation of the gene provokes an aberrant protein folding. When the protein is misfolded, it is not able to do its function. This particular condition is called "Proteopathy".
http://link.springer.com/article/10.1385%2FMN%3A21%3A1-2%3A083
If you know the structure of a protein, you are able to design or improve drugs which can directly influence the protein structure and/or function, for example antibody therapies against cancer (Cetuximab-->against EGFR, in colorectal cancer; it is a drug which was very much improved when computers prediction/simulations are used).
https://en.wikipedia.org/wiki/Cetuximab
It is hard to find out a protein's structure - for some proteins it can require years!
So you first go from the sequence of the healthy people, then you sequence their genomes, and you use this as reference for the people with certain diseases. You might find eventually some mutation is in certain loci in the genomes of people with a certain disease. Then you can study the protein structures, so you can design some new drugs which might tackle this protein. If the protein is misfolded, like the tau protein in the neurodegenerative diseases, then is good to study the structure of this misfolded protein so you can design some drugs for these protein too.
So in the end the structure is extremely important, but often times you have to study many stages of the protein folding process to understand the possible final structure that one protein might have in the body and/or in a certain disease.
I hope this can help!

I think you mean neurodegenerative not neurovegetative.

Cetuximab and nearly all other monoclonal antibodies on the market today were designed the old-fashioned way - by immunizing animals (mice in this case), screening their naturally-produced antibodies, and either humanizing it for direct use (older mAbs, like this one) or having it undergo affinity maturation via several different formats, including applying knowledge of drug/target structures (only the most recent mAbs in development). Unless you can accurately describe this in your answer, I'd just take that whole section out, because it implies the drug was designed, when in fact it was not.

Thank you for your comment, please check this link https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803018/

An article, Protein Misfolding and Degenerative Diseases, covers this question, and although it focuses on a single type of disease, this is of great importance.
To summarize, there is the potential for misfolding in proteins because of the small differences in energy between different alternative folded states, and because during synthesis some proteins expose to the solvent regions that are hidden in the folded protein and if exposed would make the protein unstable. (These latter require other proteins to help them fold.)  Thus, it is not difficult to envisage circumstances in which misfolding occurs, with concommitant loss of function and harmful consequences. The particular current interest in this is because certain neurodegenerative diseases involve misfolding of proteins. Indeed, in Alzheimers and other diseases the amyloid protein folds into an alternative structure to normal.
Although it may be a little advanced, the 10th November 2016 issue of Nature has a series of reviews on this topic, which are free to view. One by Riek and Elsberg deals particularly with the alternative structure.