text:
Why do we blow when we're out of breath?
When people are out of breath from exercising, instead of breathing normally they partially obstruct their expirations by blowing out instead of breathing out.
Why is this?
EDIT: This photo illustrates what I'm referring to.

I'm not sure I understand your question. You have to breathe out in order to breathe in again…

I don't. I start panting. This is opinion based I guess.

@canadianer: You don't understand the difference between blowing and breathing out normally?

Why did 'AliceD' mark this question as 'unclear what [I'm] asking', when her comment shows that she understood the question perfectly? I give up. No one is capable of answering, or, it seems, even understanding my simple question.

@EmmaV, after a while, thinking about it, I now understand what you are asking. Alice is clearly saying that the answer(s) would be opinion based and thus not constructive and hence put a block on any further answers. In my opinion based answer, I would say I do that so the strong air flow does not go through my teeth because it gives me a strange feeling when it goes through my teeth... Like others, I think the question could have been better expressed.

@EmmaV Do you mean why do we typically exhale harder than inhale after strenuous exercise?

What is the difference between blowing out and breathing out?

Trying to rephrase the question
If I understand the question (and what you missunderstand) correctly, I think one could rephrase the post as
When one spends some time under water and come back to the surface, one usually breath out and then breath in. This is surprising to me because I would expect the person to be out of air and therefore wouldn't need to breath out before breathing in.
Let me know if I failed to understand your question and misunderstandings
Answer
We don't incorporate the air we breath in our lungs. We only use the molecules of oxygen $O_2$ from the air (which takes ~20% of the total volume). This molecule goes in the blood, reach the cells and react with sugar to produce energy. The waster of this reaction is another molecule $CO_2$ that needs to be exhaled through the lungs.
So, really the volume and of air that we have in our lungs doesn't vary much (It actually increase a little bit as we had some carbons). Only the composition of the air that we have in our lungs changes. After some time, we need to renew this air and for this purpose we first need to breath out the air that is contain a high density of $CO_2$ before breathing in.
This is why when sticking the head out of the water many people first breath out and then breath in. Note, however that one can breath out all its air underwater and then only has to breath in when back at the surface.
EDIT
Are you asking why do we contract our lips during sport?
If yes, I think it very much depend from one person to another. There is probably no physiological advantage/disadvantage at doing so and it probably is just a consequence of expressing pain on our face.

That's not what I mean. When people are out of breath, they breath more heavily than normal, but instead of expiring gently as normal, they 'blow'. By this I mean they partially close their mouth so that there's a small opening and blow through it, often making thier cheeks bulge. Inspirations are still normal, albeit deeper. Here's an image I found quickly: http://watchfit.com/wp-content/uploads/2015/07/xshortness-of-breath-during-exercise_1-1024x682.jpeg.pagespeed.ic.qrPeKJuXUm.jpg

Your comment seems very unrelated to your post...but ok. I tried to answer to what might be your question (still unclear to me) in an edit in my answer above.

My comment is an elaboration on my question. I'm not asking why we contract our lips during sport. I personally 'blow' when out of breath because a rapid expiration when out of breath is uncomfortable. This is doubtless why others do it too. I thought that there must be a physiological explanation for it.

Well you blow to make room to breath in again, isn't it? Or you just stop inhaling altogether?!

I find it hard to believe that someone with a PhD genuinely can't understand my question, and is confusing blowing with normal expiration. Does one 'breathe' up a balloon? I make a point of always phrasing my questions as simply as possible in order to accommodate non-native English speakers, and I'm really at a loss as to how this question could possibly be any simpler to understand.

To clarify: I'm not saying people stop expiring when they're out of breath. Why would I say that? It's idiotic. I'm saying that when people are out of breath, they expire by blowing instead of expiring by breathing out normally, as a person at rest does.

Note also btw that I don't have a PhD (yet) as I am currently a PhD student. I'll delete my answer once I'll understand your question (and will then try to suggest an edit to your post).

I am not sure what is this difference between blowing and breathing out. Is it specific to the lips position or to the amount of air flowing through the mouth (or something else)?

It puzzling that my last comment has enabled you to understand my question, since the comment is essentially the same as the question. The difference between blowing and breathing out is obvious. Do both, and you'll notice the difference. Blowing is more forceful than normal breathing, and the mouth is made smaller.

And so is you question, why do we need to inhale and exhale more air when we are exercising?

You're not serious, surely. The reason why we breathe more when exercising is taught in Junior school. How is this relevant anyway?

So what is the point that interest you about blowing if it is not related to the amount of air? Is it the position of the lips?

I will soon give up trying to understand your question. It is the job of the OP to make its question easy to understand and it appears that we all struggle with yours.

No offense intended, but you might as well give up now. Stop wasting your time. It's impossible for this question to be any clearer, and yet it is still ostensibly beyond everyone's comprehension. Thanks for your efforts anyway.


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How to determine suitable Cysteine mutations?
In the lab, I'd like to generate a dimer of a protein via disulfide bonds. The interface between the two looks as follows:

Now, in the interface, there isn't any cystein I could use to dimerize the two, so I'll introduce some (bacterial transformation). But which place would be the best to introduce them? Probably not the alpha-helices or beta-sheets. But is there a general method to find the best linking site? Maybe there are program to calculate an energy minimum? Or is there a nice heuristic?
Here  a picture of a close-up of the interface.

Ive had success with Disulfude by Design, though it doesn't tell you how the suggested mutations will affect protein structure.

You need proper bioinformatics analysis to get predictions on this. Do molecular dynamics simulations for such calculation. One of most famous free tool is GROMACS.

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Range of dry matter yield per kg CO2 of different plant species
The photosynthetic equation tells us that for every sugar molecule produced 6 molecules of carbon dioxide are used.
I'm interested in how much organic matter is produced by a certain quantity of CO2. Obviously there are differences between plant species so I'm basically looking for a list of plant (categories), which tells how much CO2 does produce how much dry matter.

A plant contains about 50% of it's mass absorbed from the air, from CO2 which it converts with 45% efficiency. 40-45% CO2 fixation/respiration seems to be optimal for all plants, it's the balance of how much their cells need aerobic respiration day and night, compared to photosynthesis. That 50% absorbed from the air is fixed with H2O which provides most of the other 50%, and the rest is ashes.
According to this research:
The CO2 captured by plants is the result of the differences between
atmospheric CO2 absorbed during the process of photosynthesis and the CO2
released by the atmosphere during respiration. This difference is converted into
biomass and tends to fluctuate between 45 and 50% of the plant’s dry weight.
(the research states dry weight C measurements, they don't seem to measure CO2 absorption directly)
So it's better to search for "photosynthesis respiration ratio" to find research that measures the efficiency of the CO2 absorption:
the ratio of respiration and photosynthesis (R : P) was relatively constant, 0·40–0·45, and independent of temperature. This was consistent with earlier work by Ryle et al. (1976) [...] Some mechanistic understanding of the constancy of R : P was provided by Atkin et al. (2005), who found that respiration and photosynthesis in most examined plant species acclimated similarly after temperature change. More recently, Atkin et al. (2007) confirmed homeostasis of R : P, in Plantago spp., but this was not maintained when plants were subjected to higher temperatures than usually experienced in their habitats. Differences between photosynthetic and respiratory acclimation to temperature have been reported by Campbell et al. (2007) and Hartley et al. (2006). Cheng et al. (2000) found that the R : P of sunflower was also insensitive to changes in atmospheric CO2 concentration. Overall, the research confirms Monteith's (1981) assessment that the ratio may vary over short time periods but is constant over periods of weeks and longer.
That document has lots of research references and technical words and concepts to follow up.
It's good also to see google images for R P ratio graphs and tests.
https://www.researchgate.net/publication/263676467/figure/fig1/AS:278855131648023@1443495652845/Figure-3-Bottom-curve-simulated-10-d-running-average-leaf-respirationphotosynthesis.png
The conversion ratio is visible here, day is white, respiration is black.
https://www.researchgate.net/profile/James_Bunce/publication/43291524/figure/fig1/AS:273738792960009@1442275822297/Figure-4-The-ratio-of-average-night-time-respiration-rate-R-to-average-day-time.png

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epiphyte mats in tropical forests
I read in an ecology text book ("Ecology: Concepts and Applications" (7th edition) by Manuel Molles) that trees in tropical forests can be sustained despite the poor soil is because they extract nutrients from epiphyte mats. Trees send roots from trunks and branches to get nutrients from epiphyte mats that are located high up in the canopy. I would like to visualize these roots. Are there any pictures available (conveniently in the Internet) showing these roots?
Or are these roots usually located beneath epiphyte mats (e.g., very short) and cannot be seen unless we remove epiphyte mats?

Good question +1. In general it is good to link the book and cite it directly rather than reporting indirectly what they said.

The textbook is "Ecology: Concepts and Applications" (7th edition) by Manuel Molles (ISBN-10: 0077837282) (ISBN-13: 978-0077837280).

The book says this finding was made by Dr. Nalini Nadlarni. If I were to look at Nadlarni’s publications, there should be some information. If I cut-and-paste a paragraph from the book, “Nadlarni’s research showed that in both temperate and tropical rain forests, trees access these nutrient stores by sending out roots from their trunks and branches high above the ground. These roots grow into the epiphyte mats and extract nutrients from them. As a consequence of this research, we now know that to understand the nutrient economy of rainforests the ecologist must venture into treetops.”

Adventitious roots into epiphyte mats aren't all that uncommon, and aren't restricted to the tropics. They can occur in old growth forests in the pacific northwest (my neck of the woods). A well-developed bryophyte mat in a single upper canopy tree can store up to six metric tons of water, plus all the mineral nutrients from atmospheric deposition. For the tree, it's a huge advantage to be able to tap into that epiphyte mat rather than rely on bringing up water from their subterranean roots. As far as visualizing it goes, yes, you would have to remove the mat to see them, but they look very similar to subterranean roots. Not sure if this is helpful, but I like to think of it like this: when a new meristem is formed, it's basically undifferentiated, and if there's sufficient water and mineral nutrition it can develop into a root (or a shoot if it's getting sunlight). The tree doesn't care if that's below ground or in the canopy.

Examples of trees that do this: bigleaf maple (Acer macrophylla), red alder (Alnus rubra) in the PNW, and a wide variety in the tropics: Metrosideros collina, Cheirodendron trigynum, Ocotea spp, Xylosma spp, etc, etc. See Nadkarni's work for a more thorough treatment.

I never heard of it. Tropical forest soils may be poor, but the litter over the soil is where most nutrients are recycled and become available to trees. That's why without forest = without litter = without fertility = desert. At least in the Amazon.
Some researchers who studied the Amazonian soils are Harald Sioli and Philip Fearnside. You may find some of their old studies available on-line. If they ask some payment, try sci-hub.cc.


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Is the principle of "the least energy" a fundamental principle of evolution? How does it stand with the rule "the one who replicate the most"?
The principle of "least energy" seems to be a fundamental law of the universe (is it?). I probably use the wrong word. I'm just talking about the reason why electrons are filling first the lower level of energy or why chemical reactions happen in a specific direction, or maybe even the "Path of least resistance". Is it a fundamental law/principle or the consequence of another principle (like the weak force)?
This principle also seems obvious in living beings. But how does it fit with evolution? I first thought that between two individuals, evolution will favor the one who needs/spends less energy, but it's not that simple because the "winner" is not the most efficient, but the one who will reproduce the most (replicate its genes). So an individual who is less energy efficient (or needs/spends more energy) but replicates, more will be selected. But the principle seems to apply for two individuals who replicate at the same rate: the one who spends the least energy will be selected by evolution.
So it seems that the principle of "least energy" applies to everything, including the things that replicate (living beings) and their evolution. But it also seems like evolution favors "the one who replicates the most" first and, only after, follows the principle of least energy. But if the principle of least energy is really fundamental, how evolution was able to overtake it and put it in second place?
For example, is it accurate to say, that evolution doesn't necessarily invent the most efficient things/strategy, and fancy stuff because (amongst other reasons) it's stingy, it only follows the path of the least energy?
I feel that I'm handling the problem in the wrong way. Please correct me if that's clear for you.

EDIT: (the question has been close: I can't answer...)
this is a difficult question because it points to (at least) 3 different concept that seems conflicting, but thanks to Joe Daniel and Paul Spencer (from quora) it seems solved.

"living organisms will seek to minimize their energy output in a variety of ways. Those that do so effectively have an edge in survival and reproduction and are thus more likely to continue a population that can evolve." (Joe Daniel) "There is always selection pressure towards the systems that are most energy-efficient" (Paul Spencer)

But in evolution, the one who replicates the most will be selected, even if it's less energy efficient.
"Reproductive success is the filter that creates that evolutionary pressure on all traits, and is more fundamental than anything in terms of evolution itself" (Paul Spencer). "Conservation of energy is a distant second to surviving long enough to get offspring that survive and reproduce" (Joe Daniel)

1+2= If resources are plentiful, an individual can invest more in strategies that are costly, but increase one’s odds of success. If resources are scarce and patchy, the ones who can conserve their energies best may have an edge. (Joe Daniel)

then there is the entropy problem (It wasn't my question, I focus on energy, entropy focus on order, but it answers a part of it) :

The problem: "Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased."(Yolo123)
The solution: Earth is not an isolated system. Life causes entropy of the earth to decrease. This is offset by increased entropy of the sun, which is the primary source of energy for the earth. Overall, the entropy of the universe increases.Canadianer
(What is the difference between entropy and energy? "The more energy present in a system, the more disorder or entropy there will be. [...]  That increase in freedom that corresponds to an increase in disorder is entropy. Entropy is thus a measure of the random activity in a system, whereas enthalpy is a measure of the overall amount of energy in the system." src)
So what about the principle of least energy?
1+2+3= [it] is a theoretical concept explored by several mathematical papers that, on the surface, makes sense, if life was all about the flow of energy. But it’s not. Life is about survival, and that is often not energetically efficient. (Joe Daniel)
(An interesting implication ―which solves the seemingly paradoxical concepts, I was struggling with―: at the individual scale the principle of the least energy pushes the organism to come back to its natural state ―because it's the state that costs the less energy for it). But its natural state does not necessarily follow the 'least energy' for the reason mentioned above.)

It is possible that you thinking of the second law of thermodynamics? It would be best to be clear what that means before considering it in relation to evolution. It does indeed pose problems for cellular organization and life, but not, as far as I can see, specifically for evolution. But at the moment posing a question about something you call a fundamental law of the universe but are not sure what it is does not make a satisfactory question.

@David posing a question about something you call a fundamental law of the universe. If you read carefully, you will see that don't "call" it fundamental law, I say  it seems , then is it? and I ask Is it a fundamental law/principle or the consequence of another principle [...]?. Half of the question is about it... So to summarize, people who don't know the answer, or aren't sure shouldn't ask a question (that sin definitely deserves your downvote).

At present the question qualifies for closure on the following grounds: it lacks clarity, it lacks research, it involves several questions, the first of which belongs in Chemistry, and it has been asked before. There is a fundamental law of chemical thermodynamics and concerns Entropy (not energy) changes. As evolution is not a chemical  process I do not see how it relates to the second law, but see here.

As suggested in these comments, some research (e.g. https://courses.lumenlearning.com/cheminter/chapter/entropy-and-free-energy/ ) should help you better frame your question.

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Does this equation have a typo? (Systems Biology, singular value decomposition)
I'm reading a systems biology paper, and I'm suspecting there's a typo in an equation, but I want to make sure.
The article is "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." (Famili & Palsson 2003, http://www.ncbi.nlm.nih.gov/pubmed/12900206 / http://www.sciencedirect.com/science/article/pii/S0022519303001462). In equation 5, I wonder if the final subscript u_kr shouldn't be u_km, as the vector u_k^T is a column vector in the matrix U, which has dimensions m x m. Of course, some elements in u_k might be zero, in which case there would be less than m products in the sum, but I see no reason why there would be maximally r non-zero elements either (where r is the rank of the matrix S which has been decomposed). I worked out a simple example on paper where r < m and still got vectors with m non-zero elements. Can someone give me a second opinion on this?
Edit: Here are the main equations.
A model of a metabolic reaction network is described by a stoichiometric matrix S of dimensions m x n and rank r. For the metabolites in the model, changes in metabolite concentrations is equal to S multiplied with the vector of reaction rates, v:
${\frac{{dx}}{{dt}} = Sv}$
The singular value decomposition of S is given by
$S = U\sum {V^T}$
Multiplying on the left side with $U^T$ (The transpose of U) we get:
${U^T}\frac{{dx}}{{dt}} = \sum {V^T}v$
After matrix multiplication, we have for each row in $U^T$ and $V^T$, where $\sigma_k$ is the k'th singular value
$\frac{{d(u_k^Tx)}}{{dt}} = {\sigma _k}(v_k^Tv){\text{   k   =  1}},...,{\text{r}}$
And finally, equation 5:
${\text{u}}_k^T \cdot x{\text{  =  }}{{\text{u}}_{k1}}{x_1} + {u_{k2}}{x_2} + ... + {u_{kr}}{x_m}{\text{   (5)}}$

Can you provide the equation in your question, rather than asking people to go hunt it down?

I don't think there would be any point in presenting the equation by itself out of context. The equation is on page 3 of the PDF, right column - sorry for not mentioning that.

(a) this question has nothing to do with biology (although the paper obviously does, no biology is featured in the question) and (b) yes, it is a typo, as you can tell from it being $x_m$ and not $x_r$ and also as you can tell from equation 6 properly having $v_{k,n}$.

You are right this is a typo. Equation 5 is just a restatement of the definition of the dot product of two vectors:
$$\mathbf{u}_k^T\cdot \mathbf{x} = \sum_{i=1}^m u_{ki}^Tx_i$$
or written in another way
$$\mathbf{u}_k^T\cdot \mathbf{x} = u_{k1}x_1+u_{k2}x_2+\cdots+u_{km}x_m.$$
In the text Equation 5 is stating that one can find a linear combination of the metabolites described in $\mathbf{x}$ whose time evolution is described simply by a linear combination of the flux rates described in $\mathbf{v}$. The coefficients of the first linear combination are given by a row vector $\mathbf{u}_k^T$ in $U^T$. From this perspective, since there are $m$ possible metabolites ($\mathbf{x}$ is a $m\times 1$ vector), there have to be $m$ coefficients, so that the indices must range from 1 to $m$ in Equation 5. You are correct that $u_{ki}^T$ might be 0 for some $i$. But that doesn't change the fact that there should be $m$ (possibly vanishing) coefficients.


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What specifically allows alpha-complementation in beta-galactosidase?
I'm familiar with the use of alpha-complementation of beta-galactosidase with the pUC alpha-peptide and the M15 lacZ gene product, and would like to hypothetically apply alpha-complementation in other settings with different enzymes. I do have a few questions, but hopefully they are similar enough to all be answered here.

What specifically allows for the non-covalent association between both truncated protein products to form a functional beta-galactosidase? How is beta-galactosidase unique in that separating it into two portions still yields a functional enzyme (in other words, why wouldn't other enzymes remain functional if I split them)?
What other proteins, if any, have been engineered to perform similar alpha-complementation? What steps were taken to accomplish this?

Maybe this review is a good start: http://www.ncbi.nlm.nih.gov/pubmed/22070901

Two other (free) papers on beta-gal complementation and other split reporter systems: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835542/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137764/


text:
A question about cancer antigens and their mechanism
Can you name the most common antigen that cancer cells in general can't live without?

Are you referring to a certain type of cancer?

Welcome to Biology.SE! We encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). ——— Thank you for taking the [tour], but please also go through the help pages starting with [Ask] questions effectively on this site and edit your question accordingly. Thanks!

@tyersome I actually have searched on internet and read books but all the answers wasn't convenient

I think that you would benefit from making sure your have a firm grasp on the basics of biology. I say this because you appear to not be using the correct terminology (e.g. You seem to think that antigen is a synonym for protein, which is not correct.) This makes your question unclear and creates the impression that you won't have enough background knowledge to understand the answer to your question assuming it was made clear enough to be answerable. ...

I recommend you start your review of biology with a relatively accessible and reliable source like Khan Academy. Wikipedia is also generally a good starting point and you can then check their references. There are also online platforms called MOOCs that offer free (or very low cost) courses on a wide variety of subjects — two that I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI.

This is a hard question to answer because each type of cancer is a whole different game at the molecular level, however there is something you might be interested in called "hallmarks of cancer" (image 1) which are key features for cancer to thrive. They were originally described by Hanahan and Weinberg (2000) and have been revisited by Fouad and Aanei (2017) in an updated review. The hallmarks of cancer aren't specific genes themselves, but rather broader categories that englobe certain types of genes.
If you want to look at specific genes, we could talk a bit about what more purely data driven approaches have found. There is a very interesting work by Kandoth and collaborators (2013) that presents data from The Cancer Genome Atlas (TCGA), which is a database of different kinds of genomic features from several different cancer types. Among the results of this work (specifically on figure 2 which I include here as Image 2) you can see a table of 127 significantly mutated genes across 12 different cancer types. One gene that is well known in medical literature for being frequently mutated in almost any cancer type (situation which is also observed in the aformentioned table) is TP53 which encodes a protein that is key for genome maintenance in normal cells by participating in DNA damage and repair (which is a cancer hallmark under the "altered stress response" category). In the table you can also spot tissue-specific cancer genes such as APC in colon/rectum cancer and VHL in renal cell carcinoma.
Just to make sure you can understand the table, the gene names are presented in the right (rows) and the names of the cancer types are presented at the top (columns). The description for the cancer types abbreviations can be found here. To the left of the table there is a functional classification of the genes so you can know more or less what a given gene does in a quick manner. The values presented are simple frequencies (divide the number of samples of a particular cancer type that have the mutation over the total number of samples of that same cancer type) expressed as percentages (so they are already multiplied by 100). The final column (Pan-Cancer) shows the same idea, but taking all samples from all cancer types into consideration for the frequency calculation.
So for answering your question regarding if there is a common feature in all types of cancers: strictly speaking at the gene level no, since even the TP53 mutation which is the most common amongst all cancers might not be present in some cancers; however, looking at it by categories of genes (as one or some of the 7 hallmarks) reveals that all cancers apply similar strategies to thrive (they exhibit different mutated genes, but these genes frequently belong to the same biological pathways and participate in similar functions). I hope you find this useful (:

Image 1: 7 hallmarks of cancer (2017 review).

Image 2: frequency of mutation by gene and cancer type.
References:

Fouad, Y. A., & Aanei, C. (2017). Revisiting the hallmarks of cancer. American journal of cancer research, 7(5), 1016–1036. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446472/
Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., … Ding, L. (2013). Mutational landscape and significance across 12 major cancer types. Nature, 502(7471), 333–339. doi:10.1038/nature12634
National Cancer Institute. TCGA Study Abbreviations. Retrieved from https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations

This looks like a good answer and you've done a nice job of providing supporting references. However, please include the complete reference information since links can break. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. ...

In addition, since answers here "must be comprehensible without reference to external sources" it would be helpful to insert the figure and table you refer to into your answer Thanks!

oh ok I wasn't sure if pasting the literal image of the resource was ok. I'll modify the answer soon enough

That looks much better! +1

Thank you so much, you're answer really helped me

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text:
Can Cas13 edit DNA
Can Cas13 be used to edit DNA or is it only for RNA?
I have tried looking at literature and my understanding is that it can only edit RNA.

The Cas13 protein targets/edits RNA specifically and not DNA. That said, as you probably know, the Cas9 protein is famously used to edit DNA and was the inspiration that led the Zhang Lab to seek out the Cas13 protein for editing RNA.
If you're interested, you can read here for some additional detail on how Cas13 targets RNA and why it's RNA-specific.

The question asks "Can Cas13 edit DNA" - why is your answer about Cas9?

Maybe I didn't make it clearly but I was just trying to make the point there is something that edits DNA, but it's not Cas13. Will edit to make it clearer.

Then you probably shouldn't start with "yes" :)

Done, yes was intended to reply to "is it only RNA" but you're right that that was not very clear :).

No, Cas13 can't be used to edit DNA. Cas13 does not contain nuclease domains RuvC and HNH  domains responsible for DNA cleavage, so they cannot directly edit the genome. For that Cas9 and Cas12a is used.


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Can sleep be a barrier against aging?
I know that what I'm writing about may be a little strange, but as far as I know,when we are asleep, our human body is programmed to carry on biological functionalities in a really optimized way and we are less sensible to external stress.
So I wonder whether putting people in some state of induced coma for a long period of time (I mean for years) may reduce the effect of time and aging on their bodies to be able to awake them later ,almost as they were before undergoing the process ?
Note: I'm not speaking about the process of freezing bodies - only bare sleep.

Welcome to the site!  I've edited to clarify grammar and formatting; please feel free to [edit] if my edits conflicted with your intents.  Also, if you could show more of the research which you have already done, it would probably help us understand the context of your question.  Thanks!


text:
What is this fossilized claw found in a Belgian forest?
What is this fossilized claw found in a Belgian forest? It is 14.5 cm long and 2.5 cm in diameter.

What are its dimensions?

Why do you say it is fossilized?

Looks like the proximal end of a rib of a large mammal (cow, horse, deer). Without information about how large it is, it is not possible to get closer to an identification. It's not a claw and very likely not a fossil. It just looks old and dirty.
Here's a horse rib cage (from https://www.rodnikkel.com/content/saddle-tree-blog-from-shop-and-desk/the-rib-cage/):

Ribs in the 4-7 range seem to be a good match for shape but not as much for roundness.

It is 14.5 cm long and 2.5 cm in diameter

This isn't my area, but how can you tell that it isn't any other elongate structure from a large mamal? For example, why isn't it a horn/antler?

That's the distal end of an antler of some deer. You can tell because the texture is smooth and glossy, all wrong for a rib, and has that flange at the end which looks very different from the uncinate processes you see in some ribs but looks a lot like the flanges you see on some deer antlers. The more rugose, "veiny" texture near the base is also typical of deer antlers. My guess is that it's either a red deer (Cervus elaphus) or roe deer (Capreolus capreolus) antler fragment.
It's not a claw, because it lacks a clear flexor tubercle, articular facet, etc.

The cross-section is also very typical of a deer antler. This is what a deer antler looks like in cross-section.


text:
What kinds of fish tend to have a rapid death after being caught?
I am asking this question because I am trying to make my diet less cruelty-oriented, for this reason this question can be related to trolley problem since I am coping with an ethical problem trying to minimize the the core aspect i.e. suffering.
On the contrary I would like to know what kinds of fish suffer the least after being caught. I know that shrimps/prawns die very quickly since they cannot breathe out of the water, for instance here I have read that prawns die after  just a couple of minutes out of water. But for medium/small size fish is different, especially for those which are mass-caught. Not to mention the explosion of bowels caused by rapid pressure variation.

https://philosophy.stackexchange.com/

@JohnHadish I think technical knowledge about pain is required in order to answer


text:
What do proton pump inhibitors do?
I know that sodium azide and 2,4-DNPH inhibit proton pumps. The azide is called an inhibitor and 2,4-DNP is called uncoupler. I want to know what's the difference between the mechanisms of action of sodium azide and 2,4-DNPH in proton pumps. Why is one called an inhibitor and the other an uncoupler?

There's a decent presentation here that basically goes over what you're asking.
As an inhibitor, azides are similar to cyanide in that they inhibit complex IV by binding cytochrome oxidase, resulting in a sort of chemical asphyxiation.
Uncouplers are a little harder to wrap your head around. They embed in the membrane space, and we know that ETC and proton pumping depends on the established proton gradient across a membrane. Uncouplers uncouple the proton gradient from the electron transport chain, allowing protons to diffuse across the membrane, effectively negating the proton gradient.

Isn't OP asking about protein pumps? This answer seems to focus on ATPases. It's just all in the name, but just wondering.

The question is weird because when i think proton pump inhibitor, i think like omeprazole or benzimidazole derivatives which block the ATPase. I think the title is just misguided, because the compounds in the question body inhibit the electron transport chain.


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Solving a Pedigree Between Heterozygous Half-Cousins

A man who is a known heterozygous carrier of oculocutaneous albinism marries his half-cousin (they share one common grandparent) as shown in the pedigree below. This trait is transmitted as a fully penetrant autosomal recessive. What is the probability that this couple will produce a child with this disorder?

A. 1/2
B. 1/4
C. 1/8
D. 1/16
E. 1/64

My calculation was 1/2 (for II-2 as he must be carrier) * 1/2 (for II-3) * 1/2 (for III-2) * 1/4 = 1/32. Please help me out by proper explanation to your steps and point out my mistakes. The correct answer given is 1/64. Pedigree shown in the image below.

Also a proper attempt at answering for yourself should include your working, for example, why did you do 1/2 * 1/2 * 1/2 * 1/4  rather than 1/2 * 1/2 * 1/4 * 1/4? Therefore I think it should be closed as homework.

From what I can tell, you are not including the probability of the grandfather being a carrier (it could be the grandmother who is the carrier). Calculation should go like:
P(Child is born with disorder) = P(II-2 is carrier) * P(I-2 is carrier) * P(II-3 is carrier) * P(III-2 is carrier) * P(Child is homozygous recessive)
P(Child is born with disorder) = (1/2) * (1/2) * (1/2) * (1/2) * (1/4)
P(Child is born with disorder) = 1/64

I was just about to comment, you can Google "A man who is a known heterozygous carrier of oculocutaneous albinism" and the question has been answered on other forums. For book questions I find this is often the fastest way to get an answer.

thanks a lot everyone. but how do we get the probability of grandfather as he is the first one in the pedigree so how did u get his probability to be 1/2. please explain. @ CactusWoman

@MaryamKhan The probably of the grandfather being the carrier is the same as the probability of the father being the carrier (given that the son is heterozygous). If we assume that the father is the carrier, we know that one of his parents must be the carrier. It must either be the father's mother or the father's father, giving us a 1/2 chance of the father's father being the carrier. The fact that the grandfather is the first in the pedigree does not really matter, as we calculate these probabilities up the lineage starting with the heterozygous man.

Thanks a lot CactusWoman :-) now i understand it.
Thanks a lot for your suggestion. that really helped when i searched the question on google @ Kendall


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difference between transcriptional activator and general transcription factors?
What is the difference between transcriptional activator and general transcription factors? Are they same or different, and do the transcriptional activators first attract general transcription factors or the RNA-polymerase also, at the same time?

Activators turn genes on - they help or promote RNA transcription of the gene.  Other Transcription factors may turn genes off (prevent or reduce RNA transcription).  Some transcription factors may promote or inhibit RNA transcription depending on their environment/context.
Transcription factors is such a generic term that anything can happen in practice.  They are generically supposed to interact with the polymerase, but if some were found to interact by attracting other transcription factors that would not be a surprise.
I think 20+% of human genes are transcription factors (that is just a guess we haven't been able to characterize more than a few of them.

You here! +1, just to share my gratitude :)

As Shigeta mentioned, transcription factors are proteins that regulate gene expression which can be either positive (activation) or negative (repression). Sometimes the same transcription factor can act as a repressor or an activator under different conditions. Transcription factors have specific target genes.
General transcription factors (GTF), however are ubiquitous proteins that are generally needed by the RNA polymerase to initiate and carry out transcription. TATA-binding protein and TAFs are some examples of GTFs.
Specific transcription factors can act via different kinds of mechanisms: as you said they can recruit RNA-polymerase (but may interact with GTFs— this has not been explicitly shown, in my knowledge). Some help in altering the chromatin structure to facilitate transcription.

General transcription factors are needed for binding of RNA polymerase and also for attachment to promotor regions of genome since most of the regions of genome is tightly bound with histones promotor region and varoius other sequences necessary for attactmant for general transcription factors might not be available.As the name suggest general transcription factors are general and common for all genes.The principle that there exit vast differentiated cells arising from a single cell sharing same genome suggest that preferential gene activation is the key to differentiated cell type,each cell has its own group of mRNA and protiens.Definitly there must be other mechanism that ensure that specific a gene is activated/deactivated in cells specific transcription factors serve this purpose as mentioned above by altering the structure of genome by chromosome remodelling enhancement of transcription or deactivation  is obtained this way the transcriptional activators pave the way for prper attactment of general transcription factors and RNA polymerase to set the play for next stage recent research also suggest transcriptional activators give particular three dimensional shape to genome like protiens, to ensure gene activation by creating isolated neigbhourhoods(young et al)('rethinking transcriptional factors and gene expression' an article in MIT biology website might give deeper insight) To sum up transcriptional modulators are necessary for activation of particular genes but general transcriptional factors are necessary for all genes.


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Do you know what type of insect this is?
I found these in my appartment (we live in a half basement). It's been three so far and I can't find the thing anywhere in insect lists, etc. Could you tell me what type of insect this is?

There are 900 different species of Crickets but I would say it is a Camel Cricket based on the info provided.

As camel crickets often live in basements, you are probably right. It might be good to add a reference, for example Some hilarious info on how to get rid of then can be found here

@RHA Why would anyone get rid of such harmless insect?

This is a camel cricket (family Rhaphidophoridae); T. H. Hubbell's 1936 monograph on the genus Ceuthophilus has a key to the North American genera then known (and those added since are not found in Canada).  The photograph does resemble specimens of Ceuthophilus that I have collected and may well be that genus.


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Finding Regulatory Elements: How Have People Been Doing This?
First up, I am NOT asking about how to search for and match regulatory elements using a database. I'm asking about how people found what to search for and match in a genome, how they built those databases. My question is,
How did people identify regulatory proteins/nucleotide elements in the first place?
Did they first find the proteins we now call transcription factors and sigma factors, or did they tamper with the genome to find the regulatory parts and then traced them to the proteins?
Is there a book on the history of research gene regulation to recommend?
Also, I tried Googling. Every site recommended one database or the other. I would be grateful too if you could tell me what should I have searched for?
I am more interested in Prokaryotes, but answers on Eukaryotes would also be welcome.
Context: I'm a freshman doing research (yep. the experience is kinda crazy for me) and I'm interested in finding regulatory elements in Mycobacterium smegmatis and its phages.

where have you looked so far? textbooks? primary literature? can you give some specifics?

This should be covered to some extent in almost any textbook on molecular biology. One excellent book is Mark Ptashne's "A Genetic Switch". It's about regulation in lambda phage, a virus, but many of the principles cary over to prokaryotes as well. It has a full chapter devoted to a detailed analysis of the experiments used to identify the transcription factors and promoters.

This is one of the things I looked at: https://www.ibiology.org/ibioeducation/exploring-biology/molecular-biology/transcription/discovery-of-transcription-factors.html  But a lot of things I read was about the methods and discoveries, without much detail really on what people were thinking when they tried these things out.

@CharlesE.Grant Got it. I will check it out.

@CharlesE.Grant My school library has the 1986 edition, whereas the 2004 edition I have to buy. Is the chapter you were talking about in the older edition?

@CedarRen. For pete's sake, just walk down to your library and check it out. I was happy to offer a recommendation, but now you're asking strangers on the internet to do your work for you.

If your final goal is to understand how to carry out your project then you can focus on how such studies are carried out in current times. Scientific research in earlier times were limited by the technology available at that time.

Here's what one group thinks is pertinent: https://www.biostars.org/p/10596/#10749, besides @WYSIWYG... ze may have finished zer studies, and might like to contribute to the technology around zem: http://discuss.area51.stackexchange.com/users

@CharlesE.Grant, I recently ordered a copy thanks to you. It's a short book, and so far very interesting. Cheers.

As it can be seen from (more or less recent) discovery, most of the regulators were discovered through specifically designed experiment to exhibit one particular factor. Several examples include:

The discovery of Sp1, the first eukaryote transcription factor to be discovered (as described in the video linked in the comments)
The discovery of the Lac operon in E. coli.

None of these were intended to be screens for regulatory sequences in general. If you are looking for regulatory sequences of a specific gene, the technique of reporter gene, combined for instance with a random mutagenesis screening can provide you with a mapping of regulatory elements.
The following article might be of interest to perform a screen based on UV-mutagenesis: UV mutagenesis in Escherichia coli K-12: Cell survival and mutation frequency of the chromosomal genes lacZ, rpoB, ompF, and ampA.
If your question is more general: "all the regulatory sequences associated with one gene", then this question is generally unanswered, and can probably be better tackled first using bioinformatics analysis (such as promoter prediction, etc).

All this history hasn't stopped some from trying though has it? http://bit.ly/2lN7uKp


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Extracting DNA from a kiwi
I have two questions regarding this experiment.

Online instructions say to use 5g washing up liquid, 2g salt and 100ml tap water mixed together with a mashed up kiwi. Do I use a full kiwi ?

Instructions say to use coffee filter paper or a fine sieve. Would laboratory filter paper work or would it be too fine ?

Also, how can I improve on this method to get maximum yield etc ? All advice and suggestions welcome.

Yes, a full kiwi. The method is rather crude and the yield you get is not so high, because you will not break up all cells and also loose some of the DNA which is bound to the cell debris.

Lab filter paper of course works as well, as would a fine cloth (cheese cloth for example). The receipe is designed to work with stuff that people have usually in their kitchen, which is true for coffee filters, but usually not for laboratory filter paper ;-)

Great , and how would I increase the yield ?

With household chemicals? I don't think this will bring much. This is a demonstration and for this purpose it works pretty well. We have done this with bananas.

While it wouldn't increase the yield, I used isopropyl alcohol to precipitate (and thereby increase visibility) of extracted strawberry DNA.  Admittedly this was in a group setting (~10) so the total yield was higher, but I was could still scoop up small globs of visibly white DNA clumps in pill bottles without magnification or undue effort


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What software is there available for quantitative structure–activity relationship (QSAR) pharmacological studies?
QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what software is available to assist me in doing these studies.

On the G6G Directory of OMICS and Intelligent software, I searched for "QSAR Analysis, and received two product abstracts:
1) SYBYL®-X Suite which contained:

3D QSAR: use the power of industry leading CoMFA in a new way to
generate novel ideas for R-groups - predict the level of biological
activity or potency based on structure-activity data, Not just yes/No
activity predictions;
Cheminformatics: produce highly focused queries that avoid false
positives using a rich set of 3D queries; on-the-fly conformational
searching means you only store a single conformation of your
molecules, keeping database size small and very transportable; and...
Link to this abstract:
http://g6g-softwaredirectory.com/bio/proteomics/structure-modeling/20710-Tripos-SYBYL-X-Suite.php

2) Fujitsu GhostMiner
GhostMiner can be employed in a number of business intelligence areas and the following areas:

Bioinformatics - genetics, proteomics, Quantitative Structure
Activity Relationship (QSAR) modeling...
Link to this abstract:
http://g6g-softwaredirectory.com/ai/neural-networks/20154-FQS-Poland-Fujitsu-GhostMiner.php

Perhaps the above will help.

Click2drug is a good ressource for in silico studies.
See this link.


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How many animal species are larger than humans?
I sometimes think about just how huge humans are in comparison to most animals. Even compared to a squirrel, which is really a pretty large organism in the grand scheme of things, humans are hulking giants.
I know humans are classified as megafauna, but we're neither the smallest nor the largest animals in that group.
How many animal species currently exist where the average adult individual is more massive than the average adult human?
Sources that cite other measures of size, like height or length, might be useful, but I would expect the focus to be on mass.
Obviously, new species are being discovered all the time, and we don't have exhaustive measurements for every species, but considering how few megafauna there are, I would expect a fairly accurate estimate to be possible.

Welcome to Biology.SE. Larger in term of distance between the two extremities of the body? Larger in weights? or in volume? Would Placentonema gigantissima (9 meters long, 2.5 cm in diameter) be bigger than a human? Are you talking only about extant species?

In the last sentence you rephrase your question "How many different species are actually larger than us", do you mean animal species (as specified in the title) or any species? In many non-animal species, the concept of individual might be hard to define. There's a fungi who covers an area of almost 9 square km in eastern Oregon.

Depending on the exact formulation of your question I think that an exhaustive list might be very long. But I guess someone could come up with a rough estimate of the number of species.

Echoing remi.b's point - unless this question is narrowed down it is very broad.

@Remi.b I definitely mean animal species, I don't know why anyone would think I would suddenly be referring to fungi. I've clarified that. I'm referring to extant species. I assumed that mass would be the implicit measure for size, but I've clarified that as well. I didn't ask for a list anywhere, just a number. Listing them would be helpful, but not necessary.

I think this question is not broad at all, there have been plenty of serious estimates of species richness ~ size relationships: http://www.life.illinois.edu/ib/451/May%20(1988).pdf

Yes, the answer is a single number. That's about as far from broad as you can get.

EOL knows about (268 species of mammals with a mass >= 80.7kg)[http://eol.org/data_search?utf8=%E2%9C%93&taxon_concept_id=1642&attribute=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVT_0001259&taxon_name=Mammalia&min=80.6&max=&unit=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000009&sort=desc&commit=Search] and (5,701 species of mammals with a mass <= 80.7kg)[http://eol.org/data_search?utf8=%E2%9C%93&taxon_concept_id=1642&attribute=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVT_0001259&commit=Search&taxon_name=Mammalia&min=&max=80.7&unit=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000009&sort=desc]

@Gaurav Well that's pretty neat. I was not familiar with that website. I don't know how exhaustive EOL's data is, but that looks like the core of an answer to me.

Looks like 80.7 kg is the average for humans in North America. Google says the average for humans worldwide is 62 kg, but EOL has it listed at 68.8 kg.

I agree the question is definitely no too broad. I first voted to close as unclear, it is now clear and I am voting to reopen.

Humans weigh 62 kg on average. According to https://www.catalogueoflife.org/col/info/totals, there are 91 cetacean species, 80 of which are larger than humans.


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Hodgin-Huxley model for a single neuron
I am viewing (through edX ) an introduction course to computational neuroscience. In the second lecture, the Hodgin-Huxley model is considered. I am going over some of the questions and have encountered a problem with one of them (a picture of the exercise is attached below). I have a strong background in mathematics, but my background in biology is yet very poor. I am having a hard time connecting the biology to the math. Can anyone help with this question:

Thank you!!

This is essentially a homework. See out homework policy. You are expected to make an attempt at the answer before asking.

I think that since the question includes the answer and asks for an explanation, this is a legit question

My problem is that I don't know how to even start this question..
The formal answer of the course is that all the answers are correct except number 2.
My original answer was that 1,5,7 are correct.
But, basically, I have a problem understanding what considerations I should use..

The details you provide assume that we are all intimately familiar with the experimental facts and the a priori assumptions that went into the derivation of the Hodgkin-Huxley model, so I don't think you will find much help in this forum unless (a) the correct individual happens to see your post, or (b) you provide more background.  Given that this work was published in 5 seminal papers after World War II, I would not have thought you need to recreate the arguments to learn computational neuroscience. It's really about the molecular physiology underlying transmission of action potentials.

That is actually not the most popular representation of the model. You can have a look at this answer. You can also refer to this book - Mathematical Foundations of Neuroscience by Bard Ermentrout. It is a comprehensive book (includes mathematical models of different neuroscience aspects) and is easy to understand.

Ok. Thank you very much for your answers. I will also have a look in those references. I will attach now, the reference slides for my question. If you will have anything else to add that could enlightening my understanding I will be most greatfull. Thanks!

link

@user135172 edx has course forums where you may find more help

Where are the actual questions?

If you enter the courseware, then it is in the videos of lecture 2. it is the ex which comes after lecture 2.3

Since you didn't get the right answer to #6, let's review the basis for this model.
The basis of the model is precisely the statement in #6: an individual channel has a defined conductance when it is conducting, and if all of them are conducting then the total conductance is the single-channel conductance times the number of channels (conductances in parallel add).
Confusion comes from the fact that, in the terminology used here, an "open" channel is not necessarily conducting. The probability that a single channel is conducting is the product $r^{n_1}s^{n_2}$.
$r^{n_1}$ describes the "activation" process, while $s^{n_2}$ describes the "inactivation" process. These are two separate processes, with the activation process now known to be driven by voltage-dependent changes in the configuration of transmembrane domains of the channel protein, while the inactivation process is a charged part of the protein inside the cell that more slowly moves to block the channel when the cell is depolarized. See this summary by Clay Armstrong, who contributed much to our understanding of these processes.
So in the terminology here, a channel can be "open" (in terms of the $r$ process) but still "inactivated" (through the $s$ process) and thus be non-conducting. It can also be "closed" (in terms of the $r$ process) and "inactivated", in which case it is also non-conducting.
The way this is modeled is that $s=1$ means no inactivation, while $s=0$ means fully inactivated. So that covers question 3. This is in contrast to the activation process, in which $r=1$ is full activation.
Question 4 might be a bit misleading as there may be a hidden assumption that you are starting from being at potential $u_0$ for a long-enough time and then increasing $u$ suddenly (which is how action potentials normally are generated). In that case your understanding of differential equations should make it clear that $\tau_r$ and $\tau_s$ are the time constants for the responses of the $r$ and $s$ processes to a change in $u$. The process with a shorter time constant responds more quickly, so activation precedes inactivation (on the average). The different powers associated with the $r$ and $s$ processes ($n_1,n_2$) might confuse things a bit, but try running this model and you should be convinced.
This might seem convoluted at first, but Hodgkin and Huxley worked out this model based solely on their electophysiological studies (with help from Bernard Katz). It's amazing how this model's postulates of multiple single channels and separate activation and inactivation processes have been so well verified at the molecular level over the past decades.

I see. I think I got most of your detailed explanation. I will also look into the link. Thank you!!


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Drugs to make rats easier to trap
What drugs will make rats less cautious/sensible and/or more hungry so they'll go to my snap traps more?
What dosage and how do I deliver it to the rats?
Background info:
The rats trapped in my crawl space I imagine have limited food, if any.
The snap traps are well coated with peanut butter scent but the process is very slow -- one by one.
They have rat mites (blood-sucking parasitic barely-visible mites) and I want them out ASAP.
It's been several months because:

They reproduced down there.
One of the vents got broke open again so a second batch got in. I don't know how many. 25 rats have been trapped so far (2 today and I hear more).

I've checked the house so well. Sealed up with caulk and expanding foam every hole. Checked the roof. Sealed wire mesh on all the plumbing stacks and exhaust vents on the sides of the house.
There's really nothing else. I'm positive it was the broken foundation vent that let the new ones in. But now that everything is sealed securely and won't be broken open again, I think it's only a matter of removing the existing rats.
I don't want to poison them because then they'd die inaccessibly and their mites would swarm the house. They have to die in the traps that I check several times a day, so they can be removed before the mites spread.

If the rats become less cautious then I would suspect that it's more likely they will come in to your home and cause further problems. If you are laying traps I guess that is something you are trying to stop. You'd be better off seeking professional pest control advice

Coming from an island rat-eradication standpoint, I would second @Michael_A's point: if you're giving rats a drug with the intention of killing them, make the drug lethal.
If you want to kill using snap-traps for ethical reasons (deaths from anticoagulants are not, generally, pleasant), I would suggest habituating the rats to the traps by putting bait on an unarmed trap for several nights until the rats learn to ignore their trap-shyness, then repeating with an armed trap.

@bshane, yep, I think anticoagulants are cruel and wouldn't use them. I've updated the answer to reflect that. The producers of the rat trap that I linked in my answer have produced good literature for using traps and their traps appear to be highly targeted and effective.

@user193661, Something like the traps in my answer may work well, they use a formulated attractant and their literature may be worth a look. The suggestion from rg255 seems like a good one, a professional may be the fastest option.

I keep somewhat up-to-date with pest control measures. I haven't heard of chemicals being used to alter rat behaviour but using parasites that alter rat and mouse behaviour (Toxoplasma spp.) has been studied. The infection increases predation rates and also appears to increase the rate at which they are trapped. Toxoplasmosis also affects humans with cats being the main source of infection. I am uncomfortable about approaches that increase the prevalence of toxoplasmosis.
If you're going to the trouble of administering a drug to a pest why not make the drug lethal? The extra step seems unnecessary but I personally would opt for traps given that many poisons (particularly warfarin) seem cruel.
For traps good bait (uncooked bacon, lard, peanut butter, dog biscuits) makes rats;

less cautious/sensible and/or more hungry.

The right trap can make a big difference. This one can self-reload > 20 times and is instantaneous. The linked website contains advice for setting traps.


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How do we explain the white feathers of an albino peacock?
Peacock feathers are supposed to produce colours by surface structures modulating the light (in addition to the usual absorption/reflection mechanism)... https://en.wikipedia.org/wiki/Structural_coloration
But how does that explain the existence of an albino peacock? https://www.favrify.com/wp-content/uploads/2015/02/peacock1.jpg
Does albino mutation change the physical structure of feathers in addition to the lack of colour pigments?
Does anyone have a close comparison of the physical difference of the albino vs coloured peacock feathers?

@Tytoalba I did search a fair bit on google and visited probably 7-8 websites, but found none which discuss the albino peacock's peculiarity. I am not a biologist, so I don't know the best places for such research (other than googling)... so I am not sure my rigor of research matches your expectation.

'I am not a biologist'- me neither. :) It was just a pointer because Bio website often receives questions that show no prior research(the level is expected to be Google search mostly). Between you can always check Wikipedia, one can find almost anything on Wikipedia. Since it does have mistakes, it is always better to crosscheck. On googling 'White feathers of peacock', the peafowl link showed up, it mentions leucism at the end  of Plumage paragraph.

More specifically this site explains that the black pigment absorbs the incoming light, leaving the iridescence of the feather's fine structure to dominate. Albinos, which lack this light absorbing pigment have white feathers simply as a "reflection" of the white proteinacious content of the unpigmented eather http://www.webexhibits.org/causesofcolor/15C.html

The surface structuresa that are responsible for the structural coloration of peacock feathers are actually barbules and rods made of the very same biopolymer that is responsible for pigmentation in many other animal species, namely melanin. Just as in other animals, melanin is produced in the melanocyte cells which reside in the skin's epidermis. The conditions of albinism or leucism are due to mutations to genes responsible for melanin expression in those cells, or their absence. So although structural coloration is resposible for the colorful peacock feather, it is the same mechanism that leads to colorless feathers as in other animals.
Reference
a Zi, Jian, et al. "Coloration strategies in peacock feathers." Proceedings of the National Academy of Sciences 100.22 (2003): 12576-12578. https://dx.doi.org/10.1073/pnas.2133313100

Although melanin is a polymer of derivatives of tyrosine, and may contain cysteine, it is not a protein. But +1.


text:
How many molecules NADH are produced in the Krebs Cycle?
I don't know which source i'm going to follow.
Some say its 3 molecules NADH per cycle → 2 cycles × (3 NADH) = 6 NADH
Some say its 4 molecules NADH per cycle instead?

This is slightly depending on which reaction you want to include into the cycle. I count four:

One when Pyruvate is converted to Acetyl-CoA,
one when Isocitrate is converted to α-Ketoglutarate,
one for the reaction of α-Ketoglutarate to Succinyl-CoA and
finally one for the reaction of Malate to Oxaloacetate.

If you see the reaction of Pyruvate as happening outside of the cycle, it's only the later three.
See this image (from here) for an overview:

The alpha-ketoglutaric dehydrogenation to form Co~A.The NADH energy is released.Therefore 6 molecules of NADH is produced
You can see the above picture to understand better.


text:
What's the difference between Phage DNA and Recombinant DNA
Genetic engineering:
In my textbook the following sentences describe the two, but to me they seem the same:

The new combination of bases in the DNA (vector DNA + DNA fragment)
is called recombinant DNA.
With bacteriophage vector, the bacteriophage will infect the bacteria by injecting its DNA into it. The Phage DNA (with the
desired gene in it) then integrate into the bacterial DNA.

Without going too much into it. What is the difference between Phage DNA and recombinant DNA?

Phage DNA is the DNA in a bacteriophage.
Recombinant DNA is synthetically combined DNA used in genetic engineering.
In your case, since the phage's DNA is used as a vector, the phage DNA is the recombinant DNA, but that does not mean every phage's DNA is recombinant, since phages occur naturally. The point is, the phage DNA was altered to become recombinant DNA.


text:
I can't Identify this "bug" that seems attached to fresh cut wood
I'm a very amateur entomologist (I'm actually just an old fat hippie that loves all critters).
I don't have any chops here, but I swear I've done my due diligence and tried to figure this out. I'm asking because I'm baffled. (Leg stripes are Arachnid-ish, but thorax is completely wrong ... I just dunno...)
My girlfriend sent me a pic; she swears these things were jumping out of a seasoned firewood pile and by her words "attacking".
Location:  PA Pocono mountains, circa Kunkletown, heavily wooded area.
Now granted, there was a lot of drinking going on, it was "girls weekend out", and there was a hot tub.  I wasn't there; so I cannot actually confirm what really happened... (Of course I wish I was there, but ... nevermind)
HOWEVER - here's a pic.  You can't make this up.  Or, at least, I'm not making this up ...
What is this critter?  I think it's "insect" by the leg count I can see.  But edumicate me; this is a new one to me and I'm very intrigued.
Many thanks best!
On Edit
Perhaps some sort of "wood cricket" based on rough taxonomy of the leg configuration, and it's penchant for jumping.  Pure speculation.

I think I may have it.  gOOgle terms "giant cricket wood tiger stripes" yielded very similar critters:  So-called "Camel, Cave, or Cellar Cricket."
Order Orthoptera (Ensifera), Family Rhaphidophoridae.
Genus and Species will be next to impossible unless I can capture one, but obviously one of the North American varieties that like to hang out in damp decaying wood.
From the interwebs:


text:
What is a "pan-specific" antibody?
I am new to biology. I searched a lot to find an article that explains what "pan-specific" antibody is but I could not find anything substantial that would help me understand what it is.
An example from an article

In this report, we address this long-standing analytical deficiency by
  developing a pan-specific antibody against the pHis modification. We
  show that this antibody can be used to detect protein histidine
  phosphorylation in vitro and in vivo.

Another definition
I appreciate if someone helps me with finding a scientific explanation (article/ book) on what "pan-specific" antibodies are.
Kind Regards,

What does pan-specific antibody mean?

The combining prefix pan- means "all" or "every".
Antibodies are specific because they bind specifically to an epitope ('target') on a molecule. A pan-specific antibody is one that binds specifically to all desired targets, within a defined range.
Here are three correct examples of how the word could be used, to help you understand. Only the first two are relevant for your particular case:

In your case, there is an antibody for the phosphoprotein, the unphosphorylated protein, and both. The antibody that targets both is pan-specific because it binds both ("all", or "every") forms of the protein.
Another possible use for pan-specific is that some antibodies bind to some members of a protein family, but not all, so they are not comprehensive enough. Other time, antibodies bind to all members of a protein family, but bind additional targets, so they are not specific enough. Pan-specific is a great way to describe an antibody (monoclonal) or set of antibodies (polyclonal) that are both specific and comprehensive enough to adsorb an antigen of choice.
An antibody that binds specifically to a protein called pan.

Thanks a lot. Can you please share a link to a website or an article that I can find this sort of explanation there? It's a bit weird that I can't find an explanation about these concepts on a website! I think I'm using the wrong keywords!

It's a Greek prefix and it's commonly used. You won't get a technical definition of it, it's just jargon that you pick up over the years studying science. This goes for other Latin and Greek prefixes, like -epi or -con or -inter or -intra. Now that you know that science takes loanwords from Latin and Greek, I'm sure you'll be better prepared for novel words. For instance, you may be able to tell the difference between epidemic and a pandemic, and that pandemics are much worse.

In the paper quoted in the question the term clearly related to phosphoamino acids, but did not have the meaning suggested in answer 1 of @S_Pr. The paper was from Nat Chem Biol. and entitled:

“A Pan-specific Antibody for Direct Detection of Protein Histidine
  Phosphorylation”

The idea is that the antibody is:
‘pan’ in that it will react with all phospho-histidine residues on proteins, but
‘specific’ in that it will not react with unphosphorylated histidine residues or other phospho-aminoacids e.g. phospho-serine.

Thank you, David. I liked to vote up your answer as it was helpful as well. But, as I'm a new member I can't vote up with reputation less than 15. However, thanks.

@Tooba — No problem. It’s not a big deal and I have plenty of points.


text:
Why do protein solutions have to be alkalised in biuret test?
I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I add CuSO4. How is alkalising the protein solution before adding CuSO4 solution an aid to this process?

The directions explicitly state to add the sodium hydroxide before the copper sulfate? I've never done the biuret test myself, but I can't imagine it would make a difference. Commercially available biuret reagents are sold as premixed solutions.

Can you link the recipe you are talking about?

This is probably to prevent precipitation of copper hydroxide (see Itzhaki & Gill, 1964 - they suggest adding dilute copper sulfate slowly to the NaOH solution to avoid this). If you have the protein already alkalized and ready to react you'll get the color reaction before precipitate forms.
Commercial premixed solutions, like @canadianer mentioned in a comment, have tartrate present to prevent this (Geiger & Bessman, 1972 mention this).
It doesn't seem like it's strictly necessary to add NaOH first, but that's probably the most reliable way to do the assay without using an additional stabilizing agent.

Itzhaki, R. F., & Gill, D. M. (1964). A micro-biuret method for estimating proteins. Analytical biochemistry, 9(4), 401-410.
Geiger, P. J., & Bessman, S. P. (1972). Protein determination by Lowry's method in the presence of sulfhydryl reagents. Analytical biochemistry, 49(2), 467-473.

Wouldn’t adding sodium hydroxide solution to copper sulfate solution encourage the formation of copper hydroxide? https://en.m.wikipedia.org/wiki/Copper(II)_hydroxide

@UbaidHassan Yes exactly, which is why the OPs recipe tells them to add the hydroxide solution to the protein sample first. Might be confusing since my first reference also suggested adding copper sulfate slowly to sodium hydroxide, but that's only because the worst approach would be to add copper sulfate quickly or adding hydroxide to a concentrated copper solution. You use the same procedure with, for example calcium containing solutions that tend to form precipitate: precipitate is minimized when you keep the metal concentration low.

You mix those two chemicals to get a Cu(OH) 2 colloid, if you mixed them earlier it would settle down and not form a colorful complex (as efficiently). Base is added first because (i presume) it denaturates the protein which partly unfolds it, allowing copper ions to form complexes along a greater surface, giving clearer results.


text:
Blood acidity and bones
By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?
I ask this because i recently discovered bone is a base, as its chemical formula is approximated as Ca10(PO4)6(OH)2 where the (OH)2 suggests bone is basic and thus prone to a neutralisation reaction with acidic blood. If so, what salt would be produced?

The answer to this question What are the highest and lowest possible pH, paCO2 and HCO3 in the blood of living human? offers normal ranges for blood pH. You can see that the range is very narrow and never becomes acidic. There is a great deal of nonsense written about blood pH and food, almost all of which is complete garbage and should be ignored.

i admit the nonsense you speak of was this question's inspiration haha

Short Answer: As the comments mention, this is a hot topic for pseudoscientists to use as a selling point for their supplements. There is limited evidence that dietary acid intake significantly alters bone resorption, especially in the setting of normal renal function. This paper should answer all of your questions (emphasis mine):

Frassetto, Banerjee, Powe, Sebastian. Acid Balance, Dietary Acid Load, and Bone Effects—A Controversial Subject. Nutrients. 2018. 10(4),517.

Abstract: Modern Western diets, with higher contents of animal compared to fruits and vegetable products, have a greater content of acid precursors vs. base precursors, which results in a net acid load to the body. To prevent inexorable accumulation of acid in the body and progressively increasing degrees of metabolic acidosis, the body has multiple systems to buffer and titrate acid, including bone which contains large quantities of alkaline salts of calcium. Both in vitro and in vivo studies in animals and humans suggest that bone base helps neutralize part of the dietary net acid load. This raises the question of whether decades of eating a high acid diet might contribute to the loss of bone mass in osteoporosis. If this idea is true, then additional alkali ingestion in the form of net base-producing foods or alkalinizing salts could potentially prevent this acid-related loss of bone. Presently, data exists that support both the proponents as well as the opponents of this hypothesis. Recent literature reviews have tended to support either one side or the other. Assuming that the data cited by both sides is correct, we suggest a way to reconcile the discordant findings. This overview will first discuss dietary acids and bases and the idea of changes in acid balance with increasing age, then review the evidence for and against the usefulness of alkali therapy as a treatment for osteoporosis, and finally suggest a way of reconciling these two opposing points of view.

This paper is open-access and I recommend you read it, but the conclusions summarize their findings nicely:

7. Synthesis

We suggest the way to put all of this information together is to agree...that bone alone cannot buffer the positive acid balance that one can calculate from measures of acid production and acid excretion. In addition, endogenous acid production goes up and down in an attempt to maintain systemic blood pH...
Diets high in acid precursors add to the body’s acid burden. For the majority of people eating typical western diets with acid loads of ≤1 mmol/kg, whose renal function and acid excretory ability is normal, dietary acid loads would not be a readily detectable factor in altering bone mineral density leading to the development of osteoporosis. Other factors such as age, gender, race, and immobility are quantitatively more major factors in determining bone mass and bone breakdown.
However, body retention of only 1 or 2 mEq of acid each day, barely detectable by current measurement techniques, buffered by muscle and kidney and titrated by skeletal base over decades, could potentially result in major depletion of bone mineral. Thus, we suggest that those older subjects with diminished renal function, decreased renal acid excretory ability, and lower buffering capacity due to lower muscle and/or bone mass, whose diets contain high net acid loads could potentially benefit the most from alkali therapies.

Long Answer: Although there's a wealth of pseudoscience on the internet relating to acidemia and bone composition, there is some truth to the idea that bone can be affected by pH. An excellent model to explore this concept is chronic kidney disease, as impaired renal function causes decreased H+ secretion, which results in a chronic metabolic acidosis:

Kopple, Kalantar-Zadeh, Mehrotra. Risks of chronic metabolic acidosis in patients with chronic kidney disease. Kidney International. 2005. 67(95),S21-27.

Metabolic Acidosis

Severe chronic metabolic acidosis (i.e., the presence of excess hydrogen ions in blood) has two well-recognized major systemic consequences. First, metabolic acidosis, or acidemia, induces increased protein catabolism, decreased protein synthesis, and negative nitrogen and total body protein balance, which improve upon bicarbonate supplementation. Second, metabolic acidosis causes physicochemical dissolution of bone and cell-mediated bone resorption (inhibition of osteoblast and stimulation of osteoclast function).

Metabolic Acidosis and Bone Disease

Metabolic acidosis exerts multiple effects on bone. It causes the physicochemical dissolution of bone and cell-mediated bone resorption through the inhibition of osteoblast activity and stimulation of osteoclast function. These events are associated with a loss of calcium and phosphorus from the bone. Metabolic acidosis stimulates osteoblasts to release prostaglandins. This stimulates osteoclast function and inhibits osteoblast activity. Glucocorticoids can inhibit the production of prostaglandins by osteoblasts.
Metabolic acidosis is also associated with a decrease in the content of bone bicarbonate. Additionally, bicarbonate supplementation in postmenopausal women is associated with decreases in urinary calcium, phosphorus, and increased osteocalcin levels, indicating a beneficial effect. Figure 4 shows the mechanisms relating metabolic acidosis with bone disease3. These observations suggest that uncorrected metabolic acidosis has adverse consequences on bone anatomy and physiology.

Figure 4. The various mechanisms by which metabolic acidosis may contribute to bone disease. (From3).

From here, your questions can be answered:
Q: By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?
A: Maybe. It is possible to induce a metabolic acidosis with diet:

Adeva, Souto. Diet-induced metabolic acidosis. Clinical Nutrition. 2011. 30(4),416-21.

The modern Western-type diet is deficient in fruits and vegetables and contains excessive animal products, generating the accumulation of non-metabolizable anions and a lifespan state of overlooked metabolic acidosis, whose magnitude increases progressively with aging due to the physiological decline in kidney function. In response to this state of diet-derived metabolic acidosis, the kidney implements compensating mechanisms aimed to restore the acid-base balance, such as the removal of the non-metabolizable anions, the conservation of citrate, and the enhancement of kidney ammoniagenesis and urinary excretion of ammonium ions. These adaptive processes lower the urine pH and induce an extensive change in urine composition, including hypocitraturia, hypercalciuria, and nitrogen and phosphate wasting.

And there is existing research on short-term effects of altered diet on blood and urine pH and composition, but the clinical relevance of these values is indeterminate:

Buclin, Cosma, Appenzeller, Jacquet, Décosterd, Biollaz, Burckhardt. Diet Acids and Alkalis Influence Calcium Retention in Bone. Osteoporosis International. 2001. 12(6),493-99.

The urine-acidifying properties of food constituents depend on their content of non-oxidizable acids or precursors. Acidifying constituents such as animal proteins may negatively affect calcium metabolism and accelerate bone resorption, thus representing an aggravating factor for osteoporosis...acid-forming diet increased urinary calcium excretion by 74% when compared with the base-forming diet (p50.0001), both at baseline and after the oral calcium load, and C-telopeptide excretion by 19% (p=0.01), suggesting a skeletal origin for the excess calcium output. This observation confirms that renally excreted acids derived from food influence calcium metabolism, and that alkalizing nutrients inhibit bone resorption. Further studies are needed to determine the clinical impact of dietary counseling for avoiding diet acids as a preventive measure against osteoporosis.

But best recent evidence does not support the idea that significant changes in bone composition could be induced by diet alone (see my "Short Answer" above).
Q: ...what salt would be produced?
There are many metabolic acids, but for simplicity, we'll consider H+. Bone bases are stored as alkaline salts (e.g. calcium carbonate, CaCO3, which is really Ca2+ and CO32-). So, if H+ comes into contact with calcium carbonate, you'll make carbonic acid (with H+ displacing Ca2+ to produce H2CO3 – you excrete the Ca2+, resulting in the hypercalcuria described above). Through the bicarbonate buffer system,  that H2CO3 will be converted into carbon dioxide and water, which you excrete from your body via respiration.


text:
Do histones constitute the largest proportion of the protein in chromosomes at mitosis?
Do histones contribute more (by mass) than non-histone proteins in the chromosomes formed during mitosis?

I restructured your question in clear direct English, but wonder why this information is important to you.

If you are asking if histone mass represents a larger percentage of total chromosome mass then the answer is yes when considered at the level of the nucleosome. Each histone-octamer wraps ~147 base pairs of dna around 1.7 turns. The histone-octamer consists of  two copies of each of the four structural core proteins (H2A, H2B, H3 and H4). The sequence encoding for H2A histone family member B1 (H2AFB1) is 517 nucleotides long (RefSeq). Based on nucleotide length alone and inferring a consistent contribution to mass from nucleotides at the single base level and in triplet at the amino acid level, each nucleosome should be roughly 95% histone by mass. But this doesnt account for stochasticity in the mass and density due to DNA-methylation and to heterochromatin and euchromatin along the genome, respectively.
Consider DNA methylation, these features represent a non-zero contribution to total chromosomal mass that would decrease histone mass as a portion of the total and would not be considered if whole genome sequencing of a single organism was employed to answer this question at the genome level for a single sample. Now consider histone acetylation, this is another feature that represents a non-zero contribution to mass but swings the pendulum in the other direction. Beyond a local calculation at the nucleosome level this relationship would be nearly impossible to quantify.
During replication specifically, histone translation seems to be as tightly regulated as DNA replication.
Ma Y, Kanakousaki K, Buttitta L. How the cell cycle impacts chromatin architecture and influences cell fate. Front Genet. 2015;6:19. Published 2015 Feb 3. doi:10.3389/fgene.2015.00019
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315090/
nature has a great open source overview related this topic.
https://www.nature.com/scitable/topicpage/chromatin-remodeling-in-eukaryotes-1082

Does the 95% figure account for presence of variable-length linker DNA between the 147 bp canonical nucleosome cores?  If not then this would reduce the 95%, but I think your point would still stand.

It did not, it was a rough estimate using nucleotide sequence length as a metric of weight. Using the lengths of the sequences that encode the four core histone proteins H2A, H2B , H3, H4 in relation to the length of genomic sequence  wrapped around the complex the number is actually closer to 98 %
`>(2*(2223 +437+917+1077))/((2*(2223+437+917+1077)) + 147))

.9844527'
H3
H4
(https://www.ncbi.nlm.nih.gov/nuccore/NM_003517.2)
(https://www.ncbi.nlm.nih.gov/nuccore/NM_003528.2)

Something like 20% of the DNA is in linkers between the segments wrapped around the histones (here's a reference from plants http://www.plantphysiol.org/content/168/4/1406), so this would take the 98% down to 79%.

This furthers my point about the quantification only being possible at the nucleosome level. The linker segment is variable across the genome and represents another feature that prevents global quantification beyond the local nucleosome. Using your estimate of the linker region also incorporates a standard deviation associated with that estimate in nearly equivalent magnitude to the quantified region. Its a broader estimate of global proportion but greater uncertainty is associated with the estimate

"Genomics regions associated with active promoters/enhancers, marked by H3K4me1 and H3K27ac, contained the shortest spacing of 178 to 187 bp. By contrast, heterochromatic regions, marked by H3K9me3 and H3K27me3, contained the largest spacing of 205 bp in the human genome"
((2223 * 2) + (4372) + (9172) + (10772))/((2223 * 2) + (4372) + (9172) + (10772) + 147 +205)
Using the larger spacer value only drops the estimate to 96%

No problem @schokakola. Happy to help. It's a pretty deep rabbit hole with implications for potential experiments. If you find the answer helpful and sufficient, you can accept it and upvote it. Why are you insterested in histone mass? Or are you more interested in potential changes to histone mass during mitosis?

I am reinforcing the statement made by the previous answer. Yes, histones are the most abundant proteins in the chromosome (Ohta et al. 2010); they can contribute up to ~38% of the chromosome mass. Other abundant chromosomal proteins include toposiomerase-IIα and condensin-I (SMC proteins). Apparently many non-chromosomal proteins i.e. proteins that are not a structural part of chromosome but bind non-specifically to the chromosome, can contribute up to 12% of the total protein mass. Of the purely chromosomal proteins (68%), histones form ~48%.

  (D) The 28 classes of proteins found in chromosomes.
  (F) Estimated percentages of total chromosomal protein mass in the major classes of proteins.   From: Ohta et al. (2010)


text:
Liquid that comes out raw mangoes
What is the composition of the liquid that comes out of a raw mango when you break it off from its stem? It oozes out some sort of juicy liquid. Any idea what that is?
Also, is it edible?

It is the sap; you can see the composition of the sap (of Indian mangoes) in this article. Some plants also produce latex from injury sites. The mango sap is not supposed to be eaten as it can irritate the skin; a condition referred to as Mango Dermatitis.


text:
What the "due to" means in the definition of heritability?
According to Wray and Visscher,

heritability is formally defined as the proportion of phenotypic variation (VP) that is due to variation in genetic values (VG).

My question is, what does “due to” mean here?
My first thought is that its meaning is causal. By using Pearl’s causality framework, I’d think that we could say something like:
I have a variable T (trait), and a pool of genes (G) as cause. Also, other variables (not genes) also cause T, let’s call them U. Thus, it seems that this is a (simple) causal model behind heritability:

However, let’s say the trait is accent. It is unlikely that genes have a causal effect on this trait, so the arrow from genes to this trait would not exist. However, if we measure it in some way, we will probably be able to compute the heritability of this trait, especially because white Americans, for instance, speak with a different accent than Afro-Americans (thinking about the USA). So, we should conclude from this that the “due to” in the definition above has nothing whatsoever with causality. It is talking about correlation: how much of the variation in the trait we can associate with genes. So, if we have the following causal model (to make things simple), we would still be able to compute the heritability of a trait.

However, the only effect of gene on accent is mediated by an environmental variable (segregation), which has no direct effect whatsoever of genes.
So, my question is: does heritability depend on having a causal model? If so, are estimates done with an explicit causal model like a DAG? Do they try to control for confounding and other things that may cause a biased estimation?

Welcome to SE Biology. I have tidied up your question a little, in particularly decreasing the dead white space in your diagrams to make the whole readable. Please note that it is not correct practice to cite a journal as being responsible for a statement, unless it is an unsigned editorial. The authors bear the responsibility or should receive the cudos, as the case may be.

Thank you. I'll write better questions in the future. Lesson taken.

Related: This basic explanation of the definition of heritability

In your second model, you indicate that genes determine race, when race is not a biological category. Rather, the genes determine skin colour, which is one factor that becomes a part of how people define "race". More to your question, the model of causality is separate from the argument of which genes or environmental factors are causal for a particular trait.


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Autosomal Recessive Trait when skipping one generation
I learned recently that given a pedigree it is possible to tell whether a disease is autosomal recessive by observing if the trait skips a generation. If the disease does skip a generation, then the disease is autosomal recessive. But the converse is false. That is a disease that is autosomal recessive does not necessarily mean the disease skips a generation.
Does someone know of a proof of this fact?

Is this not just down to chance? A recessive trait may not skip a generation if the right mix of alleles are still passed to the progeny, but a dominant trait would always (by definition) be present in the offspring. I imagine there's a much better answer/way of saying this!

What you are saying is very similar to the statement that:

Absence of evidence is not evidence of absence

Suppose you have an autosomic gene A, which has a mutant allele a, causing an illness (or any other phenotype, for that matters). The particular nature of a makes its associated phenotype recessive.
You have three possibilities:
AA -> no illness
Aa (or aA) -> carrier, with no illness
aa -> ill

Now, let's take an aa individual (ill) and cross it with a sane AA individual:
aa x AA

All of the individuals of the first generation (F1) will be carriers (Aa) because the father will always give a and the mother always A.
Now if we breed them together
aA x aA

both parents have 1/2 probability of giving a and 1/2 of giving A. We will then have a proportion of:
1/4 aa
1/2 Aa (1/4 A from mother and a from father, 1/4 vice-versa)
1/4 AA

But this is just down to statistics. You have only 1/4 chances of seeing the trait reappearing, so you are much less likely to see it if they have 1 offspring then if they have 20.
Moreover, you have Aa offsprings in the progeny... this means that these could pass the mutant allele to the third or fourth generation.
Another important thing is that all we said is true if the first cross is
aa * AA

If it was
aa * aa

or
aa * Aa

The trait will (surely in the first case, and with 1/2 chance in the second) appear directly in the first generation.

Also, note that even with 20 offspring you are not guaranteed to see an aa in the F2.

A proof that autosomal recessive not necessarily skips a generation would be parents who both have the genotype and where one forth of the offspring would show the full phenotype.


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How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?
Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of degrading (or just inactivating) them.
This scenario seems more likely in eukaryotes, as they have capped 5' UTRs and a polyA tail at 3' UTRs that lend to RNA stability. How quickly and how much will an uncapped RNA degrade? What about the lack of a polyA tail?
Since prokaryotes lack these structures, I am restricted to the use of UTR regions in my particular instance. Is there any similar mechanism, whether in general or for specific proteins, that will allow me to exploit a UTR region for RNA inactivation in prokaryotes? Please keep in mind adding synthetic sequences to these UTR regions is certainly a possibility.

You can use riboswitches. Small RNAs have been shown to affect RNA stability in prokaryotes too but i think they have a stabilizing role in contrary to that of eukaryotes.

The polyA tail has a different function in bacteria than in eukaryotes, in bacteria the polyA tail seems to trigger RNA degradation, not prevent it. I've never tried to transform bacteria with mRNA, but I've injected lots of mRNA into mice, and the cap and tail are critical for expression, if they are absent the RNA is usually degraded too quickly to detect protein, at least in my bioluminescent imaging assay.

Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact lifetime). Deadenylation generally precedes 3'→5' degradation by exosome but I am not sure if that is a prerequisite. However tailless mRNAs can be stabilized by tethering Pab1p (Poly-A binding protein) to the 3'UTR. See this paper.
Figure 4 of the linked paper.

Tethered Pab1p stabilizes mRNAs that do not receive a tail. (A)
  Strategy. The HDV self-cleaving ribozyme was inserted into the 3′ UTR
  of MFA2/MS2 RNA, yielding an mRNA without a poly(A) tail (A0) in vivo.
  (B) Oligo(dT) cellulose chromatography. RNAs were extracted from cells
  carrying the ribozyme-containing construct depicted inA, or the
  control plasmid used in previous figures. RNAs were fractionated by
  oligo(dT) cellulose chromatography, then analyzed by Northern
  blotting. The ribozyme-containing RNA is not retained by the column,
  whereas the control RNA is retained. (T) Total RNA prior to
  fractionation; (+) retained by the column; (−) not retained by the
  column. The mRNA runs slightly faster in the oligo(dT) retained (+)
  sample than in the total (T) RNA, because less RNA is loaded per lane.
  (C) S1 nuclease analysis. The 3′ end of mRNA prepared from a strain
  carrying the ribozyme-containing RNA was determined by S1 nuclease
  mapping. The position of undigested probe (65 nucleotides) and of the
  protected species (43 nucleotides) are shown. The prominent 3′
  terminus lies at the expected position for ribozyme cleavage. (D)
  Decay of ribozyme-cleaved RNA by a transcriptional pulse-chase
  experiment and Northern blotting. The turnover rate of
  ribozyme-cleaved reporter mRNAs was determined in strains with (left)
  or without (right) MS2/Pab1p. Time (in min) following transcriptional
  repression are given directly at top; half-lives are at bottom. (E)
  Quantitation of results. Amounts of mRNA were normalized to the level
  of 18S rRNA, at bottom of each lane in D. (•) MS2/Pab1p; (○) vector
  alone.

Prokaryotic UTRs do not have any general paradigm. To have a controlled inactivation of a mRNA in a prokaryotic system you can use riboswitches or  cis-repressive RNA (RBS complementary RNAs). RNA-guided RNA degradation is also possible in prokaryotes using the CRISPR-Cas system. See this paper. Proteins Cmr-1,2,3,4 & 6 are required for this activity.