text:
How does the body respond to blood donation; are there any possible risks?
Can blood donation cause any harm to the donor? I have been told so, but cannot find any references supporting this claim. I have also learned that our body will replace the lost fluids within 24 hours and the RBCs within weeks. Can blood donation still cause health issues for our body?
This is not a personal medication question, and I mainly want to know how the body responds to blood loss and what mechanisms that monitor the altered levels of blood volume? To me, it would also be unethical by medical doctors to withhold the possible risks of blood donation to prospective donors, but it might also be seen as unethical to discourage a person willing to donate blood from doing so, so there might be a conflict of interest here.

If this is not a personal medical question, you should remove all references to yourself. Also, medical ethics specifically prohibits hiding information from patients.

@canadianer:I have removed

I don't understand your question. Do you want to know if blood donations are harmful for the donor?

@Chris: Yes thats what I am looking for !

Tried to clarify your question. Feel free to roll-back if you disagree.

@fileunderwater: Thank you, now it looks like a question !

How do you come to the conclusion that doctors hide risks from donors? Have you ever donated blood?

@chris The poster was encouraged to remove all personal details, so the part saying that he/she is a donor has been removed (see edit history). The last sentence on ethics is secondary to the question though, and I thought about removing it.

@Chris: I haven't concluded that doctors hide the risks, I rather inquired about it. Yes I have donated blood.

As biology and medical science have some common relationships, but medical ethics have nothing to do with biology. But this question bears biological origin and question about ethics is a bonus :)

found on internet: After blood donation, it generally takes a day or two to replenish the fluid volume in the body and three months for the regeneration of red cells to donate more blood. The total amount of blood circulating in our body's cardiovascular system is about 5 liters. Of this amount, only about 350 ml. is bled from the body during blood donation. The human body replenishes this amount of blood donated within about 48 to 72 hours of donation.

My answer below directly (and solely) addresses what I think is the main gist of the question: Are there any adverse effects on one's physiology as a direct result of donating blood?
Blood donation, at the amounts typically taken (200~500mls), will not harm you. A healthy human being produces approximately 100,000,000,000 (one hundred billion) NEW hematopoietic cells DAILY to replenish short-lived blood cells and platelets. All of these ultimately derive from the hematopoietic stem cells residing in the bone marrow within one's long bones.
As you can appreciate, with such a huge amount of turnover daily, the body is constantly churning out new blood cells. Thus, any depletion in blood cells one will experience as a result of blood donation is a fraction of what will be lost normally in daily homeostasis anyway and thus will not affect a healthy individual.
And then there are the knock-on benefits suggested by epidemiological studies, some of which are alluded in this layman article: http://news.health.com/2014/06/13/4-unexpected-benefits-of-donating-blood/
[source: I'm a hematologist]

How much amount of blood loss is considered as fatal ?

If you lose > 40% of blood volume (~2.5 L for a 75kg healthy adult male), it is most likely fatal. However, one will probably start to feel the effects (classed as hypvolemia) after >15% blood loss. As you can see, even at maximal amounts of blood donated, it is a tiny fraction of total blood volume and certainly not going to be fatal. You seem to be excessively concerned about a safe procedure that has been routinely done for over 5 decades. The biggest harm is not from donating, but from NOT donating!

Your answer and comment seems awesome and I am glad that you are worried about by excessive concerns :)

@Cantona Collar What on earth? You can start feeling the effects of blood loss (hypovolemia) after 15% blood loss? At 2.5L for a healthy adult male 15% is 375ml and you say they take 200-500mls. Seems to me from these numbers they take so much blood it approaches the quantity of blood loss which is approaching hypovolemia already.

@Zebrafish, I think you need to re-read what I wrote before typing. The total volume of blood in an average healthy human is ~5L (https://www.webcitation.org/mainframe.php)

@Cantona's Collar Right, I misread your comment. So taking 200 - 500mls of blood from a healthy adult male is taking between 4 and 10 per cent of their blood. And you say the effects of hypovolemia can be felt at 15% loss. That still seems close to the threshold to me.


text:
Should we induce fever to assist healing?
I am currently reading "The Fundamentals of Anatomy Physiology" 10th edition, and have found it an incredibly interesting book. I have just been reading about the lymphatic system, and the various Leukocytes and their roles. When it mentioned fever as an immune response, I was familiar with the concept: Bacteria and viruses operate very nicely at our usual body temperature, but not so well at around 39 degrees Celsius.
What I wasn't aware of was "For each 1 degree Celsius rise in body temperature, metabolic rate increases by 10 percent. Cells can move faster, and enzymatic reactions take place quicker." (Quoted from page 828 of that book).
Now that seems like a massive benefit (though I believe you could only really push 1 or 2 degrees before you start getting into dangerous territory), but I notice that fever is not present in all illnesses. Inflammation seems to induce fever through the wounded area, which makes sense.
So now for my question: Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever? I believe a few things would need to be considered (more than likely a lot more than I can think to list):

Increased metabolic activity would surely need a higher energy intake would it not?
Are there cells that are actually going to suffer from the temperature increase?
I'm assuming this would actually be a rather poor technique to deal with cancer as from my currently limited knowledge, it is simply a cell that is producing abnormal proteins. If this is the case, the metabolic increase would likely apply to these abnormal cells, resulting in faster proliferation. Are there other such cells/infections that will benefit from temperature increase?

Finally, what are possible downsides of long term fever if energy intake is sufficient to maintain an increased metabolic rate at these higher temperatures?

Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever?

No, not really. Pretty much the only use of hyperthermia in medicine is in the treatment of cancer. If you google "use of hyperthermia in medical treatment", you'll likely only find two kinds of hits: those for cancer treatment and those for malignant hyperthermia (a side effect of some psychotropic drugs.) The hyperthermia used to kill resistant cancer cells is high enough to destroy proteins (~113°-114°) and very localized; your entire body raised to this temperature would result in death very quickly. Lower (i.e. physiological) levers of "hyperthermia" (or hyperpyrexia) would not kill the cells.
At the turn of the century, there were many who believed in the therapeutic use of hyperthermia in the form of hot baths, hot springs, and even injection of infectious agents to produce fever(!), but the practice has fallen into disuse, probably because there were no studies which supported it.
However, hyperthermia isn't good for you; it is something to treat seriously. When the cause isn't known, the efforts used to treat it can amount to many unnecessary tests and treatments (as seen in the accident victim in the fourth reference. When it's present in a moderate amount, it can still be dangerous:

When fever occurs, many physiological stresses take place. Some of these include increased oxygen consumption as a response to increased cell metabolism, increased heart rate, increased cardiac output, increased leukocyte count, and an increased level of C-reactive protein. Oxygen consumption increases by 13% for every 1°C increase in body temperature, provided no shivering occurs. If shivering is present, oxygen consumption may increase by 100% to 200%. Some cytokines released during fever states also induce physiological stress. These cytokines can trigger accelerated muscle catabolism by causing weight loss, loss of strength, and negative nitrogen balance. Physiological stress can be manifested by decreased mental acuity, delirium, and seizures, which are more frequent in children.

It is likely beneficial in the presence of infection:

Heat shock proteins are one of the more recently studied fever-responsive proteins. These proteins are produced during fever states and are critical for cellular survival during stress. Studies suggest that these proteins may have anti-inflammatory effects by decreasing the levels of proinflammatory cytokines. Fever also triggers other beneficial effects, including an increase in the phagocytic and bacteriocidal activity of neutrophils and enhanced cytotoxic effects of lymphocytes. Some bacteria become less virulent and grow slower at the higher temperatures associated with fever. Increased levels of C-reactive protein promote phagocytic adherence to invading organisms, modulate inflammations, and encourage tissue repair.

In the absence of infection, there is no benefit to systemic elevation of temperature. For the disadvantages of continued elevated metabolic rate, one need only look at hyperthyroidism to see the deleterious effects, the worst being cardiotoxicity, even in subclinical hyperthyroidism, as well as dementia, atrial fibrillation, ventricular hypertrophy, miscarriage, perinatal morbidity and mortality, decreased exercise tolerance, etc.
Years ago, one of the most common self-inflicted illnesses was hyperthyroidism - people taking thyroid hormone replacement unnecessarily - usually because of the weight loss that occurs with elevated metabolic states. Interestingly, efforts are underway to isolste and manufacture a thyroid-hormone like substance which will cause decreased weight without cardiotoxic effects.
Hyperthermia in Cancer Treatment
HYPERPYREXIA PRODUCED BY BATHS
ARTIFICIAL FEVER IN THE TREATMENT OF GONORRHEAL OPHTHALMIA
Thyrotoxicosis in a patient with multiple trauma
Metabolic Effects of Thyroid Hormone Derivatives

"At the turn of the century, there were many who believed in the therapeutic use of hyperthermia in the form of hot baths, hot springs, and even injection of infectious agents to produce fever(!), but the practice has fallen into disuse, probably because there were no studies which supported it."  Not so. Julius Wagner-Jauregg  won a Nobel Prize given for his studies on malaria pyrotherapy. This approach was discontinued because of the advent of antibiotics, not for lack of evidence!

Hyperthermia isn't used for malaria--rather, patients were deliberately infected with malaria to treat syphilis because malaria induces high fever. Whatever the intent of your post, the claim "no studies...supported it" is badly at odds with the fact that a Nobel Prize was given for precisely such studies and so this seemed a correction worth making if we care about the faculty accuracy of biology.SE. More generally, having read a hundred or so recent studies about the effects of endogenous or induced fever on infectious disease clearance, I think you are dismissing hyperthermia too quickly.

@Corvus - there is nothing, I assume, preventing you from posting your own well-referenced, better answer?

Once I get my head around the subject fully I'll be happy to do so. It's not an easy topic to synthesize because there are so many individual facts and study results out there, and so little by way of coherent explanation for the entirety of the phenomenon. The evidence seems overwhelming that fever hastens viral and bacterial clearance, but despite numerous conjectures there is no decisive explanation for the causative mechanism by which it does this.

This has really helped me get a direction as to what I need to look at, so thank you very much for this! I shall look at all of the references as time permits and see what they say. @Corvus If you have some stuff you would like to add in to an answer with some other references and ideas, that would be good. The more information I have that indicates relevant areas, the better! Seems like hyperthermia has a huge affect on parts of the body, as I expected. It seems like the answer is something like: Yes it is good in some cases with side effects, and no in others.

@Corvus... You seem to hold the Nobel Prize up to some biblical standard... How about António Egas Moniz developer of the Prefrontal Lobotomy and 1949 Nobel Prize winner in Medicine in Physiology for "for his discovery of the therapeutic value of leucotomy in certain psychoses"? Wagner-Jauregg's treatments, while effective and a keystone in the development of neuropharmacological treats, were at best ethically questionable. Also he got lucky in that the cause of the Dementia was bacterial in nature. His research was looking to use fever as a cure for all forms of "insanity."

He used anecdotal evidence as the basis for treatment without knowing the  root cause of the problem. His "cure" worked because it happened to be caused by infection of a pathogenic bacteria. From what I read it does not appear that he knew that he was using fever to treat a bacterial infection that caused symptoms of dementia in syphilis. That doesn't constitute good science. Then there is this gem: "Other patients were deemed schizophrenic because of excessive masturbation, where Wagner-Jauregg sterilized them, resulting in an "improved" condition." from Wikipedia article on Wagner-Jauregg.

@AMR. As I thought was clear in my comment, the whole point of my mentioning Wagner-Jauregg's Nobel prize was to say that were experiments on this, and that they were in fact well known ones. I was not vouching for Wagner-Jauregg's science one way or the other. With respect to anecdotal basic of treatment, this is medicine, not science. One could make the same critique of Edward Jenner.

@Corvus In your rebuttal of anongoodnurse, you say "the claim "no studies...supported it" is badly at odds with the fact that a Nobel Prize was given for precisely such studies and so this seemed a correction worth making if we care about the faculty accuracy of biology.SE." This basically is saying that as a Nobel Prize was awarded, then the research which lead to the award was also correct, or even good. Moniz work was downright barbaric, but he won a prize. And based on what we know now of the immune system, the idea that hyperthermia was the curative agent is greatly suspect,...

if not disproven. The fact that an immune response was triggered and the leukocytes were called into action is far more likely a scenario. When the bacteria that cause neurosyphilis get into the CNS, they are in an immune privileged space, where, most of the time, WBCs cannot access. However with an infection as powerful as malaria, the immune response and all of the cytokines release make even the BBB somewhat leaky to immune cells, that can then hunt down and fight the infection. As with your reference to Jenner, they were on to something, but there wasn't proof for the mechanisms of cure.

However we likely won't know for certain, as medical ethics today would likely prevent patients from being subjected to treatment with a highly pathogenic parasite.

Also, according to the wikipedia article on Malaria, "...the inventor of this technique, Julius Wagner-Jauregg, received the Nobel Prize in Physiology or Medicine for his discoveries. The technique was dangerous, killing about 15% of patients, so it is no longer in use."

The wikipedia reference is from a Science news article from November 8, 2013 by Gretchen Vogel. It is behind a pay wall, so some of the highlights: He initially tried with tuberculin and salmonella toxin, but there was no effect. To which he thought the fever was insufficient. Then he had a patient with Malaria, so he draws their blood and gives the disease to 9 patients. 6 improved. There was only about a 50% recovery rate, and 15% fatality rate. That implies 35% either did not recover sufficiently or got worse but did not die. And "No one is sure exactly how it worked..."

@AMR "And based on what we know now of the immune system, the idea that hyperthermia was the curative agent is greatly suspect," Elaborate?

@sterid read Janeway's Immunobiology, then see if my statement makes more sense. Fever is a side effect of the cellular immune response, not a factor in the defense itself.

Fever: facts... is a dead link...

@not2qubit - It was fine 5 years ago; but thank you. It would be nice if it were still available.

Actually, hyperthermia is a known treatment for a range of diseases, including cancer.
Induced hyperthermia can be whole-body as well as local/regional and is under investigation in multiple studies (for example).

Those studies you linked to are quite interesting. I will look into some more recent studies and see what they have found. And thank you for referring to it as hyperthermia, it is a much more appropriate term!

This would be a much better answer if there was more than a yes/no, and a couple of links.

@anongoodnurse I found the links fairly helpful, but they related primarily to cancer treatment (which still nicely addresses something that I had a misconception about in my question). Are there any other things you could recommend I look into to better understand the concept I described?

@Stevo - I'll look into this and post something more comprehensive and balanced tomorrow (if no one else does!)

@anongoodnurse why do you delete your 10 comments? you should take the responsibility for your words and behavior.

lol, why did you delete yours? I deleted mine because they are not relevant to most users. But if you insist: This is a poor answer, with an opinion and a couple of links. SE strives for better. Please read "how to answer" in the help section for guidance on how to answer questions.

In terms of bacteria and viruses within humans, the reason the bacteria and viruses function well at normal body temperature is because it's normal.  If fever were a perpetual state, the bacteria and viruses would evolve to be fit at that fever state.
There is also reason to believe that one way aging occurs is through metabolism (https://www.sciencedaily.com/releases/2011/04/110427091949.htm).  Thus, perpetual fever would likely reduce life span.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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

sort: votes


text:
Why don't all bacteria have F-plasmids by now?
Some bacteria can undergo gene transfer by conjugation. Conjugation is a form of horizontal gene transfer, meaning from one (unrelated) bacterium to another (in contrast to vertical gene transfer, which is from predecessor bacterial cell to successor (daughter) cells). Conjugation is initiated when one bacterium has an F-plasmid (Fertility plasmid) and forms an F-pilus, connecting the F+ bacterium with an F- bacterium, initiating transfer of the F-plasmid.
Why is it that during evolution not all bacteria have acquired this F-plasmid?

Conjugation occurs between cells of the same species too. For this to occur cell have to be close to each other. Now, if you have an isolated population of bacteria that never gets in contact with an F+ bacteria then this population would stay F-. Also not all conjugation events are successful, mechanical perturbations can disrupt the pilus through which genetic material is transferred.
This old article can give you good details:
THE ORIGIN OF BACTERIAL SPECIES - GENETIC RECOMBINATION AND FACTORS LIMITING
IT BETWEEN BACTERIAL POPULATIONS ARNOLD by W.RAVIN

F+ shares, however, an important property of bacteriophage: after infection
  it behaves as though it were an addition to the bacterial genome. As an addition, it can furthermore exist in one of two forms: in one form, it
  is an unintegrated part of the bacterial genome, and may be  replicated either more or less rapidly than the "chromosomal" or linked genes (being
  infectious or lost through dilution, respectively); in its other form, it
  is integrated in the sense that its replication is coordinated with the
  replication of the host's genes, as though attached to them. In this latter form, found in Hfr bacteria, the F+ factor is incapable of infecting other bacteria (while permitting conjugation with them) and also prevents
  superinfection of its host bacterium by a nonintegrated F+ factor.

Taken from the linked paper. So you can see that are situations where conjugation occurs yet the F- won't become F+.
Also :

What is particularly interesting about the F+ factor is the fact that there
  seem to be a number of different  kinds. An F+ factor making a bacterium
  fertile with some  F- cultures does not necessarily  make it capable  of conjugating with others (49).

So not every F+ cell can conjugate with another F- cell.

Thank you for your answer. Also I was wondering if there are mechanisms that limit the amount of times conjugation and F-plasmid transfer can happen. E.g. "a bacterium can only transfer his plasmid once during his lifetime".

To be honest I've never thought about that question, might worth asking it.

Alright, will do. Do I just create a new question for this? (I am new to this site :-))

Yes, that is the right way.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Are there any disadvantages to HRP conjugated PRIMARY antibodies
I need to detect a FLAG tagged protein on a western blot and have to order an antibody. I'm not expecting to see a massive amount of my protein. To keep analysis time to a minimum  I am considering a HRP-conjugated anti-FLAG. Are there any disadvantages to it (e.g. sensitivity)? First hand experiences/problems?

Welcome to BioSE. It would be better if you make your question more precise? Disadvantage compared to what? Have you tried an experiment yet?

Compared to the classic incubation with primary anti FLAG or HA and subsequent detection with a secondary antibody coupled to HRP (e.g. anti goat/rat/mouse)

The obvious problem is signal amplification as pointed out in the answer. I don't have a first hand experience but I think that chemiluminescence based substrates would be better for a one-step WB.

You can compare directly coupled antibodies to the classical indirect primary-secondary systems:
Directly coupled antibodies
Advantages:

quicker workflow as only one antibody is used
eliminates the chance of a cross-reacting secondary antibody (possibly less background)
possibility to use differently labelled antibodies on the same blot

Disadvantages:

lower sensitivity because the signal is not amplified
only few labels are available
directly labelled primary antibodies tend to be expensive and you need relatively high amounts of them
the labelling can damage or reduce the immunoreactivity of the
antibody

Indirect Primary-Secondary Antibody systems
Advantages:

the secondary antibody amplifies the signal (which is especially
interesting for weakly expressed proteins)
differently labelled secondary antibodies can be used on the same
primary
primary antibodies from different species can be used simultaneously
one secondary antibody can be used with different primary antibodies
(for example for the protein of interest and the loading control)
the labelling reaction does not affect the primary antibody

Disadvantages:

cross-reactivity of the secondary antibody can lead to non-specific
bands
the method takes longer, as more steps in the process are necessary

For me the most important point is the higher sensitivity of the indirect method, for comparision see these images (from Life technologies):

Thank you for confirming my suspicions! Primary-Secondary it will be then.


text:
Can bacterial RNA be degraded at -80⁰C in a SDS solution?
I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded.
Comes from a pellet of pure liquid culture.

I now that RNA should be freezed in RNAse free water or PBS but this was done accidentally.

I will just store it for 1 week before proceeding to RNA extraction.

It's fine. Your RNA should be stable in the current state. Aside from the fact that it's frozen, meaning that any ribonuclease activity will be minimal (if any), the SDS will have denatured some of the RNase too.
However, the detergent (SDS) might impair some of your downstream activities (especially reverse transcription and PCR), so be sure to clean up the RNA well. I would suggest Qiagen columns, and doing the additional wash steps.

I think it is relatively unlikely that the RNA will degrade under these conditions. For the future, I would handle this differently:

You can centrifuge the cells and snap freeze them in an appropriate
buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing.
Alternatively, you centrifuge them, break them up with Trizol (or whatever you use for this purpose) and freeze them in this solution. This will be
safer as it completely denatures all proteins including all nucleases.

I would choose (and have done this already several times with cell samples that I couldn't process without problems) the second method.

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


text:
Why does polyploidy give an evolutionary advantage?
I would like to know what advantages polyploidy holds. I have come across a few examples during my research of polyploidy, for example human adults' hearts contain 27% diploid, 71% tetraploid and 2% octaploid nuclei, Deinococcus radiodurans can have up to 10 copies of genome, and most of the plants consumed by humans have more than 2 copies.
I have no source of any sort for these, but I think they could be advantages:

One of the most obvious one would be resistance to more physical effects.
In the case of plants it might be the increased need for protein construction during the development of the seed.

What I would like to ask is whether the ones I wrote are correct, and if there are any other possible advantage.

I have read similar questions but could not find what I was looking for.

New relevant paper: Selmecki et al. 2015. Polyploidy can drive rapid adaptation in yeast. Nature 519

First of all I am not sure if your examples are per se correct. But they might also be an additional bonus. Secondly, I would like to refer to two articles: "Polyploidy" and "The advantages and disadvantages of being polyploid".
One of the main benefits could be allowing organisms long-term evolutionary flexibility. Often adapted polyploids can undergo a proces that is called diploidization, during which genomic redundancy is removed. This means extra copies of genes will undergo less negative selection. Meaning alleles containing deleterious mutations at functionally important nucleotides are selected against. This allows more mutational freedom, leading to what is called subfunctionalization and neofunctionalization: new genes are created with slightly different or new functions. Other redundant genes are lost or become inactivated (pseudogenes).
Another example of benefits from polyploidy, this time not in an evolutionary, but in a more individual context, is the fenomenon called hybrid vigor or heterosis. Heterosis is a phenomenon in which a polyploid offspring of two diploid parents is more healthy and vigorous than its progenitors. One of the factors explaining this could be due to a protection against recessive characters, as being homozygous as a polyploid is even more 'uncommon'.

I really like the argument in the last paragraph. Reminds me a bit about genetic depression due to inbreeding.


text:
Splice in with CRISPR/Cas
I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.
CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amount of gRNA and/or of the protein.
I need to insert the gene, without the need of targeting some specific place.
Is this possible in some way with CRISPR?
I know that there may be better technique to do this, but I can only use CRISPR.

Is there a good way to detect the gene product in a living cell? Because you could just sort the cells by FACS and take the cells that have the knock in, then grow those.

Could you please define what the question actually is? If it is "can you use CRIPR/Cas9 to insert a gene in a genome?" Yes you can.

@cagliari2005,  The question is, is it possible to insert a gene with Crispr with high success rate,  when I have a very low amounts of the Crispr in the cell? I mean I actually need to reduce his high specifically - to get higher rates. Is it possible ?

What determines the specificity and cleavage efficiency is the guide RNA. As you cannot act on that I personally don't know any tricks on something like cell culture conditions which would do what you want.

Maybe you could look at conditions that increase homologous recombination rate.

Using a chemically modified guide RNA with higher melting point might help with the insertion rate, but I suspect it would also decrease the specificity.

Decrease the specificity - it's what I need, cause it will higher the insertion rate. But may you tell more about the melting point of gRNA?..

I'm not an expert at RNA backbone modifications, but I have read that Locked Nucleic Acids or ZEN modified oligos can increase the melting point. IDT may be helpful for designing the oligo, but be prepared to spend a lot on extensively modified RNA oligos.

A paper was published about a week ago in Nature Biotechnology and adresses your question, Maruyama T et al., 2015. I must say I found the authors' strategy extremely clever.
It is not about increasing efficiency by reducing specificity, but simply increasing efficiency (which is your ultimate goal anyway). What the authors did was to inhibit nonhomologous end joining (NHEJ) to promote homology-directed repair (HDR), two DNA repair mechanisms that compete in cells and of course HDR is the mechanism needed for the CRISPR/Cas9 system.
They achieve NHEJ inhibition using the molecule Scr7, a DNA ligase IV inhibitor which in turns perturbes NHEJ.
Using Scr7 they boosted by 3 to 19 fold (depending on the cell line) the insertion of the target gene. Here the graph showing these results
See paper figures
Moreover using 1μM of Scr7 over 24h on DC2.4 cells increased the % of transfected cells from 4.58% to 58.3%, a neat ~13-fold increase. Here their results:
See paper figures
Hopefully this should give you some ideas.

Interesting answer.

Looks like they also used single stranded DNA oligos for some of their short insertions (see supplementary table 7), consistent with my speculation based answer below. The longer inserts are still double stranded. Would be interesting to see if long single stranded DNA would insert more efficiently too. Just glad to see I was speculating in the right direction.

@cagliari2005, wow, thank you!! Really great.

Just a side-question: is it fine from a copyright perspective to publicly post diagrams from articles?

@TMOTTM It is not plagiarism as I am citing the source but regarding copyright infringements I think you are right in pointing that out. As those figures comes from Nature Biotechnology I am not supposed to publicly post them (I actually removed them) - see Nature policy. If they were coming from open-source journals (say PLoS one) then you can as they are publicly available.

I don't know, I was just wondering.. anyway, i can still see the figures, just in case.

@TMOTTM Now you can't ;)

If you want to have random integration you need to find gRNA sequences that are nonspecific ; everything built for CRISPR so far has been geared towards precise integration, not random integration.
Talk to an informatician about pulling out non-unique sequences from the human genome. You will then need to clone out a library of 20nt sequences that end with a PAM sequence (NGG) and chuck them into cells with another construct encoding a Cas9 and the insert.
Of course, if you simply need integration you don't need CRISPR either - you can use any bog standard lentiviral vector and you will get a stable cell line made with the gene inserted in random places. Using CRISPR for this overcomplicates things greatly.

OP says he "can only use CRISPR".

Yes I am well aware; I am also aware that this is a massively complicated and probably a very ineffective way of doing things. Not least because spiking something in with a CRISPR targeting strategy often requires homology arms of up to a kb; and in this scenario, it means one has to not only make a library of sgRNAs but also a library of his insert flanked by 1kb sequences for every locus he is trying to target.

I'm going to preface this answer with the disclaimer that I have never used CRISPR/Cas, and there is a fair amount of speculation here.
But I think that efficient CRISPR mediated knock-in probably has three parts, targeting, integration, and selection.
The targeting is accomplished by the guide RNA, which is often introduced as DNA on the same plasmid that codes for the Cas9, or can be in vitro transcribed or synthesized as delivered as RNA. However, a poster suggests that a properly designed DNA fragment can be delivered and produce sufficient amounts of guide RNA in situ to produce efficient cutting.
The integration step is where the template DNA is inserted into the double strand break by homologous repair. Homologous repair efficiencies vary greatly from cell to cell, and is often less efficient than non-homologous end joining. However, using a single-stranded DNA might increase the efficiency.
However, even if only a small percentage of cells is correctly edited, it may be possible to select those cells and grow them. NEB describes a Cas9-GFP fusion (page 4) that can be used to bind GFP to a certain DNA sequence. It may be possible to produce CFP and YFP variants of this construct and use FRET to detect cells with the knock in. (This is where the speculation comes in) With the two fusion proteins and two guide RNAs for adjacent sequences in the knock-in gene, you might be able to detect cells where a CFP and YFP cas9 are close enough that you get FRET. This might allow you to sort cells by FACS, and then grow those cells.
Of course if your knock-in is making a membrane bound protein exposed to the surface, you could just use labeled antibodies to detect that protein.

Thank you, but I don't ask how to separate the cells. I ask how to force Crispr to insert in higher success rate. How to make him less specific or what regions to target. If it's possible. And your second link about Zinc-finger nucleases and not Crispr.

The second link is about homologous recombination. CRISPR and zinc-finger nucleases are just about cutting the DNA, homologous recombination is how the new gene is actually inserted. And I don't think you're going to easily push the CRISPR success rate above 50% of all cells, the recombination rate will probably be lower. A good selection strategy can find those recombined cells and give you a population with 100% recombination.


text:
Cysticercoids of Eucestoda
I have found the following pictures representing cysticercoids of Eucestoda.
If I correctly understand the right part of the picture, I would say that the development of the scolex is portrayed on the right, as the formation of what I think to be two acetabula shows. Nevertheless, with respect to the images on the left, it is totally unclear to me, since the text says nothing about it, what the structure that seems to be encapsulating the animal is.

I know that cysticercoids develops from an oncosphere, but I do not know whether that sort of capsule that seems to be enveloping the animal is a part of what was the oncosphere's tegument -the embrionophore- that it can have gone out of and is entering again...
Does anybody reading this question know more about it? I thank you very much for any answer!

I would say that the left part of the picture depicts 2 stages of the development of cysticercoid, while the right part shows the consecutive stages in the development of cysticercus. These two parts represent different species of tapeworms in the same stage of their developments.

To say the truth, the cysticercus is drawn in another picture elsewhere, while the legenda under this one says cysticercoid... As to that sort of tailed capsule which seems to envelopes the animal on the left, what is it? Thank you so much again!


text:
Safe parameters for external nerve stimulation using electrical impulses
Introduction
I've recently stumbled upon David Eagleman's TED talk on the concept of sensory substitution and addition. Being the most inspiring thing I've seen on the internet for the last few months I've decided to give it a try and mix it with some of my coding/electronics projects.
I've settled on using electrical impulses over electrode pads to feed sensory data onto a patch of skin, instead of vibro-motors as it is more energy efficient. That being said, when planning on running electrical current through me 24/7, safety obviously comes first.
[edit]
I am targeting the lower back or the side of the hips as these parts have the least contact with the environment and won't make you look goofy. In the long run this would probably have to run on dry skin to avoid the "wrinkling effect", caused when staying in water for too long.
Questions
Main unknowns I want to sort out are:

What is the range of perceivable voltage and current that can be safely  fed through the skin without causing any damage to the nerves or any other part of the body?
Is there a risk of permanent damage or reduction of sensitivity of nerves when exposed to an electrical current for a prolonged time? Any way to circumvent this problem?
What "resolution" or input density can I hope to achieve, before signal becomes "blurry" because of cross-talk?

Welcome to Bio.SE! Interesting question. Are you planning on using the electrode grid on dry skin, on the skin using an electrolytic solution/gel or are you targeting the tongue (aka BrainPort). Your questions hinge on impedance, that's why I ask. As of now the question is too broad to my opinion.

Thanks for the support! Added some additional info in the description.

Nice question(s). I will go through them in sequence.

Safe current limits. With regard to electrical stimuli it is current density that determines safety limits. Therefore, in medical devices, it is not a matter of what is a safe maximum current level, but what is the maximum safe current level given the surface of the electrode? And in terms of skin stimulation, it is not the safety limit that is the bottle neck, but the maximum tolerable current density, which is around 0.5 mA/cm2 (Prausnitz, 1996). Higher stimuli result in pain sensations. This is one of the reasons why the BrainPort device is used on the tongue; the moist surface reduces impedance and hence the currrent needed to elicit a tactile response.
Permanent damage. As said, the tolerable sensation limit is more of an issue (a must-read in this regard is Kaczmareck et al., 1991).
Acuity. The best-possible tactile "resolution" is generally expressed in terms of tactile acuity. Tactile acuity varies across body sites, and unfortunately it is about the worst on the thigh (45 mm) and the back (40 mm). A much cited picture on tactile acuities is the following from Weinstein (1968):

These acuities represent the distance in which 2 simultaneously presented, static pressure points need to be spaced to be just noticeable (the so called two-point discrimination threshold). Although your proposed electric stimuli are different from pressure stimuli, these reported values in the figure (40 - 45 mm) give an impression on the inter-electrode distance needed. From my own work I can confirm the ~40 mm using vibratory stimuli. The unfavorable acuity of the back and external bodily skin in general was also one of the rasons to put the electrode grid of the BrainPort on the tongue, which has excellent tactile acuity.
References
 - Kaczmareck et al. IEEE Trans Biomed Eng 1991;38:1-16
 - Prausnitz, Adv Drug Delivery Rev 1996;18:395-425
 - Weinstein S. 1968. In: Kenshalo. The Skin Senses:195-222. Springfield, IL: Thomas

Thanks for the answers and references. The chart is especially eye-opening and would help placing the "display" somewhere more appropriate. I am approaching this whole matter with the hope that the brain can (learn to) subconsciously recognize information more finely than the perceived tactile acuity, which can then be a measure for base precision to be built upon.

While, for practical reasons, the tongue might not be suited for sensory addition, I am now considering other mucous membranes such as the inner part of the cheeks as viable surfaces which are more sensitive and require less power to stimulate.


text:
What would happen if we had a device that produced oxygen inside of our lungs?
Hypothetically speaking, suppose there is a device that produces a limitless supply of oxygen. The device is inhaled by a human and is resting inside the (a) lung.
What would hypothetically happen if this were possible?

Welcome to Biology S.E.! If you need additional assistance on how/what to ask please visit The Help Center.

What is your question?

We'd probably choke…

Depending on the efficiency/production of the hypothetical device, it might be toxic

Could you elaborate on the situation in which you want information about the device? i.e. in an oxygen-deprived person/athlete/underwater/etc. Also, a little more information about the hypothetical device would be useful (does it maintain normal atmospheric oxygen conc., or produce excess?)

You might need to narrow your parameters a bit.
Just things to consider:

Our lungs are not hollow organs that can accommodate an oxygen producing machine. They are basically narrow tubes that get smaller and smaller until they end in a tiny balloon-like structure - about 700 million of them. Where would the machine go?
100% oxygen is toxic to the lungs, as it is to many other things as well.
How would the oxygen diffuse to all the other areas of the lung that need oxygen? Diffusion is a complicated process in a structure like the lungs.
from what would it produce oxygen? For example, would it extract it from water? How would the body deal with the loss of moisture from the air in out lungs? Where would the excess hydrogen go?
Hydrogen is highly flammable around 29%. Would we become fire-breathing?
How would the machine not hyperinflate and thus injure the lung?
How would we get rid of CO2? We would still have to breathe in and out.
Etc.


text:
Why are killer whales found in the Gulf of Mexico smaller than ones found in the Pacific?
I recently found out that there are killer whales that live in the Gulf of Mexico, but they are smaller than killer whales that are commonly found in the Pacific Ocean. Why is it they are smaller in size?

Animals living in colder climate / environment are larger because this way they have better body surface / volume (mass) ration thus they're more resistant to cold. Animals living in warmer areas are smaller thus they have larger body surface compared to their volume(mass) to dissipate heat easier.
Check this wiki page for more details.

Has Bergmann's rule been suggested for the size disparity in Orca?

It's a general rule, but as written on the page I inked there may be exceptions, yet I do not see reason why would it not apply for Orcas.


text:
Are nucleic acids found in cell membranes?
I've found various results online and I was recently marked in on an important test as wrong when I made the assumption they were not found in the cell membrane. Does anyone know what the correct answer is in this case?  Thanks in advance.

Nucleic acids are not structural components of cell membranes (ribosomes and nucleus are the main places where they are found).
However, being open system, cell exchanges chemicals with its surrounding and cellular membrane can transport nucleic acids as well. This is why these acids can potentially be detected in the cell membranes.
If you have the exact question expression it can help with more precise answer.

Heterochromatin is anchored to the nuclear envelope by lamins, and they actually found here that this is important in expression and differentiation during development. Not saying that nucleic acid is a core component, but the interactions between that particular membrane and nucleic acid is important. An interesting tidbit to consider, IMO.

No, plasma membrane does not contain any nucleic acids – DNA and RNA. The main components of plasma membrane are lipids, glycol- lipids, phospho lipid bilayer and cholesterol.

Also contains proteins: https://www.nature.com/scitable/topicpage/cell-membranes-14052567/


text:
Evolution theory - roses spikes - being more bulgy doesn't give you advantage
I've seen spike, huge spike. And I thought that development of such spikes could be contrary to the evolution theory.

Being „little more” spiky doesn’t give you any advantage... So those individuals having one won't have smaller mortality rate than those with smooth stem.
Even more, the individuals with bulgy (more spiky) waste resources their ruggedness and have more things to feed, which should mean that they would have higher mortality rate.
So I can see no way to develop spikes on the stems of roses according to the evolution theory which embrace "small improvement". Spike is only efficient (to deter aggressor) when it's very sharp, it's either sharp or it isn't - there is little in between.
Could anybody tell me that this is bullshit (and why it is bullshit), and that I should us believe in Darwin competence?;)

Being a gardener with 50+ varieties of roses, from thornless "Zephirine Drouhin" on up, I think I'm in a position to say that thorns of any sort do give a definite advantage - especially as I'm in the middle of their spring pruning.

If you're looking for a trait which is maladapted to the natural environment then you should be looking at the rose's flower, Their flowers are a product of generations of selective breeding. Wild types have such simple flowers with so few petals they would hardly be recognised as roses. So I find it interesting that you pick out the thorns, which have such obvious utility, and would so even if they were tiny.

I think that the most important point has been given by CactusWoman, when (s)he says "Just because you cannot forsee a use for more "bulgy" spikes doesn't mean there isn't a use for them."
In addition to that, I would like to say that several plants evolved traits that were beneficial at a time where other herbivores existed and that are now useless. Those lineages did not lose their traits (yet?) just because there is a relatively low cost to making the trait in question.

Your post shows several of the very common misconception about evolutionary processes. Evolution is not all about Natural Selection. It is more interesting than that.

"small improvement"

The conception that evolution proceed through "small improvements" is either partially wrong or totally wrong.
First, because of the loaded term "improvement". Evolution can yield a population to have a lower mean reproductive success or a lower complexity, things that you could eventually see as deterioration.
Second, because changes not need to necessarily be small. Some mutations have a very big effect.
Third, because even small deleterious mutations can spread in the population and reach fixation (=and all individuals carry this mutation), just because of the joint effect of other evolutionary processes such as genetic drift. This post may help you to get a quick grasp of what genetic drift is. There are already multiple posts that emphasize the importance of other processes than natural selection in evolution to layman. Here is one of them.

believe in Darwin competence

Evolutionary biology is not anymore Darwin's evolution theory. It is way more than that. We've been working on the subject a lot since Darwin and today we have a much much better understanding of evolutionary processes than Darwin at its time. Everything is not fully understood yet and therefore there are still many people researching to better understand evolution. Of course, not to better test if evolution is true as this has been known for a long time now.

Just because you cannot forsee a use for more "bulgy" spikes doesn't mean there isn't a use for them. Furthermore, natural selection isn't about producing perfect organisms, it's about selecting for traits that are "good enough". There is also more to evolution than natural selection. The phenomenon of genetic drift can cause a neutral or slightly maladaptive trait to become fixed in the population.
In short, not every single trait is adaptive. Check out the famous paper The Spandrels of San Marco if you want to read more. It talks about how we shouldn't focus on trying to come up with an adaptionist theory for every trait and instead consider that other agents of evolutionary change, such as genetic drift, can generate non-adaptive traits.

Notably this answer about spikes is delivered by CactusWoman...

I think it's generally believed that spines/thorns/prickles are adaptive in that they deter herbivory while still allowing for pollination.  But as Gould et al. rightly point out, this would need to be tested.

@augurar Yes, it is well-known that spikes themselves deter herbivory. But the question was whether or not "more spiky" or more bulgy spikes were better than slimmer spikes.


text:
Is there a significant difference in sedentary calorie-burn between a thinker and non-thinker?
I've read that, on average, a sedentary female burns between 1,600 - 2,000 calories and a sedentary male burns between 2,000 and 2,500 calories. I've also read that the brain itself burns quite a few of these.
Let's say two people are exactly the same, and have the exact same (sedentary) lifestyle—except one of them often does intense mathematics. Is there a significant difference in calorie burn?
If so, how much is it?

Is there a significant difference in calorie burn?

No.
The brain, while only making up 2% of our body weight, accounts for ~20% of our energy use at rest. That's because the brain, being critical for survival, is a very high-maintenance organ. At rest, the membrane potentials of all neurons - firing or at "rest" - need to be controlled/maintained.
Of all the energy used by the brain, about 25% of it is needed for signal-independent function (protein synthesis, phospholipid turnover, etc.) Furthermore, there are two types of cells in the brain: neurons and glial cells. The glial cells (about 30%) use from 17 to 40% of the energy depending on whose estimates you use. The rest is needed (by neurons) for signal-related processes - maintaining/restoring cell membrane potential, etc. - only a fraction of which is used for thinking.
The brain never rests - it is highly active even in sleep, with both excitatory and inhibitory activities needing energy. Higher mental functions (e.g. doing math problems) only shifts the areas of highest activity a little bit compared to all the activity that occurs without our awareness of it.
Finally, if we could measure glucose consumption of the entire brain while daydreaming vs. doing math, we might be able to answer that question, but the truth is, brain activity doesn't occur in isolation. Someone doing challenging math problems is using more energy in other areas of the body as well; respiration rate, heart rate, muscle tension, etc. varies with the stress of the challenge, so glucose levels alone can't be relied upon (in fact, stress would increase our body's production of glucose) to indicate energy expenditure.
The end result is that in isolation, rigorous mental activity (which can be maintained only for a relatively short duration without fatigue, so it occurs in bursts) expends very little of the total energy the brain uses.

A common view equates concentrated mental effort with mental work, and it is fashionable to attribute a high demand for mental effort to the process of problem solving in mathematics. Nevertheless, there appears to be no increased energy utilization by the brain during such processes. From resting levels, total cerebral blood flow and oxygen consumption remain unchanged during the exertion of the mental effort required to solve complex arithmetical problems.

Cerebral Metabolic Rate in Various Physiological States
Does Thinking Really Hard Burn More Calories?

+1, but to be nitpicky on the energy consumption - it's 20% when in rest. During physical exercise the percentage drops

@AliceD - good point!

@anongoodnurse Excellent, excellent answer. Thank you.

Re the block quote, it's worth noting that locally, functional activity and metabolism are closely related, this is how fMRIs work (measuring blood flow as a proxy for activity).  Also, from the linked paper: "Regardless of the cause of the disorder, graded reductions in cerebral oxygen consumption are accompanied by parallel graded reductions in the degree of mental alertness, all the way to profound coma".

@augurar - I did not both those things as I was reading. My point is, or that which I was trying to get across, there is very little difference in energy expenditure overall between an awake and thinking brain and one that is furiously doing math problems. Of course a different region of the brain "lights up" on fMRI's depending on the activity (say, vocabulary tests vs. math tests), but the point remains: the question was do we burn more calories by strenuous mental activity? The answer is still "no".

@anongoodnurse Agreed, I wasn't disputing your answer, just remarking on it.

If anxiety is considered thinking then I guess there is a difference :P

@WYSIWYG - that's a good point.


text:
Does the human hand have 27 degrees of freedom?
I have counted the degrees of freedom in my hand over and over and I keep getting the number 19.
Suppose each finger has 3 degrees of freedom. Then 5 * 3 = 15. The wrist can rotate around or back and forth so that contributes to 4 degrees of freedom. In total the hand has 19 degrees of freedom.
From a cursory google search, I can notice that it is commonly agreed upon that human hand has 27 degrees of freedom. Can someone provide a good reference and explanation for this?

The first link in that search is a paper which says this: "The human hand has 27 degrees of freedom: 4 in each finger, 3 for extension and flexion and one for abduction and adduction; the thumb is more complicated and has 5 DOF, leaving 6 DOF for the rotation and translation of the wrist."

@canadianer is there a video or some sort that I can visually see how this is the case?

Why is this flagged as "unclear"? Hasn't @canadianer already provided the answer in the comment? Can't you answer it canadianer? Better to answer a question than have it deleted. Admittedly, it's quite a poor question but I am happy to edit it a bit after an answer is put forward

@AliceD I didn't answer because I don't know anything about it and the OP seems to want a better explanation. I don't think the question should be closed.

@canadianer - yes I see his video comment. Personally, I think you should answer, you have my upvote :) But I understand your position. It won't result in an accepted answer I guess. Up to you!

I think that you forgot to count the degrees of freedom of abduction and adduction present between each fingers. I've read about robotic hand recently and by a matter of fact i know that a hand has 22 DOF. Not sure though. Hope this helps.

IMO a degree of freedom allows movement in all co-ordinates along that direction. Fingers, wrist and elbow have restricted movement. I think that should bring down the DOF (https://www.cs.cmu.edu/~rapidproto/mechanisms/chpt4.html#HDR52B)

Keeping in mind that I know nothing about this, I will try to explain why the hand can be modelled with 27 degrees of freedom. This is just my interpretation of this paper, which says:

The human hand has 27 degrees of freedom: 4 in each finger, 3 for extension and flexion and one for abduction and adduction; the thumb is more complicated and has 5 DOF, leaving 6 DOF for the rotation and translation of the wrist.
To accurately model the hand, a complete model of the muscles, tendons, bones and a neurological control structure is necessary. The dynamics of such a complex model are still poorly understood, forcing the use of simplified models. Current models are too simplified for our purpose so we turn to recent work from the medical community to motivate assumptions used in a new model that we propose here. We use a 27 DOF model of the hand with the following sim- plifying assumptions:
  1. The thumb is independent of the other fingers.
  2. Adduction/abductionofthefingerjointsareindependent.
  3. Motion frequency does not affect joint interdependence.
  4. Both hands have the same interdependence model.
  5. The posture of the wrist and the rest of the arm do not
  affect the underlying interdependence structure.

Incidentally, this implies to me that there are different models of the hand with different assumptions that use a different number of degrees of freedom.
Anyways, take a look at this hand:

[source]
And now, follow along with your own hand!

finger (4 DOF): each finger has 2 interphalangeal joints between the distal, middle and proximal phalanges that allow for flexion/extension (2 DOF); each finger also has a metacarpophalangeal joint between the proximal phalanx and the metacarpal that allows for flexion/extension as well as abduction/adduction (2 DOF)
thumb (5 DOF): an interphalangeal joint between the distal and proximal phalanges allowing flexion/extension (1 DOF); a metacarpophalangeal joint between the proximal phalanx and metacarpal allowing flexion/extension and abduction/adduction (2 DOF); a carpometacarpal joint between the metacarpal and trapezium allowing flexion/extension and abduction/adduction (2 DOF)
wrist (6 DOF): between the carpals and radius allowing flexion/extension, abduction/adduction and supination/pronation (3 DOF); I think when the authors refer to translation of the wrist, they are simply saying that hand can be moved in all planes of 3D space (ie up/down, side to side, forward/backward - 3 DOF)

Since we have 4 fingers, they give 16 DOF. Adding the 5 DOF of the thumb and 6 of the wrist, we get 27. Please nobody question my reasoning. Thank you.

By the last 6DOF, the article just means the placement of the whole hand as an object in 3D space. They don't care about the radius, it's not a part of the hand.

An observations based on my hands: I think there are 3 more degrees of freedom, bringing the total up to 30DOF. I actually am able to move my metacarpals up and down independently, even quite noticably and somewhat easily for the pinky and ring fingers. Taking one as the reference, the other 3 add 1DOF each. The easiest way to observe it for me is to make a fist and alternate between squeezing these two fingers shut and trying to extend them while also resisting extension by trying to keeping the joints between metacarpals and phalanges at 90°. Or you can just move them with the other hand.

Note that my goal here was to find all visible degrees of freedom, not just "practical" ones, to make hand poses look more natural. The extra 3 I described above allow the knuckles to be in an almost straight line or in a very noticable curve, so I count them even if they are "useless". And I might as well give the joint between thumb's metacarpal and phalange just 1DOF instead of 2, for me it bends sideways about as well as all inter-phalangial joints.


text:
Why is living muscle tissue seemingly able to restore its shape under force, while dead tissue is not?
When I press my finger, even with relatively little force, into beef or chicken (say, at a grocery store), the indentation remains.
When I poke a cow with my finger, the indentation does not remain. When I squeeze my own arm, even with the same (or greater) amount of force used to alter the shape of meat with my finger, my arm remains the same shape afterwards.
What is the difference between dead and living muscle tissue, with respect to mechanisms that allow it to maintain its shape? Does living muscle tissue somehow actively maintain its shape while dead tissue cannot? Is it something more passive, such as a breakdown of something in dead muscle tissue that makes it more malleable (and if so, what)?

If you pounded your forearm with a baseball bat with time and force equivalent per ounce of muscle as using a tenderizing mallet, I guarantee you it would not spring back into shape at any time. Likely it would need to be amputated.  Likewise, punching a large cow as hard as you can doesn't mean you've done no permanent damage to any muscle fibers simply because it doesn't change shape perceptibly. You need to compare apples to apples. Active transport (of fluids, etc) doesn't occur in dead tissue. Your question needs to be reframed in different terms.

@anongoodnurse That's why I also gave the example of "poking". I can permanently alter the shape of meat with very little force (finger marks in meat at the grocery store from casual handling by customers are not uncommon), and applying that same force to my arm does not have the same effect. Does that cover the concern?

When you poke meat to indent it, a lot of what is being displaced by your finger is fluid (and it takes more that "just a very little force" or it would be unrecognizable after handling by several people) . There is no ability of dead tissue to redistribute that displaced fluid and remove the dent. It doesn't much matter the tissue - muscle or subcutaneous soft tissue in peripheral edema, for example. No active energy expenditure = no reactive movement.

@anongoodnurse It sounds like this active redistribution of fluid in living tissue that you mention is a possible answer to my question. Can you elaborate in an answer?

That's just one component. For muscle, myoglobin cross-linking also comes into play. It's a longer answer. Hence the comments.

Hence the question! :)

"Does living muscle tissue somehow actively maintain its shape while dead tissue cannot?" Yes. The answer can be boiled down to energy use and it's control. Dead tissue doesn't have it; living tissue does.

@anongoodnurse you should summarize that into an answer. Thanks.

Capillary refill time is defined as the time taken for the capillaries to refill after the blood in them has been squeezed out by pressure. It is widely used as a quick way to determine the effectiveness of the circulatory system in humans by doctors.
In a normal living organism, the capillaries will take time to refill after they have been emptied. Muscle volume consists of the cell volume (which is fixed in the absence of lysis), the blood, as well as lymph and other intracellular fluids (which will be displaced elsewhere when it is deformed by pressure).
When the organism is dead, there is no more circulation in both the blood and lymphatic systems, and therefore any fluids squeezed out by pressure will remain elsewhere, and the deformation is permanent without any regulatory effect by the circulatory system.

One difference between living and dead tissue, but specific to muscles is tonus.  In living skeletal muscle, random nerve impulses fire to keep muscles in a partially contracted, ready-to-use state.  Without this low-level tension sarcomeres, the basic units of skeletal muscle, would not recover from being poked and could more easily be pulled out of optimal position and damaged.

And yes, there are also structural changes unique to dead meat.  Rigor mortis happens when the sarcomeres exhaust all ATP after death and become trapped in a bound state.  Eventually putrefaction sets in and enzymes break off the mechanism and the muscle becomes permanently flaccid.


text:
Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?
When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are known. When there is a mixture of multiple ligands and receptors where each ligand and each receptor can interact with eachother, this is not so simple. For example, lets say you have the following set of information:
$$K_{11} = \frac{[R_1][L_1]}{[R_1L_1]}$$
$$K_{12} = \frac{[R_1][L_2]}{[R_1L_2]}$$
$$K_{21} = \frac{[R_2][L_1]}{[R_2L_1]}$$
$$K_{22} = \frac{[R_2][L_2]}{[R_2L_2]}$$
along with the $K_d$'s ($K_{ij}$) and the total concentrations of $R_1$, $R_2$, $L_1$, and $L_2$. I have not managed to find any publications where this has been demonstrated but I would be surprised if it hasn't been figured out by someone.

Are you familiar with differential equations?

The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is that they capture all the intuition without the tedious algebra.
It's interesting that you are asking for the fraction of ligand bound to receptors ($[RL]/[L]_{tot}$). Typically one is interested in the fraction of receptors that have ligand bound ($[RL]/[R]_{tot}$). This is for two reasons:

Typically the fraction of bound receptor is the physiologically relevant variable for a cell, determining the response of the cells to the ligand stimulus. Since the cell can only sense the concentration of ligand when it binds to the receptor, the fraction of bound receptor is the natural variable to study.
In most contexts, the number of receptors is much smaller than the number of ligands. This motivates the approximation found in pretty much all treatments of receptor-ligand equilibrium that the concentration of receptor-ligand complex is negligible compared to the total concentration of ligand. For cells, this is a fairly reasonable assumption. In this limit, the fraction of ligands bound to receptors ($[RL]/[L]_{tot}$) is always negligible. It's the fraction $[RL]/[R]_{tot}$ that is  interesting. Another reason this assumption might be adopted is that in practice, ligands tend to be soluble while receptors are insoluble. In this case, it is easier to control the concentration of ligand, adding it in excess to a pellet of receptors, and then measure the amount of bound receptors (maybe by radioactivity): in this experiment the total concentration of receptors is measured, not controlled, so you want your equation to be a function of your controlled variable, the concentration of ligand. This requires adopting the approximation above.

The situation in which there are two ligands binding to one receptor has been solved (in the limit that $[RL]\ll[L]_{tot}$): this case is known as competitive inhibition. In your notation, the fraction of receptor 1 bound to ligand 1 (ligand 2 is the "competitive inhibitor," i.e. rival ligand):
$$\frac{[RL]}{[R]_{tot}} = \frac{[L_1]}{[L_1]+K_{11}(1+\frac{[L_2]}{K_{12}})}$$
So I'm going to generalize to the case that there are $N$ ligands and I am interested in the fraction of a given receptor $R_i$ bound to ligand $L_j$. The equilibrium constant for this reaction is $K_{ij}\equiv [R_i][L_j]/[R_iL_j]$.
The receptor is also binding to all the other ligands, so that the free concentration of receptor $[R_i]$ is equal to the difference between the total receptor concentration $[R_i]_{tot}$ and the concentration of each bound complex $[R_iL_k]$ for $k$ from 1 to $N$. And the ligand is also binding to all the other receptors. In order to get a reasonable equation, we have to invoke an approximation very similar in spirit to the one mentioned above, namely, that the concentration of all ligand-receptor complexes is small compared to the total concentration of each ligand individually. Thus I can ignore the difference between $[L_j]_{free}$ and $[L_j]_{tot}$.
In this approximation, I expand out the expression for the equilibrium constant (using $[L_j]$ as shorthand to stand for $[L_j]_{tot}$).
$$K_{ij} = \frac{([R_i]_{tot}-[R_iL_j]-\sum_{k\neq j}^{N}[R_iL_k])[L_j]}{[R_iL_j]}=\frac{[R_i]_{tot}[L_j]}{[R_iL_j]}-[L_j]-\sum_{k\neq j}^N\frac{L_kK_{ij}}{K_{ik}}$$
Note that the sum is over $k$ from 1 to $N$ except $k=j$, which I pulled out of the sum early. I also used the definition of each dissociation constant to write the sum in terms of dissociation constants instead of $[R_iL_k]$, which makes the algebra a lot simpler.
This can then be simplified to solve for the fraction of bound receptors:
$$\frac{[R_iL_j]}{[R_i]_{tot}} = \frac{[L_j]}{[L_j]+K_{ij}(1+\sum_{k\neq j}^N\frac{[L_k]}{K_{ik}})}$$
Suppose instead of being interested in the fraction of receptor $i$ bound to a particular ligand $j$, one is interested in the fraction of receptor $i$ bound to any ligand. I'll call this quantity $[R_i\mathbf{L}]/[R_i]_{tot}$. We can figure this out by noting that
$$[R_i\mathbf{L}]\equiv \sum_{k=1}^N[R_iL_k] = [R_i]_{tot} - [R_i]_{free}$$
We obtain $[R_i]_{free}$ from the formula for each $K_d$:
$$[R_i]_{free}\equiv[R_i] = \frac{K_{ij}[R_iL_j]}{[L]_j}$$
And so using our equation for $[R_iL_j]$, we obtain (I'll spare you some of the gory algebra details)
$$\frac{[R_i\mathbf{L}]}{[R_i]_{tot}} = \frac{\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}{1+\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}$$
(these sums are again unrestricted, from $k=1$ to $N$ including $k=j$).
Happily, if there is only one ligand, these formula reduce to the regular result, namely $[L_1]/([L_1]+K_{i1})$. As another check, if all the $K_d$s are equal, then the fraction of receptors bound to any type of ligand is the same as the bound fraction for the same amount of a single type of ligand with the same concentration as the whole pool of different ligands ($\sum_{k=1}^N[L_k]$), and the fraction of receptor bound to a particular ligand $L_j$ is smaller by the fraction of the total ligand pool that is species $j$, $[L_j]/\sum_{k=1}^N[L_k]$.
If you are really interested in the fraction of ligands bound to receptors---that is, you are working in the limit in which there are tons of receptors compared to ligands, so that the number of receptor-ligand complexes is tiny compared to the number of receptors---then you can use the above equations just by switching $L$'s and $R$'s. In this case you would obtain
$$\frac{[R_iL_j]}{[L_j]_{tot}} = \frac{[R_i]}{[R_i]+K_{ij}(1+\sum_{k\neq i}^{N}\frac{[R_k]}{K_{kj}})}\qquad [R_i]\equiv[R_i]_{free}\approx[R_i]_{tot}$$
A caveat
To derive these equations, I made a pretty strong assumption that the total concentration of all receptor-ligand complexes (for different receptors as well as different ligands) is small compared to the total concentration of each ligand individually. In this limit, we can assume that the pools of free ligands of each species are so large that each receptor equilibrates with this pool independently of each other receptor (there's plenty of ligands to go around). You might be interested in the limit in which ligand binding and unbinding to one receptor affects the binding and unbinding to another receptors, so that receptors are not independent. I am not sure how to approach this problem. I'm skeptical that there will be any sort of closed form solution; in my preliminary thinking about this limit, I think I can imagine situations in which stationary equilibria are not possible: depending on rates, receptor A might partially equilibrate, depleting the pool of ligands, affecting the equilibration of receptor B, which would cause receptor B to "pull" more ligands away from A, in some sort of oscillation. However, that is just speculation, and I'd be very curious if someone could provide more insight to this case, in which receptors are able to "interact" through the pool of free ligand.
One of the take-aways of this whole analysis is that it is very helpful to be aware of the assumptions made in standard derivations that lead to the nice results we learn in biochemistry class, and how those assumptions might have to change if we generalize the system somewhat.

dzjeezz, my math is shaky, and I'm not really capable of upvoting your answer in terms of its content, but heck +1. Nice. Very nice. I really hadn't expected this one to be dealt with any time soon. kudos.


text:
What exactly is neuroplasticity, and can it be demonstrated with a simple experiment?
As far as I know, neuroplasticity is about restoring brain functions by moving some functions to other still functional. Neuroplasticity is more prominent in children than in adults.
What are other examples of neuroplasticity that are unrelated to pathologies? Can it be demonstrated by a simple experiment outside the laboratory? Are learning, or simply the getting used to new things examples of neuroplasticity?
For example, after wearing red-cyan goggles, I see a color mismatch for some time after I take off the goggles. Is it related to neuroplasticity or some other thing?

Can you please include a link for your definition of neuroplasticity? This is not how I understand the term at all.

@anongoodnurse, I just remember reading about it somewhere before. Wikipedia gives this intro: Neuroplasticity, ..., is an umbrella term ... — it refers to changes in neural pathways and synapses due to changes in behavior, environment, neural processes, thinking, emotions, as well as changes resulting from bodily injury.

This is not something you want to be testing in any kind of "home experiment".  I agree with @anongoodnurse, your last example is a bit muddled in terms of its reliance on long-term plasticity.  Your first sentence has some ring of truth to it, as this phenomenon has been observed in the congenitally blind, for example (see http://en.wikipedia.org/wiki/Cross_modal_plasticity), but there is no "movement" per se.

I have voted to close this as a medical advice question due to the "experimentation" aspect, but if you rework it a bit, there are some interesting questions here.  Take a look at some of the work done on lateral connections/silent synapses in the motor and sensory cortexes particularly after cerebral infarct or TBI and you should have plenty of fodder for an outstanding and well-researched question.

@jonsca et al., I have edited the question and removed self-help referencing. I vote to re-open as it is a valid question.

Your question is basically a matter of defining brain plasticity or more broader, neuroplasticity. According to a well-cited paper in Brain (Cramer et al., 2011) neuroplasticity is defined as:

[...] the ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function and connections.

Hence, the term can be, and indeed is used very broadly. A more elaborate definition in the same article should answer you question as to whether learning and habituation can be considered to be associated with neuroplasticity:

Neuroplasticity can be broadly defined as the ability of the nervous system to respond to intrinsic and extrinsic stimuli by reorganizing its structure, function and connections; can be described at many levels, from molecular to cellular to systems to behaviour; and can occur during development, in response to the environment, in support of learning, in response to disease, or in relation to therapy. Such plasticity can be viewed as adaptive when associated
  with a gain in function [...] or as maladaptive when associated with negative consequences [...]

Your vision example, however, is more appropriately referred to as adaptation. Although it strictly spoken falls under the above definition of plasticity (...reorganizing its... function,  color adaptation is (at least in my opinion) too short-lived (minutes) to be associated with plasticity.
Lastly, as to experiments - Although learning a chunk of material from a textbook as a homework assignment is definitely related to plasticity, it cannot be seen as proof; it is the result of neuroplasticity. Experiments showing plasticity can and have been done with imaging (most notably fMRI) or with electrophysiological approaches (patch clamp studies showing long-term potentiation reflecting learning). These techniques cannot be applied outside the laboratory, as they require advanced and pricey equipment, careful experimental design, and not least importantly ethical clearance.
Reference
 - Cramer et al., Brain 2011;134:1591–609
Further reading
 - Color adaptation: What is the science behind the   inaccurate perception of colors?


text:
RNA polymerase question
In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second.
Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs?
My answer: A codon is 3 base pairs so I start by dividing 3510 by 3 and then by 20 to get 58,5 seconds.
Question 2: Your bacteria can produce a Lac Z mRNA about every other second. How can you explain this?
My answer: I am very lost on this one. I thought that the mRNA would be as long as the gene so wouldn't this be 58,5 seconds not roughly 2 seconds??

Multiple RNA Polymerase transcription complexes engaged on the lacZ gene at the same time, staggered along the gene.

Either the gene is present in multiple copies (especially possible if it is in a plasmid) or multiple RNA polymerases are transcribing it, each beginning from the start site one after the other with some amount of time delay, much like multiple ribosomes translate the same mRNA to increase rate of protein production.


text:
What are iPSC cells, and what are their applications?
I also searched it on internet, and just basically know it's related to the Stem Cells, but there are too many resources, can anyone help me find out more about them, like their applications? They really interest me.

have you seen this page? http://stemcells.nih.gov/info/basics/pages/basics10.aspx

From this article: iPSC's or induced pluripotent stem cells are somatic cells that have been driven to acquire an induced pluripotent cell state.  Somatic cells can be any cell of the body except sperm cells, egg cells and undifferentiated stem cells. Investigators can induce these cells to 'return' to a stem cell like state by forcing the expression of key transcription factors, and by genome-wide remodeling of epigenetic marks.
There is an entire spectrum of different iPSC's that can be generated, but much is not yet known. Future applications include using them for regenerative medicine, drug discovery, etc.
Recently there were several articles published in nature:

Stem cells: A designer's guide to pluripotency
Genome-wide characterization of the routes to pluripotency

amongst others. Also you can check out http://www.stemformatics.org/ for more information on stem cells and research being done.


text:
Are there mechanisms that limit the amounts of time conjugation and F-plasmid transfer can happen? If yes, what are they?
Not all bacteria have acquired F-plasmids through conjugation. Some of the mechanisms for this are unsuccesful conjugation events (mechanical disruption), no transfer due to integration in bacterial chromosome, etc (See previous question and answer).
Now I am wondering if there are also mechanisms that self-limit the conjugation and transfer of F-plasmids. For instance that a bacterium can only transfer its F-plasmid once during its lifetime.

Yes there are many such mechanisms.
One of the simplest, but perhaps most easily overlooked, is metabolism.  Conjugation requires ATP.  In environments with low levels of nutrients, heterotrophs might not have enough "extra" ATP to fuel the conjugation process.  Note that both donor and recipient need to expend ATP in conjugation.  The donor needs to make the nicking enzyme, the pilus, and extrude the DNA into the recipient, and the recipient needs to synthesize DNA from the single-strand DNA that it has received.


text:
Why are triacylglycerols broken down before being absorbed?
So when dietary fats are in the small intestine, they are emulsified by bile salts in order for action by lipases to occur.  Lipases degrade the triacylglycerols into monoacylglycerols, diacylglycerols, free fatty acids, and glycerol, and these are taken up by intestinal epithelial cells.  Once taken up, these are reformed into triacylglycerols.
My question: why do these have to be broken down in order to be absorbed, and what is the driving force for reformation of triacylglycerols once absorbed?

Your question does not have a clear answer yet, as stated in Metabolic regulation: a human perspective / Keith N. Frayn. – 3rd ed (2010) on page 39.

There is still debate about how fatty acids cross cell membranes.

On that page they claim that a simple diffusion transport is possible through a 'flip-flop' mechanism, where the fatty acid inserts itself in the membrane and then experiences a reversal movement. The kinetics of the process seem to be in agreement with the observed utilization rates.
Also, it is claimed that there is growing evidence specific fatty acid transporters like FAT and FATP (fatty acid translocase and transport protein) play a key role in the process. They might join forces with the fatty acyl-CoA synthase, consuming ATP. ATP consumption activates them, i. e provides energy, for the acyl-CoA formation (not in order to move against gradient). The activated state would enable them to both move into the cell and regenerate a triacylglycerol.

Why do these (triacylglycerols) have to be broken down in order to be absorbed?
I would say that the hydrolyzed products (fatty acid and glycerol) are more readily internalized because their structure is simpler. Fatty acids can perform the flip flop mechanism, but whole triacylglycerols might not (I am not sure). There is a fatty acid binding protein that may help maintain the fatty acid importation gradient too.
What is the driving force for reformation once absorbed?
It is the secretion of chylomicrons loaded with regenerated triacylglycerols. Since they are secreted, they don't pile up inside the enterocyte (intestine cell) and the equilibrium in the synthesis route (the monoacylglycerol esterification pathway) favors the production of triacylglycerols.
Remarkably, not all fatty acids are reesterified, those of short length (< 14 carbons) are not compatible with the acyl-CoA synthase and enter the plasma in a free state. That happens when digesting dairy products.

So there is a mechanism for efflux of triglycerides, but not for uptake?

I'd like to just add on with some more detail.  According to this, gastric lipase cleaves 15-20% of fatty acids in the stomach.  The rest is completed in the duodenum by lipases secreted by the pancreas.  Bile salts, phospholipids and cholesterol coat these lipid particles to prevent them from coalescing.  The reason is because lipases have adapted to oil-water interfaces.  Therefore breaking down dietary fact into "into an emulsion of fine oil droplets enhances the action of lipases.  The smaller fat globules have an increased surface area and are more easily accessible to active pancreatic enzymes for further breakdown."
As for your question on the driving force of why they are reassembled, "several enzymes reassemble the fatty acids and monoacylglycerides to reconstitute triglycerides.  Subsequently, the enterocytes package the reconstituted triglycerides with proteins and phospholipids into chylomicrons."  These chylomicrons travel into the blood stream through the lymph system where they go to adipose tissue and muscle cells for further breakdown.
Barbara E. Goodman
Advances in Physiology Education Jun 2010, 34 (2) 44-53; DOI: 10.1152/advan.00094.2009

Triglycerides are "huge" molecules relatively speaking compared to carbohydrates like glucose or amino acids like alanine. Within the intestinal lumen they are broken down by lipases and solubilized by bile for absorption, which also enhances the activity of pancreatic lipase. So, to get into the enterocytes of the small intestine they need to be broken down. However, once they are reformed you can't just excrete them into the venous circulation because there are exceedingly hydrophobic and can't circulate in their native form. In fact, they first pass into the intestinal lymphatics before entering the arterial circulation. Before this happens, though, triglyceride particles and other lipids like cholesterol are packaged onto lipoprotein molecules for their transport. These lipoprotein molecules are still large, but they have proteins (i.e. Apo-B48) that act as signals to the peripheral tissues for particle uptake into the muscle, adipocytes, etc.

Thanks for your contribution. References are appreciated at Biology.SE. I think it is a great answer, but without references no one can follow up on your information.

Yes, many answers come from the top of my head too, but everyone can claim to be an expert and start selling nonsense :) Like in your previous answer I simply added a wiki link. Personally I don't like wikis and prefer primary literature instead of open-source stuff, but if you are reluctant adding primary literature, some links to credible sources are an easy alternative

Could the reason that triglycerides being neutral and non-polar, require the aid of additional proteins for their transportation but when broken into glycerol and free fatty acids, the individual components being polar are more easy to transport. Also, in terms of storage, the triglyceride form is better because of its non-polar properties and that it would remain relatively inert in the cytosolic environment.

Some points that you mention have already been covered in other answers. Can you please [edit] your answer to add some more details so that your answer provides additional information?

Welcome. Answers need to be founded on credible sources. Please cite relevant references to allow other users to background read on your material.


text:
Location of TFBS in genome
I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it.
What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?

Lots of annotated SNPs are located nowhere near  any part of any gene, so you would be quite fortunate to (a) find a SNP that maps close to a gene of interest. It would be even rarer for a public SNP to map in top of a relevant TFBS. If you had some SNPs from an unpublished study that might be cool

I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser.
For the actual question TFBS are located pretty much everywhere, including exons (as described here), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - here a reference).

what about the binding affinities? Is there any tool where I can insert my notrmal sequence and a sequence with snp and it will predict the difference? I know sTRAP(http://trap.molgen.mpg.de) is suitable for that, however the online results differ from r-version results

@Tonja This page contains some suitable software. If you know what TF you are looking at, you might want to look at this page.


text:
Understanding recombination scoring in family pedigrees
I am having some problems understanding recombination, and I am not sure what element I am missing here. This figure is an example from my text book. The pedigree belongs to a family with an autosomal dominant disease, typed for a marker with alleles A1-A6.

So, all meioses are phase-known, meaning we know which combination of alleles was inherited from each parent. Apparently this leads us to be able to unambiguously score III1-III5 as non-recombinant (N) and III6 as recombinant (R).
This is were I get lost, I don't understand how it is possible to unambiguously score each individual as N or R. Also, if the disease is dominant, how is it possible that III6 is affected, as both alleles originate from the both unaffected I1 and II2?
EDIT: Blue colour in the pedigree means the person is affected by disease, white symbolizes unaffected individuals. I believe the red stars symbolizes that the person carries the disease gene. That would mean blue corresponds to not carrying the disease gene. If this is the case The red colour of III2 is a fault in the figure.

Could you add some details to your question to annotate the image? Also in my opinion this is quite homework question, which is off topic here at Biology SE, unless you share your efforts / research to solve the question.

I don't understand how recombination scoring works, and I thought I'd use this image from my text book to provide a basis for illustrating it. It wasn't meant as help with home work, but I understand your remark :-). How can you deduce from given alleles which is recombinant or not?

Okay so not homework :) but it would still help to know what all the stars etc mean on the image. For me at least...

To be honest I have no clue... I believe its purpose might be in emphasizing heterozygosity, but I don't think this is correct: if blue star corresponds to allel A2, then III2 and III5 should also have a blue star...

You need to add what the stars and colors are referring to.

Ns are not non-recombinant at the genomic level. What you know is that they do not show recombination events at the risk allele locus as subjects carrying the marker A1 show signs of the disease and similarly healthy subject do not carry the marker A1. Hence they are called non-recombinant. On top of that 3rd generation subjects (excepted III6) show combinations of alleles reflecting inheritance of one allele from each parent.
What is very important is that A1 is not the allele, it is the marker for the risk allele. This means that A1 is not directly the allele but a region of DNA close to the allele provoking the disease, sufficiently close to be co-inherited most of the time with the disease allele.
For III6 you actually know that a recombination must have happened as this subject obviously carry the risk allele (shows the disease) yet not the marker associated with it, therefore a recombination event happened between the marker and the disease allele.

-I've re-read the question a few more times, and what you say makes sense. I've focused too much on the picture than the text itself. My bad, guess I'm a bit tired. I've deleted my answer as yours is obviously better.

One slight remark though - On molecular level basically everybody is recombinant, but multiple recombinations can restore the original gene / allele combination, practically only those offsprings / individuals are considered recombinant who exhibit different combinations than his/her parents.

@poka.nandor You are exactly right. In the context of genetic linkage, the term recombinant is usually used at a given locus and not at the genome-wide level this is why III1-5 are considered non-recombinant, they actually are non-recombinant at the disease risk locus. Good point.


text:
Ethanol production by fermentation?
As bacteria are involved in the production of ethanol through fermentation and ethanol is also used as antiseptic that kills bacteria, so how and why bacteria are involved in the synthesis of such alcohol which is lethal for itself(bacteria)?

Yeast can produce up to 16-17 v/v% ethanol without dying according to this article. Yeast is a primary industrial ethanol producer, it produces ethanol even under aerobic conditions, in contrast to bacteria that usually ferment sugar to ethanol under anaerobic conditions. Bacteria can also withstand up to several percent v/v concentration ethanol in their media. Check this paper for details. They produce ethanol because it is a natural byproduct of their cellular metabolism. Under anaerobic conditions sugar as the primary energy source cannot be oxidized and utilized as well as in aerobic conditions.

Alcoholic fermentation converts one mole of sucrose into two moles of ethanol and two moles of carbon dioxide, producing two moles of ATP in the process.

from: http://en.wikipedia.org/wiki/Ethanol_fermentation
Anaerobic bacteria follow this path because fermentation of ethanol does not require oxygen. This byproduct is secreted from the cells. In natural environments ethanol either dilutes in the media bacteria live in or can be taken up by acetic acid bacteria and used as an energy source.


text:
Is it possible for a human to wake up in a wrong way?
There's an old folk saying that goes like "He got out of bed on a wrong foot" - to indicate that the person's day is going poorly because of the way that person woke up.
Is it is possible for a human to disrupt the awakening process, causing negative cognitive side effects for the rest of the day? If so, how long does it take to restore normal cognition?
There's this related question that I asked - if different parts of a human brain can be asleep independently of each other? This question is a variation on that one, and specifically deals with the process of awakening or activating brain regions in the morning.
I'm aware of the concept of "Sleep inertia". However, it does not seem to be the phenomenon in question, as sleep inertia is frequently mentioned in the context of napping. (where napping over a certain time leads to sleep inertia). Additionally, sleep inertia has been described in terms of decline of motor activity, and not as cognitive side effects lasting for a whole day.
From personal experience, it seems that I'm doing best if I get out of bed immediately following a natural awakening, even if it is rather early, as opposed to snoozing for another 30-40 minutes.

I want so badly a response to that...

I think the "sleep inertia" you refer to is the reason - if you are woken by your alarm during a particular cycle of sleep this would have an effect lasting all day [haven't looked this up - anecdotal]. This would then be referred to as having woken up on the wrong side of the bed (which is just a saying not a literal reason why you are having an off day).
Could be due to all sorts of reasons though, including nutrition, recent physical activity, stress, alcohol/drug consumption... etc!

I'd say anytime a human hasn't slept enough, of course how much is enough sleep depends on the individual.

Isn't sleep paralysis another kind of disrupted sleep phenomenon?

I did a quick search and found some research in this area. Sleep inertia is the technical term for feeling groggy for a while after waking up.
In a review article by Patricia Tassi, Alain Muzet (Sleep inertia. Sleep Medicine Reviews. Volume 4, Issue 4, August 2000, Pages 341–353), they define sleep inertia as

Sleep inertia is a transitional state of lowered arousal occurring immediately after awakening from sleep and producing a temporary decrement in subsequent performance.

and also says,

Depending on the studies, it [sleep inertia] can last from 1 min to 4 h. However, in the absence of major sleep deprivation, the duration of sleep inertia rarely exceeds 30 min.

Same article reviews several studies (first report in 1964) on sleep inertia relating to sleep stages:

Abrupt awakening during a slow wave sleep (SWS) episode produces more sleep inertia than awakening in stage 1 or 2, REM sleep being intermediate.

So yes, sleep stage seems to correlate with "waking up in the wrong way" as @CactusWoman suggested.

Good find, I especially appreciate the up to 4 hour timing information. This may also interact with caffeine, which is frequently consumed in the morning. Apparently caffine half-life is about 5.7 hours (http://www.caffeineinformer.com/the-half-life-of-caffeine)

Sleep occurs in stages. There are three stages of non-REM sleep followed by REM sleep. Natural waking occurs during the REM stage. If your alarm goes off while you are in the middle of deep sleep, you are going to feel different from if you had woken up naturally. That's why there's a market for alarm clocks designed to wake you up during light sleep.

do you have references for this "feel different" claim?

I have an "alarm clock" which is silent but slowly brightens a lamp over the course of a half hour or so. It is called the Sunrise Clock, I got it about 20 years ago. Normally I awaken a few minutes before it goes "click" and begins to come on. If I set an actual alarm, I wake up about 1 minute before.