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Why does applying pressure to a venipuncture site prevent haematoma?
From what understand, when drawing blood, a phlebotomist puts pressure on the venipuncture site while withdrawing the needle to prevent a haematoma.
I'd like clarification;

How does this prevent a haematoma?
And why is it not necessary until withdrawal?
I assume it's not necessary, and counterproductive to apply pressure prior to withdrawal, besides complications or unusual procedures etc?

My best guess at a rough idea if what's happening is simply pressure restricts flow out of the vein, so slowing blood leaking into surrounding tissue, helping clotting? Or maybe it increases vein inner wall cell damage, releasing agents triggering faster clotting?
Thanks

I wonder this as well - always thought the purpose is to pressure-close the capillary ends to prevent a sudden rush at the moment the needle is withdrawn.

Prevention of hematoma (as we say in the colonies) is by causing hemostasis within the vessel (here, a vein). Careful pressure during withdrawal, followed by firm pressure after withdrawal until primary hemostasis is achieved reduces the rate of hematoma formation.
Thorough mechanistic studies being absent, we can still confidently make some statements about what is likely happening, based on our knowledge of physics and hematology.

Why is it not necessary until withdrawal?

Good venipuncture technique results in a single puncture of a vein that is no larger than the needle. With a single puncture, during the blood draw, all blood exiting the vessel enters the needle and the collection tube. This is why pressure is not necessary until withdrawal of the needle.  In fact, pressure at this point may cause the needle to damage the vessel at another site, allowing blood to exit into the tissue.

How does pressure prevent a hematoma?

On withdrawal, external pressure to a punctured vessel that is greater than the internal pressure of that vessel will stop the flow of blood, preventing blood from entering the tissue.  At a standard venipuncture site, e.g., the antecubital vein, it takes approximately 2-10 minutes for primary hemostasis (in the absence of aspirin, or otherwise poisoned or disordered platelets). If you prevent flow out of the vessel during this period, you'll prevent formation of a hematoma. There are other mechanisms at work here that help, e.g., vasospasm, so you may still avoid a hematoma without pressure, but the rate of hematoma formation is higher when this isn't done

Does it increase vein inner wall cell damage, releasing agents triggering faster clotting?

Possibly, but the primary mechanism is simple physics. Increase the pressure until a plug is formed, and you prevent blood from exiting the vessel into the tissues.


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Do immortal organisms exist?
Do organisms exist that are able to live indefinitely if they are not killed by external factors?
Under external factors I would consider things like predators and natural disaster but not illness by bacteria for example.

See http://biology.stackexchange.com/questions/6884/why-is-the-hydra-biologically-immortal

the biggest issues for immortality are internal factors - senescence (aging) is a planned death on a cellular and organismal level.  the above referenced question is a pretty good review of answers. Aubrey de Grey is another good google term to understand proposals which may reverse aging.

If you're referring to the elves of Middle Earth, I'm sorry no they do not exist.

I'm not, I was more looking after some bacteria species. Or maybe some sort of tardigrade..

Umm, that was supposed to be a joke...

I find your distinction between internal and external factors a bit arbitrary. What is your motivation for excluding bacterial infections as external cause of death?
You might be interested in what happens in plants. Here is an example, where the plants get cloned and seem to be able to do this for an indefinite amount of time, but they loose their fertility:
http://www.wired.com/wiredscience/2010/08/aspen-immortality/

I think a lot of this answer hinges on the (artificial) choice of how to distinguish what constitutes an "organism" versus a collection of organisms.

Duplicate: see this http://biology.stackexchange.com/questions/6884/why-is-the-hydra-biologically-immortal and http://biology.stackexchange.com/questions/7010/is-there-any-kind-of-immortality-in-plants

@StevenRoose see this book (http://books.google.co.uk/books?id=4wEspn9gUdoC&pg=PA109&lpg=PA109&dq=extrinsic+causes+of+death&source=bl&ots=Cj-gAk94ZC&sig=wfo9x9I614_TyYEyGa6kUaUoZS8&hl=en&sa=X&ei=HTDbUfrIMsfXtAbasYCYDQ&ved=0CEsQ6AEwAw#v=onepage&q=extrinsic%20causes%20of%20death&f=false) page 108. It defines extrinsic and intrinsic causes of death - as someone studying aging and lifespan I can tell you these are standard definitions and bacterial/viral infections are considered extrinsic.

The immortal jellyfish, Turritopsis dohrnii http://en.wikipedia.org/wiki/Turritopsis_dohrnii

The most amazing thing about this is that if you own one of these creatures, than you can call it "My immortal".

hydra vulgaris & stuff i suggest to read "mortality patterns sugest lack of senescence in hydra" Daniel E. Martinez

I now found this Wikipedia article on biological immortality. It's pretty much what I was looking for.
Wikipedia describes the phenomenon as follows:

Biological immortality refers to a stable or decreasing rate of
  mortality from cellular senescence as a function of chronological age.
  Various unicellular and multicellular species may achieve this state
  either throughout their existence or after living long enough. A
  biologically immortal living thing can still die from means other than
  senescence, such as through injury or disease.

It has a list of such organisms as well, consisting of

tardigrades
hydras
turritopsis nutricula, some sort of jellyfish
lobsters*
planarian flatworms

Addendum: This blog post takes a good look into the myth of lobster immortality. It seems to be as much a myth as the result of any substantial observation.

It would be helpful to summarise the content of your links for future readers

Yes. The Bristlecone Pine, Pinus longaeva, is one example. This species boasts the oldest individual living organisms, and also has been convincingly argued by Lanner and Connor (2001) to show no evidence of senescence.
While the Wikipedia page on Biological Immortality (as of June 2013) unfortunately ignores plants, the pages on Negligible Senescence and Longest-lived Organisms list many plant seeds, clonal groups, and individuals.

 Lanner R, Connor KF. 2001. Does bristlecone pine senesce? Experimental Gerontology 36: 675–685.

This is indeed a correct answer, as many organisms listed on other answers show some aging. The entire list of (presently 7) organisms, including P. longaeva, which do not show signs of senescence is given in a subsection of the reference AnAge database, which collects information on aging of every species: http://genomics.senescence.info/species/nonaging.php

The immortal jellyfish (Turritopsis dohrnii) is capable of biological immortality.

It's one of few known species capable of reverting completely to a sexually immature, colonial polyp stage after having reached sexual maturity as a solitary (free-floating) individual (called a medusa).

Theoretically, this process can go on indefinitely, effectively rendering the jellyfish biologically immortal

 Image source: Piraino et. al. 1996

Citations
Piraino, Stefano, et al. 1996. "Reversing the life cycle: medusae transforming into polyps and cell transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa)." The Biological Bulletin 190(3): 302-312.

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Viral susceptiility of Nose and eyes
I read that opening in our face like nose and eyes are one which get us infected with numerous communicable diseases like  cold , flu ebola etc.
Both these organs have preventive mechanism like nose hairs, eye lash , etc.
Which one of eye and nose does protect human better from airborne virus and bacteria?

Between the eyes and nose, which offers better immune protection

Neither. Both are mucous membranes lined by epithelial cells. Each is their own niche (and the nose has a number of sub-niches), with particular receptors, environmental factors, and immune factors that interact with pathogen factors. The interaction between the two produces the tissue tropism of a particular pathogen. Each is colonized with many commensal microbes, with some overlap (see Murray Medical Microbiology Ch 7 and this study of the eye). As far as "airborne" transmission, vs. inoculation by physical contact, the nose and nasopharynx are important structures in respiration. The eye is not.

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Serological assays measuring antibody response
Given that an appropriate immune response to a bacteria may be thwarted in an individual, including not producing all of the antibodies which are known to occur in people who have been infected, or producing insufficient amounts of antibodies specific to a bacteria --- Are all serological tests using antibodies as a basis for detection of a systemic infection inherently flawed? In this instance, I'm assuming appropriate application of a test and competent laboratory methodology. But, equally important, what criteria can routinely be used to consider the efficacy of a particular antibody test, across the board.

Can you give some example conditions under which the immune response may be "thwarted"? Are you talking about immunocompromised individuals, or something else?

Infections, such as flu, mono, and CMV can temporaCrily, suppress immune function so we don't produce antibodies to new antigens.  If these infections are known -- fine. Would be considered when evaluating results from subsequent antibody tests.  But, the primary infections I mentioned may be subclinical for symptoms and still effect overall immune function.  So, I'm wondering if or how results of antibody tests "adjust" for this factor.  Is it a consideration when evaluating antibody tests?  This is the flaw I wondered about and still may not be clear enough.

Antibodies used for serological tests are performed in vitro, and are not required to be effective for eliminating the pathogen. For an infected individual, antibodies may play a role in neutralization, opsonization, or activating the complement system (checkout Janeway's Immunobiology for more details). There are a number of reasons why antibodies may be present and not trigger an effective response down these pathways.
For example, E. Coli O157:H7 produces Shiga toxin and there are immunoassays to test for the presence of the toxin in feces (1). Only low amounts of the toxin is needed to cause disease. Antibodies against the toxin have been seen in individuals with the disease, suggesting the toxin is not a strong enough challenge for an immune response Discussion of (2).
You could go case-by-case for each of the immunoassays and see why their targets are difficult to turn into therapeutics.

Can you add sources to the first part of your answer?

Are all serological tests using antibodies as a basis for detection of a systemic infection inherently flawed?

No
Every diagnostic test must be interpreted in the context of the clinical features of an individual and according to the data about that particular test. Tests of serum for antibodies are no different. See Cecil Medicine Chapters 8 and 9 for a discussion of this. A key passage:

Most tests do not provide a definitive answer about diagnosis or prognosis, but instead reduce uncertainty

Except in cases of passive immunization (e.g., transfused IVIG), the presence of a specific antibody in a serum sample indicates both exposure to an antigen and an immune response. What exactly this means depends on the individual and the test. Though not generally the test of choice for diagnosing active or chronic infection, some antibody tests are excellent indicators of infection in many individuals. A good example would be antibody to HIV.
As with any diagnostic test (again, see Cecil), antibody to HIV was evaluated relative to a standard, giving us a sensitivity (how good the test is at finding disease when it is present) and specificity (how good the test is at excluding disease when it is not present). It's not perfect (I've seen one false positive in my career), and it is not useful in the first few weeks after exposure, but, in general, it is an excellent diagnostic test.
Antibody tests are used for many other things, and again, as with any diagnostic test, they are evaluated for that purpose. Sticking with the use of these tests in infectious diseases, Hepatitis B antibody tests are an interesting example, since antibody to different antigens mean different things. Surface antibody, for example, indicates immunity either from exposure and clearance or from immunization. Core antibody indicates exposure to the virus itself, since core antigen is not present in the vaccine. As with most antibody tests, the antibody class can also give you useful information. IgM antibodies typically represent the initial immune response, where IgG antibodies represent a later response, and either clearance or chronic infection.

Are all serological tests using antibodies as a basis for detection of a systemic infection inherently flawed?

You're thinking theoretically. Serological assays aren't theoretical, they're empirical.
When any assay is being characterized, it will be correlated with a particular outcome. Serological assays are no different. So long as there's a strong correlation with the targeted phenomenon, it doesn't matter if they're theoretically "flawed" (whatever that means); if they tell you what you need to know, then they're functional.
If every time a serological assay reads 40 or higher, an individual can be shown to be infected and every time it's less than 40 the individual isn't protected, then it doesn't matter what theoretical problems there might be with the assay, it can be used to predict infection. For that matter, if every time a ceramic saint wept salt tears it correlated with infection, then the saint test would be perfectly valid in the clinic, no matter how flawed the theory is.
How do you correlate your assay to the presence of infection, or whatever? Typically there are gold-standard tests that are perhaps too time-consuming, or difficult, or expensive to routinely run, and the serological assay will be cross-referenced to that for validation, and then hopefully approved by whatever regulatory body is in charge (in the US, often the FDA).
Don't confuse theoretical reasons with practical considerations.

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Could we eradicate mosquitoes?
Researchers have proposed the application of CRISPR/Cas9 and gene drive to genetically alter wild mosquito populations such that they don't transmit malaria. The government of New Zealand has announced a program to eliminate several invasive mammals from that island, also using gene drive (among other things).
Could we use this technology to completely eradicate from the world all species of mosquito that prey on humans? Also, could we accurately predict the extent of the resulting ecological disruption so we could decide if it was worth it?

"Primarily opinion-based"?

Could we use this technology to completely eradicate from the world
  all species of mosquito that prey on humans?

Yes, implemented correctly, a gene drive has this capability.

Also, could we accurately predict the extent of the resulting
  ecological disruption so we could decide if it was worth it?

The current scientific and political consensus is that, no, we can't predict the potential consequences with high enough confidence to move forward with such a large-scale manuever.
One of the leading scientists studying and improving gene drives, Kevin Esvelt at the MIT Media Lab, instead supports a "daisy chain gene drive" which is pre-programmed to weaken with each successive generation, allowing humans to effectively control the spread of gene drives to a specific geographic area and time frame.


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Fraction of naive T-cells in CD4+ T-cells isolated from whole blood?
Many papers isolate CD4+ T-cells from whole blood.
I am wondering approximately what proportion of naive T-cells there will be from such a sample? Are these predominately naive T-cells or are there more memory and effector cells?

are you looking for absolute numbers or relative amounts?

I updated the question. I just want a ballpark estimate. I do not have a biology background :)

Stemcell Technologies has a really good wall poster for this. You can enumerate roughly 80,000 to 760,000 naive CD4+ T cells from peripheral blood per mL. This is 1-10% of leukocytes.
One of the things you need to remember about memory cells is that they do circulate, but it follows that among the circulating subsets of memory cells, they highly express markers for lymph node localization such as CCR7 and CD62L. Their presence in the blood at a given time is influenced by a number of factors including disease state.
Likewise, effector cells are programmed to localize within infected or distressed tissues through the actions of chemokines and chemokine receptors. The presence of effectors will depend on the same sort of factors, and as effector T cells, they are typically either made anergic and die by apoptosis or differentiated into memory cells.


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What is the name of this plant I found in a park?
I found this on Garret Mountain in Paterson, New Jersey, USA. Does anybody know the name of this plant?

@Always_Confused For a good botanist, most species can be identified even without flowers. If this would have been a North-European species, I'd probably be able to tell you what it was.

Today i saw them also in dover, nj usa. The enviroment is swamp area. Same in paterson park. Their sizes are around 30 cm, 40cm. Actually i see them all over the new jersey. I did not realize any flower.

I think this is Lysichiton americanus,  skunk cabbage. It has these large, rolled-up leaves and grows in wet habitats as you describe. In Europe, it is an invasive species, but in America it is native. I am not 100% sure, because I don't know if there are any similar species in the US.
EDIT
As Anongoodnurse pointed out, I was right to be unsure. This is Eastern skunk cabbage, Symplocarpus foetides. This species occurs in the Eastern parts of the USA.

I found that also they call skunk cabbage.


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Do mutations in one bacterial strain have the same effect in other strains within the same species?
I would assume so, since they are the same species after all. I am asking this because I am doing a bioinformatics project for school and I cannot find any protein mutations for the specific bacterial strains that my department has managed to isolate. The proteins I have identified as stress proteins are within their genomes, but there is no known mutations I have found while perusing the literature. Mutations for these proteins are present in other strains though. Any help would be greatly appreciated.

Different strains of the same species have differents genotypes (ie different alleles and therefore express different proteins).So if your protein A in strain 1 has some effect, it could have the same effect in strain 2, but not necessarily.
Indeed lets imagine that protein A interact with protein B in strain 1 to produce an effect. If protein B is absent in strain 2, or different, protein A will have no effect. My point is if you have a mutation in one strain, the same mutation would not necessarily have the same effect (although it is very likely) in an another strain beacause both strain don't express the same proteome.

Hi welcome to Bio.SE! We ask that answers be well supported and/or cited in order to improve the quality of our answers in this community. Please provide support/references for your answer.

Hi. Sorry, I did not know that. I'm afraid I have no english reference to cite. It is just basic population genetics : in a population the individuals are not clones but show genetic diversity.

If you provide sources, it will probably be reasonably simply to find English translations, so don't worry about that :)


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Material(s) That Tissue Can Grow Into And/Or Not Be Rejected?
I once watched a special on Dr. Roger Leir, a doctor made famous for removing supposed ET implants. Whether they were as such or not isn't important for this question. What is important is that he documented the removal of several devices that were at least partially made of material that tissue would somewhat grow into so that the body wouldn't reject it.
The question is: what, if any, such materials exist? Of course what the body won't reject and what it will grow into are two different things. I'm interested in both. It would also be helpful to know where people tend to discuss this and what companies are working on it. This is a question of biology and material science.
When I think of materials that won't be rejected, the only thing that comes to mind are materials made out of tissues themselves (like cat guts). Of course, we have things like pacemakers and all manner of implants but I don't know to what degree the body accepts them. Keep in mind that devices wouldn't have to be made entirely of such materials, just the outer shells of them.

You might be interested in the emerging science of tissue engineering, including "growing" organs on a scaffold, either artificial or biological in origin. Simpler transplants have already been successful.


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How does formaldehyde/PBS or methanol fixation of cells affect lysosomal pH?
The question is fairly simple - does formaldehyde or methanol fixation in preparation for immunocytochemistry/immunofluorescent staining affect the pH of the lysosomes?
Some background: I'm trying to look at the intracellular trafficking of a fluorescently-labeled lysosomal enzyme. Cells are grown in vitro and treated with the labeled protein, which is taken up into the cells via receptor-mediated endocytosis. The protein-receptor complex targets the late endosome-lysosome pathway, where eventually the acidic pH of the lysosome causes the two to dissociate and the receptor to recycle, while the enzyme stays and does its thing. I've labeled the enzyme with two different dyes - Alexa Fluor 488, which is supposedly pH-insensitive between 4 and 10, and pHrodo Red, which has greatly-increased fluorescence as the pH drops. Alexa488 is the brightest of the Alexa dyes, and is widely used in all sorts of applications. pHrodo is not as bright (as far as I can tell, it's been difficult to find comparisons), but its pH-dependence helps lower the effect of non-specific extracellular binding, and it seems to work in my system so far.
So what's the problem? I'm developing an assay that will measure the ability of certain substances to block the uptake of this enzyme into the cell. Since I'll be measuring a lack of signal, the higher I can get the uninhibited signal to be, the better. Like I said, pHrodo works OK, but it could be better. The problem is that my Alexa-labeled protein has an extremely low signal to noise ratio, when I would have expected the exact opposite. I'm wondering if, in my system, the Alexa dye really is somewhat pH-sensitive, and is not fluorescing as well when in the acidic lysosome. I'm encountering a few other issues as well, and while before I was performing live-cell imaging, I'm starting to toy with the idea of fixing the cells first, as that will positively impact some other things I want to try.
Hence my question: Will fixing the cells with 4% formaldehyde in PBS (standard ICC/IF protocol) affect the pH of the lysosomes? Would methanol fixation do the same thing? Any other suggestions for increasing signal?

i don't have a definitive answer.. fixation can also affect the dyes.. formaldehyde can react with the fluorophore and make it insensitive. pH should change on fixation because it dehydrates the sample.

Yes, they will both affect pH.
In addition to the above comment, both, but methanol especially dehydrates samples - removal of water will most definitely affect the pH in organelles. This will be time dependent. Both duration of fixation, and time after fixation before you assess the cells will affect the pH of the organelles.
Because you fix the cells in a non-aqueous environment (I presume you're using standard fixation), you don't use buffer during fixation. We might be able to answer better if you post the general protocol you follow.

thanks for answering! I actually fix with 4% formaldehyde in PBS, so it is an aqueous environment, as I mentioned in the question.

In my opinion, cell fixation shouldn't change the pH. However unbuffered formalin will oxidize and lower the pH, but using PBS should buffer around pH 7.
Maybe Glutaraldehyde fixation would also be an option, if the others are not working...
I found this website by leica very useful, maybe it will also help you:

http://www.leicabiosystems.com/pathologyleaders/fixation-and-fixatives-2-factors-influencing-chemical-fixation-formaldehyde-and-glutaraldehyde/


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Do High Iron Stores (but within the healthy range) Make Sun Exposure Damage Worse?
Ultraviolet damage from sun exposure is related to the creation of free radicals. Iron is often involved in exacerbating damage by free radicals.
Having lower iron stores is associated with reduced risk of diabetes. Could having lower iron stores reduce UV-related damage from sun exposure?
=========================================================================
I add some references after being asked in the comments:
On iron and free radicals: Iron, Free Radicals, and Oxidative Injury
UV-light and free radicals: Ultraviolet light-induced free radical formation in skin
About high ferritin making diabetes worse:
"Compared with those in the lowest quartile, subjects with diabetes in the highest ferritin quartile were 55% (P = 0.029) more likely to have microalbuminuria."
Source
Elevated serum ferritin levels predict new-onset type 2 diabetes

Can you add some references for your claims?

Chris, I added some references in the question.

Your references seem to have nothing to do with UV related damage.


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Why sister chromatids and daughter cells but not brother chromatids and son cells?
In biology, why do we have terminologies in terms of female relatoinships such as daughter cells and sister chromatids and not in terms of male relationships. When did this custom started and is there a reason for it ?

During the days when philosophers used to debate, they tended to regard  reproduction as a feminine trait. So naturally organisms/cells capable of producing offspring are also given a feminine trait. The parent cell is often called the mother cell, and the daughter cells are so named because they eventually become mother cell themselves.
I presume there exists a similar argument for sister chromatids, in that they are identical. When they separate, they are usually termed as undivided chromosomes.

Can you back up this answer with a citation?

@MarchHo Tough to provide a scientific recommendation for this as this is common knowledge. I can link to other places on the web where they say the same thing though..https://answers.yahoo.com/question/index?qid=20070810035548AACEcrl

Abit like why we call ship and storm she. There has yet to be a storm or hurricane called Bob..

@JayCkat But there are plenty of hurricanes with male names!

hmm looks like my reference on meteorology is a bit old. Looks like the practice of naming hurricanes solely after women came to an end in 1978 when men's and women's names were included in the Eastern North Pacific storm lists. In 1979, male and female names were included in lists for the Atlantic and Gulf of Mexico. I feel old.


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Does body fat percentage effect storage of fat soluble compounds?
Would a person with a higher body fat percentage store more of a fat soluble compound, or store for a longer time, than a person with a lower body fat percentage if they both consumed the same amount in the same time frame?

Does body fat percentage effect storage of fat soluble compounds?

Generally, yes.
Phenytoin, an anti-seizure drug, provides a good and well studied example.  The key issue here is that, for phenytoin, plasma half-life is proportional to the apparent volume of distribution of the drug.
(Apparent) volume of distribution is a pharmacokinetic property of a drug. It is the volume a drug would need to be dissolved in in order to achieve the concentration of the drug in plasma. For fat soluble compounds, this can be quite large, as the drug is primarily partitioned into fatty tissues, leaving a low concentration in plasma. Empirically, phenytoin's volume of distribution is higher for more obese patients, and (by the same reference), the half-life is proportionally longer.
As is often the case, though, it depends on the drug. For some lipid soluble drugs, an increased rate of metabolism by the liver in obesity compensates for the increased volume of distribution; for others, obesity doesn't have that much of an impact on volume of distribution in the first place.


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How do our eyes see an inverted image?
How exactly do our eyes see an inverted image of what we are looking at?
Does it have something to do with the shape of our lens (i.e. convex)?

This isn't particular to eyes. Anything without mirrors would show the same behavior.


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Can oral baking soda effect tumor cells in mice
Could anyone explain me please, how exactly (according to research article in Cell journal) adding the baking soda in drinking water can influence the acidity of tumor cells? What about homeostasis and ph buffer systems?
In this article in Cell, discussed in this news source, in addition to a number of experiments with cell lines, a live mouse model with xenograft tumors was used to show the effect of oral bicarbonate on tumor acidification, and support the in vitro results re: the effect of tumor associated acidification on the circadian clock.
How is it possible that oral bicarbonate could make tumors in these mice less acidic? Wouldn't the physiological buffer system prevent any changes to the pH in tissues?

its Ludwig Institute for Cancer Research, they like baking soda stuff)
full name of article is "Acid Suspends the Circadian Clock in Hypoxia through Inhibition of mTOR"

Welcome to SE Biology. This is a question and answer site that is self-contained. The questions should be complete and comprehensible without reference to external sourses. Your question refers to an article in a journal, and its title presuposes a knowledge of some previous controversy with which you are engaged. I appreciate your feelings, but this is not the forum on which to express them.

@David I read the post script as context for why the OP was asking, possibly defending against a potential accusation that this is a personal medical question. The question itself seems to be on topic, since it's about the impact of oral bicarbonate on acid base homeostasis. Maybe it would be helpful to edit out that paragraph...?

It would really help if you had links to the exact studies you are talking about.  Links to articles talking about the studies are not what's needed.    The 2018 Cell paper is not about mice getting drinking water, but cell lines.  So what paper are you talking about that has mice drinking water?

@swbarnes2 it uses both cell lines and a live mouse model (with SCID mice). Look at figure 7K: Immunohistochemical pS6 staining of HCT116 xenograft tumors hosted by mice drinking tap water or 200 mM sodium bicarbonate ad libitum throughout tumor hosting (up to 3 weeks).

Okay, they do mention that, but they got the samples from another lab?  A link to the original paper there would say much more about the "drinking water changes the tumor" angle than this one.  And on an unrelated note, the use of FPKM in the RNA-seq is painful.  It's been deprecated for years.

@swbarnes2 the effect is well established and has been used in this mouse model for nearly 20 years. See my answer :)

OP, I've edited your question to try to make it the biology question more obvious (as well as its relationship to the study that prompted it. If you don't agree with the edit, feel free to roll it back!

@swbarnes2 I'd say that the "oral bicarbonate increases sensitivity to rapamycin" angle here is NOT what got this article a spot in Cell. It's the mechanism for the abolishment of the circadian clock. Baking soda cleans cancer is a more compelling (and misleading) news bite, though.

@DeNovo — Then I suggest you edit the post radically to fit your interpretation of the question. At the moment the question is unacceptable in my opinion. If you don't, then I have no qualms about doing it for you.

@David and OP I made one more edit, which I believe makes clear the question and keeps it clearly on topic. OP, if you don't like this (or any edit) feel free to roll back.

@DeNovo — That's fine. Makes your excellent answer worthwhile.

What can oral baking soda do?
If your question is (which I don't think it is):

Does baking soda cure cancer?

The answer is that there is no support for that statement.
If your question is:

Can oral bicarbonate alter the pH of tumors in a mouse model?

The answer is yes.
This effect has been observed in this mouse model and replicated many times
This is an effect that has a been used for a while, and was first demonstrated in this 1999 article in the British Journal of Cancer.  The addition of bicarbonate increases the buffering capacity in the live animal model, preventing the acidification of the tumor. It does not increase the pH of other tissues.
How does this work?
The idea here is not that adding a base increases blood or tissue pH directly, but it increases the amount of a physiologic buffer in a situation where that buffer has been depleted or is insufficient, allowing a better response to a pathologic excess of acid. Your question suggests you believe that an oral acid or base load will not change the pH of body tissues. This is true in normal physiology because there is a robust system of buffers. The primary extracellular buffer actually is bicarbonate. However, in diseased states, the buffer may become depleted or be insufficient. Oral (as well as intravenous) bicarbonate therapy is used in humans in several disease states, including certain forms of metabolic acidosis (Cecil Medicine, Ch 63, 120) and kidney disease (Ch 124, 128, 132). What is happening in these cases, and in the mouse model, is not a change in pH from the normal set point, but an increase in buffering capacity that allows the pH to return to the normal set point.
I would caution, though, that just because oral treatment is used in certain specific forms of acid base pathology, however, does not mean that there is support for the various forms of quackery that use arguments about flushing acids from your body, or using alkaline water as a general health tonic. It does address the question about whether it is very strange that orally administered buffer would impact a tissue with excess acid. It's not (strange).
The effect of changing the pH in the tumor microenvironment
The effect in the study behind the article you referenced, as well as others, is an increased sensitivity to cancer chemotherapy in otherwise resistant tumors. This is not horribly surprising, and doesn't mean by any stretch that baking soda cures cancer or that, e.g., an acidic diet causes cancer.  Other studies, including this one (also in this very particular mouse model), show decreased invasion and metastases, also presumably because of the increased buffering capacity (and decreased acidifcation of the tumor and tumor microenvironments), so there may be other possible effects.
There has been a good deal of interest since 1999 in human studies adding bicarbonate to other treatments, but none have been published that I'm aware of, though I haven't checked the clinical trial registry.
EDIT:
On checking the clinical trial registry, on first glance it looks like some safety and tolerability studies have been completed, but it would take a fair amount to do a full analysis of what has been done and what hasn't. Maybe someone else wants to do it and include it in an answer? I'm fairly certain I would have seen and remembered an article showing that bicarbonate cures cancer in humans, though, so I don't think that's on the list :)

I added some edits here to be clear that baking soda is not a miracle cure. An unsuccessful google news search looking for news reports of the 1999 study reminded me that there is an entire subsection of quackery built around faulty reasoning about acid-base balance.

Although i'm a girl, i'm not so stupid to read tabloids or believe in quasi-science. The problem was i had no answer for people who believe in soda miracle, because they literally put this article to my face, with a spoon of soda. My question was not about "cure cancer by soda", it was about mechanism of influencing of baking soda taking peroral to tumor's acidity, i just couldnt understand how it works on the biochemical level. Thank you for the answer, i will read articles deliberately.

Hi @DariaMorozov. I didn't mean to imply you believed in the quackery. That seemed clear from the way you phrased your question. I just wanted to make sure my answer wouldn't be misinterpreted by others as evidence for a baking soda cure.


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Is there any advantage of having mitochondria for aerobic respiration?
If we consider the pathway of breakdown of glucose which includes glycolysis, the citric acid cycle and the electron transport chain, all these processes takes place in some  prokaryotes and eukaryotes. In prokaryotes all these processes take place in cytoplasm while in eukaryotes the last two processes take place in mitochondria.
So is there any advantage of performing the last two processes in the mitochondria? Does it yield more energy? If there is no advantage, what is the point of having a mitochondria (at least for this process)?

From the evolutionary point of view, the eukaryotes acquired these metabolisms (except glycolysis) from their prokaryotic endosymbionts. Not all prokaryotes have the ETC. The free living ancestor of mitohondria is supposed to be the alpha-proteobacterium.
Now, glycolysis is a common pathway in lot of lifeforms perhaps because of abundance of glucose. TCA cycle is coupled with ETC at certain steps which makes it essentially a part of aerobic metabolism.
The reason for having a dedicated organelle for respiration
ATP synthesis is a membrane process. Imagine a large prokaryotic cell- as big as an animal cell. Such a cell cannot take care of its energetic demands which primarily consists of protein synthesis with the given area of membrane i.e it needs much more ATP-synthases than it can have to cope up with the energy demands of maintaining such a huge cell (this index is approximated based on surface to volume ratio). Therefore it is wise to harbor multiple efficient organelles i.e. mitochondria which themselves have just a small essential genome and proteome to maintain.
For a better understanding, please read this article. I just loved it.
There is also a book by the same author about mitochondria called Power, Sex, Suicide.


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How did the genetic code evolve?
The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is coded by 6 codons, tryptophan is coded only by one codon.
[I am aware that the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last base that does not affect the amino-acid that is encoded.]
I therefore do not think that the genetic code can be entirely be explained by “it happened to occur that way the first time” (at the origin of life or in the last universal common ancestor) “and it never changed”.
So, my questions are:

Why are some amino acids coded by a several codons while others are coded only by one or two?
Specifically, why is methionine coded by only one codon — AUG — which has also to serve as a start signal?
In general, how (by what mechanisms, selective pressures) has the genetic code evolved to give this pattern of redundancies?

This is an area of ongoing research, and I don't think you'll get a great answer. There are some ideas about the early evolution of the code, and there is some variation among extant life, but it is hard to say how it evolves because it evolves so rarely.

This question (actually two questions) allows only speculative answers, and is not likely to find one here, given the complexity of any serious argument. However it has been popular and so there is little point in suggesting it be closed. Instead I have tidied it up and tightened it up, without changing the essential question(s).

This question is closely related, and the fascinating link posted by @JohnSmith is a good read.
In short, with a four-base system, and a codon size of 1, you get four possible amino acids.  Silly system.  A codon size of 2 gives 16.  Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids.  Codons of size 3 gives 64 - plenty of room to work with and it covers all your forseeable amino acids, and then some, without being too wasteful.
The redundancy, known as degeneracy, is pretty straightforward.  There's room to expand, and any redundancy/degeneracy will only reduce the likelihood of errors.  That's a huge benefit.  For some amino acids, the first two bases are enough.  That third position can be quite tolerant to mutation, which is very beneficial to organisms.  It appears to be even more fine-tuned, to the degree that redundancy often not only reduces the likelihood of mutation but also reduces the damage caused when a base does mutate.  Swapping a hydrophobic AA for another hydrophobic one is less likely to cause aberrant protein function, and anything with a U in the middle is probably hydrophobic.  Convenient!  I'll also note that, while it's not perfect or even a significant correlation, the more popular amino acids tend to get more redundancy; tryptophan is traditionally the least common AA.
Finally, there are a few non-proteinogenic amino acids, so, as the linked question/answer above points out, maybe in the future there will be more amino acids.

This fails to answer any of the three questions posed.

It seems that duplicate codons make translation more robust and resistant to translational misreading. There are four theories that explain existence of duplicate codons:

Stereochemical theory
Coevolution theory
Error minimization theory
Frozen accident hypothesis

They are not mutually exclusive and “Origin and evolution of the genetic code: the universal enigma” paper attempts to reconcile them:

Mathematical analysis of the structure and possible evolutionary
  trajectories of the code shows that it is highly robust to
  translational misreading but there are numerous more robust codes, so
  the standard code potentially could evolve from a random code via a
  short sequence of codon series reassignments. Thus, much of the
  evolution that led to the standard code could be a combination of
  frozen accident with selection for error minimization although
  contributions from coevolution of the code with metabolic pathways and
  weak affinities between amino acids and nucleotide triplets cannot be
  ruled out. However, such scenarios for the code evolution are based on
  formal schemes whose relevance to the actual primordial evolution is
  uncertain. A real understanding of the code origin and evolution is
  likely to be attainable only in conjunction with a credible scenario
  for the evolution of the coding principle itself and the translation
  system.

From my understanding the idea is that codons are grouped by selection for physico-chemical properties of corresponding amino-acids so a random one nucleotide mutation wouldn't change properties or a corresponding amino-acids too dramatic.

Some elements of response to your question.
First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on minor tRNA (while the ribosome waits for the proper tRNA). This may have very important impact on the folding of proteins (see for instance this paper: http://dx.doi.org/10.1371/journal.pone.0002189). Having several codons for common amino-acids may actually be a powerful fine-tuning too for the folding of proteins.
Second, as in some cases (splicing, selenocysteine insertion, what else ?), the secondary structure of the mRNA produced is extremely important, the organisms must be able to tweak the sequence of RNA to leave room for that to happen, and that can only happen if there are lots of amino acids for which there is latitude to tweak the produced mRNA sequence.
Third, it is false that the genetic code is universal. There are some evolutions of the genetic code, see for instance the specific case of methionine in mitochondria: http://dx.doi.org/10.1073/pnas.0802779105.

This fails to answer any of the three questions posed.


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How does the body detect irreversible binding to receptors?
I have read an article on Wikipedia about irreversible agonists and antagonists. These permanently bind to a target receptor on a cell. However, the receptor protein is then internalized and recycled by the body after the binding occurs. How does the body detect when a protein has been irreversibly bound in such a way? Is there some pathway involved in that or are proteins simply regularly recycled by the body?
Article: https://en.wikipedia.org/wiki/Irreversible_antagonist

I've edited your question to, I think, clarify what you meant by "damaged". Usually, "damaged" proteins refers to, e.g., oxidative damage, or some change other than that of a ligand binding (even if irreversibly), and "how does the body detect damaged proteins" is, i think, a different question from the one you are asking.

The process of downregulating a receptor by internalizing and degrading it in response to (sometimes prolonged) activation or (sometimes prolonged) failure to activate is what pharmacologists call desensitization (in either context). You can read about this generally in Goodman and Gilman's Pharmacological Basis of Therapeutics, Chapter 3, under the subsection "Receptor Desensitization and Regulation of Receptors". There are a number of mechanisms, not all well understood, but the basic idea is that when a signal is constant (either always on or always off), it no longer has any value as a way of providing information. Receptor regulation, or desensitization, is a mechanism for, effectively, resetting the cell or tissue. Removal of the receptor can be followed by recycling, or protein synthesis and return of new receptor to the site.
One well studied mechanism for desensitization is seen in G protein coupled receptors (GPCRs), such as some Dopamine receptors. It is well reviewed here.
To answer your specific question, binding that leads to desensitization is detected the same way any other binding is detected. A receptor produces a signal on binding (or stops producing a signal). The downstream effect of that signal includes a process that involves internalization of the receptor from a location where it can receive signal.
Here that process is mediated by phosphorylation by GRKs (GPCR kinases), which allows for binding of arrestin, and so on...

It would be great if you can provide some information on whether this feedback is thresholded (like sigmoidal kinetics or similar dynamics).

@WYSIWYG i don't happen to know the dose response relationship here. I'd welcome an answer that adds this information.


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research on brain-eating amoeba
Are there any alternative treatments for brain-eating amoeba?
I've spent about 6 hours trying to find information about this and haven't had any success.

Sorry, this is a science list. We don't do "alternative medicine", nor can we recommend research projects to students. This is a site for questions about biological processes.

I'm voting to close this question as off-topic because it is asking for recommendations for research topics, and not about biology.

This is off-topic indeed but to foster interest, intravenous amphotericin B and rifampicin was used with varying success. Miltefosine has shown efficacy. In almost all cases the infections are fatal without intervention or luck, however.

Naegleria fowleri & other protozoa like Acanthamoeba castellani are sometimes referred to as "brain-eating" amoebas. The latter due to the severity of the disease they can cause and the remarkable inefficiency of the treatments administered at the moment of diagnosis. If you wanna know more about this I would suggest reading this paper
https://aac.asm.org/content/aac/59/11/6677.full.pdf
Although if you are a beginner in the field of microbiology you will probably have trouble understanding a paper like that. If this is the case I would suggest reading the introductory chapters of a general medical microbiology book first. The one I started with was Murray's Medical Microbiology from elsevier saunders; I know there is a spanish edition (which is what I read) as well if you happen to prefer that instead of english.


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How do we know the brain flips images projected on the retina back around?
Why do we turn images upside down again rather than dealing with them directly, still vertically rotated after passing through our lens?
I don't see how that would cause any problems, and how we'd ever be able to figure out if we are presented with flipped images after getting used to interacting based on visual input, whether flipped or not.
What am I missing?

My head of Biology has regularly mentioned an experiment where individuals were given glasses that inverted their vision - after a period of time their brain compensated and re-inverted the image (presumably the same happened when the glasses were removed).  Interesting stuff - I'll see if I can find a link.

That'd be appreciated :).

So, what is the exact question you are asking? The title asks something different from the question's body...

The body merely adds the 'why' aspect, the question as stated in the title is also in there: 'I don't see (...) and how we'd ever be able to figure out if...' - Both are interesting and very much related.

@Chris Some preliminary experiments on vision without inversion of the retinal image - the original article from 1896.  More recently (and for me disappointingly :L) a lot of doubt has been put onto the thought that the field of vision was corrected - people were still very much aware that the image was inverted even if they could deal with it The myth of upright vision. A psychophysical and functional imaging study of adaptation to inverting spectacles

Thank you for your efforts. This article seems to point out we can function normally despite inverted vision, i.e. without (the return of) upright vision. So as stated in my first post, why bother with flipping images after the retina if we can deal with the input either way? And how do we know we do?

Closely related question on CogSci.SE

The question assumes there is something like a little projection screen inside the brain -- something that has an "up" and a "down".  It's not like that; there are just an array of retinal cells transmitting pulses to a set of neurons.  Retinal cell A talks to neuron 1, cell B to neuron 2, etc.  neurons 1 and 2 are not physically arranged in space in a way that matters to image perception.  There is no little man in there watching a little screen.  See the CogSci question that jonsca linked to.

@mgkrebbs: the retinotopic mapping of images in the visual cortex is very precise. There is no projection screen in the brain but the image is processed in a very precise spatial manner.

@nico: Of course the neurons maintain precise connection relationships with neurons carrying signals from spatially adjacent areas of the retina. Nevertheless, there is nothing about the arrangement that makes it "upside down" and thus requires further processing to "flip" it.

@mgkrebbs: OK, we agree. I just misunderstood your previous comment :).

The basis of this question is a common misconception, and unfortunately the accepted answer by @CHM is also based on this common misconception. The misconception is based on the homunculus falacy: the tendency for people to think that the image that lands on the retina is somehow 'assembled' and presented for something (the 'consciousness') to view. This is not the case.
As the comment by @mgkrebbs explains, there is no orientation (up or down) in the brain, there is only neural firing. The information of the visual scene is distributed over the brain, and information does not have physical properties like orientation. Although as @nico pointed out the neurons that process the information do have a spatial structure that mimics that of the retina, this is a topological property (i.e. stimuli that are close on the retina are processes by neurons that are close in V1) and such a topological property does not induce an orientation.
The root of the problem is really that the question "How do we know the brain flips images projected on the retina back around?" is a pseudo-question. Although it is grammatically well-formed, it makes no semantic sense. When the image is 'in the' (i.e. being processed by the) brain it no longer has physical properties like orientation. Thus you cannot ask if it has been flipped or not.

So is the retinotopic arrangement inverse top-to-bottom of the input from the retina? In that case it's still a valid question why the pathways from one half would at some point cross over with those from the other half and not just stay on the side they are.

@Armatus: that is a different question from the "upside down" problem though (which, by the way, on the retina is a purely physical issue do the lens that turns the image upside-down).

@Armatus The cross-over is a good question, and you should ask it on CogSci.SE. However, I feel that the question (and the accepted 'answer') was instead about the lenses vertical and the common misconception of orientation of images in the brain, not about why we have opposite hemispheric mapping..

You can talk about a perceived image without invoking the homunculus fallacy. The brain certainly re-orients (or perhaps orients) the image that is projected on the retina, but it is a complex integration of retinal and extra-retinal stimuli. See my answer.

I think you're oversimplifying the problem. Think about gravitation.
Take this informal example: at any point on a massive sphere, you can define "bottom" such that any massive object with weight less than that of the sphere is subject to an attractive force towards that point. The direction of the force points in the direction of the "bottom".
Assuming this holds true for every massive object, the following is logical: for the purpose of orientation, it is a lot more energy efficient for an organism to simply invert the image using brain circuitry than invert every single sensory input to effectively reverse the definition of "bottom", which follows from physical laws to which the organism is invariably bound.

My answer was initially posted in response to this duplicate question. Since this post was made earlier, the question I answered will likely be closed as a duplicate. I think my answer has something useful to add, so I've added it here, with a little more discussion in response to the other answers:

How do we know the brain flips images projected on the retina back around?

You examine your own visual sense and, possibly, if you're examining patients on a neurology ward, examine theirs as well. Here @CHM's answer is on point, as our sense of gravity (through the vestibular system) is one of the senses integrated into our ability to visually perceive up as up and down as down. It also reflects the confusion expressed by a particular patient with Reversal of Vision Metamorphopsia (see below) when an upside down cup of tea didn't spill out. This doesn't require anyone to invoke a little man watching a video projected somewhere in the occipital lobe. You just ask yourself (and the stroke patient) to describe the world around them. If it's upside down, if people seem to be standing on their heads, you present them with a series of letters with a different orientation and ask them to identify the normal (right side up) letters.
Here is the bulk of my answer to the earlier question, which describes the various inputs the brain integrates in order to produce a visual perception of a right side up (and left-side left) world.
Your retina is presented with an inverted image, but a healthy brain  (re)orients the image. I would note that you can talk about the image an individual perceives without invoking a video playing in the brain.
The spatial orientation of a perceived image is a complex process that seems to involve integration of information about the relative position of objects from the light perceived by the retina, about the position of the eyes from the muscles of the eyes, and about the position of the head from the vestibular system and muscles of the neck. It may or may not involve other body position information from the cerebellum and proprioceptive cortex.
As with much of our knowledge about the localization of function in the human brain, the evidence for the importance of these various streams of information comes from cases with lesions at a number of different locations that produce brief disruption of the integration of this information, a syndrome called Reversal of Vision Metamorphopsia.
For one patient:

He saw people walking on their heads, and the floor next to his bed appeared to be over his head

For another:

People were seen walking on their heads, the windows close to the ceiling were within reach of his hands, and a cup stood "upside down" on the shelf but the "tea did not spill out" (all the objects including the shelf were upside down).

Typically this (Reversal of Vision Metamorphopsia) is the perception of a completely inverted image as in C above (left becomes right, up becomes down), but other reversals have been reported (A, D, and E above).


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Why do neutrophils need to die after pathogen phagocytosis?
From referenced article below, neutrophils need to be removed because its granule contents and oxygen metabolites (used for killing phagocytosed pathogen) are harmful to the surrounding tissue. Thus, the process used for this is that neutrophils undergo apoptosis, then are phagocytosed by macrophages.
However, I do not see why neutrophils need to first die to be phagocytosed by macrophages. Do macrophages not phagocytose living cells?
Source: http://www.sciencebrainwaves.com/the-immune-cell-the-neutrophil-the-good-the-bad-or-the-ugly/

Once the pathogens have been dealt with, and to completely resolve inflammation, neutrophils need to be cleared from the tissue... For removal, neutrophils firstly need to die.

Macrophages can certainly phagocytose living cells, as you can read in Sompayrac's "How the Immune System Works", Chapter 1 and 2, but they do need an "eat me" signal of some kind in order to do it. For a bacterium that might be lipopolysaccharide and mannose. For endogenous cells, there is a balance of "eat me" and "don't eat me" signals. Apoptosis, in addition to neatly packaging up potentially toxic intracellular components, involves downregulating the don't eat me signals and upregulating the eat me signals. Macrophages can phagocytose live cells that seem to have some sort of problem (for example, tumor cells), but they are much more efficient at phagocytosing apoptotic cells.
As far as why the neutrophil has to die, in addition to making them more efficient targets for phagocytosis, they die pretty quickly anyway. There is some debate about the exact length of their life span, but from the time they're released by the bone marrow, the average circulating life span is probably less than 24 hours, regardless of whether they exit the blood stream as part of an inflammatory process or not. The exact function of this short lifespan is the source of some speculation, but we do know that, after being recruited in the inflammatory response, apoptotic neutrophils help suppress that inflammation, playing an important role in regulating the processes that sent them out into the tissue in the first place.
Sompayrac's book is a good overview, but if you want to read the gory details this is a good review.


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What is a "mechanistic study"?
I believe a "mechanistic study" means a study where a medicinal product is being used but the purpose of the study is to investigate the patient or disease, not the medicinal product.
How does this differ from any other type of study?  What is the purpose of this study?  Why would we not be interested in the medicinal product?
Please provide a very simple example that a non-scientist could understand.

A mechanistic study aims to uncover a mechanism. It can be a mechanism of the disease (exactly how does the disease do damage to the body), or a mechanism of a drug (exactly how does the drug prevent or repair the damage) that is being investigated.
Understanding mechanism, be it mechanism of disease or mechanism of the drug, is very important toward targeted improvements of treatments, as opposed to trying lots and lots of compounds, hoping that someday we'll find one that's better.
Non-mechanistic studies involving drugs aim to show that the drug provides a clinically relevant health benefit over competing treatments, or to determine the safe dosage of a drug. At that point, the mechanism of action of a drug is known to a reasonably large extent.
In short, there are many different things that need to be known for drugs to reach the market. Mechanism is one of them.

"There are many different things that need to be known for drugs for each the market. Mechanism is one of them." This is incorrect according to the regulatory authorities I'm familiar with. The standard is safe and effective. Many drugs have been approved before we understood anything about their mechanism of action (e.g., Lithium). Some we still don't understand much about (e.g., Levetiracetam).


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Is it possible to make a contagious cure to a virus?
In a TV series I've been watching The Last Ship, - spoiler alert - a scientist develops a cure for himself for a virus, but actually continues to remain a carrier, and sort of weaponizes the virus accidentally, killing 3 billion people. In response, another scientist develops a cure for that virus, a vaccine, and eventually makes that contagious by close contact as well, based on data gathered from the lungs of the scientist that infected/vaccinated himself with the weaponized version.
The science behind this might be totally ridiculous, or potentially realistic / possible I don't know. Is this possible? Can a vaccine / cure to a virus be engineered into a contagious version, to cure everyone in a chain reaction?

Cure or prevention? There are several vaccines that can and do spread, such as the smallpox vaccine (vaccinia)

Arrived at this question looking for the same thing, though from a different TV show - Doctor Who, S02E01, New Earth, in which the doctor cures thousands of infected humans by disinfecting a few, and getting those few    to pass the "cure" on. The way it was actually done was ridiculously unrealistic, but raised an interesting question for me.

There's also this, very directly related to your question: https://www.geneticliteracyproject.org/2015/10/19/tnts-the-last-ship-shadows-ebolavirus-crisis-how-realistic-is-a-contagious-vaccine/

Fun question!
I think that to make a transmissable ("contagious") antiviral vector, you would need to design a virus that can infect people and that codes for something like an antiviral drug compound, which targets specific viral proteins.
As easy as that was to write down in one sentence, I think that execution would be extremely challenging.
Making the anti-virus out of another virus seems necessary to me, as there is little alternative. You would need something capable of efficiently spreading from host to host, that can generate many copies of its therapeutic payload and that is relatively simple to engineer. A virus is the only thing that I can think of that fits the bill.
You could theoretically engineer an antiviral virus that is mostly non-pathogenic to other people, although this wouldn't be perfect. Even if it didn't code for specifically pathogenic proteins, it is a foreign molecule that is likely to raise an immune response, risks integrating into an important location in the host genome and would divert cellular energy to production of its proteins and away from other cellular processes.
Say that you get this to work, that it's minimally harmful to its host and can effectively target the more pathogenic virus, against which you've designed it. What happens when the job is done? Is it still in the host body, pumping out more copies of itself and/or its antiviral proteins? If so, then it could end up causing more damage to the host in the long run, as it uses host resources to fill cells with no-longer-helpful foreign molecules.
Given more thought or time (than I have), you could probably image more ways to tweak the design of this theoretical anti-virus, but as a brief answer, I think that the above considerations can give you a quick idea of what it would take to bring this system from the realm of science fiction to that of hard science. :-)

Can a vaccine be contagious?

Yes.
Most currently used human vaccines are not transmissible. That is to say on vaccinating one individual, the vaccine cannot infect another individual. Oral poliovirus vaccine (OPV) is an exception. OPV is a live attenuated vaccine that replicates after administration (as all live attenuated vaccines do). Unlike other live attenuated virus, the virus in OPV sheds in substantial amounts and can be transmitted from person to person. Transmission is, as with other enteroviruses, fecal-oral, via contaminated food and water, hands or fomites (see Murray Medical Microbiology, Ch 56).
Vaccine derived virus can circulate in communities for some time. This is, in some ways beneficial, because it allows for more broad vaccine coverage and improves herd immunity, but can cause problems. Vaccine derived poliovirus can revert to what we call neurovirulent poliovirus, causing what we call Vaccine Associated Paralytic Poliomyelitis. In the US, we use a formaldehyde killed inactivated poliovirus vaccine (IPV) that does not replicate and is not transmissible. It is less effective at producing an immune response, but cannot cause disease. Strategies for a global move to IPV are an active area of investigation.

The original vaccine was the infectious disease cowpox, which elicts a good enough response from the immune system to smallpox that it effectively prevents the infected from getting smallpox.  It's just not particular contagious among humans.
But it might be possible to engineer a virus which has a very mild disease course, but is antigenically similar enough to something nasty that it provides protection, and is contagious.
But delivering a medical treatment without consent is ethically dodgy.

It turns out vaccinia virus is different from cowpox virus, but it is transmissible, even recently.  Good answer! I'll upvote if you add a reference.

Definitely possible, assuming you have access to sci-fi technology.
Consider a virus specifically rigged to produce epitopes (the immunizer) matching pathogenic infections. It has to survive in its host while causing negligible damage and having reasonable access to the bloodstream for immune recognition.
Next, it would have to be extremely specific to a narrow type of cell preferably exposed to the air. Immediate obvious candidate cell hosts are palatal tissue cells - exposed to the air plus reasonable bloodstream access. In this case, full upper respiratory tract is largely a non-starter since it would likely cause constant allergies similar to a rhinovirus.
Minimum damage principle: the most practical approach would be a partial lysogenic cycle where the contagious "antivirus" contents stay in host cells for a limited period of time (after which the foreign DNA/RNA is programmed to destroy itself), creating copies which grow off the surface of the host cell and shed. Preferably the contagious antiviral particles would immediately deactivate themselves on entering a host cell that happens to be strapped for resources (if the concentrations of certain needed materials are insufficient, then deactivate).


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Religion and Genetics
Are there studies that investigate the heritability of "believing in supernatural" (or related concepts)?

the perception of paranormal perception can be due to some brain development disorders. (At least I know that they arise because of lesions in certain areas). In such cases if there is a gene involved, these traits may be heritable.

sorry the perception got repeated.. another sort of impairment of brain function :P

How do you define a measurable scale for believing in supernatural things?

Oh there are some tests for self transcendence.. not for religious beliefs though..

This is an interesting idea, I'll just watch and see what happens with it!

See this related CogSci question, but the answer cites the same references as below.

There are several twin studies showing, that the tendency to be religious has a genetic component. Not which religion you choose, because that is a cultural thing, but how serious you are abot it. I am lazy for a detailed report, but this blog can lead you to the studies: http://www.scilogs.eu/en/blog/biology-of-religion/2011-03-12/religiosity-genes-again-confirmed-by-another-twin-study
Also this article: http://www.popsci.com/science/article/2013-08/what-twins-reveal-about-god-gene
EDIT after a few years - I was informed one link is broken and the other contains no citation. So I checked for new material today and wikipedia has a cool passage how genes and environment affect religion. Wikipedia saves the old version, so this is from March 8 2018, article Religiosity.
"
The contributions of genes and environment to religiosity have been quantified in studies of twins (Bouchard et al., 1999; Kirk et al., 1999) and sociological studies of welfare, availability, and legal regulations [15] (state religions, etc.).
Koenig et al. (2005) report that the contribution of genes to variation in religiosity (called heritability) increases from 12% to 44% and the contribution of shared (family) effects decreases from 56% to 18% between adolescence and adulthood.[16] "
15 Nolan, P., & Lenski, G. E. (2010). Human societies: Introduction to macrosociology. Boulder, CO: Paradigm Publisher.
16 L. B. Koenig, M. McGue, R. F. Krueger and T. J. Bouchard, Jr. (2005). Genetic and environmental influences on religiousness: findings for retrospective and current religiousness ratings. Journal of Personality, 73, 471-88
https://en.m.wikipedia.org/wiki/Religiosity#Genes_and_environment

Sadly the first link is now broken (and the second link does not contain any reference to peer-reviewed paper). This is a common issue with referring to popular science articles.

You updated your question shortly after I updated my answer. Did you feel misunderstood by my update ?


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How does GC-content evolve?
Background
GC-content refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs plus the number of AT base pairs.
$$GCcontent = \frac{N_{GC}}{N_{AT}+N_{GC}}$$
Question
How does the GC-content evolve and why does the GC-content differ between populations/species/lineages? Does it evolve under Genetic drift only? Under selection? Intuitively, I'd say that the ratio of the probabilities of mutating from A or T to G or C should be an important factor driving the evolution of the GC-content. Does it? Does the overall mutation rate influence the GC-content? What other traits/forces influence the evolution of the GC-content?

GC base pairs are more stable than AU/AT base pairs. I could imagine situations in which this plays a role, though I don't know if this is actually a relevant effect.

Yes it is probably an important factor. Note that if this difference in stability is the only thing that explain the evolution of GC-content, then I'd expect that very little variation would exist between species and the equilibrium point should be given by $$\frac{P_{CG \space |\space AT}}{P_{CG\space |\space AT}+P_{AT\space |\space CG}}$$, where $P_{CG\space |\space AT}$ is the mutation rate from $A$ or $T$ to $C$ or $G$.

I think the key work here is 'evolve'.  Overall GC/AT ratios change by mutations, whose rate is constant.  The probability that given a mutation event that one base will be substituted by another one has been modeled in several ways where the probabilities of different mutations may or may not be the same.
Overall the GC content will tend to close to 50%.  What causes GC rich genomes to become GC rich (60-70%) are that mutations to GC base pairs have selective advantages either in regions or in the genome overall that cause them to be retained. The mutation rate may be no different (or even lower) in GC rich organism (many of them are deep underground or deep underwater.  GC rich genomes occur because AT->GC mutations convey an advantage and they stick around.
The reasons that the GC content migrates away from 50% fall into two categories I will call entropic and selective.
By entropic I mean specifically that coding sequences for genes and other features such as binding sites on the DNA or other features such as centromeres, which will cause the overall ratio to vary from 1 because the sequence is constrained by the information it contains.  While coding regions have a ratio higher than 1, GC content tends to hover around 54%.  Eukaryotes have GC islands and etc, but this also does not overall change the GC content
So gene rich genomes and typical functional features of the genome do not really explain some of the spectacularly high GC contents found; up to the 70% range.  While the link above looks at GC bias in coding regions, its a given that any part of the genome that is merely a spacer between elements with specific functions will freely vary to GC if it is useful.
Selective factors for high GC content include high pressure and temperature environments for instance, which usually strongly bias to high GC content by this mechanism.  You can imagine how this works: high GC content genomes are thermodynamically more stable and can survive the extra molecular collisions of higher energy of those environments more readily.
GC rich genomes are not simple adaptations to live with.  All the genes for DNA oriented processes such as transcription, chromosome packing, DNA polymerase have to adjust a lot. As the organism adapts to hotter temperatures or higher pressures, each individual protein produced will have to also change to be stable and function in the new conditions.  As such, these changes happen only over long evolutionary times.  This is probably a good part of the reason why the archaea niches have not been superseded by eubacteria in all 1+ billion years since life has been on Earth.

Thanks for your answer. I am not sure I understand though. Let me try to rephrase differently and you'll correct me.Temperature or any factor that modifies the state_to_state specific mutation rate will modify the GC-content influence the GC-content and those factors are likely to vary from species to species explaining the differences observed.

Also the kind of sequence we consider (and the amount of DNA sequence that are of this type in a given genome) influence the GC-content. Coding sequences for example are not free to vary their information too much (usually it is only the third base pair that is free to vary). Did you say anything else? Did I understand?

I tweaked my answer. in short though, the mutation rate may be no different for these organisms, coding sequences can migrate to 70% GC.  its all selection in certain environments.  lmk if i'm making a good case here.

Everything is clear now! I got what I missunderstood ;) Thanks a lot.

Glad to hear it!  There is now a lot of research going on to identify processes which mediated and accelerate adaptation and therefore evolution.  On this level there isn't so much controversy I think...


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What is this strange-shaped fruit?

The fruit has form of a cube or icosaheder. It is green but quickly becomes black. The meat of ripe fruit is easily separated from the seed, is sweet and tastes as dried plum. The seed has strange icosahedrical form, like two pyramids connected.
The fruit is seen on Mediterranean coast of Israel.

I don't have the answer, but a warning: the flowers, to the degree I can see them, look like the family Apocynaceae -- 5 petals, tubular, twisted/overlapping petals.  Break off a leaf and see if there is white sap, another characteristic of the family.  These plants are typically very toxic, at least the sap containing parts.  However, the fruit looks pretty atypical for the Apocynaceae, and I don't know if the fruit in the family is typically toxic.  But I guess you've already done the experiment!

@Bryan Hanson: And if the OP never posts again, we can reasonably assume that it was indeed toxic :-)

You funny! Let’s hope we get a positive report!

Now I have the answer, and if you are reading this soon after eating the fruit you should probably seek medical attention.
Looks like Cascabela theviata which is in the Apocynaceae and the Wikipedia article makes clear that the fruit is also poisonous.

I did not eat it, only tried yesterday morning, I experienced no problems so far.

@Anixx that's good to hear!  I think it could have been unpleasant...

I did not swallow it, that's why possibly there are no effects. But I testify it tastes like a dried plum.


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Do endosymbiotic organelles have Latin classification?
Do endosymbiotic organelles such as chloroplasts or mitochondria have Latin classification?

You might find this article interesting Mitochondrial Evolution

As any other organelle, endosymbiotic organelles do not have a systematic name. However, their descendant prokaryotic organisms do have a genus name.


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Are there any biological obstacles prohibiting lighter-than-air organisms?
Why there are no organisms that use cavities filled with lighter-than air substances (e.g. hydrogen) to fly and remain in air?
Given that there are a lot of fish and algae that use similar cavities to float, it is surprising that no organism utilized the same mechanism to fly.

I don't know of any organism that uses cavities soley to fly; birds have air sacs to help them fly, and very light bones. https://en.wikipedia.org/wiki/Air_sacs

@Ro Siv what's the purpose of air sacs filled with normal air? It only worsens aerodynamics.

This tends to be a question like If a trait would be advantageous to an organism, why hasn't it evolved?

Because organisms would need to develop an electrolysis system or a steam refractory apparatus. Rather energy consuming. Better to flap some wings I reckon.


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Do people need nitrogen from air for health?
Can people breath totally nitrogen-free atmosphere for a long time? I know, nitrogen is essential for life, and in big quantities, but maybe people can take it entirely from food, from proteins, etc?

Some short comments - Nitrogen gas is pretty much inert and nutritional nitrogen is mainly obtained from the diet. Inhaling pure oxygen will kill you in the longer run. So what exactly is your question? If N2 gas has dietary value, or whether nitrogen-less air where ~79% of some other non-toxic gas substitutes for N2 can sustain life, or whether 100% O2 can possibly sustain life?

Do people need nitrogen from air for health?

No. This is well established!

Can people breath totally nitrogen-free atmosphere for a long time?

Yes. Also well established!

I know, nitrogen is essential for life, and in big quantities, but
maybe people can take it entirely from food, from proteins, etc?

As expounded on in the comments by AliceD, nitrogen gas (N2) is entirely taken in by humans from their diet, since atmospheric N2 is pretty inert. It is also not necessary for gas exchange to take place in the lungs.
Some extra questions as an addendum:

Can one substitute N2 in atmospheric air with another gas, and sustain human life?

Yes. All side effects would be attributable to the effects of the substituting gas (e.g. it may be heavier or lighter or equally or more reactive than N2).

Can 100% O2 sustain human life?

No, and such a case has never been recorded. Oxygen toxicity following hyperoxia is very dangerous. Ironically, too much oxygen damages lung tissue and epithelial membranes via oxidation and render the lungs unable to exchange gases correctly; and so death by suffocation follows in such extreme cases such as with 100% O2.

A pedantic point: dietary nitrogen is 'fixed' nitrogen, not N(2) which (to quote the Wikipedia article) is 'metabolically useless" to all but a few (very important) microorganisms. N(2) is, however, primarily responsible for 'the bends' (decompression sickness). (Nitrogen 'fixation' is why the Harber process is so important)

Is it known that none of the microbes in the microbiome require nitrogen in the air from inside the intestines for protein synthesis?

Do they have on ISS nitrogen-based air?

I think negative effects of oxygen come frm its partial pressure, not from its percentage. Thus, 100% oxygen at 20% atmospheric pressure should be harmless, no?

Oxygen toxicity depends on partial pressure, sure. That relates to how many O2 molecules there are. Fewer make it less toxic, no doubt. But the act of breathing in low atmospheric pressure is more difficult too, it's another problem entirely. During inhalation, lung volume increases, lung pressure decreases below that of atmospheric pressure. This draws air into the lungs. At lower atmospheric pressure, less total air is drawn in, so breathing is more difficult at lower atmospheric pressures (or at higher altitudes due to the same phenomenon). So you're describing a trade-off.


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How does sugar enter neurons if they don't use insulin?
I heard somewhere that as opposed to other cells, neurons do not use insulin to get their sugar supply.
Why is that?
What is the alternative mechanism? I assume sugar can't just enter the cell without some kind of help from a protein, is that true?

Insulin is not directly involved in sugar uptake. It accelerates sugar uptake by upregulating glucose transporters and activating glycogenesis.
Neurons have many glucose transporters including GLUT1 and GLUT3 which are responsible for glucose uptake.
Moreover, insulin being an endocrine molecule has effects throughout the body including neurons. So neurons need not secrete insulin.

It's important to have vital cells not require insulin for glucose uptake. This includes organs such as the brain or cells such as red blood cells. They get glucose by diffusion which only stops if glucose levels get ridiculously low, which is most commonly seen in a diabetic that's taken too much insulin.


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Heterozygosity under genetic drift
The wright-Fisher model of genetic drift is:
$$p_{ij} = \binom{2N}{j}\left(\frac{i}{2N}\right)^j \left(1- \frac{i}{2N}\right)^{2N-j} $$
,where $\binom{2N}{j}$ is a binomial coefficient.
From this equation one can infer that the expected heterozygostiy should decrease by $1-\frac{1}{2N}$ at each time step because:
$$E[x_{t+1}(1-x_{t+1}) \space|\space x_t] = (1-\frac{1}{2N})x_t(1-x_t)$$
I don't understand this equality. That might be very simple though! Can you help me making sense of it?
source

To derive it, first use that $E[x(1-x)]= E[x-x^2]=E[x]-E[x^2]$ and that $E[x^2]=\text{Var}[x]+E[x]^2$ to rewrite the left-hand side:
$$E\left[x_{t+1}(1-x_{t+1})\right] = E\left[x_{t+1}\right](1-E\left[x_{t+1}\right])-\text{Var}\left[x_{t+1}\right].$$
The equation for $p_{ij}$ is just saying that $2Nx_{t+1}$ is binomially distributed with $2N$ trials with success probability $x_t$, so $E[x_{t+1}]=x_t$ and $\text{Var}[x_{t+1}]=x_t(1-x_t)/(2N)$. (Note that $\text{Var}[\alpha x]=\alpha^2\text{Var}[x]$.) Plugging these values into the equation above gives the form you're looking for.

I feel close to the understanding! Can you help me understanding why $$E\left[x_{t+1}(1-x_{t+1})\right] = E\leftx_{t+1}\right-\text{Var}\left[x_{t+1}\right].$$

@Remi.b: If Var(x)= E(x(x-1)+E(x)-E(x)^2 = E(x(x-1)) + E(x)(1-E(x)) then -E(x(x-1)) = E(x(1-x))= E(x)(1-E(x)) - Var(x). See, e.g., math.ubc.ca/~feldman/m302/binomial.pdf –  daniel 11 mins ago

@Remi.b It should be: http://www.math.ubc.ca/~feldman/m302/binomial.pdf

You are welcome. Sometimes you don't see a tree in the wood :-)

My bad. It was just a cite for the variance. Sorry.

The notation at this site resembles that in your question but preserves the $\frac{x_t}{2N}$ notation for probability of selecting an allele.
$$E[\frac{x_{t+1}}{2N})(1 - \frac{x_{t+1}}{2N} )|x_t] = (\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) (1 - \frac{1}{2N})  $$
The expression $(\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) $ is the probability of heterozygosity at step $t.$
Your expression says that the expected heterozygosity at step $(t+1)$ is equal to the heterozygosity at step at $t$ multiplied by $(1-\frac{1}{2N}).$
For a population of size $2N,~(1-\frac{1}{2N})^{2N}\approx 1/e,$ so large populations are insulated from this effect and small ones may lose genetic diversity rapidly.
A typical explanation can be found here. The notation at this site condenses the expression $(\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) $ to $H_n$ and explicitly says it is $1 - F_n, $ in which $F_n$ is the probability of homozygous at step $n.$


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Have we ever observed two drosophila lineages that evolved reproductive isolation in labs?
Background
The standard definition of species refers to the concept of reproductive isolation. If two lineages are found to be reproductively isolated, then we consider these two lineages to belong to different species. My question concerns evolved reproductive isolation in Drosophila sp. following labs due to experimental evolution.
Question
Have we ever demonstrated that two Drosophila sp. lineages that could initially interbreed (in nature or in labs) evolved through artificial selection (and drift and mutations) in labs to finally not be able to interbreed anymore either due pre- or post- zygotic isolation (see wiki)? Or, in other words, have we ever demonstrated that two drosophila lineages evolved to become different species (reproductive isolation definition) in labs experiments?
If not, have we ever observed some partial reproductive isolation such as inbreeding depression for example?

Note: This question is motivated by @LotusBiology that could not receive the answers she/he was waiting for because he/she failed to ask questions that are possibly answerable! So I wanted to ask this question that somehow addresses this question he/she asked (now on-hold)
For more information about the concept of species, please have a look at How could humans have interbred with Neanderthals if we're a different species?

Reproductive isolation in not only Drosophila but other species is the basis of Daniel Matute's research (http://dm-incompatibilities.org/).

Rice and Salt$^1$ bred fruit flies for 35 generations and from one line of flies created two groups that were isolated from each other reproductively. They could not interbreed because they no longer bred in the same environment. Depending on one's definition of 'species' this could be a case of artificial speciation.
$^1$Rice WR, Salt GW (1988), Speciation via disruptive selection on habitat preference: experimental evidence". The American Naturalist 131 (6): 911–917.

Also there was one experiment by diane dodd...mate preferences of fruit flies changed.

Diane Dodd's experiments on Drosophila pseudoobscura would be another example of lab-based speciation.
http://www.jstor.org/stable/2409365?__redirected
To summarise - four populations each adapted to feeding on a starch-based diet and a maltose-based diet were evolved in the lab to test effects on mating preferences; compared to what is expected by random, using chi-squared tests, 11 of 16 combinations showed greater isolation than expected by chance - strong evidence for assortative mating.
An alternate link to the PDF of the paper is here http://www.sulfide-life.info/mtobler/images/stories/readings/dodd%201989%20evolution.pdf

Reference:
Dodd, Diane M. B. (September 1989). "Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura". Evolution 43 (6): 1308–1311. doi:10.2307/2409365.

Can you summarize the results so that if the link dies the answer will still have value?

@AnkurChakravarthy The link no longer works I am afraid. Can you please edit it and as JamesJenkins asked, can you please add a short summary of this article or post your link in a comment. Thanks a lot!


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How are Mono and Diglycerides metabolized without the Free Fatty Acids of Triglycerides?
Having difficulty figuring out what the body does with ingested mono and diglycerides if the usual process of TAG metabolism includes the FFA released from the TAG returning to the MAG to recreate a TAG in the enterocyte, whereas with MAG and DAG consumption, those FFA don't exist. There are many studies (Nagao, 2000, Takatoshi, 2002 and others) confirming that DAG oil consumption leads to weight loss, which is seemingly obvious as the fat cannot be stored without the FFA getting repackaged into TAGs for storage in the adipose tissue. I have not found any studies on what actually happens to the MAGs in lieu of its normal course. I would much appreciate if someone could direct me to literature discussing this process or help me better understand it. Many thanks! Anyone?

Inside the intestinal lumen, di- and triacylglycerol are hydrolysed to free fatty acid and monoglyceride by lipase.
These diffuse through the plasma membrane of enterocyte where they will   used to resynthetize triacylglycerol, and ultimately the lipoprotein chylomicron for transport into the general circulation.
Contrary to what your question seems to imply, the glycerol to which the free fatty acid are affixed is not necessarily coming from the food: glycerol is routinely produced by glycolysis. (This notably also happens in the adypocytes). There is no requirement that food contain a ratio three fatty acid to one glycerol to be fully absorbed - if the weight loss property of DAG are true, it may be through  a different mechanism.

My question was not where the glycerols come from as there are present in MAGs and DAGs as well. The question was that without the extra FFAs which exist in TAGs, the MAGs which are entering the enterocyte do not have the usual accompanying FFAs to re-synthesize into TAGs.

Hello! This question was deemed worth of an answer, so why not upvote it? Vote early, vote often to encourage new users and keep the community alive!


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Can someone help me identify this queen ant?
I found this queen ant near a river on the 14 july in Braga-Portugal, it was on a river bank, and it measures around 8 mm. Can someone help me identifying the species? thank you for your time :)

The small space between the thorax and the abdomen indicates this queen has only one petiole segment (no post-petiole). The large size and absence of an elongated first abdominal segment indicates the subfamily Formicinae. The morphological features necessary to go further with a formal identification are not visible, but from the general aspect of the ant it is likely to be a Lasius or a Formica.
See ref below:

Seifert, Bernhard. Die Ameisen Mittel-und Nordeuropas. Lutra Verlag-u.
  Vertriebsges., 2007.