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Are there any papers arguing against vaccination in French?
Disclaimer: This question is NOT about challenging the safety or efficacy of vaccines. It is only asking for tips on providing credible references that may show harmful effects of vaccination, if any.
In my French class, we were asked to debate an issue in current events. My topic is vaccines in children or adults.
The challenging part is that I was assigned to argue against vaccination, and I have to back up my arguments with credible sources (not blogs) that are in French. Hopefully some of you could point me towards some links to articles or research papers in French.
Please avoid discussion on safety and efficacy of vaccines, including local and global policies on their use. I just need help with this topic for my French class

What about looking into positive studies and say that all distributions have negative-side tails that cause death etc. In real science there are studies like "X is good for you", only "in p% cases X helps to increase Z by q%". Take (1-p)% cases and use that as an argument

*there are no studies like X is good for you

Out of curiosity, did you pick this topic or did your teacher?

Strangely, it seems that all of the debates about science aren't actually based in science at all. Vaccines, evolution, global warming, etc…

Maybe instead of a direct approach you can find arguments on why death by disease isn't so bad after all?  But seriously, you're not going to find much in biology; you might be better off looking for non-scientific arguments.  For example, some religions view disease as an expression of divine will and discourage medical treatment.

I'm voting to close this question as off-topic because it asks evidence for a wrong claim. There are no evidences yet for vaccines having bad effects. This question is also likely to attract anti-vaccination supporters who may claim this post as a support for their cause.

@WYSIWYG so when people get disease after&due to vaccination it is OK? science is about measuring real effects, not saying that something is bad or good.

@WYSIWYG - asking for references for any claim should be on-topic. Whether it has proven correct or incorrect. Stuff being considered correct now is proven incorrect tomorrow. Isn't that science? Moreover, the Wakefield study  is an important study, as it stands example for total non-sense making it into one of the most respected journals worldwide.

@aandreev and AliceD I am not questioning the scientific process. I am just saying that the way the question is worded, it is likely to get into controversies. We can always say no it doesn't happen like that as per the research till now and many of you have said that. Questions about specific formulations of drugs/vaccines are fine. This post needs to be protected if not closed and even then there may be people with enough rep who will come up with theories. We can't keep moderating it forever.

You could find credible sources arguing against specific vaccines but not against vaccination in general. That's like looking for credible sources arguing that the earth is flat.

@terdon: That would actually be my strategy: find many credible sources arguing against several specific vaccinations, and paint the pro-vaccination crowd as zealots trying to stuff vaccines down everybody's veins.

Not an answer, but just a hint -- I know that there's an angle that condemns vaccines because they (some of them) contain aluminium compounds, which in turn is claimed to cause Alzheimer's disease. Highly controversial and certainly not my POV, but perhaps this provides you with a couple more keywords.

can we probably add a disclaimer that question is not for discussing vaccines, but for providing credible references that show harmful effects of vaccination?

There is no scientific dispute that modern vaccines are brilliant. The anti-vaxxers rely only on pseudo scientific fear mongering and ludicrous, offensive campaigns to further their profiteering. The only (off topic) debate to be had is whether or not one has the right to refuse vaccination for non-medical reasons and (rather selfishly in my opinion) rely on herd immunity, which is very risky for the individual.

I wish you good luck, as 99.99% of the anecdotal claims out there that conclude vaccination is bad are based on unfounded rumors.
Note that much of the negative public opinion is based on a fraudulent (and retracted) paper by Wakefield in The Lancet (1998). Unfortunately for you, however, it is in English.
My French is a bit rusty, but if you go to Google Scholar and type in a search term like vaccination results in autism (les résultats de la vaccination dans l'autisme) or Wakefield vaccination autisme something might pop up in French that advocates against vaccination.

I do wonder if Wakefield regrets the damage he has done. 5% of children under 7 in California are not vaccinated. Measles is a preventable condition! One I've never had to endure!

You will not find good, credible sources arguing against vaccination. However, spewing nonsense is not necessary for winning your debate. You can collect good, credible sources arguing against specific vaccinations and use them to paint the opposing side as pro-vaccination zealots who unquestioningly want to stuff vaccines down everybody's veins.
Vaccines, like other treatments, have to be approved by health authorities, and therefore, the possible side effects are being studied in clinical trials. All you have to do is find a few cases where there side effects were a bit more severe than anticipated.
A good start for your research could therefore be publications about the risks of vaccination. On Google Scholar, "risques vaccination" brings up hits like Risk-Benefit assessment of hepatitis B vaccination in France (in French) that can give you a good basis for gathering material against vaccination.

@AliceD: I reverted some of your changes to keep the original meaning of my post. If you feel the first paragraph remains problematic, I'd rather take it out completely.

If you don't mind - I've taken it out. As it was previously, it could have lead to anti-vaccination people (ab)using your answer in favor of their stand point. OPs question is kind of problematic in that it may lead to endless debate

@AliceD: I tried another version that states why am trying to give the OP what he needs rather than what he seems to be asking for.

The Wakefield study has collapsed as fraud, and there are no credible sources that make persuasive scientific arguments against being vaccinated in today's world -- not even in French.

did you mean "in English"?

@MarchHo I meant "in French". Apparently certain types of humor fail to translate well to the written word.

The only angle I can think of that isn't "Haha, I can't believe these people are allowed to vote" is that the enemy we know is better than the enemy we do not know.
I see no reason why the classic argument of selection pressure doesn't apply. (See Warfrin(spelling?) resistance in rats, the resistant rats required more vitamin-k, thus more time out in the sun, so in a warfrin free environment are at a disadvantage, but thrive in an environment with warfrin)
Unfortunately (fortunately) evidence doesn't really support that, in fact we have eradicated several diseases already entirely and nothing replaced them.
(Long comment sorry)
By the way! Do tell us some of the arguments that come up!

I don't think the resistance angle helps much here, but if one wanted to pursue it, this question is relevant: http://biology.stackexchange.com/questions/30166/why-vaccines-do-not-cause-bacterial-resistance/

@Corvus indeed, no doctor is going to say "Let them die!" (side note: "overprescription of antibiotics" is a hot topic in the UK because bacterial resistance is actually becoming a problem! However that's not vaccination)

Also @Corvus thanks for that link, I was wondering while I was writing!


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Explanation of the ‘cherry red spot' in Tay Sachs disease
In Tay Sachs disease, a hallmark symptom is a cherry red spot in the macula of the eye surrounded by a halo of white.
I understand that the ganglion cells, which are higher in numbers around the macula rather than in the macula, accumulate gangliosides due to the hexosaminidase deficiency, and thus cause the surroundings of the macula to appear white, but I don’t understand why the macula is red.
It is said that in Tay Sachs disease, the macula is the only normal region of the eye, but isn’t the macula supposed to be yellow, as it is referred to as the yellow spot?
Moreover, I’ve read that the red color comes from the choroid blood vessels, but isn’t the choroid black? It contains blood vessels, yes, but it is pigmented. The hindmost layer of the retina also happens to be a pigmented epithelium. So what is the explanation of a cherry red spot?

Short answer

The fovea centralis is colored red in both the healthy retina and Tay-Sachs affected retinae. The macular region around the fovea has a yellowish hue. You are confusing fovea and macula in your question.
The reddish hue from the fovea comes from the well-vascularized choroid layer below. The choroid is not black, it is colored red due to the presence of many blood vessels. You are confusing choroid with the retinal pigment epithelium, which is indeed black.

Background
The macula includes the fovea at the center, also called the fovea centralis, which forms the very center of the retina. The macular region around the fovea includes the perifoveal and parafoveal areas. The macular region around the fovea has a slight yellowish appearance to it due to yellowish pigments present in the cone axons (Fig. 1) (Kolb, 2012).

Fig. 1. Healthy retina. The macular region is seen in the center, The parafoveal region has a slight yellow/orange hue to it. Note that the landmark yellow circle at 4 o'clock, with the vessels sprouting from it, is the optic nerve head. source: Webvision.
Below a Tay-Sachs affected retina showing the hallmark cherry red spot (Fig. 2):

Fig. 2. Tay-Sachs affected eye. The fovea centralis appears red. source: Prezi
The only normal part is the fovea centralis, appearing in its native red color, i.e. the cherry red spot.
The choroid plexus is well-perfused and is, therefore, red. You are confusing it with the pigment epithelium, which is pigmented (Fig. 3).

Fig. 3. Layers of the eye. RPE = Retinal Pigment Epithelium. source: Retina Eye Specialists
Reference
- Kolb (2012), Simple anatomy of the retina. In: Kolb et al. (eds.), Webvision. The organization of the retina and visual system. Salt Lake City, UT, Moran Eye Center

But is the RPE is present in the fovea too? I don’t understand why the fovea doesn’t appear black when the rest of the eye’s interior does.

The retina does not appear black. See the images above. Note that the black borders are outside the eye.

But where does the black appear then in the eye? Isn’t it important for the eye’s interior to be black to absorb backscattered light? You mentioned the RPE is black, but this should be visible, should it not?

It's a very thin structure.

So the RPE is so thin that you can’t really see the black? But what about the whole part where the pigmentation helps absorb scattered light? I’m just thinking that if, upon hitting the RPE, light is absorbed and not scattered, then there is no light reflecting back into the observer’s eye and the eye’s interior would appear black. If the eye’s interior doesn’t appear black then that does mean that light is being scattered about in the eye.

The black RPE contributes to the "normal" color of the eye fundus in photos of the retina. Albinism is a condition of absence of black pigment, and then you can see the eye fundus without pigment. Compare the two images below

Welcome to Biology.SE! It isn't clear that this answers the original question, which was about Tay Sachs not albinism. In addition, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Please take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site and then [edit] or delete your answer accordingly. Thanks!

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Why do spiders make their web near the ceiling and near a light source?
Why do spiders make their webs near the ceiling and near light sources ?
Is their an advantage for spiders in doing that? For example do they catch more insects when their web is near a light source because prey insects are drawn to it, hence giving those spiders with a well-lit web a better chance of survival?

probably...

same reason you put light inside of your bug lamp?

Possibly related?

Because many insects (their food) are attracted to light. This attraction is called phototaxis.
Hypotheses for why insects are attracted to light

The leading hypothesis for why so many insects are attracted to light is that before artificial existed, insects were using the light from the moon in order to navigate. They would keep themselves at a given angle relative to the light source in order to navigate straight.
Another hypothesis is the presence of light indicates that the pathway is clear.
A third hypothesis is that some insects may confuse artificial light source with the other sex. This appeared to be true for moths for example

These three hypotheses are not mutually exclusive.
How do spiders chose their habitats
For more information about the abilities of spiders to find a good habitat, have a look at this very interesting answer.

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Can we produce synthetic red blood cells lacking antigens?
I had an idea come to me during Biology class and I immediately asked my teacher, but she couldn't really answer the question, so I'll ask it here.
What are the limiting factors in the production of synthetic red blood cells with no antigens? I mean, we do have the human genome mapped, but am I naive to think that we have genetic technology capable of doing this?
If red blood cells are too complex to manufacture, is it feasible to manufacture much smaller particles of just hemoglobin inside small spheres of cell membrane and use that as a temporary replacement for red blood cells?
(I was at a medical research talk a while ago and one professor was explaining that there are many other proteins bound onto a red blood cell that aren't of the ABO or RH system. Normally this isn't a problem for recipients who only occasionally received transfusions but for people who need a long-term supply of blood, their bodies do get sensitized to the foreign proteins and will eventually start attacking the foreign red blood cells).

Actually there are such particles. It is estimated that about 20% of the hemoglobin (HGB hereafter) is in HGB vesicles (HbV hereafter) formed by RBCs. So sure, it is possible to use small particles instead of RBCs, but these vesicles have major and minor antigens on their surface. According to some of the articles they cause other complications too by blood transfusions and they are destroyed by the immune system within 3 to 7 days. So they don't solve the problem.

In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells
Artificial Oxygen Carriers (Hemoglobin-Vesicles) as a Transfusion Alternative and for Oxygen Therapeutics
Red blood cell vesiculation in hereditary hemolytic anemia
The red cell revisited--matters of life and death.
Red blood cell microparticles and blood group antigens: an analysis by flow cytometry
Hemoglobin-Vesicles as Oxygen Carriers
Physiological Capacity of the Reticuloendothelial System for the Degradation of Hemoglobin Vesicles (Artificial Oxygen Carriers) after Massive Intravenous Doses by Daily Repeated Infusions for 14 Days

HGB vesicles without major and minor antigens are not a perfect solution either (I think), because the immune system tends to attack such things. For example by viral infections the MHC1 levels are low (in cells with nucleus) to avoid T cell response and the NK cells does not like that, so they destroy such cells. I am almost sure something similar would happen with this kind of vesicles as well. At least afaik. the immune system checks not just the presence of these antigens, but their composition as well. So if a RBC is under stress, then it changes the antigen composition on its surface and the leukocytes destroy it if necessary. According to some of the experiments PEG can cover HbV antigens and increase immune compatibility, so having less surface antigens seems to be a better choice than having more.

Development of a Synthetic Blood Substitute Utilizing Hemoglobin Vesicles
Biocompatibility of Hemoglobin Vesicles, a Cellular-Type Artificial Oxygen Carrier, on Blood Cells and Plasma Proteins In Vitro and In Vivo
Artificial Oxygen Carriers, Hemoglobin Vesicles and Albumin−Hemes, Based on Bioconjugate Chemistry
Hemoglobin Vesicles, Polyethylene Glycol (PEG)ylated Liposomes Developed as a Red Blood Cell Substitute, Do Not Induce the Accelerated Blood Clearance Phenomenon in Mice

HGB vesicles have another problem. The HGB inactivates in them without reduction (metHb formation). Only Fe2+ HGB can carry oxygen. This can be solved with methylene blue according to this study.

Red Blood Cells Donate Electrons to Methylene Blue Mediated Chemical Reduction of Methemoglobin Compartmentalized in Liposomes in Blood
Inhibition of methemoglobin formation in aqueous solutions under aerobic conditions by the addition of amino acids

We cannot use free HGB either, because it would decrease the NO levels and lead to endothelial dysfunction. I think to small particles would have the same effect because of increased surface.

Mechanisms of Slower Nitric Oxide Uptake by Red Blood Cells and Other Hemoglobin-containing Vesicles
Microparticles in stored red blood cells as potential mediators of transfusion complications
Removal of Cellular-Type Hemoglobin-Based Oxygen Carrier (Hemoglobin-Vesicles) From Blood Using Centrifugation and Ultrafiltration

According to other studies RHSA-heme (serum albumin bound to synthetic heme) is another option. It seems to be safe if you replace only 20% of blood volume (of rats). I think a complete transfusion is not safe, because it would reduce the NO levels as we already discussed. I have not found an experiment which does complete transfusion.

Safety evaluation of an artificial O2 carrier as a red blood cell substitute by blood biochemical tests and histopathology observations.
Exchange transfusion with synthetic oxygen-carrying plasma protein “albumin-heme” into an acute anemia rat model after seventy-percent hemodilution

So there is ongoing research in the topic. There is progress, but none of the current solutions is perfect I think.

Artificial blood substitutes are being researched and developed as alternatives for replacing RBCs for oxygen carrying capacity. Regular human blood has a shelf life of only 42 days which limits their utilization over more extended periods. This necessitates the development of blood substitutes which can be stored for longer duration. In addition, blood substitutes have universal compatibility, and therefore their application is not restricted by typing and cross-matching. Blood substitutes are extremely necessary in case of acute and chronic blood loss from injuries and accidents where a shortage of oxygen to cells affects the survival of patient by inflicting permanent damage to tissues.
Blood substitutes market is categorized into two segments viz. Perfluorocarbon-based oxygen carriers (PFBOC), and Hemoglobin-based oxygen carriers (HBOC). PFBOCs are based on inert components which replace hydrogen with fluorine. HBOCs consists of hemoglobin derived products sourced from humans blood, bovine blood, microorganisms and transgenic animals.

Artificial blood Substitute is an artificially developed substitute for red blood cells which is use for transporting oxygen and nutrients to the body cells and transporting back carbon dioxide, ammonia and other waste products away from cells.
Six potential application markets have been identified based on the possibility of replacing donor blood in critical medical treatments-
Injuries,
Cardiovascular diseases,
Malignant neoplasms,
Neonatal Conditions,
Organ transplants,
Maternal condition

Welcome - The question is on antigens in specific and hence your answer doesn't address the question. Further, your answer is not references or supported by credible web links. -1


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Resource for finding what proteins bind?
I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a given protein binds or otherwise interacts with?
I am aware of Uniprot and Phosphosite which have proved useful but I am wondering if there are others that I am not aware of.
Again: the question I am trying to answer is "which proteins from list A interact with proteins from list B and vice-versa?"

"the question I am trying to answer is 'which proteins from list A interact with proteins from list B and vice-versa?'" You and every biophysicist on the planet.

Go to the NAR database site and look for protein domain databases. You have multiple options. Here is the link.

This is definitely a good resource. It looks like most of the tools are very specific. I am hoping to find something more general; like string-db.org

STRING is one available tool http://string-db.org/ and allowes you to do multiple sequences/names. I would also take an indepth look at what expasy has to offer http://www.expasy.org/proteomics. It is a large collection of bioinformatics tools (far too many for me to go through) and almost always has the tool you want.
(As a side note Expasy also has tools in genomics, structural bioinformatics, and many more, check the left hand tabs on the website for the full list!).


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What information can Uniprot give me about phosphorylated forms of proteins?
I have a list of proteins formatted like this:
Protein Name        Gene Name
4E-BPI              EIF4EBP1
4E-BPI_pS65         EIF4EBP1
4E-BPI_PT37_T46     EIF4EBP1
53BP1               TP53BP1

Its my job to pull the following from Uniprot:

Subcellular Location information (this is easy)
Information about phosphorylated forms

The first thing I did was compile a list of Uniprot IDs for each gene's human form that I could plug into the Upload List function.
Next, I used Uniprot's "Customize Results Table" page, to add the "Subcellular Location" column to the output. Do you know columns will provide information about the phosphorylated forms of these proteins? I added columns PTM > PhosSite and PTM > PhosphoSite but they return the Uniprot ID or nothing at all.
Is there somewhere else in Uniprot that I can look for information about phosphorylated forms of proteins?

You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as PhosphoSite. To get the actual modified residues, click on "PTM/Processsing" (sic) further up the page and then select "Modified Residue", and in your results table you'll get a list of all phosphorylations, glycosylations, acetylations, etc.

This is the relevant help entry, should you want more information on these annotations. You can use the advanced search with Keyword '597' to only retrieve proteins that have phosphorylation annotations.


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What if a Point Mutation is seen in only half the coverage for its location?
I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact.
I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20.
My primary question is: how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?
I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and heterozygotes at this SNP-position.

Yeah, its a human. That's a really great answer; I can't believe I didn't think of such an obvious explanation.

Just to ascertain this- check the quality scores (phred), sequencing lanes, replicates etc at the SNP region: to make sure that it is not an artifact.

@WYSIWYG: the probability of this being an artifact is negligible given the systematic nature of the phenomenon: it's not about two reads having one mismatch.

I totally agree.. If it is really half the reads sort of situation. However, it is always good to confirm that there are no other hidden patterns.


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Why does ear wax taste sour?
Why does ear wax taste sour?
I am interested in both the physiochemical mechanisms and the evolutionary reasons behind the sour taste of earwax.

Well, I am curious - How do you know ear wax tastes sour ?!

I know because... for science.

Earwax, also called cerumen, is slightly acidic (1), with a pH of about 6,  and acidic foods or substances taste sour. The composition of earwax, upon which its taste depends, is related to its functions. Earwax aids in cleaning and lubrication of the ear canal and has an antimicrobial effect. The antimicrobial effect is in part attributed to its acidity, which might give an evolutionary reason for the sour taste.
From Wikipedia:

Cerumen is produced in the outer third of the cartilaginous portion of
  the ear canal. It is a mixture of viscous secretions from sebaceous
  glands and less-viscous ones from modified apocrine sweat glands.[4]
  The primary components of earwax are shed layers of skin, with 60% of
  the earwax consisting of keratin, 12–20% saturated and unsaturated
  long-chain fatty acids, alcohols, squalene and 6–9% cholesterol.[5]
(...)
While studies conducted up until the 1960s found little evidence
  supporting antibacterial activity for cerumen,[15] more recent studies
  have found that cerumen has a bactericidal effect on some strains of
  bacteria. These antimicrobial properties are due principally to the
  presence of saturated fatty acids, lysozyme and, especially, to the
  slight acidity of cerumen.


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What does this equation about DNA replication mean?
Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why?
$\ce{dNTP + dNMP_{n} -> dNMP_{n +1} + PPi}$
I found that dNTP means deoxy nucleotide triphosphate and dNTP means deoxy nucleotide monophosphate. Deoxy nucleotide monophosphate is a monomer in DNA, but dNTP isn't.
I also would like to know if there is an equation like this in other processes in the central dogma (such as transcription and translation)?

NTP stands for nucleoside triphosphate. A subtle difference. With nucleotides, the phosphate is implied.

The notation you are referring to is a way to express the elongation of a nucleotide strand (Fig. 1).
dNTP + dNMP(n) → dNMP(n+1) + PPi
means
Existing strand  +  deoxynucleotidetriphosphate  →  elongated-strand  +  pyrophospate.

Fig. 1. Elongation of DNA. Source: Concepts in Genetics.

This reaction holds for DNA replication as well as transcription.
Translation is all about protein synthesis from amino acid precursors. Each subsequent amino acid is coupled to the growing peptide by a peptide bond between the carboxyl of the growing peptide and the amino group of the new amino acid. A water molecule is eliminated during the reaction (Fig. 2).

Fig. 2. Peptide bond formation. Source: An Introduction to Molecular Biology
Hence translation can be written analogously to replication as:

amino acid + peptide(n) → peptide(n+1)
However, also in this polymerization reaction energy is needed and amino acids are activated while they are bound to the messenger RNA (mRNA) through the action of ATP. Moreover, during translation the ribosome (i.e., the protein synthesizing machinery) uses another source of energy to move across the RNA template, namely GTP. Hence, the net reaction can be written as:

amino acid + peptide(n) + ATP + GTP → peptide(n+1) + AMP + GDP + PPi + Pi
Note that this notation in itself is not a dogma as other ways are in use to denote DNA and RNA synthesis. According to Merriam-Webster a dogma is:

A belief or set of beliefs that is accepted by the members of a group without being questioned or doubted.

It's incorrect to say that amino acids are not activated. tRNA charging is the activation step of protein synthesis and creates an ester bond with high and negative free energy of hydrolysis (whose cleavage subsequently drives peptide bond formation). tRNA charging requires ATP. A net equation for peptide synthesis could be written as amino acid + peptide_n + ATP -> peptide_(n+1) + AMP + 2Pi. This equation (like that discussed in the question) is over simplified, but gets the point across.

@canadianer - Great point, will include shortly

Additional point to what @canadianer said. Each elongation step requires a molecule of GTP per codon. So the reaction for translation elongation should be: amino-acid + Peptide(n) + ATP + GTP → Peptide(n+1) + AMP + GDP + PPi + Pi

@WYSIWYG - I edited the answer. Thanks. I must say that both mRNA activation and the ribosome movement are both indirectly related to the translation reaction. The direct substrates are mRNA and the growing peptide. ATP and GTP are indirectly involved. So I reverted to my old answer and added your comment alongside Canadianer's in a separate section for clarity's sake. Thanks for your suggestions and the edits!

DNA is a polymer of dNMPs (dAMP, dTMP, dCMP, and dGMP). That's why you could describe DNA by dNMPn (n base length). When another dNTP is added to DNA (dNMPn), one pyrophosphate (PPi) is released. It is obvious that the length of the DNA results in n+1 bases.


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(How) Does the human digestive system process petroleum jelly, aka petrolatum?
Does the human digestive system processes petroleum jelly? In other words, does it pass through the digestive system without any interaction, or is it absorbed and/or metabolized?

Liquid paraffin was used as a laxative (i don't know if it still is).

There are controversial case reports about systemic absorption of paraffin used for constipation. These reports mention systemic effects of paraffin absorption and one of them report liquid paraffin accumulations in
abdominal visceral organs. (full text article about paraffin)

Liquid paraffin is indigestible and is absorbed only to a limited
  extent following ingestion.

+

As inert substances the ingested mineral oils mostly are excreted
  intact in feces and to some degree in urine. However, some absorption
  form the small intestine has been observed (Stryker 1941). Using
  radiolabeled mineral oil, it was established that the amount absorbed
  in rat was appr. 1.5 % (Ebert  et al. 1966).

  (full text article)

Is paraffin the same as petroleum jelly? I was under the impression that paraffin was a more-or-less natural wax, and that petroleum jelly is a byproduct of oil refinement.

@mHurley In the scope of the question it is the same. https://en.wikipedia.org/wiki/Petroleum_jelly


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What is a substance that is safe to eat, not absorbed and not metabolized?
I would like to know whether there are substances that are safe for humans to consume, are not absorbed and do not interact with any digestive process.
So, food is disqualified because although it may be safe, it is processed by the digestive system and is metabolized. I'm looking for things that go entirely unprocessed (other than passage).
One such material, or a discrete class of materials is sufficient.

Would dietary fiber count?

Dietary fiber stimulates the intestinal movements. I think the phrase '...do not interact with any digestive process' effectively kills any answer, including laxatives and dietary fibers.

This is by no way an opinion-based question.

Dietary fiber might qualify for what I was thinking about; perhaps I just asked the question poorly. Either way, it isn't nearly shocking enough ;-)

Several sugar substitutes stimulate taste buds but are [largely] indigestible. Whether they are safe in a health sense is debatable.

Simethicone is one example. It is a mixture of silica gel and dimethicone (polydimethyl siloxane); they are individually inert too.
Simethicone/dimethicone is used as antigas (they help the gas bubbles coalesce). It does have a laxative effect, though.

Do you have any reference for that?

@rg255 Wikipedia is a basic reference; added that. It is kind of a known fact. I don't know of pharmacology databases. Looking for one.

Wiki is good enough there I think

Yeah, Wikipedia is fine for my purposes.

How about gold. You can find it on foods, but it is inert and also not absorbed.

any reference to that?

[...] gold nanoparticles [...] absorption across intestinal barriers and accumulation in secondary target organs after oral administration: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267526/

So gold nanoparticles can be taken up and subsequently deposited throughout the body

I doubt there's any research on macroscopic lumps of  pure gold and digestion, but i suspect they're entirely unaffected by the process.

I can look for a ref for this, but we use gold as a tracking source that does not get absorbed/digested. But nanoparticles are a bit unique, it isn't so much the compound as it is the size that facilitates their absorption and subsequent tissue trafficking. So @AliceD, your answer is a bit misleading, because you could really say this for a large swath of materials regardless of how much they get absorbed as Resonanting says, as a 'lump'.

@TheNightman, nice one. But my comment is not an answer, its a comment only. I'm just playing devil's advocate. As I commented under the question, I think this question is all-exclusive. I'm considering close-voting it because of its opinion-based nature.

Well, this might reveal the real answer to my question, which MIGHT be "anything will be absorbed if it's small enough."


text:
How to make a fake auditory signal?
My question is about making fake auditory signals. The ear collects sounds from the environment, which are transformed into a neural signal by the hair cells in the inner ear. This signal is sent through the auditory nerve to the to brain, where it is decoded into a hearing sensation.
Now can we make fake signals and feed them into the auditory nerve to bring it to the brain? E.g., instead of the ear collecting sound, could we use an electrical instrument for collecting sound and convert this signal into a neural signal in the auditory nerve?

It is possible to electrically trigger the auditory nerve but I am not sure how well can (with the current technology) it reproduce the normal hearing.

Devices that bypass the hair cells in the inner ear and directly stimulate the auditory nerve are called cochlear implants. Cochlear implants are used to treat deafness caused by the loss of hair cells in the cochlea. The hair cells are the sensory cells that convert sound vibrations into electric neural signals (Purves et al., 2001). With state-of-the-art devices, the better performing implant wearers are able to talk over the phone(!) An exclamation mark is in place, because it means they can understand the spoken word without the need for lip reading or sign language. Hence, cochlear implants are the answer to your question, but they definitely are not designed to generate fake signals. Instead, they are used as an effective treatment for deafness and are capable of transmitting meaningful speech information.
Cochlear prosthetics consist of an array of typically 20-24 electrodes that are inserted in the scala tympani of the cochlea. The inner ear is tonotopically organized, which means that high frequencies are coded in the base of the cochlea, while low frequencies are encoded in the tip. Hence, each electrode stimulates a separate frequency band (Fig. 1). By using a microphone and sending the acoustic signal through a filter bank, a number of auditory frequency bands can be obtained equal to the number of electrodes in the implant. After this speech processing step, the acoustic frequency bands are converted into trains of biphasic pulses. These pulse trains are sent to the electrodes in the cochlea, which then activate the auditory nerve directly, effectively replacing the degenerated hair cells in the inner ear (Stronks, 2010).

Fig. 1. Cochlear implant. Source: Mayo Clinic.
References
- Purves et al., Neuroscience (2001) 2nd ed.
- Stronks (2010). PhD thesis, Utrecht University

AliceD I got it . when i say fake signal  i mean the signals that are not generated by the real haircells. the exactly things that you said was in my mind.Can you show me a refrence that introduce this Cochlear implant completely with details ?

@Nimda - I linked a PhD thesis which has a nice introductory text on cochlear implants. Please refer to section 1.5. The other sections in chapter one may also be of interest as they deal with normal functioning of the ear as well.

:) @AliceD I had a small doubt. I thought there is a continuum of frequency sensing- something like firing rate proportional to frequency. If it is so then how stimulating just six physical zones can produce all types of tonal perceptions? In other words- is it easy to differentiate the neurons that sense frequency vs those that sense amplitude? Even if you suggest me a review, it would be fine.

@WYSIWYG -  :) here 2 :)  I'm not exactly sure where you obtain the '6' from, but you are pretty much spot on that 7 channels are enough for speech understanding. The gross reduction of the nr. of inner hair cells (16k)  to the nr. of effective channels (~7) still leaves enough info for speech understanding. The trick is the efficiency at which the auditory system retrieves temporal information. Electrical info is temporally very fast, but spatially very crude. You are spot on.

@WYSIWYG - cont. There is just one neural cell type that is stimulated here: the spiral ganglion cells. They sense mainly amplitude. Frequency of stimulation is extremely fast in present stim. strategies, in the order of thousand to tens-of-thousands Hz. Frequency (i.e., pulse rates) in itself are irrelevant. It is place-coding (akin to perceptual frequency/tones) and intensity coding (akin to perceptual loudness) out of which the temporal changes contain the most relevant info.

@AliceD I don't know why I said 6. Anyways, thanks for the info. You can add this to the answer as well. :)

@WYSIWYG - with your permission I'd rather leave this in-depth analysis of electrical stimulation to the comments :)

@AliceD Your choice. It is your answer.

As @AliceD mentioned, cochlear implant is one of the earliest achievements of neural engineering. However, there are orders of magnitude more inner hair cells (IHC) and even more auditory nerve fibers (AN) in human cochlear than the current cochlear implants offer electrodes. If you are interested in a more detailed model of IHC to AN signal transmission, there are tons of research, for example:

Meddis, R. (1986). Simulation of mechanical to neural transduction in the auditory receptor. The Journal of the Acoustical Society of America, 79(3):702-711.
Walsh, E. J. and McGee, J. (1987). Postnatal development of auditory nerve and cochlear nucleus neuronal responses in kittens. Hearing Research, 28(1):97-116.
Sumner, C. J., Lopez Poveda, E. A., O'Mard, L. P., and Meddis, R. (2002). A revised model of the inner-hair cell and auditory-nerve complex. The Journal of the Acoustical Society of America, 111(5):2178-2188.
Heinz, M. G., Colburn, H. S., and Carney, L. H. (2001). Evaluating auditory performance limits: I. One-Parameter discrimination using a computational model for the auditory nerve. Neural Computation, 13(10):2273-2316.

There are only 2 auditory nerves. You probably meant AN fibers?

@AliceD correct! thanks for pointing it out. Fixed.

Looks good now :) +1;   20+ auditory nerves would become interesting anatomy :)


text:
Do genetic modifications exist to enhance the taste of tomatoes?
GM tomatoes seem less tasty. Has there been any research on GMOs with regard to taste?
Can scientists introduce a gene to, let's say, tomatoes, which would enhance the flavour? If not, why?

I'm voting to close this question as off-topic because it is poorly researched.

I think the primary reason commercially available tomatoes have poor flavor has more to do with being bred for hardiness and stability while being shipped and on the shelf. These features were selected in favor of taste and were not added by what most consider "Genetic Modification"

If you trim this question down to the first two sentences I think it becomes quite good. Strong answers should probably consider geraniol synthase etc.

I have a feeling additives would be easier than genetically enhancing taste.

@GoodGravy If you could identify the "flavor genes" that were lost during breeding, you might be able to add them back while maintaining the hardiness. Whether or not this would be cost effective is another issue.

@user137 Flavour is a really really tough one from a genetic perspective. For example sugar content would be the result of several genes and their interactions between one another. Up-regulating some may not revert the flavour. Fibrosity would certainly be a similar story. Of course there is also the more subtle taste factors like metals and complicated carbohydrates which they are struggling with in artificial meat. I agree with your cost summary. Whereas there might be a single gene switch to make the crop drought-proof, taste is far more complex task for a far more trivial outcome.

@GoodGravy About the only thing I could think to do would be to compare the genome or transcriptome of poor tasting tomatoes to good tasting ones. This would probably produce a long list of differences to sort through.

@user137 You can see why additives might be simpler :P A simpler way yet would be selectively breeding the better tasting crops for a few generations and see if that sorts things out... Old school, but it doesn't involve a $1,000,000+ project!


text:
Does a virus have a well defined shape?
I assumed a virus to be something with a very specific geometry,
similar to a crystal, but more complex.
In an answer to
What is the size (diameter) of the SARS-CoV-2 virus? some SARS-CoV-2 virus particles are shown.
It looks like they do not have the same geometry.
They may be soft and influenced by external forces, but they could also be of different, but similar shape. Also, they could simply be defective in some way.
I assume a structure of the size of a virus is not rigid. Assuming no external forces, would multiple exemplars  of the same kind of virus have the same shape?
Can a virus have a different molecular arrangement, but be equivalent for biological purposes?

You should check literature on VLP (virus like particles) for vaccine purposes. They spend a lot of time charactering their modified virus shells a lot as capsid protein don't tolerate fusions well.

The caption to the figure in the source linked in that answer says Figure 3. Visualization of 2019-nCoV with Transmission Electron Microscopy.
Negative-stained 2019-nCoV particles are shown in Panel A, and 2019-nCoV particles in the human airway epithelial cell ultrathin sections are shown in Panel B... They've been through quite a lot and I'm not completely sure those techniques can faithfully preserve the shapes of the virus particles.

Some parts of viruses are consistently shaped, in particular anything that is made of multiple copies of a protein sticking together. There are methods to determine the structures of these regular components to high precision, like single particle analysis (eg. zika) and X-ray crystallography (bacteriophage HK97). Other parts of the virus are less consistent, either because they are flexible or because they are produced slightly differently each time. The nucleic acid core is often arranged semi-randomly, and the lipid envelope of many viruses can vary greatly, dependent on the process by which parts of the host cell's membrane is pinched off to create new viral particles. Here's an example of pretty extreme variability of influenza particles, based on what cell type they have infected. Virus particles with different shapes can be just as infectious, but if they are too large the number of new viruses produced by an infected cell may be too low.

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


text:
Is there a balance or feedback between O₂ and CO₂ in the atmosphere?
Is there, globally, a balance of the concentrations of oxygen and carbon dioxide  in the atmosphere?
Plants convert CO₂ to O₂,
and with the concentration of O₂, the tendency of plants to oxidize to CO₂ increases. That is, plants burn better with more oxygen.
Based on this there may be a feedback of increasing CO₂ concentration to increasing O₂ concentration back to increasing CO₂.
This feedback requires that plant growth increases with increasing CO₂ concentration.
Otherwise there would be only a limit to the oxygen concentration as at some concentration of O₂, even a wet rainforest burns explosively.
Does a feedback loop like that exist?

Actually no.  Even if there were a feedback loop, CO2 concentrations are only a few hundred parts per million.  Convert all the CO2 to O2, and you change the percentage of O2 in the atmospere by less than 1%.  Also, ~78% of the atmosphere is nitrogen.

Yes, increase in CO₂ concentration increases the rate of photosynthesis in plants. The rate of photosynthesis is linealy proportinal to CO₂ concentration in range up to 225ppm  and  slowly increases range 225-650ppm.[Limiting Factors in Photosynthesis, Plant Physiol. (1984) 75, 82-86] (Now CO2 concentration is about 400ppm).
You can read more in Educational article on Nature journal website or in
More scientific review on the topic.

Not generally true in nature.  The rate of photosynthesis is almost always limited by factors such as the availablility of sunlight, water, and soil nutrients.  It's only when all those other factors are in sufficient supply (which probably happens only in the lab) that CO2 concentration becomes a factor.  And since atmospheric CO2 hasn't been below 280 ppm for at least 10,000 years, rates below that level are hardly relevant to modern conditions.


text:
Can cracking fingers cause Arthritis?
I have been cracking my fingers for 2-3 years and on the first year I was told that I'm going to get arthritis because of it.
I've been researching this since the first year and I've never gotten an answer. Most people say either Yes, No or I don't know.
Arthritis is mainly cause by bones rubbing together and cracking fingers is just air sockets poping.
I've asked my biology teacher and he said that he's not sure. He then explained to me that the cracking sound from people cracking their fingers is just air sockets poping.
So can finger cracking cause arthritus?

I believe this has been answered on skeptics

Thanx @RoryM I think your link answers my question. So in conclusion, Cracking your fingers causes some harm but it's so negligible it's not worth worrying about.

Similar: http://biology.stackexchange.com/q/19850/6422

@Cornelius It is similar but it doesn't answer my question. Sorry for the reeeaaallly late answer. Although I did get the answer that I was looking for from http://skeptics.stackexchange.com/questions/1325/is-popping-your-knuckles-bad-for-you


text:
How do roots absorb water instead of presence of waxy - material suberin in the form of casparian strips on the wall of endodermis?
I found that in the endodermis, the tangential and radial walls have deposition of the waxy, and hence water-impermeable, material suberin in the form of casparian strips. The endodermis comes before the vascular bundle so how is water absorbed in roots?

Read this (especially the function part):
https://en.m.wikipedia.org/wiki/Endodermis


text:
Why are lips covered with specialized skin?
I found out some interesting facts while studying our lips:

They are covered in glabrous skin, while most of the skin surface is hairy;
The outermost layer (stratum corneum) of the skin is far thinner than on any other part of our body;
They lack pigmentation (melanin);
Their pink colour is due to underlying capillaries.
Their only source of moisture is our saliva. They lack sebaceous gland;

What is the reason behind this specialization of our lips?

Why is it not covered with the thicker skin type found elsewhere on the body? The lips are not more sensitive than the fingertips for example (see figures below), i.e., the pressure thresholds are similar (upper graph) and the two-point discrimination thresholds as well (lower graph).

Source: Dreamviews

Source: Institute Balseiro

I edited your question and removed my answer. You're right! Sensitivities are similar on fingertips and lips! That is interesting... I edited your question. +1 Feel free to roll back if you don't like the edits.

No no there is nothing to troll . I respect you mam . Thanks for your support :)

LOL - That was a typo :) I meant "Feel free to roll back" :-)

@Pi5 you need not address people as Sir or Ma'am. One reason is you may not know who is a Sir (male) or Madam (female) just from their profile names. Other reason is that respect can be shown without such salutations as well.

What did I say about cell differentiation? Same reason. Specialization of cells for a specific purpose so they express different genes than skin cells. They are the begin or the alimentary canal. This differentiation occurs very early on in development.


text:
What is this bug found in a garden in Utah?

Apologies for the poor quality of the photo.
I found this bug in a garden in Utah.  The body was flattish, with teal markings (lighter than it looks in the photo) with an interesting pattern of three dots along the back, and a pink cone projecting down to the rear.  It was about the size of my smallest fingernail.
From the searching I've done, the shape and the light "rim" on the outside of the shell look like a June Bug or a Stink Bug, but this one was not as green and the markings seem a lot more pronounced.
Is it a pest to be concerned about?

Based on the pattern of yellow spots it might be a Say Stink Bug.
Check out this list of common Utah stinkbugs

The 12 - 17 mm size is consistent with OP's description and the fact that this insect is often found on ornamental shrubbery is consistent with finding it in a garden.

The picture on Wikimedia is an even closer match.  So much easier to find when you know what you are looking for.  Thanks.


text:
What is the connectivity between on-center & off-center bipolar cells?

Do rod-photoreceptors only form synapses with on-center bipolar cells (and on-center ganglion cells in the next step)? If so, why is that?
Why do rod-cells only connect to on-center cells, while the cones connect to both on- and off?
Am I correct in saying that what happens in the bipolar cell as a response to light stimulus on a photoreceptor depends on i) Wether it is an on-center or off-center bipolar cell - and of course where the light stimuli is focused on the bipolar cell (periphery or center), or ii) What kind of receptors the on-center and off-center bipolar cells have? This is the part where I get really confused, because I read somewhere that what kind of receptors On/Off-center bipolar cell have, is not something set in stone? So saying that On-center bipolar cells have AMPA receptors and will, as a result of that, react in a specific way to less Glutamat release would be wrong?
How does this release of neurotransmitter works together with central / periphery stimuli. Let me try and use an example, You have an on-center bipolar cell. What will happen if light is focused on the center of this cell's receptive field? And what will happen if it is focused on the periphery? Let's just say that the light hitting the center of this cell's receptive field causes it to be depolarized. But is it really the light hitting the center which causes this effect, or is it the decrease in Glutamate release from the photoreceptor that causes this effect? If the latter, then what does it really matter if the light hits the periphery or the center of the bipolar cell's receptive field? The photoreceptor is hyperpolarized by light either way and less Glutamate will be released no matter what.
Also, in order for this to make sense, the light that enters the eye is absorbed by the photoreceptors pigmentmolecules, but some of the light also has to hit the receptive field of the bipolar cell in order to decide which signal to be transmitted? So not all of the light is absorbed by the photoreceptors then?
If the light hits the periphery of an On-center bipolar cell, you will have an inhibitory effect, is that right? And the other way around, if the light hits the center of the cells receptive field, you will get an excitatory effect? But I am curious as to how this also has to do with the kind of receptor that the on-center bipolar cell has (AMPA or MGluR6).

Please limit yourself to one clear question per post.

I suggest that you split this up into several simpler questions.

First off, the post is quite lengthy and contains various sub-questions. I will answer the first two questions in detail, but only after starting with an abstracted overview of photoreception in the retina. By the looks of it, your basic understanding of photoreceptors and secondary visual neurons is incorrect. Clearing the general neurophysiological workings of the retina up should get you on your way in understanding questions 3 - 6.
Synopsis of information flow in the retina: sensation of light
In Fig. 1 a schematic of the retina is shown. It basically consists of three layers. Layer one contains the photoreceptors, namely the rods and the cones. These primary sensory neurons absorb the light with photopigments and generate electrical signals in response to that. The photoreceptors, in turn connect to the second layer, namely bipolar cels, horizontal cells and amacrine cells. These cells are responsible for the center-surround structure of the receptive field of the last layer of cells (Fig. 2), namely the retinal ganglion cells in the front of the retina, whose axons pass across the surface of the retina and form the optic nerve (Kolb, 2017).

Fig. 1. Retina. source: Quasar Group
Note that there are no light-sensitive cells in the retina besides the rods and cones (barred the retinal melanopsin ganglion cells, but please forget that for the sake of simplicity). This one detail should basically clarify the sub-questions 3 - 6 in your post. The first two questions I will address next.

Fig. 2. ON and OFF center responses. source: McGill University
Regarding the retinal bipolar system and your first two questions:

Do rod-photoreceptors only form synapses with on-center bipolar cells (and on-center ganglion cells in the next step)?
  and
Why do rod-cells only connect to on-center cells, while the cones connect to both on- and off?

Rod bipolar cells in the mammalian retina are of the ON type. In contrast to the cone system, rod bipolar cell signals are split into ON and OFF components by amacrine cells. The cone system piggybacks then on the cone system; Rod ON signals flow from rod bipolars to amacrine cells to ON cone bipolar cells. Rod OFF signals are generated between amacrine cells and OFF cone bipolar cells (Nelson & Connaughton, 2017). See Fig. 3 for an overview of the retinal connectivity between rod and cone bipolar cells.

Fig. 3. Retinal circuitry. source: Nelson & Connaughton (2017)
References
- Gouras, Color Vision: In: Webvision: The Organization of the Retina and Visual System (2017)
- Kolb, Simple Anatomy of the Retina. n: Webvision: The Organization of the Retina and Visual System (2017)
- Nelson & Connaughton, Bipolar Cell Pathways. In: Webvision: The Organization of the Retina and Visual System (2017)

This is a great answer, I think it's worth adding that there are more than just ON/OFF Bipolar cells, about 11 according to Nelson and Connaughton. There's a bit more about specific types of OFF bipolar cells here: https://www.ncbi.nlm.nih.gov/pubmed/26500507. So it's possible that the different classes of bipolar cells have slightly different receptors, or respond slightly differently, so "not set in stone".


text:
small RNA bioanalyzer traces showing miRNA enrichment for sRNA-seq
I am bioinformatician trying to support some small RNA-seq experiments. All bioanalyzer traces that I have seen for RNA at the small RNA range show at peak at 22. But probably it depends on the protocol for the RNA purification (in this case only experience with RNeasy Qiagen).
I would like to know if some of you have some examples/experience of good bioanalyzer results after RNA purification that have been sequenced and got a big percentage of miRNA detected.
Currently I have a example where there is a broad peak at 25 and in some cases a small peak at 22. After sequencing there is almost not data. So at some point we lost the data. Trying to figure out if the bioanalyzer was good at that point, or already was something wrong.
thanks.


text:
Do macrophages get nutritional value from the pathogens that they eat?
X-posted on reddit AskScience here.
I know that macrophages engulf foreign bodies and transport them to various waste excretion pathways (sorry if the terminology is wrong), and if the foreign bodies are cellular in nature, they get trapped in phagolysosomes and get digested by enzymes.
Does the macrophage get any "nutrition" by destroying the cells, the same way that a person would if those same cells were to pass through their digestive system? Is there any chemical energy produced by the catalysis that the macrophage then uses, e.g. pyruvate for its mitochondria? Or scavenged cellular components that it can use to build its own cytoskeleton?

Maybe there is a study showing if  labeled phosphate of phagocytosed bacteria ending up in the macrophage DNA or mitochondria? I will search for this.

I've found an old paper using radioactively labeled bacteria to track their fate in macrophages. According to the data, both $^{14}$C and $^{32}$P are reutilized in the host cell.
COHN ZA. (1963). The fate of bacteria within phagocytic cells. I. The degradation of isotopically labeled bacteria by polymorphonuclear leucocytes and macrophages. J Exp Med. Jan 1;117:27-42.

It would make sense that nutrients are consumed from the breakdown of the phagocytosed object. Gotta love some of these old papers probing fundamental (yet relatively minor, by today's standards) questions

In this article it is described that starved macrophages 'consume' heat inactivated bacteria through phagocytosis with enhanced ability. Starving can also induce (macro)autophagy and the pathways are connected with phagocytosis,in the macrophages under investigation it was shown that autophagy did not play role in the enhanced ability of phagocytosis. The paper however does not mention anything about macrophages utilizing the resources obtained by the digestion of the bacteria. although it would seem logical. I'll keep looking.
Edit:
I found a text book that says:

in general cells of the macrophage series have two major functions. On f their functions ,as their name ("large eater") implies, is to engulf and, with the aid of all the degradative enzymes in their lysosomal granules, break down trapped materials int ismple amino acids, sugars and other substances, for excretion and reutilization.

Source : IMMUNOLOGY A Short course 3rd edition by Eli Benjamini, Geoffrey Sunshine and Sidney Leskowitz 1996 pages 23-24. ISBN 0-471-59791-0. I only have printed copy, but I'll try to find online version.
The other function is antigen presenting.
Thus I can say that yes macrophages and other cells do utilize resources from digested pathogens.


text:
Fastest and slowest action potential
When our instructor asked us about the speed of action potentials in cells, I told him that action potentials and two-wheelers travels at similar speeds. He thought that this is an 'interesting' way of looking at it.
Needless to say after the class I tried to figure out the minimum, average and maximum speed of action potentials in neurons. Wiki helped but its not authoritative. Some place it says that the fastest is 110 m/s and other place it is 120 m/s. While slowest one varies between 7 m/s (in Rana frog) to 0.5 m/s (Nociceptors) on Wiki. The average speed would be hard to calculate.
I am looking for any references where slowest and fasted action potentials are described. They would be interesting cases to write a note for classromm.

You can search on Bionumbers.
Here is what I got after searching action potential:

Speed of action potential along non-myelinated invertebrate axons of ~10μm diameter = less than 1 m/s
Action potential speed in myelinated axon = 50 ... 100 m/s
Velocity of action potential in pyramidal tract at 37°C (in Cat Felis) = 164 m/s

It offers you references for every number.


text:
Can a neuron make a synapse onto itself?
I was wondering if a neuron can make a synapse to itself? I suspect that it would be extremely unusual for a neuron to do this. Anyway, has anyone seen even a single instance of this?
Is the process by which a neuron 'knows' not to make a synapse onto itself is known?

A synapse from a neuron unto itself is called an Autapse. Not a whole lot is known about them. Tamas et al. (1) give a summary:

Van der Loos and Glaser (1972)proposed the word “autapse” to describe
  a transmitter release site made by the axon of a neuron and its own
  somatodendritic domain. In addition to their original Golgi study in
  rabbit neocortex predicting the existence of autapses, possible
  autaptic contacts have been described in dog (Shkol’nik-Yarros, 1971)
  and rat (Peters and Proskauer, 1980; Preston et al., 1980) cerebral
  cortex, monkey neostriatum (DiFiglia et al., 1976), and cat spinal
  cord (Scheibel and Scheibel, 1971). (...)
  Although autapses formed in cell cultures have been used extensively
  to study the physiology of synaptic mechanisms (Segal, 1991; Pan et
  al., 1993;Shi and Rayport, 1994), few proposals have been made for the
  functional significance of inhibitory autaptic innervation in
  vivo(neostriatum, Park et al., 1980; Aplysia buccal ganglia,White and
  Gardner, 1981).

Thanks for the references. I'll probably wait for few more days before accepting it as answer. Let's see if someone can comment on why autapse are rare.

@dilawar it would also be interesting to know what function,if any is done by such neurons. If they do not have a significant role they would most likely be rare.

There isn't enough research out there to explain the role of autapses however having read a selection of the latest research I can perhaps explain some of the proposed theory. Autapses may self inhibit or self excite. In the latter, one of their roles is thought to be to make a rhythmic action potential. This allows the brain to have an action potential which fires rhythmically if needed. Autapses of this nature have been identified in Interneurones for this purpose of continual activity.
Then there is even less researched areas. Imagine you need a neurone to fire twice to certain neurones but once to others or other similar requirements. A mixture of autapses with self inhibition and self stimulation properties can achieve this elegantly in a short space.
Things like this however aren't required frequently. Usually interconnecting neurones is sufficient, however possibly in places of high rhythmic activity or fine control these autapses may be helpful.
http://www.sciencedirect.com/science/article/pii/S0960982203003634


text:
Can geckos climb a wet surface?
We know geckos can climb vertically or even upside down a surface like glass. But can they do that on wet glass?

Yes , they can! (Obama)

Short answer
Yes they can, but with less efficiency.
Background
Efficiency of sticking to a glass surface decreases about 20-fold when the gecko's feet are wet (Stark et al., 2012). On dry glass, Gekko gecko holds on with about 18 N, which is about 18 times their own body weight. Hence, the gecko attachment system is over-designed (Knight, 2012). Wetted toe pads reduce the adhesive force significantly down to 0.9 N. A wetted glass surface does not significantly affect the grip of Gekko gecko, except after the gecko takes multiple steps. Hence, geckos can cling to wet surfaces, but only when their feet are not getting too wet.
Note that gecko attachment is not based on suction, such as the suction cups seen in octopus. Instead, geckos cling to surfaces with Van der Waals forces. Van-der-Waals-based adhesive systems take advantage of weak intermolecular forces between two surfaces. Upside is that these forces are not surface specific, allowing geckos to climb trees, rocks, walls and even glass windows.
Geckos achieve their strong attractive force to the substrate by utilizing small hair-like structures on their toes called setae, which are made primarily of keratin (Fig. 1). Setae contain flexible spatulae which make intimate contact with rough and even dirty surfaces.

Fig. 1. Left panel: Close-up of the underside of a gecko's foot as it walks on vertical glass. Source: Wikipedia. Right panel: Images of (A) dry and (B) wet setae using the same digit of an individual tokay gecko (Gekko gecko). The image in A was taken prior to exposure to water and the image in B was taken after 30 min of soaking in water. Source: (Stark et al., 2012).
The drawback of using Van-der-Waals forces for grip is that the Van-der-Waals forces only exist across surfaces very close together, and an intimate contact between the spatulae and the substrate is required for van der Waals forces to be effective in the gecko adhesive system (Stark et al., 2012). Wetting of the feet decreases the Van der Waals interaction with the surface.
References
- Knight, J Exp Biol 215, i
- Stark et al., J Exp Biol; 215: 3080-6


text:
How does an increased amplitude affect nerve conduction velocity?
My professor said that increasing the amplitude (the amount of depolarization e.g. depolarizing from -80 mV instead of -50 mV) leads to a greater conduction velocity.

Do you mean that larger-amplitude action potentials have larger speeds? In that case your example is incorrect, as an action potential generated from a resting potential of -80 mV has a larger amplitude than an action potential generated from a resting membrane potential of -50 mV.

@AliceD yes that's what I mean, -80mV has a larger amplitude and will have a greater conduction velocity through the neuron as compared to a 50mV resting potential. Why is this?


text:
Can people with AIDS get a fever?
It's my understanding that fevers are an immune system response to infection. Like the body's cells can take more heat than most viruses or bacteria.
So if that's the case then can you even get a fever if you have a non-functioning immune system due to AIDS?

With AIDS, the whole immune system is not non-functional. The condition results in a severe drop in CD4+ T-cells, which is what primarily predisposes AIDS patients to secondary infections.
Fever can be an immune response to infection, but it is not directly affected by the loss of CD4+ T-cells. Rather, fever occurs due to a complex cascade of events triggered by pyrogens, which causes a release of prostaglandin E2 (PGE2). In the hypothalamus, PGE2 signals a systemic response for the body to generate heat. More on the pathophysiology of fever can be read here.
AIDS patients still produce PGE2 in response to pyrogens (such as compounds produced by bacteria). Therefore, AIDS patients can certainly get fevers. In fact, AIDS patients may be more likely to get fevers because they may produce more PGE2.


text:
Fruit-bearing tree identification
Just moved into a new house in Puerto Rico and I found this tree in the back garden. Can anyone tell me what tree this is, and whether its fruit is edible?

Telling us where on Earth you're located would be helpful...

It is in Puerto Rico.

I think this is a Canistel (Pouteria campechiana):

The fruit are yellow when when ripe, but the form and also the leaves look very similar. The fruit are edible raw, you can find some more information here.

+1, but OP also asks if its fruit is edible?


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Visualising a subset of the tree of life
I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess at their evolutionary relationships?
The best site I managed to find so far is http://itol.embl.de/itol.cgi, which allows you to select specific species from the main tree to plot into a sub-tree, but the tree itself is rather small, so more detailed comparisons cannot be made.

So you mean a site that can produce a phylogenetic tree for a group of chosen species, based on an underlying database of phylogenetic relationships?

@fileunderwater Yes, that would work.

I have a similar project, this option you need could be added in the future. Take a look: http://dao.url.ph/tree/tree.php

http://phylot.biobyte.de/ performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables).
For example, the input of tree elements

Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia
  radiculosa,Paramecium tetraurelia,Tetrahymena
  thermophila,Cryptosporidium muris,Cryptosporidium hominis,Blastocystis
  hominis

generates the tree

Really cool resource!


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Request for an ID of two spider species found in Australia, NT
These two spiders were found in the Northern Territory in Australia in July (winter time). Both arachnids were shot during the night (I suspect them to be nocturnal), and both were found close to the ground. They do not build webs I think (way too big).
The upper spider is quite big, pretty much hand-sized, and about as big as a bird-eating spider. I think the guy with us told us it was a species of wolf spider (if I recall correctly - I'm unsure). The bottom hairy spider with its nice camouflage is somewhat smaller (if I recall correctly), but still well sized.
I have been searching for their names, but the amount of spider species is overwhelming and Australians tend to focus online resources on the poisonous ones. I'm fairly sure these two are harmless.

The bottom one is most certainly a Huntsman. Something akin to a Holconia immanis, aka the Sydney Huntsman. The picture is difficult but a characteristic Huntsman typically has 2 front legs that are longer than the back legs. And of course they tend to be larger spiders.

 Holconia immanis. source: Wikipedia
The top one looks like a type of brushed trapdoor spider (family Barychelidae), typically composed of such species as Idiommata scintillans, which are known as silverbacks or goldbacks depending on the color of the hair on their head (ref).

Idiommata sp., the 'Silverback'. source: Archne.org.au

I've taken the liberty to add some sources and pictures. Please feel free to undo. Thanks!!!


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E. coli bioreactor or E. coli fermenter?
I have a Requirements Specification in Russian for a "Fermenter" that would be used for "E. coli cultivation". This E. coli strain would be used to make a generically-engineered drug. The "fermenter" would consist of two "reactors" of 200 and 2000 liters, linked by a "pipeline system for transferring the half-finished product between them".
Would the whole thing be called a "Bioreactor" or "Fermenter", or are the two terms interchangeable here?

I don't think that there is a clear division between bioreactor and fermenter and the terms are often used interchangeably, but they do carry a difference in connotation (and marketing). The term "bioreactor" implies complexity, research driven, and/or maximal cell growth. Bioreactors are more state of the art and are used primarily for studying microorganisms or producing difficult to grow cells or for peak production of cells- while the term "fermenter" implies production of a substance besides or other than just the cells and might have the connotation of utility.  Fermenters also carry a historical connotation of brewing beer, wine, and other fermented food stuffs or materials. Also, it's important to bear in mind that bioreactors are used for fermenting, because bioreacting is not a real word.
If you just need a simple design for producing the bacteria or a bacterial product, then the term fermenter might be more appropriate. If you need computer control, or if you are using it to investigate/research growth and/or production parameters then you could call such vessels bioreactors without the risk of looking foolish. I think the best way to describe the difference is probably by example, but instead, I tried to itemize some of the distinguishing details, as follows:
Fermentors commonly have all or some the following elements: Agitator (of simple design), pH meter, temperature control (jacketed vessels are common), pipes for transferring nutrients, water, etc., and a sampling port (maybe). It may be made out of wood or clay, but if it is made from steel, plastic, glass, or other modern materials, that certainly wouldn't disqualify the term fermenter, but I would probably not call an oak barrel or a clay pot a bioreactor.
Bioreactors generally have the same things as fermenters, but bioreactors also usually have some or all of the following additional elements: oxygen probe, air or oxygen pump(s) and diffuser(s), other gas ports, additional ports/pipes for pH monitoring and control (often a programmable computer controlled pump is used for multiple solutions), electrolyte balance, radial or axial impellors- which operate at hundreds or thousand of RPMs, a vapor condensor (maybe), spectophotometer (for cell density measurements), nutrient processing data, and any variety of data measurement and/or recording is the often the point of interest, or when growth of tricky or finicky cells is necessary (especially like hybridomas, phytoplankton, or perhaps generally eukaryotic cell culturing). Also, there are different kinds of bioreactors like wave bioreactors (often in bioreactor bags on shaker tables instead of having an impellor).

In general, sterility is more important for bioreactors whereas many fermenters (or fermentation products, like yoghurt) can kind of take care of themselves, or a certain "cleanliness" will work. In both cases, steam sterilization is common. Again, the division is a bit blurry, and the terms might be used interchangeably by some people, like a jacket (light) versus a coat (heavy).
So, for your specific example, it would definitely be a fermentation system (not a bioreaction system), but regarding whether to call the vessels bioreactors or fermenters is more of an opinion, I'm afraid; but personally, I would probably say the fermentation system has two fermenters, since the idea is to produce a product and it sounds like they may be simple vessels. However, if the system has on-the-fly computational checks and balances, then I might be tempted to call the vessels bioreactors (if dazzle demands it).
Also, the smaller (200 L) vessel could be called an inoculation vessel without any connotations.


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ID of a pair of similar-looking birds in NT, Australia
I spotted these two birds in Yellow Water, Kakadu NP. They were not in each other's vicinity, so it's not a pair in the sense that they were mates (not that I can tell at least :-).
Their appearance is quite similar, so I'm expecting they are the same species of bird. They look like egrets to me, which are common water fowl in the wetlands of Kakadu. However, they may in fact be different species altogether. One has these speckles on the wings, the other one doesn't, by the looks of it.
Can anyone help me ID these birds?

Where: Yellow Water Region in Kakadu NP, Northern Territory, Australia;
Size: Not too big, my guess is about 20 to 40 cm from beak to tip of the tail (about a foot or so);
When: Southern hemisphere's spring, early September; the end of the dry season;
Time of day: afternoon.

I think these are most likely nankeen night heron (Nycticorax caledonicus). The only that does not fit is your size estimation. See the images (from here):

I think the first image shows a bird which still has parts of its juvenile feathers, which look pretty different (from here):

A lot of information about these birds can be found here and here.

How. On. Earth. Can. You. Manage. To. Do. This. So. FAST?  And so complete with the juvenile identified?! I've been searching for this for ages. :-)

The size estimate was rough. I gave a more proper range now.

@AliceD Magic. Seriously: I had luck being around when the question popped up and finding the right bird relatively fast :-)

@AliceD: what field guide do you use? The Slater field guide for Australia (http://www.publish.csiro.au/book/6145/) is very good, as is the  Australian Bird Guide (http://www.publish.csiro.au/book/6520/#author. Full disclaimer: my PhD supervisor is an author, but the plumage detail in ABG is stunning).


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Meaning of "Antibody is 50% w/w pure of interfering proteins"
From Google Patents, "Preparing antibodies from cho cell cultures for conjugation":

An isolated antibody or ADC is typically at least 50% w/w pure of interfering proteins and other contaminants arising from its production or purification but does not exclude the possibility that the monoclonal antibody is combined with an excess of pharmaceutical acceptable carrier(s) or other vehicle intended to facilitate its use. Sometimes monoclonal antibodies or ADCs are at least 60%, 70%, 80%, 90%, 95 or 99% w/w pure of interfering proteins and contaminants from production or purification.

Does it mean that even after purification the antibody solution may have an amount of impurities totaling to up to 50% of the antibody itself, in terms of weight? That the total weight of impurities may reach 50% of the antibody weight?
Maybe "an isolated antibody" is an antibody just after it has been produced? But the mention of "purification" confuses me. Why then such a high impurity content?

Patents are not the best source for reliable information, and obviously are not that readable. In this case they mean that of the purified product (usually that what comes of a protein A column I think), at least 50% of the weight is antibody. Or less (silly patents).
Commercial purification of antibodies (and proteins in general) is usually not that thorough. Most of the times what you'll get is just culture supernatant with cells removed, maybe some ammonium sulfate precipitation fraction or if it's thermostable just the proteins that are left after the production-solution is heated.


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Use of beta-2 microglobulin staining to assess frozen tissue sample integrity
In a Russian paper I'm reading the authors use staining for beta-2 microglobulin (B2M) to make sure that a variety of frozen tissue samples still express antigens on their surface, so that these samples could be used to assess the activity of an antibody they are researching.
The authors write that "since virtually each cell expresses B2M on its surface, this assay ensures that other antigens have remained on the surface of the examined cells as well".
Is there a special term for this kind of check? Is this anti-B2M staining a routine procedure, and are there papers dedicated to this procedure? I haven't found relevant papers.

I'd say it is not common practice to look for B2M, although I guess there will be heavy users would would disagree.
Without seeing the paper I cannot be sure, but I guess they are using B2M as a housekeeping gene, that is, a molecule whose presence and quantity is largely unregulated in living cells, and which is commonly used in labs as reference. Biological samples vary greatly in their content. It is hard to tell if a molecule is made or destroyed in response to a treatment, by merely measuring, and finding more or less of it. But if the ratio between the aforementioned molecule to an unregulated molecule goes up, you can be more sure it responded to the treatment. That is called an internal control. You may be familiar with "normalization to actin" or to GAPDH in immunoblot and qRT-PCR.
The use you are describing is diverging from the typical use of housekeeping genes in a lab, and not optimal for what they were trying to show. Since it's there in pretty much any tissue measured by immunoblot, B2M is expected to be present in any tissue assayed by microscopy. If a tissue slide lacks B2M, it is likely spoilt. But if it has B2M, it doesn't make it 100% certain that other, scarcer, more unstable molecules have been preserved as well. It would be ideal if they looked for the specific molecule they were studying; but if many of their samples were supposedly devoid of the latter, they had to replace the ideal with something more practical.
Note that I am using "molecule" in an ambiguous manner. With antigens in the referenced paper, it's obvious B2M is used as a reference protein. But housekeeping genes, including B2M, are also used as internal control for mRNA measurements ("gene expression").


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Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)
I came across the term ISHH in my document and discovered that it stands for In Situ Hybridization Histochemistry. I's translating to Russian a document that uses this abbreviation.
Example from the PubMed:

We then validated these findings by using a combination of tools, including the analysis of an additional brain region in an independent subject cohort, cross-validation with an alternate custom microarray platform, and follow-up with in situ hybridization histochemistry (ISHH).

Is there any difference between ISH and ISHH, or are these just synonyms for the same method, in situ hybridization?

Helpful histochemistry def'n: "the branch of science concerned with the identification and distribution of the chemical constituents of tissues by means of stains, indicators, and microscopy."

The term appears to be in use as a synonym.  PLOS ONE is a good journal, and in it Okubo, 2016 write "The protocol for ISHH was described in detail previously [22]."  Where [22] is Yamanaka, 2007, describing a classic ISH protocol.
Note that both papers use good old fashioned nuclear tract emulsion for S-35 labelled probes.  The ISHH protocol is in its own section separate from IHC.  It seems a bit odd because no literal "chemistry" is involved in recognizing the target - the RNA probe binds non-covalently and emits radiation.  However, as noted in the question discussion, IHC is formally defined (OED) as "the branch of science concerned with the identification and distribution of the chemical constituents of tissues by means of stains, indicators, and microscopy".  For example, though I have seen immunofluorescence and immunohistochemistry used to describe mutually exclusive visualization options, noncovalent binding of fluorophore-labelled antibodies is described as "fluorescent IHC".


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What is a "membrane holding potential"?
What is a membrane holding potential? I have come across this term but haven't been able to find a definition.
From "Voltage-gated sodium channels as therapeutic targets in epilepsy and other neurological disorders", legend to Figure 4:

Voltage-dependent and frequency-dependent inhibition of voltage-gated Na+ channels by Na+ channel blockers (A) Inhibition of Na+ currents by phenytoin is dependent on membrane holding potential. The top traces show currents evoked by depolarisation to 0 mV, with control (a standard physiological saline solution) and with 50 M phenytoin. In each of the four pairs of current traces, the larger trace is the control. The traces on the left were elicited from a holding potential of 130 mV, whereas the traces on the right were from a holding potential of 65 mV. The control current at 65 mV is smaller, due to greater inactivation induced by the more depolarised holding potential. Moreover, phenytoin is a much more effective blocker at the more depolarised holding potential. This is more evident in the bottom traces, in which the amplitudes have been scaled so that the control currents are the same size. (B) Phenytoin block builds up during repetitive channel activation. The graph shows normalised current amplitudes of whole-cell Na+ currents over the course of depolarising pulses to 0 mV, from a holding potential of 85 mV, applied at 2 Hz. Red dots indicate discrete measurements. Dashed line indicates a baseline to monitor decline in amplitude. (C) Voltage-dependent and frequency-dependent inhibition of Na+ channels by phenytoin and other antiepileptic or local anaesthetic drugs with a similar mode of action (green diamond) are qualitatively explained by a modulated receptor model. In this model, the drug binds with higher affinity to inactivated channel states than to resting channel states. Biophysical and molecular data suggest that the modulated receptor site is within the inner vestibule of the ion-conducting pore.

The membrane holding potential is the voltage level set by the experimenter in a voltage-clamp recording.


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Are sensory receptors neurons?
Background
There are many receptor types in the body, with various functions and various mechanisms of transduction. Receptor cells are considered to be part of the peripheral nervous system, as they are the first step in conveying information from the periphery to the brain.
Many receptor cells do not fire action potentials. Action potentials are widely considered to be a key property of neurons. Instead, receptors often operate by graded responses. For example, upon illumination photoreceptors gradually hyperpolarize. Cochlear hair cells gadually depolarize when the stereocilia are bent into one direction and hyperpolarize when they go in the opposite direction. Hence, many receptors are in fact analog sensors, whereas spiking neurons can be considered to be operating in binary (all-or-nothing) mode.
Given their similarities and differences, are receptor cells classified as neurons?
Credits: This question was formulated after a discussion with @OneFace on the question "Relationship between nerves and axons"

Lol I was planning to ask this! Good question though. I am specifically interested in knowing if mechanoreceptors can be considered neurons.

Lol - I thought to ask and answer. so it allows more input here. It is a question that has been on my mind for ages.

Short answer
Receptor cells are specialized neurons

Background
There are, globally, three types of neurons (Eckert's Animal Physiology):

Sensory neurons: these cells transmit information from external stimuli (e.g., sound, light, pressure), or from internal stimuli (e.g., blood oxygen level or head orientation);
Interneurons: these cells connect other neurons within the central nervous system;
Motor neurons: these neurons carry effector signals to effector organs, causing contraction of muscles or secretion by gland cells.

To illustrate these classes of neurons let's consider the visual peripheral system. Fig. 1 shows a schematized representation of the retinal circuitry, connecting the photoreceptors to the ganglion cells of the optic nerve (interneurons):

Source: Instituto Balseiro
The photoreceptor's response is graded. Notably, the bipolar cell, being an interneuron has also a graded response. The bipolar cells convey the signal, in turn, to the ganglion cells that translate the analog, graded signals into a binary, neural spiking code that enters the optic nerve.
Receptor cells are considered neurons, but they are highly specialized. Although interneurons may come in various shapes and sizes, they are not so specialized as receptor cells. The photoreceptor, for example, has a highly specialized dendritic region containing the photosensitive pigment and membrane stacks that capture light.
Another receptor is the Pacinian corpuscle, a vibrotactile mechanoreceptor of the skin:

Source: Pixgood
In this case, the receptor cell is in fact a myelinized and spiking neuron that functionally much resembles an interneuron. Just as the photoreceptor, the dendritic part does not connect to another neuron, but is highly specialized structure designed to sense a physical external stimulus. In case of the Painian corpuscle, it is an onion-like structure consisting of many lamina. These lamellar structures substantially change the receptor's response to mechanical stimuli. Specifically, it allows the corpuscle to respond rapidly to pressure changes and allow it to faithfully transmit vibratory stimuli.

Reference

Eckert, Animal Phsyiology:
 - Chapter 5 - The Physiological basis of Neuronal Function
 - Chapter 7 - Sensing the Environment

I think there are more types of neurons. Several cortical/hippocampal neurons cannot be called interneurons (a term generally used for modulatory neurons)

I agree with you that interneurons are often said to be inhibitory. However, I extracted this info from Eckert. A quick Google search indicates it is an ambiguous term, but Eckert's definition is pretty widely used.

I think you can add a statement that the gene expression profiles of these cells closely match that of other kinds of neurons (compared to other excitable cells). They also have the same developmental origin and therefore they can be classified as neurons. Regarding point#1: I had looked at expression data from retina as well as brain; I am just telling an observation from the back of my mind. Need to verify that.

Neither hair cells (fig 1) in the inner ear nor taste receptor cells are neurons. They are modified epithelial cells (i.e. during development, they come from non-neural ectoderm). Additionally, Merkel cells in the somatosensory system (which might or might not be doing the actual transduction) are also derived from skin.

@alexforrence - thus you are saying that embryonic germ layer defines what a neuron is? In the end, neural tissue comes from the neuro-ectoderm, which is basically derived from ectoderm. Hence, neurons arise from the ectoderm.

That's why I emphasized non-neural ectoderm. It seems like a pretty good place to draw a line in the sand. I don't think that this answer addresses the question completely; I'll try to write up one in the next couple of days.

@alexforrence - I am looking forward to your answer!

@alexforrence Question is what is the right classification method- gene expression profile or developmental origin. I don't think the latter makes sense when we now know about iPSCs. Even though these cells may originate from epithelial cells, I guess they are functionally neuronal.

@WYSIWYG I think that's where part of the confusion is coming from. Non-neural cells are allowed to do a lot of the things that neurons do (release neurotransmitter, de/hyperpolarize, etc.). Developmental origin and gene expression go hand in hand; the signaling during development (based on location of the cell) can drive or suppress expression.

@alexforrence - One of the main reasons I think receptors are classified as neurons is that their connecting afferents are called secondary neurons: http://en.m.wikipedia.org/wiki/Spinal_cord, meaning receptors are primary neurons

It's just confusing semantics. That refers only to the somatosensory system, where the primary sensory neurons sit in the dorsal root ganglion. Making a blanket statement across all sensory systems is the problem.

@alexforrence - it is the same in the retina (photoreceptors connect to secondary neurons) and likely this applies to other sensory systems as well.

I am confident receptor cells are neurons. Whatever their gene expression profiles or origin in embryonic tissue.


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What is the evolutionary reason behind human preference for salty foods?
It's been established that food palatability is related to it's caloric density. This hypothesis is used to explain why humans are partial to sugar and fat. But it is also said that humans are partial to salt.
Given that salt has no calories, are there evolutionary reasons that explain why humans have a preference for salty foods?

The body needs more than energy to survive.
Salt is vital to the body's function. Ions of sodium and calcium perform numerous vital functions, but are particularly related to the function of the nervous system and contraction of muscles. Accordingly, seeking out sources of salt makes sense in a natural environment in which salt is relatively unavailable.


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Can coronavirus contaminate public water systems?
It's been reported recently that people are panic-buying stuff as the coronavirus epidemic worsens. I've even noticed that the local grocery store is low on hand sanitizer, paper towels, and bottled water.
I did some reading and traced links back to the DHS's ready.gov website, and it recommended preparing a 2-week supply of food, water, medicine, and hygiene products for ISOLATION, though I expect if you're sick you're supposed to plan a trip to the hospital. Most of that makes sense to me. The exception is the supply of water. We have public water systems that send drinkable water to us, so why do we need to prepare a stash?
I tried finding an answer online, but I couldn't. The only guess I have is that coronavirus can contaminate the public water system, and it's not guaranteed water treatment will work. Who here has the know-how on waterborne viruses and water treatment to address this speculation?

What if one person at the water plant gets sick, and the place is closed down and the other workers quarantined until decontamination is carried out? NB: I know noting about water plants, but no, the water system won't get "infected".

SE Biology is concerned with the mechanisms of biological processes, and questions are generally answered by people with biological rather than medical or epidemiological expertise. Although I understand your concern about the coronavirus outbreak, your question is not about the biology of the disease and is clearly off-topic here. I advise you to consult more appropriate reputable sources of information, some of which are listed here.

do you know how I can close this as off-topic? I can't delete it because the site says it has an answer

Try medicalsciences.SE

Viruses can survive a few days in water, i.e. SARS can survive 22 days in lab grade reagent water and 7 days in pasteurized sewage. That is the time the virus takes to be at 99% of it's original concentration. (from "survival of surrogate coronavirus in water").
Viruses can also spread via swimming pools, i.e. hepatitus A and norovirus have been associated with swimming pools. (from "a review of waterborne viral deseases associated with swimming pools").
Boiling water will kill viruses. Children have very little reaction to the virus when they carry it, so it's likely that they act as a transmitter more than water does. I'm not worried about it at all by the way, just do what the doctors advise.

I f you deleted your answer the OP would be able to delete his question which he now recognizes is off-topic.

Perhaps transfer it to the medicalsciences.stackexchange.com

@com.prehensible
"Children have very little reaction to the virus when they carry it" - that's of interest to me as I wonder if it has been the basis of vaccine and treatment therapies research for other parts of the population. Please share further information if you have it. Thank you !

search for "juveniles immune coronavirus" "covid child immunity" you'll find some info although it is a complete mystery, nobody knows even what the T-cells for the new virus are and it's unkown why the effects are so variable.


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How to interpret figure on somatic mutation frequencies
In paper Mutational heterogeneity in cancer and the search for new cancer-associated genes, Figure 1 defines:

Somatic mutation frequencies observed in exomes from 3,083 tumour–normal pairs. Each dot corresponds to a tumour–normal pair, with vertical position indicating the total frequency of somatic mutations in the exome.

Is the figure representing with each point a tumor/normal pair because somatic mutations (differently from germline mutations) are assumed to not be present in the normal sample?


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How to preprocess htseq counts for gene expression (TCGA)
I want to prepare a matrix of gene expression to analyse TCGA LAML data.
The required data is available at TCGA LAML - Gene expression quantification.
The following is an example of the kind of data retrieved from the TCGA data portal:
ENSG00000000003.13  9
ENSG00000000005.5   1
ENSG00000000419.11  661
ENSG00000000457.12  1434
ENSG00000000460.15  1211
ENSG00000000938.11  405
ENSG00000000971.14  251
ENSG00000001036.12  786
ENSG00000001084.9   4423
ENSG00000001167.13  5038
ENSG00000001460.16  246
ENSG00000001461.15  2773
ENSG00000001497.15  1932
ENSG00000001561.6   1693
ENSG00000001617.10  55
ENSG00000001626.13  8
ENSG00000001629.8   4629

Each row displays, for each gene, the quantification of read counts by the htseq tool.
My question is, how do I have to preprocess the data (e.g. regarding gene length) before using data for subsequent analysis?
In this case I will not consider normalisation (such as loess) and batch effects removal (e.g. with combat).

This entirely depends on the type of subsequent analysis so the question isn’t really answerable without more information. However, in general I recommend you familiarise yourself with a standard RNA-seq analysis workflow.