text:
Can TGF beta family induce all somatic stem cells?
I think this is not possible.
Conclusion about this preview article TGF-$\beta$ family signaling in stem cells:

While TGF-$\beta$ family signaling regulates stemness of normal and cancer stem cells, its effects are diverse and depend on the cell types and physiological state of the cells.

Can TGF-$\beta$  induce all somatic stem cells?

What do you mean by induce?

@Chris Induction. You can think it as sending a positive signal. I think it does not need growth value. Only that some process is induced to start or made stronger - not inhibited here.

But what do you want to induce? Differentiation? Migration? Proliferation? Retreat into a nice? This is a pretty broad topic at the moment.

TO be induced by a TGF-$\beta$ ligand, a cell has to express one of its cognate receptors

Signalling in the TGFβ pathway normally puts a brake on the progress of cells through the cell cycle - it counteracts the action of myc for example, partly by regulating the expression of myc. In Burkitt's lymphoma myc escapes this regulation because of a chromosomal translocation, tipping the regulatory balance over to uncontrolled cell growth.
This anti-proliferative action of TGFβ signalling is so critical that you might expect it to be ubiquitous in cells, and the expression atlas entry for the TGFβ receptor is consistent with this.

So in naturally occurring somatic cells, the answer is yes because this antiproliferation action. Think now about induced somatic cells (those artificially derived from somatic stem cells). Can this same behaviour occur in all induced stem cells? I do not understand if this behaviour can proceed into processed cases and when we do not have such a behaviour on stem cells derived from somatic stem cells.


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What are the naming conventions for mutations of proteins?
I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50.
Please can someone explain the naming convention for this? i.e. what does the 'E' stand for? Does the number refer to the amino acid that has changed?

I know that usually both amino acids and the position are named, for example BRAF V600E means an exchange of valine against glumatic acid at position 600 of BRAF.

What your example is referring to is the change in the glutamic acid (E) amino acid (AA) residue, which is in position 36. This is denoted so that people/scientist would know what has been changed and usually there should be another letter after that number such as Y, which is tyrosine, to denote what it has been changed to, if it is a substitution. Then there is the delta (∆) symbol to denote deletion, and usually a number range e.g. 36-50 or just a number e.g. 70 appears after it to denote if a protein has been truncated in a certain AA range or if the entire protein from that AA is truncated, respectively. Sometimes (quite often now a days) the delta symbol is followed a protein domain name such as SH3 or RA to denote that a protein domain has been deleted and people use all sorts of naming variations for a protein that has been altered from its native sequence, which can be confusing!!
These are just some conventions, which isn't documented very well and you just figure them out when reading a few papers but I would welcome any edits for a good source for protein change annotations.
EDIT:
Since as pointed by Alan Boyd response, MalE is an E. coli gene encoding Maltose Binding Proteins, then my answer will not apply for any protein AA changes as correctly pointed out and elaborated on in Alan Boyd response.

MalE is the gene that encodes the maltose-binding protein in E. coli. If you look at the genotype of any E. coli strain you will see similar nomenclature. Everything in the answer from @Bez is correct, but in this case the E has nothing to do with glutamate.
The numbers are probably just arbitrary numbers that were assigned to the individual mutations, but you would need to provide a link to a source before this could be confirmed.

source: Stack Exchange

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

sort: votes


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Ni-NTA purification, problem with the chaperone protein
I'm trying to purify the protein by Ni-NTA affinity chromatography. It seems that my protein (size about 54 kDa) is co-purified with chaperone protein (probably GroEL  - as the band is around 57kDa).
I tried the method where 4M glycerol and ATP is added to the wash buffer 1 and then I incubated this with the resin for 2 hrs in 4C, but it did not help.
Has anyone met such a problem before? I will be grateful for any advices.

If chaperone proteins are not an expected binding partner to your protein/peptide fragment then you need to use imidazole in your lysis and wash buffer ranging from 1 to 10 mM depending on how stringent you want but 1 mM worked for me. Can go higher than 10 mM if the problem does not resolve but don't go too high since imidazole is also used to get the purified proteins off the nickel beads as an elution buffer!

My lysis buffer and first wash buffer contained 10 mM Imidazole, then I made second wash with 10% buffer B in A, and eluted protein with buffer B contained 250 mM imidazole. The band of chaperone protein appear in 'second wash' fraction  and 'elution' fraction but mostly in 'elution' fraction.

The go higher, try 25 or even 50 mM in your wash buffer (and maybe lysis buffer). I know someone had this very exact problem and increasing imidazole concentration solved it! I can't remember the exact conc they used but it was between 20-50 mM (that I remember for sure!). However it might effect your purification yield, but thats the compromise you might have to make. If you have high amounts of purified protein, then it shouldn't matter!

Also try increasing your wash numbers since two is far too low! Try 5 perhaps. I do 3-5 washes.

Also in what system are you over-expressing your protein since what you are seeing at 47 could be the result of post-translational modifications (http://www.embl.de/pepcore/pepcore_services/cloning/choice_expression_systems/comparison_expression_systems/index.html), which can increase the MW of your protein from 54 to 57 kDa! i.e. what I'm saying is how do you know you are co-puryfying a chaperone?

I did western blot, so I know which band is my protein - it is below the bigger band. It is T7 expression system which is started by adding IPTG to medium in final concentration of 0.1 mM.

ah, so you did an Ab based assay of your protein after pulldown with Ni beads and the second protein did not produce any signal? or you just did a coomassie stain in a SDS-PAGE gel? Although it's commonly said in science that in E. coli you don't get post-translational modifications but it does happen! (http://www.sciencedirect.com/science/article/pii/S1874391913004533) so my question is what have you done to exclude the possibility that the higher MW band is not your protein?

I don't see how "did a western blot" would not involve antibody-based staining, though.

I was confused as to whether at which stage (coomassie stain or WB) the OP was observing the extra bands when referring to WB (as commonly done) was not referring to commassie by mistake. This was just for clarification purposes.

Is it possible to clone your gene of interest onto a new plasmid (preferably with a GST/avidin/alternative tag)? If all else fails, this would probably remove the problem with elution.

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What is the best file format to store gel images?
I store many gel images which are included in my Latex notebooks. The geldoc software normally produces TIFF files, however, Latex only accepts PNG or JPEG.
If I am going to store only a single copy of my DNA agarose gel images, which format is a good idea? PNG, or JPEG? Is there a good reason to keep one copy in TIFF and one copy in another format for every gel?

I asked this here because an answer would require understanding of what sorts of information is recorded when a gel photo is taken, and how valuable they are for research purposes. I'm open to the idea of migrating it elsewhere (for instance SuperUser) if that seems more appopriate.

JPEG is a lossy format. So save it as PNG. All these are raster graphics; all of them store images as pixels only. The differences lie in the compression methods and resolution.

BTW This question appears to be off-topic because it is about image formats which is not in the realm of this forum.

You have to convert it into a .png. This is accepted by PDFLaTeX and since it is also a loss-less format this shouldn't be a problem. As this is a LaTeX question, this is off-topic here, and should be asked at tex.stackexchange.com, which I can really recommend for all sorts of questions around LaTeX.

@Chris I think the major issue here is not TeX-specific, it is more about good practices for documentation of scientific data.

@MadScientist Agreed.

I agree with Mad Scientist response. More often than not the images I produce from microscopy or imaging are TIFF (my raw data files) and TIFF (the raw data) is more reliable for things such as pixel densitometry analysis (used for quantification analysis).

Always keep the raw data files! This is always a good idea for scientific data, and the only exception should be if the raw data is prohibitively large and it is not feasible to store it completely. This is not the case for gel images, so I would always keep the originals, and then use a cropped and edited copy in a suitable format for documents.
The original image has the full amount of data, any conversion can potentially destroy data. For example, some imaging systems produce images with more than 8 bit color depth. Converting to another format will in many cases reduce the color depth to 8 bit as many programs and some image formats like JPEG don't support higher color depths.
JPEG is lossy compression, I would always prefer PNG. You might have to use JPEG at some point because of the file size, but that should be at the latest point possible.

No reason to ever use jpg. PNG is also a compressed format.

But Jpeg can compress by an order of magnitude more, by the nature of its lossy compression. PNG will compress in a similar manner to ZIP and so the gains are fair less.

@terdon The lossless compression of PNGs still results in much larger images than JPEG. I personally use PNGs for almost everything, but there are situations where you need smaller files and where JPEG can be acceptable.

True. I'm just leery of JPG since they can easily get corrupted. Personally, I'd probably just convert the TIFFs to EPS and deal with those.


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How is the fluoride in toothpaste absorbed?
How is the fluoride in toothpaste absorbed by our body? Does the tooth absorb the molecule directly, or is it absorbed by the mouth?
The answers to this question suggest that some materials can be absorbed by the mouth, but fluoride is absent. Additionally, many municipalities add fluoride to tap water which I should imagine is actually absorbed in the stomach by a different mechanism than that of toothpaste.
Note that toothpaste generally comes with stern warnings not to swallow. Looking at the ingredients it seems the only thing that may be harmful is the fluoride itself. Therefore I suspect that toothpaste has a much higher fluoride concentration than tap water, which supports the notion that its fluoride is absorbed by a different mechanism than tap water.

The chemical mechanism by which fluoride protects teeth is the remineralization of hydroxyapatite $\ce{Ca5(PO4)3(OH)}$ in the tooth enamel into fluorapatite $\ce{Ca5(PO4)3F}$:
$$\ce{Ca5(PO4)3(OH) \ (s) + F- \ (aq) -> Ca5(PO4)3F \ (s) + OH- \ (aq)}$$
This reaction occurs at the surface of the enamel, i.e. directly within the mouth.  The fluoride ions participating in the reaction are dissolved in the saliva and other fluids present in the mouth.
Thus, the fluoride does not need to be absorbed into any part of the body (although, as part of the remineralization process, it can be said to be absorbed directly into the tooth enamel), and, in particular, there is no need for it to be swallowed.  Indeed, because of potential adverse effects of high levels of fluoride when absorbed into the body through the digestive tract, swallowing strongly fluoridated dental care products like toothpaste or mouthwash should be avoided.
That said, any fluoride that is swallowed and absorbed into the body, e.g. through fluoridated (or naturally fluoride-rich) drinking water, can still contribute to the remineralization of teeth, simply because some of it will be secreted back into the mouth as part of saliva.
While the fluoride levels in saliva (assuming a safe level of fluoride intake) are much lower than those in, say, toothpaste, your teeth will be constantly exposed to the fluoride in saliva, whereas they will only be exposed to toothpaste for a few minutes each day.  Thus, while the rate of remineralization due to systemic fluoride may be much slower than that due to e.g. fluoridated toothpaste, the total amount of remineralization per day may well be of a comparable magnitude.

Thank you! This is exactly the information that I was looking for, including both the mechanisms by which the fluoride gets to the tooth.

From different sources, I think that it can be safely assumed that fluoride stays in the mouth and is absorbed by the teeth while brushing unless ingested (reference). Most dental doctors agree that the fluoride is not absorbed in the mouth and that it may be retained on the surface of your oral mucosa, where it is then available to help re-mineralize your teeth after acid exposure (reference).
Fluoride levels in toothpaste differs according to the company that is producing it.

It may appear after the label "Active ingredient" or as a component
  under "Ingredients" on the toothpaste tube. Whereas previously
  fluoride content was given as a percent of volume (% w/v) or weight (%
  w/w), it is now accepted that the most efficient method of informing
  people of the amount of fluoride in a toothpaste is to give the "parts
  per million" fluoride (ppm F). Most manufacturers now give fluoride
  content in ppm F. The EU has prohibited over the counter sales of
  toothpastes with a ppm F value of 1500 (reference).

Of course ingestion of the toothpaste will lead to the fluoride being absorbed by the stomach.This could increase the dietary recommended intake of fluoride leading to fluorosis and many other issues (reference). There is also a study estimating the fluoride absorbed from toothpastes through ingestion. In the study, it states that

Measuring changing fluoride levels in saliva appears to be an
  acceptable non-invasive technique for following systemic fluoride
  absorption(reference).

The 1984 issue of Clinical Toxicology of Commercial Products lists Fluoride as "more poisonous than lead and slightly less poisonous than arsenic". Lead has a toxicity rating of 3, Fluoride has a toxicity rating of 4 (reference).
Hence it is recommended that the brushing habits of your young ones be supervised to check ingestion of toothpaste and use the appropriate amounts of toothpaste for brushing.
Health effects of fluoride can be read about in this article.
The action of fluoride on teeth and treatments with fluoride is very comprehensively given in this article.

The tooth bone directly absorbs the fluoride, then? It passes through the enamel?

@dotancohen Most articles call it absorb but I would like to say deposited. and no it doesn't pass through the enamel but becomes part of it which is why the term absorbed is used.

Thank you. If the enamel is the final destination of the fluoride, then how does digested fluoride get there? By the saliva only?

@dotancohen For fluoride in the mouth, I would have to say that saliva would be the way to get to the teeth.

I'm a bit dubious about that "more poisonous than lead" quote: it's repeated (in various mutated forms) on many anti-fluoridation websites, but I wasn't able to find anything like it in the claimed source (which, apparently, is actually a book, not a journal issue). That said, Google provides only a rather inconvenient form of snippet search access to the book, so, without an actual copy, I can't be quite 100% sure that it's bogus.

@IlmariKaronen the same thing is repeated here http://fluoridealert.org/issues/health/ and the obsevation is made in terms of acute toxicity.

Fluoride is absorbed mostly in the stomach and small intestine.

Several aspects of fluoride metabolism - including gastric absorption, distribution and renal excretion - are pH-dependent because the coefficient of permeability of lipid bilayer membranes to hydrogen fluoride (HF) is 1 million times higher than that of F(-). This means that fluoride readily crosses cell membranes as HF, in response to a pH gradient between adjacent body fluid compartments. After ingestion, plasma fluoride levels increase rapidly due to the rapid absorption from the stomach, an event that is pH-dependent and distinguishes fluoride from other halogens and most other substances. The majority of fluoride not absorbed from the stomach will be absorbed from the small intestine. In this case, absorption is not pH-dependent. Fluoride not absorbed will be excreted in feces. Peak plasma fluoride concentrations are reached within 20-60 min following ingestion. ... Many factors can modify the metabolism and effects of fluoride in the organism, such as chronic and acute acid-base disturbances, hematocrit, altitude, physical activity, circadian rhythm and hormones, nutritional status, diet, and genetic predisposition.

Source: Buzalaf MA, Whitford GM. Fluoride metabolism. Monogr Oral Sci. 2011;22:20-36. doi: 10.1159/000325107. Epub 2011 Jun 23.
Fluoride concentration:

tap water: maximum contaminant level goal is 4.0 mg/L or 4.0 ppm [1]
optimally fluoridated municipal water: 0.7 parts per million (ppm) of fluoride ion (F) [2]
toothpaste for adults: 1000 ppm or 1100 ppm F from three fluoride compounds. These are sodium monofluorophosphate (MFP), sodium fluoride (NaF) and stannous fluoride (SnF2) [2].

When ingesting toothpaste, fluoride is less absorbed from dicalcium phosphate dihydrate toothpaste [3].

References:

http://water.epa.gov/drink/contaminants/basicinformation/fluoride.cfm
American Dental Asociation http://www.ada.org/EPUBS/science/2012/may/page.shtml
Drummond BK, Curzon ME, Strong M. Estimation of fluoride absorption from swallowed fluoride toothpastes. Caries Res. 1990;24(3):211-5.

If the toothpaste is not ingested, then how does it get to the stomach and small intestine? Just whatever seeps down the throat? Why not just take a fluoride pill then, which would give a more controlled dose, instead of relying on however uncontrolled amount seeps down the throat.

Dotancohen, if fluoride is in the digestive tract, isn't the most likely source fluoridated water?

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

authors: евгений иванов


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What does 'H' in BamHI stand for?
It's not explained on the wikipedia page. So if, apparently, 'H' is not relevant, why is it part of the name? And if it is relevant, why is it not explained?

These enzymes are named by the bacteria and the strain from which they are isolated. For BamHI this is Bacillus amyloliquefaciens strain H. In the beginning the enzyme was named BamI, which was later changed to BamHI.
See these two references:

Isolation of a sequence-specific endonuclease (BamI) from Bacillus
amyloliquefaciens H.
Recognition sequence of specific endonuclease BamH.I from Bacillus
amyloliquefaciens H.

The same is true for all the other restriction enzymes, so is EcoRI the first restriction endonuclease isolated from Escherichia coli strain R.


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How does heat shock transformation work?
What exactly happens when competent cells like DH5ɑ are heatshocked with DNA present? How does the DNA get inside the cells?
Specifically, why are all the steps necessary? What if you heatshock right after adding DNA? What if you don't put on ice after heatshock? What does the calcium chloride do? What actually happens when cells are "competent"? What governs transformation efficiency (besides obvious things like amount of DNA or cells)?
To make it clear what I'm talking about, I use a protocol like the following:

Take cells out of -80C and thaw on ice for 5 min.
Add 1 ul (~500 ng) plasmid DNA to 50 ul cells, mix gently with pipette tip.
Leave on ice for 30 min.
Put in 42C water bath for 45 sec.
Put on ice for 10 min.
Add 950 ul LB, put in 37C for 1 hour.
Spread 300 ul of the culture on LB-agar plates with appropriate selection.

I usually get thousands of colonies from this (in fact, often 1:10 or 1:100 dilution is necessary so I can actually get isolated colonies). Even if I skip the outgrowth, I still get hundreds.
I don't have my competent cell protocol, but basically I use that one rubidium chloride that everyone uses: DH5ɑ cells are washed with some buffers, suspended in a solution with CaCl2 and RbCl, then frozen in liquid nitrogen. I never actually measured, but usually the concentration of cells in the frozen aliquots is about 10 times as many as you would get from an overnight liquid culture (they are spun down and resuspended in a small volume).

I think it is still true that no-one knows "exactly" what happens. There is a piece of received wisdom that by growing cells at 37C then shocking them at 42C, the membrane becomes more fluid (true) and this helps DNA to cross this barrier. If anyone writes an answer with evidence for this I for one will be very interested.

@AlanBoyd I have heard many scientists also claim that nobody knows. I have always found it bizarre. How can such a simple, popular technique not be well understood? Are the experimental techniques to study it not available? Or does nobody bother because they think even if they figure it out, nobody will cite it or care?

I also learned/was told the same mechanism is responsible for E. coli transformation as written by Alan Boyd. This paper (Large-volume transformation with high-throughput efficiency chemically competent cells. Focus 20:2 (1998)) seems to get referenced a lot about the procedure; however, I do not know if the study offers any mechanistic explanation of heat-shock based E. coli transformation as I cannot seem to be able to access/find it.

Can't be sure about this but natural competence is affected by environmental stress.. May be it is the same case with chemically induced competence. See this post.

Heat shock transformation alters membrane fluidity creating pores:

A sudden increase in temperature creates pores in the plasma membrane of the bacteria and allows for plasmid DNA to enter the bacterial cell.

Reference: Journal of Visualized Experiments. Bacterial Transformation: The Heat Shock Method. 2014. http://www.jove.com/science-education/5059/bacterial-transformation-the-heat-shock-method

The change in temperature alters the fluidity of the semi-crystalline membrane state achieved at 0oC thus allowing the DNA molecule to enter the cell through the zone of adhesion.

Reference: Anh-Hue T. Tu. Transformation of Escherichia coli Made Competent by Calcium Chloride Protocol. 2008-2013. American Society for Microbiology

... heat-pulse (0 degrees C42 degrees C) step of the standard transformation procedure had lowered considerably outer membrane fluidity of cells. The decrease in fluidity was caused by release of lipids from cell surface to extra-cellular medium. A subsequent cold-shock (42 degrees C0 degrees C) to the cells raised the fluidity further to its original value and this was caused by release of membrane proteins to extra-cellular medium.

Reference: Panja S, Aich P, Jana B, Basu T. How does plasmid DNA penetrate cell membranes in artificial transformation process of Escherichia coli? Mol. Membr. Biol. 2008 Aug;25(5):411-22. doi: 10.1080/09687680802187765. PubMed PMID: 18651316.


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Local storage of NCBI database in MongoDB
My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I just learnt about MongoDB. Is it possible to somehow convert the sql schema code to mongoDB architecture? Also, are there any real advantages to implementing the dbSNP database as MongoDB?

This question appears to be off-topic because it is about pure bioinformatics implementation issues, not biology. Also: why would you want to use MongoDB, given you just heard about it and don't know the advantages?

Why bioinformatics is off topic in a biology website is beyond me.  Lots of biologists don't know how to do taxonomy or behavioral observation which was most common 40 years ago.  Many are molecular biologists, but its not required for all biologists.  Nobody can define what is in biology these days, why in such a hurry to declare what is out?  This is a highly subjective judgement.

@shigeta I usually put the line pretty far on the informatics side when deciding whether a question is off-topic, but this question is a bit far on the informatics side for me. The main question, how to convert an SQL database to MongoDB is better asked on a specialized site. But there is a question below that that might require some biology knowledge, and that is whether a NoSQL approach is useful for an SNP database.

@Venkat if you edit your question with indications of biological relevance, then it will assist its reopening!

I've played with mongoDb.  It is a nearly schemaless data store - each record (analogous to a row) can have nearly any entry name set except for a unique ID that mongoDb uses.  In practice most of your records will have the same labels and names
Leaving SQL for noSQL is turning out not to be a great win.  MongoDB will excel in retrieving records quickly and processing records by their content.  It has some constraints too compared to SQL.  It requires that the main index be stored in RAM, which might or not be an issue.   For very large datasets mongoDB can be configured to shard the data automatically - splitting it up over a cluster of machines for high throughput fast processing applications.
If you need flexibility in your data record and you have a good machine (or a good cluster) to put it up on it could offer some advantages. We have a reasonable store of dbSNP on a recent MySQL machine and it performs okay.  Not thousands of transactions a second, but we can do reasonable throughput of record processing.


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How do penicillin resistant bacteria grow slower in the presence of penicillin?
We put 2 flasks inoculated with Bacillus cereus in 37⁰C: one with 100μg/ml penicillin +  50μg/ml chloramphenicol and the other without penicillin. We found that the OD is higher in the one without the penicillin. These strains are supposedly penicillin resistant as verified by growing them in a test-tube containing penicillin (5mg/ml) at 30⁰C. It contradicts my hypothesis that they should have the same growth rate because of the $\beta$-lactamase secretion that would destroy the penicillin. I can't find any explanation in the web.
help me

You need to add a lot more detail for any answer to be possible. Which kind of bacteria were in there? Were they resistant to Penicillin. Did you work sterile?

the bacteria was bacillus cereus. as far as i know weve worked sterile (they gave us the bacteria). i didnt mention two other things: 1. we onother erenmyer that contain penicillin (0.2 ml) and chloranphenicol (0.1 ml). 2. the real changes in the OD began after 90 min.

Can you please edit your question and add information about the bacteria, resistances and, media and all the other things that may be important. Additionally: This sounds a lot like a homework question, so please add some interpretation of yourself.

You could also show a diagram with OD measurements over time for both cultures.

Resistance to penicillin in B cereus is due to chromosomal genes, but not all B cereus strains are penicillin resistant. Do you know for certain  that you used a resistant strain?

@ebeginner To make it short: You used a penicillin resistant strain of B. cereus and the culture that was grown without the presence of penicillin was growing faster? How was the difference in OD? Was it 0.05 or 0.5 or what?

the differnce was between 0.05-0.1.

i dont know for certain. but later on we put the bacteria in a test tube that contain penicillin (in a higher concentration) and it pruduce penicillinase.

forgot to mention: we put that in 30 degrees

@ebeginner So please use the edit function of your question (directly below it) and edit your post so it contains all relevant acts of the experiment. I don't want to collect them from the comments. If you could add a figure with the growth curves, that would be great.

ey chris, ill add the curves later (they are not available now). do you think that the low concentration of penicillin (100 ml/u) wasnt inough to induce penicillinase ? later we put it in 5000 ml/u and it induce it/

@ebeginner One last time: Please add all info to the question. Then I will answer them.

@ebeginner: I edited your question.. see if it is consistent with your experiments. Add more details such as 1) When did you finally take OD measurements 2) Did second flask contain chloramphenicol 3) Did you perform any other tests for penicillin resistance

Your hypothesis is incorrect.
You must be assuming that lactamase destroys the antibiotic with perfect efficiency. This is incorrect.
You must be assuming that the population will remain genetically stable. This is doubly incorrect. Firstly the penicillin will select highly resistant bacteria which suffer a greater fitness burden from expressing the lactamase. Second, in absence of penicillin, spontaneously arising mutants which suppress the lactamase are free to proliferate.
You must be assuming that carrying capacity is identical for Pen+ and Pen- media. Trivially, you claim your experiment disproves this, but the assumption is also baseless since this need not be the case.
Furthermore, your results are inconclusive. You lack crucial controls, such as putting the bacteria from the Pen+ into Pen- and vice versa to see if the growth difference is intrinsic. You have not only failed to provide the error of your measurements, but have failed to provide the quantitative measurements themselves, so we do not even know if the difference is statistically significant.
Lastly, there are several basic things which you could rightfully expect us to assume, but have nevertheless failed to provide. For instance, you do not say if the populations are clonal.

Can you provide a ref. for "suffer a greater fitness burden from expressing the lactamase," and explain why it would slow growth, if that's what you are getting at? Thanks.

@daniel Assuming not every cell in the population expresses the exact same amount of lactamase, it stands to reason that some of them make more of it than others. It is well known that expressing arbitrary proteins, or antibiotic resistance, by itself constitutes an energy burden. I cannot provide references unless OP clarifies the experiment.

Not questioning your assertion, just wanted to read further if you had a ref. The question is a bit vague and I think your second paragraph is correct. If the results are qualitatively accurate it's an interesting question. How is the difference in growth rates allocated between the 'fitness burden' of resistance and the ability of non-resistant mutations to proliferate in the pen.-free nutrient? That's why I was interested in a ref if you have one. +1


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Can botulinum toxin be grown or kept from denaturing in an UNWRAPPED 50 pound hay bale?
Botulinum toxin is the neurotoxin protein created when botulism spores grow. The requirements for growth and/or for keeping the toxin from denaturing would seem to be very difficult to create in bale of hay.
There are well documented incidents of botulism in horses who are eating hay, all the references I found were centered around hay in large plastic wrapped bales.
I have been involved in an event where the presumed DX is botulism secondary to ingestion from hay from last year.  In this case the hay is second cutting timothy hay (making it 6 plus months old), in rectangular 50 pound (22 kg) bales that are not wrapped, have been barn kept, and when purchased from the vendor where stacked in rows 4 feet wide, by 6 feet (2 meters) high. The bale then spent more then a week on an shelf (chrome platted heavy wire) with good air circulation.
Three pet house rabbits appear to have been effected. with 2 dead and one recovering from a case of descending paralysis.  Several tests are underway, but my understanding is that it may be difficult to conclusively show either the botulism in the rabbits, or significant presence of 'botulinum toxin' or 'clostridium botulinum' in the hay (samples from the mangers of effected animals are being tested).
Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria?
Note
If there is an awareness of a plant based neurotoxin that would cause similar symptoms that may be growing in the hay field please offer that in an answer at Gardnening.

It's been a long time since I knew the ins and outs of botulinum toxin, but I do seem to recall that it's pretty resilient. Botulism is pretty distinct as far as symptom progression. I'll see if I can do more research and return.

@MCM, thanks it would be really great if you could shed some light on this.

As an addendum to Spinorial's answer, and after some research, the Center for Food Security and Public Health specifically lists hay / grass / decaying vegetable matter as a potential source for C. botulinum growth in their (very informative) Botulism PDF.

All species of Clostridium can produce spores, dormant
  forms  of  the  organism  that  are  highly  resistant  to
  disinfectants,  heat  and  environmental  conditions  that  kill
  vegetative  cells. These  spores  can  survive  for many  years
  until  favorable  conditions  allow  them  to  germinate  and
  grow. C. botulinum spores are common in the environment...
  ...
  Different  strains  or  groups  of  C.  botulinum  may  have
  somewhat  different  requirements. For  instance,  the  acidity
  necessary  to  inhibit C. botulinum  type C strains  is reported
  to be pH 5.1 to 5.6, but other organisms can survive a lower
  pH. Each group also has an optimal, minimal and maximal
  temperature  for  growth.  For  example,  some  group  II
  organisms  may  be  able  to  grow  in  foods  at  refrigeration
  temperatures  (3-4°C/ 37-39°F), but group  I organisms  and
  type  C  toxin-producing  strains  are  inhibited.  Because  C.
  botulinum  does  not  compete  well  with  other
  microorganisms,  growth  is  more  likely  to  occur  if  other
  bacteria  and  molds  have  been  killed  or  inhibited.  C.
  botulinum  spores  can  survive  cooking  and  some  food-
  processing  conditions  that  kill  vegetative  cells,  then
  germinate and grow in the cooked food.

As for your question...

Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria?

Could the toxin survive? Probably. The toxin itself isn't particularly hearty, BUT...
Could the spores survive (and go on to create the toxin)? Definitely. The spores survive direct heating/boiling, very low pH environments, and desiccation. For instance, botulism from canned foods can occur from eating the food (and toxin) directly - but you're supposed to throw it out if it look suspicious because even if you cook it and inactivate the toxin, the spores are still present after cooking. The spores can find anaerobic environments inside the body and germinate, then produce toxin afterwards.

Clostridium botulinum toxin is present ubiquitously in soil. As such it is more than plausible that hay bails, which come into contact with soil can and I should expect almost probably will be infected with these bacteria. However it is not the mere presence of the bacteria itself which causes poisoning, it is the toxins they produce when the appropriate conditions are met. These toxins are produced as a consequence of spore formation.
Traditionally in human cases, the presence of toxins has been linked to home canned foods, where there is an anaerobic environment with a ph < 4.5 (http://cid.oxfordjournals.org/content/41/8/1167.full). It is conceivable that such an anaerobic environment exists within a hay bail (even if not wrapped). The following site from the ontario minestry agriculture and food (http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_haylage.htm) suggest that the pH certain methods of hay bailing have pH < 5. This would seemingly confirm hay as potential source for botulinum toxins.
With regards to testing the hay for C. botulinum I would expect there to be a very high chance of finding this, due to soil contamination, however this does not imply this was a definite source for poisoning. A more conclusive test would be for the toxin. So in summary it is logical to suggest that hay could be the toxin source, but this does not mean it was the source.

This is a very good answers, full of information.  I choose to award the bounty to @MCM as that answer more directly addresses the root question about the toxin surviving. Thank you both for your answers.


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Is it theoretically possible to treat filaggrin deficiency with a dietary supplement?
http://f1000.com/prime/reports/m/3/2/

"Filaggrin is a highly abundant protein expressed in the uppermost part of the epidermis that is critical to the formation and hydration of the stratum corneum—the outermost dead cell layers responsible for the barrier function of the skin. Filaggrin deficiency leads to a 'leaky' skin barrier that allows higher than normal water loss (explaining the dry, scaly skin), as well as allowing entry of allergens through the epidermis where they trigger inflammatory and allergic immune responses (atopic eczema and allergies)."

Not that such a supplement exists, but is it biologically possible to treat filaggrin deficiency with something taken orally?

THe cause of the deficiency has to be ascertained before thinking about therapy. FOr e.g it could be because of improper diet or it could be because of a mutation.

It may be possible to upregulate the filaggrin gene in skin cells. https://www.ncbi.nlm.nih.gov/pubmed/24055295

Direct replacement of a protein through oral supplementation is extremely unlikely. Our digestive tract is designed to break down proteins into their constituent amino acids.
In the stomach pepsin breaks proteins into polypeptides which then pass into the small intestine. At this point (second part of duodenum) multiple enzymes (proteases) enter having been released from the pancreas in response to eating. These enzymes further reduced the polypeptides into smaller components such as you end up with component parts of the original protein.
These component parts are then transported across the intestine into the blood through cells lining the intestinal lumen (enterocytes). Enterocytes also have proteolytic action on long chains of amino acids.
As a result of this process, the original structure of the ingested protein is destroyed. However you do end up with the constituent amino acids. If your fillagrin or any other protein deficiency is as a result of lack of nutrients then in response your body may be able to synthesise the required protein. If on the other hand your deficiency is due to a gene defect, despite having the building blocks for the protien you will continue be deficient.

I highly doubt it. Filaggrin is a human protein which is expressed in the skin and stored as profilaggrin. The profilaggrin has a molecular weight of about 350 kDa (which is rather big) and is cut into smaller units of filaggrin, which then crosslinks kreatin fibers of the epidermal keratinocytes. This enhances the durability of the skin. Mutations in the filaggrin gene have been associated with dry skin and excema. See here for more information:"Filaggrin - revisited."
To supplement the profilaggrin, you would have to bring this rather large protein into the skin. You could think about making a cream with the smaller filaggrin in it to promote crosslinking of the upper skin. The question here would be how effective such a treatment ist and how deep the crosslinking would be.

Yes, according to this study 4g of histdine administered daily does the trick: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5634381

Welcome and thanks for your answer. Link-only answers are discouraged. It's great to link a research paper, but try to extract the answer and underlying proof from the paper and synthesize your answer, preferably with other sources as well. As of now, acknowledging the post is referenced, it still is a question comment rather than an answer.

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


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What is Pan for in pan-caspase?
A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?

can you tell the context of that phrase? If in case of inhibitor it could mean that it inhibits all caspases. Similarly with antibodies: a pan-caspase antibody would bind to all caspases.

there is no specific context but i now realized that it is usually used as pan-caspase inhibitor in the articles i was looking at. just to be sure: can we then say that pan is the opposite of specific?

yes you can say that.. but we generally use the term "caspase-x inhibitor", where x is that specific caspase

The term pan, in my opinion, is perhaps one of the most vague that exists in science! I can partley answer this question (ironically as vague as the term pan) by referring you to the term pan-neuronal. A pan neuronally expressed genes has features, which include the expression of many "generic" genes required non-specifically for neuronal function, such as components of the synaptic vesicle machinery, so pan-neuronal genes are not neurone class specific (http://www.wormbook.org/chapters/www_specnervsys/specnervsys.html). So with that token pan-caspases are a term referring to a general caspase activity/function/structure and not a specific caspase type activity but I would welcome any corrections or edits to this response.

Pan is referring to all. So a pan-caspase inhibitor is a molecule that inhibits all caspases indiscriminately.
Note that pan means all in Greek.


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Science experiments at home with Minimal Cost
What is a good recipe for making agar at home for a minimal cost? Are there materials that could be found in the kitchen cabinet?

why not just buy dehydrated agar powder and add water and sterilise through autoclave (which is basically oven or steam baking)? Thats how they make it in media kitchens!

Dried agar (Agar agar) is used in food recipes. You can add potato/dextrose or whatever you think your bugs will like and it's already very cheap. It's often in the oriental food aisle or baking supplies aisle of grocery stores. Surely you don't want to grow the algae?

Instructions
1
Place a coffee filter in a strainer and hang the strainer over the opening of the clear bowl.
2
Slowly pour the broth into the filter, making sure that the broth doesn't overflow from the sides of the filter. If the filter becomes clogged with particles, remove the used filter, replace with a clean filter and continue pouring the broth.
3
Remove the strainer and filter from the top of the bowl and observe whether the broth appears clear (i.e., there are no suspended particles in the liquid). If particles are floating in the liquid, repeat Steps 1 and 2 using a second clear bowl and a fresh coffee filter.
4
Place the pot on the stove and pour the clear broth into the pot.
5
Add 16 ounces of distilled water to the pot containing the broth.
6
Turn on the stove and adjust the heat to medium-low. Heat the broth to a simmer (i.e., small bubbles appear near the side of the pot).
7
Add 1 teaspoon of the agar-agar powder to the simmering broth (approximately 2.5 grams) and stir the mixture until the powder is dissolved. Make sure to stir the powder to dissolve and prevent the gelatin from sinking to the bottom of the pot (where it can burn).
8
Repeat Step 7 until all agar-agar powder has been dissolved in the broth.
9
Continue stirring the broth for about 1 minute to ensure that all powder is completely dissolved.
10
Turn off the stove, place the lid on the pot and let the liquid cool for at least 15 minutes.
11
Arrange the sterile petri dishes in a row for easy assembly, but do not remove the lids.If desired, place a trivet to hold the warm pot. If you're using lidded custard cups instead of petri dishes, sterilize the custard cups by placing the cups and lids inverted (upside down) on a foil-covered cookie sheet and bake in the oven for at least one hour at 375 degrees Fahrenheit. Make sure the sterilized cups and lids are completely cooled before use.
12
Carefully touch the outside of the pot to check that it is warm to the touch and place the pot on the trivet. If the pot is too hot to touch, wait at least 10 minutes to let the pot cool.
13
Remove the lid and set aside. Place the ladle in the pot.
14
Remove the lid from one petri dish and dispense nutrient broth to fill the dish halfway. Cover the dish immediately with its cover.
15
Repeat Step 14 for each of the petri dishes.
16
Allow the nutrient broth to solidify in the petri dishes for at least 1 hour, undisturbed.
17
Gently shake the petri dishes side to side to check that the nutrient broth has completely solidified. If the broth is not completely gelled, wait another 20 minutes before checking again.
18
Cover a table or flat surface with a roll of paper towels to create a sterile work area. Tear off a sheet of paper towel and fold it four times to create a thick, rectangular wad. Set this wad on one end of the work area.
19
Transfer one petri dish to the sterile work area and remove the lid. Carefully turn the dish over and place one end on the side of the folded wad, so that it lies inverted and slightly angled (with a slight gap by the paper towel wad).
20
Turn the lid over and place it above the petri dish on the sterile work surface. If water droplets appear on the lid, gently shake this moisture off before placing on the covered surface, but do not touch the inside of the lid.
21
Repeat Steps 19 and 20 for each petri dish, positioning one side of the inverted dish on the side of the previous dish rather than the paper towel wad. The dishes will appear as a staggered set, with gaps on one side so that excess moisture can evaporate.
22
Look at the inverted petri dishes to check whether the moisture on the sides of the plates evaporated. Once all moisture has cleared, turn the plates right-side up and immediately cover with the lids for use.
23
Inoculate the nutrient agar on the plate by wiping a swab containing the desired culture on the nutrient agar surface before covering with the lid. Turn the petri dish over so that the solid is on top. Store the inoculated petri dish with the solid on top for culturing and the lid on the bottom to catch any moisture, loose particles or growth.

What type of broth is involved?


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Electrodes in the brain and 'repetitive orgasms'
The advent of chlorpromazine in 1955 put an end to one of the more bizarre chapters in American psychiatry.$^1$ Dr. Robert Heath implanted wires or delivered injections of acetylcholine (a neurotransmitter) deep into the 'septal regions' of the brains of men and women with various physical and mental disorders. His discovery of the brain's 'pleasure center' actually preceded the discovery of the same center in rats by about 20 years [Baumeister, below, at 272].
In one of his papers$^2$ Heath describes intense orgasmic experiences on the part of his patients in response to his treatments, which he dutifully records on EEGs.
His description of Patient b-5 is especially interesting. He relates: "The patient became more attuned to her environment, answered questions more rapidly and accurately, and solved simple mathematical problems with more ease...and in most instances, within another 5 to 10 minutes, this [heightened attunement] culminated in repetitive orgasms." [Heath, below, at 12].
In addition to refreshing my interest in solving simple mathematical problems, this article made me wonder whether this area of research had been resumed in some form. Many of the ethical and technical problems discussed in Maumeister's article seem surmountable, especially in light of computer-aided visualization of brain structures. Not to mention that a kindred treatment, ECT (electroshock), which can still actually be done involuntarily, has seen something of a comeback in the U.S. since the 1940s. ECT is basically controlled destruction of brain tissue, which seems to cast Heath's work in a kinder light.
So my question is whether this thread has been taken up or whether, as one VIP put it, the absence of evidence is evidence of absence. I was unable to turn anything up.
Thanks for any enlightenment.
$^1$ Baumeister, The Tulane Electrical Brain Stimulation Program: A Historical Case Study in Medical Ethics (2000), J. of the History of the Neurosciences 9 (3): 262-78. See page 270.
$^2$Heath, Pleasure and Brain Activity in Man, (1972) Journal of Nervous and Mental Disease 154 (1): 3-17.

This question belongs to Cogsci.


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Prokaryotic Ribosomes
During bacterial protein synthesis, when ribosomes attach to the cytoplasmic membrane and form a polysome, to what molecule are the ribosomes attaching? Is the polysome held to the cytoplasmic membrane by just a single connection between one ribosome and the particular attachment molecule?

Do "ribosomes attach to the cytoplasmic membrane"? Membrane-bound Ribosomes Define the Rough ER. Ribosomes are not membrane bound. A polysome represents a cluster of ribosomes, bound to a mRNA molecule.

Here is a good article on bacterial protein synthesis: http://mmbr.asm.org/content/69/1/101.full

According to "Microbiology: An Introduction" by Batzing, Ch. 2 p. 24, "During protein synthesis, bacterial ribosomes attach to the cytoplasmic membrane.."

According to Smith et al., 1978, bacterial ribosomes don't necessarily bind directly to the membrane, but through the nascent chain, in which case nothing is truly attaching to anything..


text:
level of organisation of proteins

Is there any disulphide bond in a quaternary structured protein?
If yes, please provide examples.
In tertiary structured proteins, what is(are) the most important characteristic(s)  of tertiary structured proteins?
a) globular in shape
b) have both alpha helix and beta sheet
or, is there any characteristic that I do not mention?

Aha, this is not a homework question, just that I feel like I do not understand protein quite thoroughly. Anyone can help?

Interesting protein structure trivia question!
Disulfide bonds form more or less spontaneously when two sulfhydryl groups from cysteines are close enough to each other in the proper orientation in a reducing environment.  So given this, its possible for them to exist, even though in most cases the distance between the cysteines in a disufide bridge is small and intra-domain.
Inter-domain disulfide bonds are rare.  The most common example is that some immunoglobulin domains in antibodies have an intrachain disulfide bridge.  I also found reference to one in a starch synthetase from rice.
In tertiary structure, the overall shape is an important one.  Globular shapes are the most common, but elongated protein folds, triangular folds,  rings, disk-like structures made out of wedges are popular examples of how protein structures can do amazing things when selection requires them to.

Surely immunoglobulin molecules are excellent examples of the involvement of disulphides in the quaternary strucure of proteins?

sorry i didnt use the same term, but i did mention this.

Apologies Shigeta, I just didn't see it, possibly because I was still puzzled by the term 'intra-domain". I know what that means, but it doesn't map on to quaternary in my opinion.

i didn't bother to explain.  I felt that a disulfide between two cysteines in different domains on the same chain would be a result of similar forces as a quaternary disulfide.  I didn't really have to go there in the reply though


text:
Do mitochondria use ATP in order make another ATP from glucose?
Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?

During ATP production through the citric acid cycle, some ATP is used to transport necessary molecules for the reactions.

piruvate molecules are actively transported into the mitochondrial matrix [2]
two NADH equivalents from glycolisis are transported into the mitochondrion and consume two molar equivalents ATP [1]
protons leakage across the mitochondrial membrane leads to reduced ATP from NADH and FADH2 [1]

In theory, one molar equivalent of glucose can generate 38 equivalents of ATP. The actual number is only 25 [1].

References:

Wikipedia contributors, "Citric acid cycle," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Citric_acid_cycle&oldid=610117265 (accessed June 26, 2014).
Wikipedia contributors, "Mitochondrion," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Mitochondrion&oldid=614223751 (accessed June 26, 2014).


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Why do flies fly in circles?
Lying on my bed, doing nothing I recently noticed flies usually fly in small circles, right under my ceiling lamp. Worth noting - the lamp was off as it was middle of a day. And those flies kept flying like this for hours, not moving anywhere else! Later I noticed it repeated every day, pretty much the same pattern. Why is that?

Flies use any object they can find as a landmark.

The flies patrol well-defined airspaces underneath landmarks like lampshades. ... Male flies approach a landmark from below and, in the absence of other flies, settle to patrol an airspace close to the landmark. A second male approaching the same landmark chases, or is chased away by, the patrolling fly when it comes too close and may eventually settle to patrol 10–30 cm below the airspace occupied by the first fly. ... The position of male patrolling stations relative to the landmark suggests that females might arrive at landmarks from the side (and not from below, as males do), thus crossing the dorsal visual field of patrolling males.

Source: Jochen Zeil. The territorial flight of male houseflies (Fannia canicularis L.) Behavioral Ecology and Sociobiology. August 1986, Volume 19, Issue 3, pp 213-219


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Has an artificial symbiotic relationship ever been created?
Have 2 organisms ever been introduced to create a symbiotic relationship that doesn't occur in their natural environment?

Can you please give your definition of symbiotic relationship? No everybody uses the same definition. Some use it as an equivalent to mutualism. Some uses to describe any kind of relationship and I've heard people using it as "obligate mutualism or commensalism".
What kind of barrier to their relationship existed in their natural environment? If you consider a symbiotic relationship to be any relationship and you accept any barrier preventing their interaction in nature, then almost any example of introduced species would answer your question.

@Remi.b I've been thinking on this, and it's a good question, but I'm not sure how to answer it. I was just thinking of pairs that don't normally interact in nature, but were introduced (with or without genetic alteration) in an artificial setting to induce a cooperative or symbiotic relationship with benefits that either replicate their symbiotic relationships with other organisms, or else create a new beneficial relationship.

does domestication count?

Here are some examples:

symbiosis between genetic modified yeast cell populations (Shou W et al. 2007)
symbiosis between green algae and embryonic chick connective tissue (Buchsbaum R et al. 1934)
symbiosis between EcoBot II and microbial fuel cells (Ieropoulos, Ioannis, et al. 2005)

Do not forget domesticated animals that we now keep as pets. It's not unreasonable to argue that the relationship between dogs/cats and humans has a symbiotic character. The pet gets foodand shelter whereas the owner benefits in other ways, e.g. companionship, deterrence of enemies, herding,...

I thought of that initially, but the mutual benefit varies wildly when considering abusive/neglectful pet owners, and like my cat for example, she offers nothing in return. She overeats and ensuingly throws up on the regular, stands in my way wherever I'm trying to go, and deters very few enemies...very few indeed.

So if your cat actually offers nothing, why do you still own her? What I want to say by that: the pure presence of a cat often suffices to make their owner more comfortable. If a cat would not have nothing to offer, no one would have one as a pet...
Anyway, you would certainly agree that at least dogs perform useful tasks in some cases.

well I do enjoy giving her smooches on the whiskers, so I suppose there is some benefit.  I'm not sure if that qualifies as a symbiotic relationship, but maybe a re-defining of the word is in order to include the aforementioned smooches.


text:
How specific is the adaptive immune response?
When you read about the adaptive immune response, you are often told that the response is specific to each pathogen - that the response is tailored. My question is - to what extent is this really true? And if it is true, how is the response tailored?
I understand that the B cell receptors (and, consequently, the antibodies produced by plasma cells in response to a pathogen) are highly specific. A pathogen will bind specifically to a B cell receptor on a particular B cell and particular antibodies will be produced for that pathogen. Again, T cells are specific for each pathogen.
But, it strikes me that there doesn't seem to be that much variation in what antibodies do. Each antibody is particular to its pathogen, but all antibodies work by doing the same few things, e.g. opsonisation, or inhibiting viruses from infiltrating cells. Yes the antibodies may be specific, but to what extent is it true that the antibody will produce a specific response to a specific pathogen? I mean, does the antibody for staphylococcus affect staphylococcus differently from the way the antibody for listeria affects listeria?
Again, each CD8+ Tc cell is specific to its pathogen, but they then seem to go about killing their target pathogen in very similar ways - inducing apoptosis or lysis via perforin and various cytotoxins. So, again, would the CD8+ Tc cell for influenza respond differently to the CD8+ Tc cell for norovirus?

You are correct, specificity is in the antibody etc, but the killing/clearing mechanisms are the same in all cases.

The adaptive immune response is highly specific and is made to fit a specific antigen. The antigen binding sites are located on the ends of the two short arms of the Y-shaped molecule, as seen in the figure below:

The recognition site is made of the ends of one short immunoglobulin chain and one long chain. The ends (shown in yellow in the figure) are also called variable regions and are the key to the big variety of different antibodies.
When B cells develop, there B cell receptor (which is basically a membrane bound antibody) is tested if it reacts to components from the own organism. If not, they are released into the periphery (blood stream). These B cells are then called naive, since they haven't come in contact with an antigen. They express a B cell receptor which usually only has a weak affinity to an antigen - but the body produces quite a wide variety of these cells. (see the second figure).

When the body comes in contact with an antigen (like a virus), it is taken up by the so called professional antigen presenting cells (dendritic cells, macrophages, B cells) of the immune system, broken down into small pieces and these are presented to the immune system. This activates the affinity maturation of the B cell receptor, somatic hypermutation and finally the clonal selection of the cells, which produce the antibodies with the highest affinity (the strongest binding) to the antigen.
There are estimates that the human immune system can produce around 10 billion different antibodies. This variability is achieved by the genetic variability of the mutation of the variable region of the antibody (the whole process is nicely explained here).
For further information on this topic I can recommend reading the following articles:

Development of the immunoglobulin repertoire.
Immune receptor editing: revise and select.

The reaction of the body afterwards is always the same, as you state yourself. The specificity of the adaptive immune response is "only" mediated by the specificity of the antibodies. This also makes the system very strong against new pathogens, since only one part of the system needs to be adapted, while the cascades behind it (like apoptosis) are always the same and can be activated fastly if needed.
This can cause some problems, too. Think about self-antibodies, which occur in autoimmune diseases. Here the body can not distinguish between a legitimate immune response against a foreign antigen and those, which are from the own body.

Rather than saying that it is specific for an antigen, won't it be better to say that it is specific for an epitope ?

To make it more prescise: It is specific for an epitope of a specific antigen.


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Is there a good explanation for this swarming pattern?
A film clip would be helpful here. A few days ago I noticed a swarm of newly hatched flying bugs about 20 feet away from me with the sun behind them so the shape of swarming (such as it was) was easy to make out. Several times, after creating various spiral shapes or chaotic masses they returned to a sort of 'holding pattern' which I either never noticed or never saw before. To a pretty good approximation the bugs arranged themselves in what seemed like an "oscillating drum head" pattern that is well approximated by a rotated sinc function. The peak at zero is a little exaggerated here but the bugs were more or less dispersed on a shape like:

subject to a light breeze and continuous adjustment. I know that people have studied swarming behavior and made models but are there any that account for this one? It has a lot of significance in ODEs and engineering but I never associated it with swarming behavior.
Thanks!

It is a fascinating phenomenon. There is some research on swarming behaviour, see e.g. Collective motion, and in general some research by Tamas Vicsek and Ian Couzin research groups.

I watched some youtube videos but couldn't find any swarming that looked like rotated sinc function.
The following is nothing but the guesses of someone who doesn't know much about swarming!
One pattern that is often found (through computer simulation and empirical observation) in swarming is a simple 2D rotation.

Let's first consider only the static form of the shape you observed. This shape might be the consequences of multiple rotating layers. Do you remember what kind of dynamic had the individuals within your sinc function?
Oscillation is a pattern that is also sometimes observed in swarming. The oscillating behavior might be the result of inertia. Just like a pendulum, individuals that are far away from the group accelerate continuously in the same direction up to the point they reach the middle of the group. Then they undergo a inverse acceleration up to the point they reach a null speed and then start their cycle again. This inertia depend on the number of neighbors they align their movement on are low. For example, it has been shown in I don't remember which species of birds (I can't find the reference) that each individual align their movement according to only the 6th closest neighbors.
For more information about the 3 basic rules (separation, alignment, cohesion) that allow swarming behavior, have a look to the wiki page
In short, I hypothesize that thanks to the underlying 3 basic rules of swarming, the patterns of rotations and inertia together allow to explain your observations.

Yes, I can't rule out multiple rotating layers. +1


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Equation for accurate prediction of PCR yield
It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 grams of DNA. This is clearly absurd and not the case.
Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an upper bound - but even so, a very uninformative one), and in practice, yields will fall far short of it because:

Every single duplex of DNA does not denature at each cycle
Primers do not bind to every single molecule of DNA at each cycle
Not every DNA strand gets bound by a polymerase at every cycle
Not every polymerase that binds manages to complete the entire product in time in every cycle
The reaction inhibits itself by depleting dNTPs
The heat denatures the reaction by degrading enzyme

In fact, cursory examination of qPCR output often follows saturation kinetics:

Mathematical methods for modeling qPCR are obviously well developed.
My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?
For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).

An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.
Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in terms of copy number or in terms of moles; the number of DNA molecules of interest is what the reaction is operating on, and the mass of product generated is a function of the length of the product (and, to a lesser degree, on the composition of the product).
The following discussion is sourced from this URL: https://www.csun.edu/~hcbio027/biotechnology/lec3/pcr/p.htm
According to Perkin-Elemer, copy-number amplification of 100,000 fold of the targeted sequence of DNA can be expected from a PCR with 0.1 ng of Lambda phage DNA (a well-characterized and standard DNA isolate) in a 100 µL reaction with > 25 cycles of denaturation, annealing, and extension.
In the above 100,000-fold amplification example, if the targeted amplicon were to be 500 bp in length, the estimated molecular-weight of duplex DNA of 500bp is 325,000 g/mol (based an average base-pair having a molecular mass of 650 g/mol).
The Lamdba Phage genome is 42,502 base-pairs in length.
42,502 bp × 650 grams/mol/bp = 2.762×10^7 grams/mol.
0.1 ng Lambda DNA -> 0.1×10^-9 grams.
0.1×10^-9 g ÷ 2.762×10^7 g/mol = 3.619 × 10^-18 moles.
3.619 × 10^-18 moles × NA (Avogradro's Number) = 2.179×10^6 copies, or 2,179,000 copies.
2.179×10^6 copies × 100,000 = 2.179×10^11 copies.
2.179×10^11 copies ÷ NA × 325,000 g/mol = 1.176×10^-7 grams of sequence.
1.176×10^-7 grams is equal to 0.117 µg or 117 ng.
An amplification yield of 100,000x after 25 cycles would mean at each cycle 1 template would yield 1.58 templates for the next round of synthesis.
How was this calculated? If c is the number of copies made per round of synthesis, then:
c^25 = 100,000 = 10^5
so c^5 = 10
and so 5(log c) = log 10 = 1
so log c = 0.2 and c = 1.58 (approximately)

(Or you could calculate the 25th root of 100,000 on a calculator, if you prefer.)

If we obtain 1.58 copies instead of the theoretical maximum of 2 copies, then the efficiency of the reaction could be said to be 79% (because 1.58/2.00 = 0.79).
One reason this calculation is important is that a slight loss of efficiency is magnified through the amplification. A reaction may appear to have not worked if the efficiency drops (in each cycle) by just a few percent. Optimization is critically important in the polymerase chain reaction.

Here is a useful website for calculating the molecular mass and number of copies of double-stranded DNA molecules based on their length in base-pairs. http://cels.uri.edu/gsc/cndna.html

The equation is correct, but there's an additional asymptotic limit to a maximum concentration of product depending on the starting concentration of NTPs, template and primer pairs in solution too.


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Is there any measure by which the Germans today could be called a genetically superior race?
The Nazi eugenics programs are well known. Despite their controversy, I cannot find any indication on their effectiveness. Were there ever and studies done on the (arguably subjective definition of) superiority of German genetics due to (or possibly in spite of) these programs?
Do we even have a way to objectively measure genetic superiority or fitness? In the case of a lack of such a measurement, the idea could be qualified for purposes of this question as:

Lower instances of genetic disease.
Lower instances of mental retardation, criminal tendencies, and mental illness.
Higher general academic achievement.
Healthier, longer lived population.

Note of course that I am not promoting or condoning eugenics in any way. I am only interested in knowing if the results were effective (i.e. achieved their goals), without comparing the programs' possible benefit against its obvious drawbacks. All contemporary discussion of the programs concentrate only on the drawbacks, unfortunately.
EDIT: Before anyone accuses me of bigotry or crimes against humanity, I will mention that my grandfather lost all seven of his siblings, his parents, and all the rest of his entire family to this same regime. My grandmother lost five of eight siblings, both parents, and all the rest of her entire family to this same regime. What these people did to Jews, Gypsies, and the feeble was terrible and I do not excuse it. This question is intended only to concentrate on the scientific issue of forced, deliberate genetic improvement, a form of "breeding" if you will.

There was already some discussion on the topic.

@har-wradim: Thank you, I'm surprised that I could not find that! Please mark this as a dupe (already answered), I don't have permissions to do so on the SE site.

That answer still has no answer, so I'm able to mark yours as a duplicate. You can close it yourself if you wish.

@har-wradim For me it is not a duplicate. This question is not about the efficiency of Nazi eugenic programs, but about the intrinsic genetical superiority of German race (or lack of thereof).

@PiotrMigdal I have nothing against this question, I'm even "glad" that this topic got a new chance.

But in any case there is some overlap, so I would suggest to edit this question to remove this 'effectiveness of eugenics' part (since it is a dup). And in any case, saying "Is it true that X because of Y?" is much harder than "Is is true that X?". See my answer - an I am trying to answer only the simpler variant.

To the extent this question means anything it could be asked without the inflammatory context. As it is, it is too broad and reflects badly on the site. It is also partly a dupe.

Why should they? This would imply that there is some "superiority" in some humans above others. This programme selected people by external criteria (tall, blonde, blue eyes), why should any of this lead to superiority? Genetics is much more complicated plus not everything that we are is inherited in our genes. A lot is society and behaviour. The question doesn't really make sense to me.

I think this is very much a duplicate of the question mentioned above & (despite the authors efforts) agree with Daniel that it reflects badly on the site - the underlying question is largely inoffensive but the concept of superiority is not necessary and likely to cause unnecessary deviation from the question itself. Personally I think that the essence of the question is "Has the eugenics program implemented by the Nazi regime left any real effects on genetics & genetically caused traits in the populations of the people it affected?"

I agree that the question as intended was a dupe, however the comments and Piotr's answer are terrific and the truth is, I find the direction that the question went in to be a valuable contribution. Thus I've edited the title to reflect the new direction in which the answer went and to keep it distinct from being a dupe. It is also less inflammatory. Thank you all for your wonderful contributions and insight.

I am leaving the word 'superior' aside (it's ill-defined and strongly valuing).
In any way - unlikely. If any ethnic group is 'superior' (at least, intellectually) - then, ironically, Nazi main victims - Ashkenazi Jews. But while there is some genetic component, it is impossible to disentangle it from societal and historical factors. Here are some links, is you are interested.
When it comes to Germans, as far as I remember, they are not a group genetically distinct from, say Poles. Yet Slavs were considered by Nazi also an inferior race, to be enslaved or eradicated.
In any case, culture and socioeconomic factors seem to be much stronger than (relatively small). In particular, for Germany itself, there was a huge difference between West and East Germany, prior to the fall of Berlin Wall. It can be hardly explained by 'genetical superiority' of West Germans. An excerpt from Race, IQ, and Wealth by Ron Unz:

Consider, for example, the results from Germany obtained prior to its 1991 reunification. Lynn and Vanhanen present four separate IQ studies from the former West Germany, all quite sizable, which indicate mean IQs in the range 99–107, with the oldest 1970 sample providing the low end of that range. Meanwhile, a 1967 sample of East German children produced a score of just 90, while two later East German studies in 1978 and 1984 came in at 97–99, much closer to the West German numbers.
These results seem anomalous from the perspective of strong genetic determinism for IQ. To a very good approximation, East Germans and West Germans are genetically indistinguishable, and an IQ gap as wide as 17 points between the two groups seems inexplicable, while the recorded rise in East German scores of 7–9 points in just half a generation seems even more difficult to explain.

See also The East Asian Exception to Socio-Economic IQ Influences and The Myth of American Meritocracy (on how ethnicity can affect admission) by the same author.

Thank you. As for being the same race as the Poles, I thought that the Germans are Aryans, genetically distinct from Slavs but rather the same people as the Persians / Iranians.

@dotancohen Then if you mean than, it is a duplicate of Did the eugenics program in Nazi Germany have a measurable effect? (with answer: WW II with all of its killings, migrations, changes in economy and politics had much stronger impact, and most likely it is impossible to separate it). And no, Germans are not closer to Persians/Iranians than to Poles. This Aryan thing is a myth, not supported by science.

I agree that as intended the question was a dupe, however the comments and your answer are terrific and the truth is, I find the direction that the question went in to be a valuable contribution. Thank you very much for your learned insight. I learned more than I expected to learn. Oh, and being an Ashkenazi Jew I find the linked Wikipedia article astounding, though I find it disturbing that the topic is notable enough to warrant a Wikipedia article.

@dotancohen In any case, SE has no-dupe policy. So I guess unless you edit question, it will be closed. If you like my answer, could you edit it to ask about superiority of Germans, without speculations or relations to effectiveness of any eugenics? (In short: if there was some truth in Nazi propaganda on the genetic superiority of Germans) BTW: I didn't note your surname. :) With respect to topic notability - it is hard to miss a great number of scientific and cultural achievements (especially in the 20th century) due to people of Jewish ancestry.


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What is this red liquid produced by a fungal colony?
In a jar, where I had some orchid plants, a fungi start growing few days ago. I removed the plants and let the fungi to expand and grow more.  After some days, red drops started to appear on the surface of the fungal body (images below).
Does anyone know what this probably can be or recognize the fungi? Is it an antibiotic or something else?

Take this with a massive pinch of salt (which is why I'm posting it as a comment) but I guess the reason the colonies have turned red is that the fungi processes Fe(III) so perhaps this review might shed some light as to what it is you are looking at (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC100245/).


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Confusion regarding seedless grape and the normal process of germination
In general, does seedless grape by definition contains seed or is the seed small enough that the process of ingestion creates the illusion that there is no seed?
If the latter is true, is the seedless grape capable of germination?
Lastly does the fruit part of the seeded grape function as an incentive for animals to ingest it and provide nutrients for seeds in the form of feces, or can it function as nutrient itself?
Thanks

The seedless grape technically has a seed, but the seed has no hard outer shell and is microscopic/invisible. These seeds aren't viable. Technically you could isolate out the seed tissue from the grape and grow it in specialized germination medium, but that process also works for any other part of the grape plant. Hooray cuttings! Certainly the seedless grape would not grow if you put it in the ground.
The fruit part of the seeded grape is 'bait' to get animals to ingest the grape and carry the seeds within inside their digestive tracts. The goal is distance, but the surrounding feces provides bonus nutrients. The fruit is not designed to feed the seedling grape, but instead to act as bait for herbivores. The grape is mostly sugars and water, which makes them excellent bait but not amazing plant food. Plants can make sugar from the sun and pull water from the ground, but nitrogen and phosphorus are harder to come by.
Contrast fruit (which are for animals) with coconuts, which are examples of large fruit storing lots of calories for the seedling itself. The coconut flesh isn't as sweet as fruit, and it's much harder to get at.


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What are these strings used to describe animals?
For example, what's a $dt^{sz}$ hamster? (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/).
What's a Rgs9-Cre/+;gtROSA/+ mouse? (http://www.sciencedirect.com/science/article/pii/S2212877813000719)

Those describe the genotype of an animal (or plant, virus etc.).
The nomenclature can be very varied and domain-specific, but for those two examples:
$dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred during breeding, without specific human intervention) which gives predisposition to seizures.
They are described in this paper:
Spontaneous seizures: a new mutation in Syrian golden hamsters. - Yoon et al. - J Hered 1976

SPONTANEOUS motor seizures with tonic muscle spasms and severe paralytic states have been observed in inbred line BIO® 86.93 of Syrian hamsters
  (Mesocricetus auratus auratus). These animals had been inbred for 23 generations and maintained by Bio-Research Consultants. The seizures, which last from 2 to 5 hours, can be precipitated by mild stress, and occur in
  animals between the ages of 30 days and 60 days. Breeding tests have shown that the condition is transmitted as a simple recessive; accordingly, the gene symbol
  sz is proposed for this condition.

The lowercase indicates that the mutation is recessive that is, you need to have two copies of the mutation to see its effect (its phenotype).
dt comes from dystopia, another symptom of the mutation.
As for Rgs9-Cre/+;gtROSA/+ mouse, the genotype is a bit more complex.
Whenever you see /+ it means that the animal is heterozygous, that is, it only carries one copy of that specific gene.
For instance these are transgenic animals producing the bacterial protein Cre under the Rgs9 promoter. A promoter is a sequence of DNA that controls the expression of a certain gene. In this case the DNA sequence for the promoter of the gene Rgs9 was attached to the DNA sequence for Cre. This new construct was then inserted into the genome of the mouse.
The result is a mouse in which the cells that normally transcribe the Rgs9 gene also produce Cre.
This mouse line was then crossed with a reporter mouse line called gtROSA26, which expresses a certain protein called $\beta$-galactosidase in a Cre-dependent manner.
The gene for the galactosidase is present in all the cells, but only where Cre is present (in our case the Rgs9 positive cells) it will be transcribed.
Eventually the crossing leads to the expression of $\beta$-galactosidase in Rgs9 positive cells.
$\beta$-galactosidase has the nice property that it can change the colour of certain chemicals to blue, which allows to easily visualize the cells that produce it. This can help you answer questions like: "where is the Rgs9 gene transcribed?".
Wikipedia has a neat page on Gene nomenclature with lots of links to nomenclature guidelines.

These strings are specific genotypes of these animals. They often denominate mutations or transgenes.
For the hamster $dt^{sz}$ stands for dystopic, the sz comes from the first denomination of this symptoms as seizure. See here for a brief explanation.
For the mouse you have both alleles named: Rgs9-cre is a transgene, + in this context always stands for the wildtype. So this mouse has one allele of the transgene Rgs9-cre while the other allele is wildtype for it. Transgene constructs with the cre-recombinase can be inserted into the genome upon induction, which is a useful tool to modify genes. This needs to be done in mice which harbour the gtROSA transgene, which denominates a specific genetic background for the mice.
See here for more details:

"Promoter traps in embryonic stem cells: a genetic screen to
identify and mutate developmental genes in mice."
Identification and targeting of the ROSA26 locus in human embryonic
stem cells.

Thank you! Do you have any suggested books/articles/material for me to read as a primer to this material? I need to be familiar with this stuff to be working in a research lab.


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Does the most common definition of "allele" include a change in phenotype?
I'm prepping an activity for my biology students on cystic fibrosis. There are about 2000 different mutations of the CFTR gene that cause CF. Since the final phenotype is pretty much the same, can I still claim that all these mutations represent different alleles?
I like to point out that genes tend to have more than two alleles - it's something that students really struggle with. But if every allele needs to have a different phenotype based on the standard definition, then this isn't ideal.
Thanks for the help.

I agree with the answer given by @Bez. The problem arises because the term "allele" was coined in an era when the only way to observe (or infer) the existence of different forms of a gene was through the associated change in phenotype (i.e. genes were not observable directly). Now that we can document single base changes via sequencing, the link to observable phenotype has been completely severed, but the idea of alleles as alternative forms of a single gene is still useful.

Yes, allele is an alternative form of the same gene which can be produced through any variations/mutations of a gene, such as deletion, segmental duplications, inversions, insertions through transposons, even a SNP or point mutation (http://en.wikipedia.org/wiki/Allele) and as correctly stated many alleles do not produce any observable/discernable phenotypic variation. A gene can have many alleles in a given population, but do not confuse allele with gene homologues (which I suspect what you were alluding to above in the second paragraph), which are similar versions of a gene such as RIN1, RIN2 and RIN3 (http://homepage.usask.ca/~ctl271/857/def_homolog.shtml).


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Are Asian people genetically predisposed to be shorter than Europeans?
People in different countries have different average heights. For example, Wikipedia's article on human height states that Australian men have an average height of 177.8 cm, and Australian women 163.8 cm, whereas Japanese men have an average height of 170.7 cm, and Japanese women 158 cm.
Are these differences in height due to environmental differences between people in different countries, or does genetic differences play a role?
In particular, are Asian people (people from Far East countries like Japan) genetically predisposed to be on average shorter than people who are of European descent?

Related: Height and natural selection in humans?

I would advise against the use of the term "genetically programmed". "Genetically predisposed" would probably be a better term

Note: This is too long for a comment, so I will post it as an answer, even though it is merely an example and not a full answer to your question.

An example of the environmental influence on human body height can be found in the statistics assembled by the Swedish conscription service from 1840s to 2010 (when general conscription ended). During this time the average height of Swedish men (aged between 18-21) increased from 167.4 cm (in 1841-45) to 180.2 (in 2004), an increase of 12.8 cm or 7.6% (Werner 2008, unfortunately in Swedish, but tables 2 and 3 should be understandable). Here is a graph of the data found in the paper:

During this time Sweden has gone from what would have been a bottom-20 position in the wikipedia list of average human heights (close to contemporary India or Mexico) to a top-10 position. This is clearly not due to changes in the genetics of the population, but to changes in the environment (probably mainly due to nutrition). I know that many countries have gone through a similar development, and this is usually refered to as a secular change or trend in body height and weight (see e.g. Roche, 1979 and Loesch et al., 2000 for further examples).
Nothing of this naturally contradicts that genetics is a powerful determinant of human height. However, it shows that the average height in two countries cannot be compared in a meaningful way (at least if you want to infer genetic differences) without knowing something about the nutrition status and the average living conditions in both countries. The situation is rather that genetics is setting the limits of potential height, but that environmental factors will determine the actual outcome. This is also discussed in the paper above, but there are certainly better references to be found in English. In the reference list (#9, #10) you can also find examples of how there are also well-known genetic determinants of e.g. short stature in some human populations (in this case decreased insulin-like growth factor I receptor expression and function in African Pygmys, see ref #10)

Why is it clear that the height change in Swedish men is not due to genetics?

@canadianer Because we don't expect such dramatic changes to happen in frequencies of gene alleles in a human population of that size given the shortness of the period, absence of severe bottlenecks or strong directed selection and polygenic nature of the trait.

See @har-wradim answer. Remember that 150 years is only a couple of human generations, and this drastic change is would require an extremely strong selection pressure. For the most part, this increase in height is caused by the shift from a poor mostly agricultural population to an industrialised, well-fare nation. Also remember that a similar shift has been observed in many industrial countries.

This also doesn't disprove that there is a correlation between genetics and height, it only proves that there are other factors besides genetics. For this, we should analyze a group of Japanese living at least since the second generation in a Western country.

@vsz Agree, and this is also what I'm saying in the last paragraph.


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Classification of degree of infested areas by pine processionary moth on regions
I'm making a thesis about pine processionary moth distribution on the regions of algeria!
i'm making tests about if there are spatial autocorrelation of this insects on the regions.
and i'm doing also hierarchical clustering of (degree of infest, small defoliation, medium defoliation, and high defoliation, and lattitude and longitude coordinates ) on each region to see the regions that have the same caracteristics on the variables i muntioned above!
The problem is that i need some information about the effect of geographical location and climat on this specific insect ?
i have made some statistical tests, and i have found that each year have diffirent cluster caracteristics for this regions, so can anyone help me to know why it's diffirent each year ?
the final thing, if anyone could suggest to me some links, to previous some study on another country maybe , so i can take an idea of what do i have to include and do , and to compare also with my results ?


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Is the sense for salt depending on the electrolyte level in our body?
I often noticed, after (heavy) physical activity like cycling, running, swimming or working an isotonic drink (to recover the electrolyte level) tastes less "salty" compared to when drinking it before the activity.
Is this possible or am I just hallucinating?
The object of this (if it's real) could be:

to save us of taking too much salt
to reduce the reluctance against salt if our body is undersupplied (with sodium ions)

My guess is, that the electrolyte or particularly the sodium (chloride) level in our body influences the cells/nerves that sense the taste for salt on our tongue.
Wikipedia says this:

Salts, sweet, sour and umami tastes causes depolarization of the taste cells, although different mechanisms are applied.

So, I imagine it like this:

If there is enough salt in our body, the cells are saturated with e.g. sodium ions (higher polarization since there are more ions)
NaCl and other salts (probably KCl too) will then dissociate into Na+ and Cl- (etc.)
The Cl- will then attract more Na+ from the cells causing deplolarization
Our brain converts these signals into the proper perception

But maybe I'm just hallucinating... :)

Is this possible or am I just hallucinating?

Certainly possible, but I'd peg the mechanism closer to Sensitization or De-sensitization of the neurons involved so that when you finally ingest some salt the sensation is different. The sodium and chloride levels of the ingested material wouldn't have a direct effect on the level of De-/Sensitization, but rather how low your stores are or how long you've gone without.

So, I imagine it like this....

What you broadly described is how regular sodium receptors work. They will work that way regardless of what you've been doing, and doesn't really explain an increase or decrease in your ability to taste salt - the signals will fire either way.
Check out the action of the Capsaicin receptor and how it changes sensitivity over short periods of time. I'm betting the phenomenon you're describing will be closer to this (an increase or decrease in the number of sodium receptors in response to the abundance of salts or lack-thereof) than an immediate mechanism from the drink itself.

Who else than MCM from Salt Lake City can answer this? :D -- So it's more the fact that consuming the salty electrolytes desensitizates the receptors, so they are less sensitive when consuming the electrolytes one or two hours later? Would you also say this is not directly related to the thesis of my first two bullet points (that we want to take salt if undersupplied and to avoid it if oversupplied)? From animals I know that they're searching for soil/plants that provide salt. So there must be some urge to get it (this is another question, actually).

@try-catch-finally - ;-) The desensitization is one potential reason. Subjective occurrences are pretty difficult to pin down. It could be short term desensitization, or your brain could simply be paying more attention to other ingredients (water) after such a long workout. If it's within a few hours then it's probably an attention modification - de/sensitization can work on that short a time scale, but not usually. I would say that the phenomenon is not related to your thesis. I'll add another comment.

@try-catch-finally - Regular "taste" is depolarization. For sodium that simply involves the influx of the ions over the cell membrane of the taste buds, and that will cause a depolarization without other mechanisms. That happens when you eat something with Sodium, regardless of what you taste. Taste is left up to interpretation in the brain, and the brain is great at ignoring stuff that doesn't really matter. If the drink tastes less salty, it wouldn't be the mechanism occurring - but it would be the mechanism occurring less often, or just as often but less noticed.


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How are minerals formed by biological processes?
News to me is that about 4500 of the 4900 minerals on Earth have been created by life. What are some examples of such processes? Are some minerals formed inside the human body?

News to me is that about 4500 of the 4900 minerals on Earth have been created by life.

After reading the article, this isn't what was said.
What was said is that life increases mineral diversity on a planet, most notably through biproducts reacting with existing minerals (like Oxygen - a biproduct of photosynthesis - reacting with iron to create iron-oxide).
So, life doesn't create new minerals, but it does change the abundance of elements at the surface which can undergo reactions with pre-existing minerals to form other minerals.
Not all of the 4500 "new" minerals on the Earth can be attributed to life. We don't know how many new mineral formations have formed because of life, but the article suggests the theory that increased surface diversity of minerals might be a good indicator of life.

biproduct-> by-product?

@daniel - Sorry, yes.


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difference between ischemia and oxygen-glucose deprived medium
Ischemia is roughly defined as insufficient blood flow to a specific region of the body and in the literature it is generally considered as causing oxygen and glucose deprivation in the tissue and therefore cells. Can we induce ischemia by depriving cells from oxygen and glucose in the medium or does it require more than that and ischemia is more complicated?
edit: i know the definition of ischemia maybe i should have said 'mimick' instead of 'induce'. Anyway, here is the better version of my question:
Ischemia is defined as blood flow shortage in a tissue and it is one of the main causes of non-apoptotic cell death. In an article i was reading, the authors claim that they induced ischemia in the glucose-serum containing medium. Does this mean they deprived the cells from oxygen and thus mimicked ischemia? Is this the way to create ischemia in a cell culture? What other ways can there be? Should not cells also be deprived from glucose?

Ischemia leads to tissular hypoxia and glycopenia due to an insufficient blood flow (e.g. due to atherosclerosis or thromboembolic diseases). Ischemia always result in hypoxia.
Hypoxia can occur without ischemia (e.g. due to anemia).
Tissular glycopenia can occur without ischemia (e.g. due to hypoglicemia).
Ischemia is a shortage in blood supply. Depriving cells form oxygen and glucose isn't the same as cutting their blood supply.


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What species of butterfly is this?
This big fellow came to visit my kitchen (in Hong Kong) a bit earlier.
It is brown with some longitudinal white stripes, banana/boomerang-shaped patterns towards the middle, and an eye-like marking on each forewing tip. Picture below.
What kind of butterfly is it?

I helped it find the exit in the meantime, not before taking a lot more pictures.

Can you please add where your kitchen is located?

People can't search by image very easily. Could you please add a text description of it to help people find it?

@HighlyIrregular I'm not sure how to describe it.. brown butterfly (well.. moth) with white stripes? Any suggestions?

@aditsu, something like that is good. The marking on the front tip of the wing looks a little like an eye too. I'd describe some of the other markings as boomerang or banana shaped, and v-shaped.

@HighlyIrregular I added a description, you can suggest changes if you want.

It isn't a butterfly, it's a saturnid moth -  Samia canningi, also known as the wild eri silkworm moth.
There is a good image on Flickr here, and some more information here.

Oh wow, something about its coloring and behavior seemed to say "moth", but I couldn't believe that a moth could be so big and so beautiful.

It's related to the largest sprcies of moth - the Atlas moth.

A lot of those Samia look alike, I'm impressed that you could identify the exact one.


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Why isolated, recombinant plasmid DNA without any restriction is often detected in agarose gel electrophoresis as three DNA bands?
I don't understand why three bands are found without any restriction digest. Please answer me as soon as possible.

today, i have seen fourth band first time after plasmid(pNL4-3) isolation

These are the three forms of the plasmid: supercoiled (smallest 3D-structure, runs fastest), linear (runs in the middle) and relaxed, nicked plasmid (runs highest). You can have another fourth band, which is the circular single stranded plasmid (runs faster than the supercoiled version). See the following figure (from this article, which I recommend reading):

Thank you a lot. I have another question,                  How many DNA fragments are generated from a circular plasmid DNA, when this DNA is restricted by EcoRI three times and each of these EcoRI fragments is restricted one time by PstI?

Can you please make this a new question? And if an answer is satisfactory answering your question, can you please accept it? This is a nice gesture towards the people who anwer.

Thank you Dear  Chris. I accepted your ansewr. I got confused again. I found in wikipedia that relaxed plasmid(mentioned that both strand are uncut) is different than open circular(one strand is open). But here both are considered as same. In case of second question, Already I asked as a different question and I didn't get any answer. waiting for response. Thank you