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How can synonymous mutations lead to cancerous or tumorous phenotypes?
After analyzing DNA sequences of an oncogene from many human cancer patients, you found that synonymous substitutions occur in a specific codon of this oncogene. Assuming that these synonymous substitutions do not exist in normal populations but do contribute to tumor development, what would be possible mechanisms that would explain how such alterations can lead to tumor phenotype?

Can you finish the title of the question?

What are your ideas regarding this question? Have you thought about any possibilities?

I think you assumed that synonymous mutation means silent mutation. But this is not correct.
From Wikipedia (synonymous mutation) :

Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations, however this is not always the case. Synonymous mutations can affect transcription, splicing, mRNA tranport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent

From wikipedia (Oncogene):
The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic methods of activation:

A mutation within a proto-oncogene, or within a regulatory region (for example the promoter region), can cause a change in the protein structure, causing

an increase in protein (enzyme) activity
a loss of regulation

An increase in the amount of a certain protein (protein concentration), caused by

an increase of protein expression (through misregulation)
an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell
gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell

A chromosomal translocation (another type of chromosome abnormality)

There are 2 different types of chromosomal translocations that can occur:

translocation events which relocate a proto-oncogene to a new chromosomal site that leads to higher expression
translocation events that lead to a fusion between a proto-oncogene and a 2nd gene (this creates a fusion protein with increased cancerous/oncogenic activity)

the expression of a constitutively active hybrid protein. This type of mutation in a dividing stem cell in the bone marrow leads to adult leukemia
Philadelphia Chromosome is an example of this type of translocation event. This chromosome was discovered in 1960 by Peter Nowell and David Hungerford, and it is a fusion of parts of DNA from chromosome 22 and chromosome 9. The broken end of chromosome 22 contains the "BCR" gene, which fuses with a fragment of chromosome 9 that contains the "ABL1" gene. When these two chromosome fragments fuse the genes also fuse creating a new gene: "BCR-ABL". This fused gene encodes for a protein that displays high protein tyrosine kinase activity (this activity is due to the "ABL1" half of the protein). The unregulated expression of this protein activates other proteins that are involved in cell cycle and cell division which can cause a cell to grow and divide uncontrollably (the cell becomes cancerous). As a result, the Philadelphia Chromosome is associated with Chronic Myelogenous Leukemia (as mentioned before) as well as other forms of Leukemia.

You might be especially interested in the second point (An increase in the amount of a certain protein)

Therefore, there is nothing impressive to find some synonymous mutations that are involved in oncogenes.

This paper here talks about how synonymous mutations are over-represented in oncogenes and cause mis-splicing of the gene.
http://www.sciencedirect.com/science/article/pii/S0092867414001457#bib22
In addition to that, synonymous mutations could also work by affecting a regulatory region like a transcription factor binding site, enhancers, etc., leading to enhanced or decreased expression of the corresponding gene.


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On which strand does the promoter sit?
My book keeps giving different indicators as to whether the promoters are on the coding or template strand.

It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that the -10 and -35 regions are binding sites for RNA polymerase.
It also says that CAAT and GC, unlike -35 in prokaryotes, can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand, with the transcription complex attached.

All the sequences are written 5'-TATAAA-3' (for example). This also implies they are on the coding strand, since the template strand will then be 3'->5' which is the direction that transcription happens in.
Obviously I'm confused, and hope someone can clarify this. In which strand can I find the promoters? Does stuff act on the promoter sequence itself, or its complementary sequence? If the promoter can also be on the other strand, should it be reversed?

The promoters are usually on the coding strand (which is the one which is transcribed) in front of the transcription start site.

@Chris I don't think it is correct to say that the coding strand is transcribed - the coding strand of the DNA has the same sequence as the RNA produced by transcription (except T>U). The other strand of the DNA is the template for the synthesis of the RNA.

You are right. I still get confused by this every now and then. Thanks for correcting.

It occurs to me that there is a usage of "or" that can confuse. Above "are on the coding or template strand" might as well be written "are on the coding strand un-commonly also known as the template strand". However, clearly the author wants to know on which side promoters are on, physically.

Refering to "...can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand..." There lies no contraction; why do you say "and then" (sounds German to me:-). In other words, promoter may lie on the one side, for the one side there is graphics given. That seem to be coherent, from the side of the textbook.

Anyway, can you offer some link or say what textbook you were reading? Any other? Me, I was surprised to find out that promoter "sits", see below, in the template/anti-sense strand, as I learnt, before, that is may sit on the coding strand, Thanks to your question I now may assume it's different for prokaryotes. Do you know of any parallel rule/exception issue with eukaryotes?

The answer to this question depends upon the definition of the word 'promoter'.
In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to form the closed complex. The next step is the switch to the open complex involving separation of the DNA strands.
Articles describing investigating the interaction of the σ factor with the DNA (e.g. here) refer to the protein making contacts with base pairs. I conclude therefore that the original question doesn't make sense - a promoter is a dsDNA entity even though we might describe it in terms of the sequence on one or other of those strands. So, for example, in a promoter the consensus -35 sequence - 5'-TTGACA -  would be present on the coding strand (upstream of the coding sequence), but the promoter property of the sequence is due to the presence of this sequence and its complement on the other strand.

"The next step is the switch to the open complex" - difficult to imagine that polymerase does not need the strands already open to bind.
From the abstract of the link you gave, sigma seems specific to species. One sigma for each species. Is is relevant to the question?
"...the promoter property of the sequence is due to ...  and its complement on the other strand." By "property" you mean that - as both strands have stayed together  - the promoter might as well be defined by the sense strand, which is called the coding strand, may I say "denominating strand"?

Again, according to your answer, at least with eukaryotes, the promoter physically never lies or acts in the coding/sense strand, right? (This is so essential...)

Promoter doesn't sit anywhere.. it is just present .. the transcription factor sits on it :P
Jokes apart.. Adding a little more information to Alan Boyd's answer:
As Alan Boyd points out, the terms coding or template refers to the region that is being transcribed.
Usually the Transcription Factors (TF) that bind to DNA have a dsDNA binding domain and therefore bind to both the strands. However, the sequence recognition domains are specific and usually scan the DNA 5'-> 3', subsequently recruiting RNA-polymerase in the same orientation. But there are additional aspects to this:

Promoter/regulatory elements are usually upstream but are also downstream of the TSS in several cases
The activity of a promoter element depends on the TF that binds to it. Some TFs can control the entire genomic locus i.e they affect several genes- both upstream and downstream.

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Are these bat social calls?
I'm currently researching bat social calls (not echolocation calls) and have been given a series of samples (in .wav format) and wanted to know if what I can hear is actually the social calls. Below is a Graph representation of the a sample from the data I have:

This looks fine to me. From this, I can clearly tell where the social calls are. If I play at the specific peaks, then it sounds like a bat "chirping." However, I've been told that social calls cannot be played back, and, therefore humans cannot hear them. I'm just trying to figure out what these noises, or, chirps might actually be.
Here is a link to the .wav file:
Thanks for your help :)

Come on, edit your question and ask it.

Ha ha! Yes it seems at first sight that such question would fit this website. So, as @Chris said, edit this question (including the title) and directly ask your question on bats and social calls.

@user1326876 Have you gotten any explanation other than "its impossible" why you cannot record the social calls?

@Chris - The social calls are recorded. I was told "it's impossible" to play the social calls back, since, they were recorded real-time and cannot be detected with just a standard media player.. But if this is the case, what am I hearing when playing these files back?

It could not fit in a comment..
You recorded bats. You are interested in social calls. Socials calls can be recorded by your microphone but they cannot be read by standard media player because...

the standard media player are limited to certain frequencies
your speakers cannot produce such high sounds
your ears are not able to hear many of the frequencies emitted
you formatted your records in a format that cannot hold very high frequency (for reason of optimizing data compression)

You might use some program like Adobe Audition in order to easily visualize the frequencies (vs time) of your record. (It might also help you finding all harmonics or performing Fourrier analysis)

This wiki article says :

Social Calls
This is a wide subject and there is still a lot to be discovered about bat social communication and how they use social calls in roosts and when flying. Generally a bat social call is not tonal, in other words it does not consist of a musical type note. Some bat detectors do not produce an accurate recording of a bat social call. Typically bat social calls use a lower frequency range than echolocation calls, and can thus be heard further away. Sometimes a bat will make a social call while echolocating which can cause confusion.
We can see and hear how the lower frequency social calls are heard at a greater distance than the higher echolocation calls as the bat approaches and departs. Zooming in on a spectrogram, social calls are atonal and repeated rapidly about five times in each call. The social calls are interleaved between the echolocation calls. They show a ragged frequency distribution around 20 kHz. Note the FD detector divides frequencies by 10.
The echolocation calls are single "hockey stick" calls at a higher repetition rate. At this scale the hockey stick shape is not very clear, but the end frequency can be measured as 45.2 kHz. A doppler shift is recorded as the bat approaches. The frequency was measured as it passes

I believe the first one. But, if this is the case. In the sample I gave in my post. What is it exactly I'm hearing? I have performed the a FFT on the signal, but, it still does not give any indication to where the social calls actually are.

For example, could it be that the person who has recorded these bat samples has already made it possible to hear the calls?

You want to know when you hear socail calls. Well, if social calls of your bats are around 20 kHz (at what frequency do you expect to find these calls?), then you might find signals on the frequency spectrum around 20 kHz. If someone modified the records by shifting the frequencies, he would have probably notice it somewhere. That would be surprising. But the best is always to contact the dude who took these records

Okay, thanks! I'll take a look at the FFT and see if anything comes up at the specific frequency range. Is there a chart or something for different kinds of bats at what frequency they can be heard at?

I am affraid there not enough study to create such a chart (But I don't know much!). you may try this article though. If you know which species you're dealing with you may find some studies that compared individual-specific or group-specific social calls

Thanks, but, this does not answer my question. What exactly can I/you hear from the recording I posted? If they are not social calls, what are they?

Did you have a look on this two Wikipedia articles (I know, its not a scientific ressource but sometimes a good starting point): Bat species identification and Bat detector. They go into some of the details discussed here.

I know it does not answer. I don't quite know to what frequency these sounds we can hear correspond. But anyway, I would recommend to you to contact the guy who made the record he will probably manage to help you a lot.

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What is the smallest oligocelluar organism?
What is the smallest oligocelluar organism?
How many cells does it have?
EDIT
The question is motivated by this comment@Philosophy.SE
EDIT as recommended in comments
I'm looking for an example of an organism made of very few (the fewer, the better) sister cells (obtained by mitosis or aggregation) that are morphologically and functionally different. I would accept examples of species that exist in different "conformation" (unicellular and multicellular).

I thing the answer depends on what you will accept to consider as multicellular. If you use a very broad and open definition, than the answer will probably be "2 cells".

@Remi.b do you know an example with 2 cells? But in fact I  thought about organisms where different cells serve different tasks...

No I don't have an example right now. As someone already voted to close, I would suggest you to re-edit your question and make sure we understand what you ask for. For example, you might say that you're looking for an example of an organism made of very few (the fewer, the better) sister cells (obtained by mitosis) that are morphologically and functionally different. You can also say that you would accept examples of species that exist in different "conformation" (unicellular and multicellular). I think/hope this would be a valid question.

I can only support Remi's comment. The question is pretty broad at the moment.

@Remi.b thanks for your suggestions. I hope you don't mind that I borrowed from your comment...

@Chris better now...?

Seems much better to me! +1

From my point of view definitely.

Volvox is a genus of chlorophyte that has been used in several studies as model organism for understanding the transition from unicellular to colonial or multicellular (I don't mean that multicellular and colonial mean the same thing!). If I am not mistaken, the species of this clade present quite a good transition from unicellularity to multicellularity. Some species create a bottlneck while reproducing, while others don't for example. One might investigate a bit the clade in order to answer draks …'s question.

This might interest you (I haven't read it though!)

The classic example, though I am sure there are others that are smaller, is the slime mold Dictyostelium discoideum:

It can have up to 100,000 cells and exists as both single cells and as a multicellular organism (emphasis mine):

Dictyostelium amoebae grow as separate, independent cells but interact to form multicellular structures when challenged by adverse conditions such as starvation. Up to 100,000 cells signal each other by releasing the chemoattractant cAMP and aggregate together by chemotaxis to form a mound that is surrounded by an extracellular matrix. This mechanism for generating a multicellular organism differs radically from the early steps of metazoan embryogenesis. However, subsequent processes depend on cell-cell communication in both Dictyostelium and metazoans. Many of the underlying molecular and cellular processes appear to have arisen in primitive precursor cells and to have remained fundamentally unchanged throughout evolution. Basic processes of development such as differential cell sorting, pattern formation, stimulus-induced gene expression, and cell-type regulation are common to Dictyostelium and metazoans.

100.000 is quite a lot, C. elegans has 956 cells which would surely classify into the smallest. Some of the algae mentioned above can have even lower cell numbers.

@Chris well yes but dicty cell counts go from 1 to 100.000 while the worm is always at 956. The interesting part is that dicty exists as a single celled organism as well.

Slime molds are faszinating. And as we see, this question is not easy to answer :-)

@draks... thanks for the accept but there are probably more extreme examples.

true. It was the "independent cells but interact to form multicellular structures when challenged" that I was looking for. And acceptance is revertible :-)

nice example @terdon

@terdon I personally see no point: C. elegans doesn't always have 956 cells, zygote is a single cell. I don't think "Dictyostelium" is the right answer given the current wording of the question.

@har-wradim hello and welcome to the site. There is no such thing as "the correct answer" on the stackexchange network, the OP chooses to accept whichever answer suits them and that answer is, by definition, the "best". It may be wrong or incomplete but if the OP feels it answers their question then that's that. As for dicty, the cool thing is that it exists and can live as both a single cell and as a multicellular aggregate. The worm cannot and the zygote is an "unfinished" animal, they are completely different.

Quite late for a welcome, but you are right.

Actually, a clever point. I would also mention syncitial organisms, which are formally multicellular, but have no cell boundaries between cellular "loci".

@har-wradim yes please post an answer...

@draks I think har-wradim is talking about Plasma molds.

Not sure, whether it fits in your requirement (since it was not clear for me with the terdon's answer), but I'd also mention plasmodia and other cases of species with syncytial organization: they have multiple nuclei, sometimes have even macroscopic sizes, but formally there is only one cell boundary within their body.
(If we broaden this definition, we may also include all kinds of protists with multiple nuclei: from diplomonads (which have two equal nuclei) and ciliates (most of which have two functionally differentiated nuclei) to Pelomyxa or giant foraminiferans with huge numbers of nuclei.)
Some examples:

Myxosporidia, once thought to be a group of protists and now believed to be highly aberrant metazoans - are parasites of fish (first generation) and some invertebrates (second generation), which form highly differentiated plasmodial bodies in their hosts.
Orthonectids, a group of "lower metazoans", have a biphasic life-cycle with sexual generation represented by oligocellular free-living males and females, which produce zygotes developing into parasitic plasmodia.
Myxogastrid slime molds are famous in having plasmodial fruit bodies: they are relatives of Dictyostelium and have a similar life-cycle with mono-nuclear amoebae, which conjugate and produce the plasmodium. So, these are still formally "unicellular" even as fruit bodies.
Some algae have plasmodial organization with the most famous case of Caulerpa, species of which "are unusual because they consist of only one cell with many nuclei, making them among the biggest single cells in the world.".
Cannot recall right now the name of the group (can someone help?), but there are amoebae, which are "normally" unicellular, but able to aggregate on rich food resources to form trophic plasmodium.
Lots of other cases.


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Do swarms show intelligence?
Can you think of collective and swarm behaviors as "intelligence"? Would such a concept apply to a) ant colonies and b) fish swarms?

Intelligence is something which has to have a definition, and there are many, but I would cautiously say no.
The reason that I say this is because swarming behavior can be largely reproduced by a simple set of rules - matching distance to your neighbors and direction and speed as well.  To me this really removes any intention or even conscious element to swarm behavior although its clear individuals do make decisions, they don't have to be more intelligent than a mouse looking for food or other kinds of animal behavior.
That being said, others have literally built definitions of intelligence inspired by swarming - a decentralized sort of mind which makes decisions based on the interactions of component individuals.  You could argue that our own brains are a similar sort of ensemble, and therefore no more different than our own intelligence if we look closely enough.
So take your pick really.

When we talk about "artificial intelligence" we are talking about the ability to solve problems not directly specified in the code. It doesn't need to have "intention" or "conscience", as @shigeta suggests. So, I'd say swarms are intelligent, it's just another "hardware" where intelligence appears. Like shigeta said, our own mind is not different in essence from a swarm (just many times more developed).


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Why does sulfonamid not inhibit the growth of Rickettsia?
Sulfonamid is an antimicrobial agent, why has it no effect on the growth of Rickettsia?

Sulfonamides competitively inhibit the enzyme dihydropteroate synthase, which is involved in the tetrahydrofolate synthesis pathway in most bacteria. Rickettsia lack this enzyme target, and thus possess a natural resistance to the antibiotic. As tetrahydrofolate is an essential compound, it is believed that Rickettsia possess an alternative enzymatic process which is not susceptible to sulfonamides, or the bacteria simply acquire the compound (or its immediate precursors) from their environment.

richettsiae lacks folP gene which encodes for dihydropteroate synthase and folA which encodes dihydrofolate reductase enzymes. This shows that richettsiae lacks the target of sulfonilamides. therefore sulfonilamides are ineffective to inhibit its growth and thus if given may lead to increased mortility and morbildity.
reference:http:escholarship.org


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Gene transfer between Gram positive and Gram negative bacteria?
How does transfer of genetic material occur between Gram positive and Gram negative bacteria?

By horizontal gene transfer.. but would you add more details to your question ? then the answers can be specific.

Do you want the exact mechanism ?

Have a look at this two links:

Exchange of genetic information
and
Gene transfer between distantly related bacteria

Especially the second should answer a lot of questions.


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Definition of "Regime of selection"
How would you define Regime of selection (or Selection regime)?
In addition to a accurate definition, a developped example would be very welcome!

I'll kick this off with an attempt at a definition: a selection regime is
the set of selective pressures on a population

As in, "alteration of selection regime resulting from harvest" (Mooney & McGraw 2007)
or "Human-induced nutrient input can change the selection regime and lead to the loss of biodiversity. For example, eutrophication caused speciation reversal in polymorphic whitefish populations through a flattening of littoral–pelagic selection gradients." (Hirsch et al 2013)

 Hirsch PE, Eckmann R, Oppelt C, Behrmann-Godel J. 2013. Phenotypic and genetic divergence within a single whitefish form - detecting the potential for future divergence. Evolutionary Applications 6: 1119–1132.
 Mooney E, McGraw J. 2007. Alteration of selection regime resulting from harvest of American ginseng, Panax quinquefolius. Conserv Genet 8: 57–67.

The best answer so far I found is this one (see Baum and Larson 1991):

The criterion of historical genesis is applied using the concept of
"selective regime," the aggregation of organismal and environmental
factors that combine to determine the expected action of natural
selection on actual and potential character variation.

Baum, D. A., and A. Larson. 1991. Adaptation reviewed: a phylogenetic methodology for studying character macroevolution. Systematic biology 40:1.
In this article you can find this example:

For example, the hypothesis that a given floral trait is an adaptation
enhancing the efficiency of bird-pollination would be tested by
scoring subject taxa as having either the selective regime
"bird-pollinated" or an alternative one (e.g., "insect-pollinated").

Then, you would be able to determine part of the selective regime of the floral trait. I say part of it because it's almost impossible to know all the abiotic  and biotic factors that can trigger a change in a trait variation.
Hope that helps.


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Evolutionary history: did any organs start out as autonomous organisms?
I've read that the cell nucleus was once an autonomous organism that was "enslaved" by the larger cell at the time of the Eukaryotic Revolution. Are there any organs in the human body that we know of that started out as autonomous organisms (of course they would be unrecognizable in their current form)?

Very short answer
No!
Long answer
It is not the nucleus who was an independent organism but the mitochdonrion (organelle) (One might discuss this point and say that both are correct, it is just a philosophical issue of the identiy of the eukaryotic cell). The plastids (the chloroplasts for example) were also independent organism. In consequence, in every cell, we have DNA in the nucleus and DNA in the mitochondria. The mitochondria is contained in every cell of our body and is transmitted via the ovule (and not the spermatozoid) to the offsprings.
Now let's think about your hypothesis that one of our organ (let's say, our liver) might have been an independent organism in the past. Therefore, this organ would contain different DNA than the rest of the cells of our body. How would you transfer the DNA of your liver to your offspring? Well, it is hardly imaginable.
Moreover, it has been argued that because we now have a complex and efficient immune system, a endosymbiose would be very unlikely.
But no, none of the cell in our body come from a previously different organism. But every cell of our body is some kind of chimera of two previous cells. Note: the vast majority of our DNA are present in the nucleus and not in the mitochondrion.
For more information about endosymbiose, have to look to this and this (wiki articles)
It seems much more easy to have two organisms that stay together during reproduction when reproduction is mediated by striking.
You may find some funny examples (border cases) of two organisms that don't separate during reproduction in corals (zooxanthella), leafcutter ants (and their fungus), parasitoid bees (and the virus that females create in their ovary) and lichens

Remi.b is perfectly correct if the question were restricted to humans (and yes, nucleus is not thought to be a result of symbiogenesis; actually some bacteria have similar structures).
But in the animal kingdom there several cases when certain organs "start(ed) out" as more or less separate organisms:

Many parasites have dwarf males and giant females (which actually feed on the host). These females when reaching maturity recruit actively swimming males, which upon attachment to female genitalia functionally become testicles and get nourishment from the female. The resulting organism can be viewed as hermaphrodite (although "self-fertilization" results in crossing). This phenomenon was described for example for Rhizocephala (Crustacea).
Similar cases are known for free-living organism: for example, in some species of the deep-sea anglerfishes males are dwarf and after attachment to females become "parasitic".
Siphonophorans (colonial Cnidaria) have several distinct organs (swimming bubble, locomotive organs, hunting tentacles and so on), but this differentiation is achieved via specialization of individual members of the colony - zooids. One can argue, that these organism were never separate, but for example one can still tell, which organs are medusae and which are polyps, each one of them "is homologous to a free-living solitary animal". In other colonial hydroids one can find something reminiscent, but the degree of integrity of the whole colony never reaches that of Siphonophorans.
In some species of bryozoans (which are colonial as well), several zooids (they are called "heterozooids" in this case) devote their lives to defend or move the colony, becoming highly specialized organs of the colonial organism.
There are probably other systems fitting in the question, can't remember right now.

I'm leaning toward down voting this - I think, though it is good, it doesn't answer the question. It seems the OP is interested in cases where organisms have been "captured" and used as organs by animals, specifically humans, in an evolutionary transition context rather than phenomena within a single generation. The closest analogy I can think of is the mitochondria, formerly a free living cell, which was engulfed by cells to be used as an organelle millions/billions of years ago.

@GriffinEvo.. The case of zooids is acceptable.. though there is no evidence of enslavement... Perhaps this term can be excluded because even for mitochondria we dont have an evidence that they had been actively enslaved

good point about the zooids @WYSIWYG - downvote removed


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Why would lactate be high in diabetics?
Why are lactate level high in diabetes? For example, type II diabetes are resistant to insulin. If those patients are insulin resistant their gluconeogenesis should be working at a high rate and, because of that, lactate uptake by the liver should be removing lactate from the blood.
Alternatively, type I diabetics don't produce insulin, so the ratio insulin/glucagon would always be very low and gluconeogenesis should be stimulated... So I don't understand why lactate levels are high in diabetes... Can someone help me?
PS. This question came up after doing an experiment in school, with diabetic rats and normal rats. Diabetic rats had higher levels of lactate and my professor said that it was because the diabetic rats don't perform gluconeogenesis and so, lactate accumulates in the plasma. But it doesn't make sense for me.

I talked with my teacher and he said that one of the reasons that can contribute to this state of high lactate in diabetes is that diabetes patients are more likely to use aminoacids as gluconeogenic precursors than lactate, so lactate will accumulate in their blood. Hope this helps someone in the future.

This condition is also known as "lactic acidosis" and can be pretty dangerous, since it influences the pH of the blood.
When we metabolize glucose to produce ATP and NADH it is metabolized finally to pyruvate in a process called glyolysis (I am not going into detail here since this is nicely explained in the Wikipedia). Pyruvate can then be used further in the body in the Gluconeogenesis, the Citric acid cycle and other pathways.
If a lot of energy is needed Pyruvate is converted by the pyruvate dehydrogenase into acetyl-CoA.
The problem with diabetes is that the pyruvate dehydrogenase can be inhibited in diabetes. If the body then needs a lot of energy pyruvate will be converted into lactate which is released by the cells into the bloodstream.
Gluconeogenesis cannot be activated since this needs either Pyruvate, Acetyl-CoA or Oxaloacetate as starting material. The other problem with this process is that this happens in the liver and when the glucose is released into the bloodstream, it cannot be taken up by the cells due to the lack of insulin.
The conversion from Pyruvate to Lactate is katalysed by the Lactate dehydrogenase and needs NADH + H+ as a co-factor. The image below is from the Wikipedia article on Lactate dehydrogenase.

This reaction is highly exergonic which means its preferred direction is to the right side. To change this and make Pyruvate from Lactate you need an excess of NAD+ which usually only happens in the liver.
There is also an epidimiologic study available showing a strong correlation between elevated blood lactate levels and diabetes type II: "Association of blood lactate with type 2 diabetes: the Atherosclerosis Risk in Communities Carotid MRI Study."

Thanks, It was clear and explicit! But, one thing, can't you use that lactate to form piruvate by lactate desidrogenase and build a source of pyruvate to gluconeogenesis? Because if you think in the glucagon/insulin ratio (in type I) or insulin non-action in type II , the gluconeogenesis would be stimulated.

Yes, and it dependends on the redox state of the cell, right? So if there's NAD+ sufficient, lactate should be converted to pyruvate... But okay, I'm beggining to understand why it can happen, although it's not clear for me the full mechanism. Thanks! :)

Part1- What is not completly clear for me is how the accumulation is so noticeable since, by the way I was thinking, some gluconeogenesis is still ocurring. For example, in a normal person, insulin would bind to receptors and stimulate mTOR--> Akt --> akt would inhibit gluconeogenesis. But in Diabetes Type II, that mechanism would not occur because the receptors wouldn't sense insulin, so gluconeogenesis would actived.

Part2-Now imagine that the rat is in the fasted state, it would be using fatty acids as fuel source, so there will be a lot of acetil-coA in the mitocondhria and NADH. If there's a lot of acetil-coA, piruvato desidrogenase would not be active, some glucose that would have been turned to piruvate would be converted to oxaloacetato by pyruvato carboxilase. So OAA and lactato could begin the gluconeogenic pathway... what am I thinking wrong?

Yes, because Gluceoeogenesis uses energy to make glucose. The body on the other side needs energy badly (otherwise it wouldn't go for lactate. The production of lactate also consumes a lot of NADH (which is needed as you stated yourself in Gluconeogenesis) so it really doesn't make sense to build up (and use and conserve energy) and use it up at the same time.

Hum, ok! In the case of diabetes, if gluconeogenesis is not active in the fasted state, would ketone bodys be the only fuel for the brain?

Under certain circumstances this can happen. This is why diabetic patients can smell after acetone when they have problems with their insulin.

Ok, now it makes sense. Because of the high NADH/NAD+ ratio, oxaloacetato would be shifted to malate and would not react with the acetil-coA released by oxidation and fatty acids. acetil-coA would go to ketone body synthesis, and with no oxaloacetato, there will only be one precursor left which is lactate. NADH could drift lactate to piruvato, but since it is being exported means that there's a lot of energy expanding going on, so It's not acceptable to use energy to make glucose! Thanks a lot :)

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text:
Aerobic vs anaerobic respiration comparison
The following graphs compare glucose decomposition in yeasts (in anaerobic vs aerobic conditions respectively)
My question is, why doesn't the first one look like a straight line as the second one does? Don't they actually follow similar processes?

Sorry, my German's (i think) a bit lacking.  What are the axis?  Also, they are similar but not identical processes.

y: Glucose concentration, x: time

@ZaferCesur you might want to expand on why you think this question has not yet been answered by the existing answer (clearly you think so because it has a bounty) and is this also from some kind of homework assignment etc?

I think the reason as to why glucose concentration is faster in the aerobic case than the anaerobic one, is perfectly explained by Chris. To summarize:-

The energy requirement of the organism in both the condition remains more or less
  constant. Since aerobic respiration generates more energy per glucose,(38ATP)
  it takes more time for the same concentration of the glucose to be
  depleted, than it takes in the case of anaerobic respiration where
  less energy is released.(2ATP)

The non-linearity in case of anaerobic respiration can probably be explained thus:-
In the aerobic case, glucose is oxidised to water and carbon dioxide, both of which do not influence the respiratory process. The first step of glycolysis, the phosphorylation of glucose has a very negative free energy change, i.e. is practically irreversible. Therefore a dip in glucose concentration will not affect the rate of energy release and therefore the rate of energy released will stay constant resulting in a linear graph. But in the anaerobic case, the final product is un-metabolised ethyl alcohol. The conversion of pyruvic acid formed as a result of glycolysis to ethyl alcohol is not so strongly irreversible(smaller free energy change), and at high product concentrations, becomes considerably reversible. This means that the ethyl alcohol produced will affect the rate of glucose metabolism, and will retard it by negative feedback (Le chatelier's principle). This will lower the speed of glucose utilisation at low concentrations of glucose, i.e. high concentrations of ethyl alcohol. This reduce the value of slope at lower concentrations of glucose in the graph, and hence produces the non-linearity.

Your graphs show two things: Starting at the same concentration (150mM/l) the metabolization of glucose is not linear under anaerobic conditions. The other observation is that under aerobic conditions the glucose is metabolized much slower.
This is because under anaerobic conditions on 2 molecules of ATP are generated from the metabolization of one molecule of glucose (for all the details on the biochemical pathways look into the "Ethanol Fermentation" article in the Wikipedia) while for the complete respiration of one molecule of glucose under aerobic condition generates 32 molecules of ATP (2 from the Glycolysis 2 from the [Citric acid cycle], aswell as 26-28 in Oxidative Phosphorylation (Electron Transport Chain and Chemiosmosis) 3).
So to generate enough energy the yeast has to metabolize the glucose much faster when the conditions are anaerobic which explain the form of the graph, while under aerobic conditions the graph stays linear. The metabolization starts in both cases with the glycolysis, but afterwards is different. Aerobic conditions produce water and CO₂, while the anaerobic conditions produce ethanol and CO₂.

I think in anaerobic conditions they are fermenting, what is different from respiration. Respiration produces much more ATP from single molecule of glucose, because the biochemical path is different, involves more steps, each one producing a little energy.
Also note that, on the graph on the right, the X-axis goes up to 6. Which means glucose is being processed much faster on the left. Maybe that's because mitochondria are numerous and can process the sugar faster?
As for the curve, I can only think that fermentation is so slow that the ATP produced is being consumed by the cell in the same rate. With respiration, the ATP is produced in big amounts and thus begins to accumulate, what regulates the process to slow down. But I may be missing something important here.

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text:
Mass Spectrometry Terminology
I began reading this paper (http://www.biomedcentral.com/1471-2105/14/56) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere.  Consider the following line:
"The resulting peptide signals in the LC-MS map are referred to as features while the selection of features for fragmentation with MS/MS is called precursor ion selection."
I'm not sure what an LC-MS map is, so I can't properly understand what features or precursor ion selection are: can someone define these terms for me with examples?

LC-MS stands for Liquid chromatography–mass spectrometry. The LC-MS map shows the separation of samples by polarity and mass.

As I understand precursor ion refers to the tryptic peptide ions prior to fragmentation after the first round of MS.

LC-MS map they refer to is the projection of two separation method (Liquid Chromatography - Mass Spectroscopy) results into an imaginary plane. It's a conceptual map. From this map, peptide signals referred to as "features" (article uses this term) are selected for the next level of fragmentation and then MS again.
Figure 1 of the article you cite simulates a small fraction of this larger map.

In a liquid chromatography coupled to mass spectrometry (LC-MS) analysis, as analytes elute from the chromatographic column they are sprayed through a hypodermic needle maintained at a high potential difference relative to the mass spectrometer. Combination of this potential difference and the pH of the LC buffers causes the analyte molecules to pick charge. Analyte ions are then pulled into the MS and guided using lenses. Then these ions are separated based on their m/z (mass-to-charge) ratios inside an analyser and then detected using a detector.
At any given time, detected signals are typically represented on a 2-D map/graph between m/z on the x-axis and ion intensity/relative abundance on the y-axis. This is called as MS1 scan or precursor ion scan. Now, depending on the mode in which LC-MS analysis is being carried out, precursors are selected for fragmentation and further MS measurements, which is called as MS/MS or MS2 or product ion scan. Several of these MS1 or MS2 snap-shots can be used to construct a elution time profile for every ion. For an ion having a specific m/z ratio, this can be represented as a 2-D map between retention time on the x-axis and ion intensity on the y-axis. Area under this profile can be used to estimate the ion current of an analyte and under the given conditions it is proportional to the abundance of the analyte in the sample.


text:
DNA fingerprinting
I would like to make my own DNA fingerprint - just for fun to have my "autoportrait":).
I was looking around a bit and all the commercial kits you can have are very expensive. Can you suggest me a cheaper way to do it - which DNA extraction protocol do you recommend?
I have access to restriction enzymes, we have several different pcr polymerases (Herculase, pfu). Can this be used to make PCR with human DNA?
I found this list with primers for different STR loci. http://www.cybertory.org/resources/CODIS/#Primers
If I understand it correctly I have to extract DNA, digest it with restriction enzyme and make a pcr with each of primer pair and than load it to a gel and make a picture. Am I getting it right?
Thank you for your answers!

You might be interested by this Ted talk

What about SNPs instead of fingerprinting or STRs? There are some companies which perform genotyping at hundreds of thousands of loci for acceptable money.

The idea is that I do it by my self not just send DNA to some company.


text:
Predicting host-pathogen gene interaction networks
Background
What we have are:

~20 genome sequences for a host species that come with gene annotations
Several sequenced genomes for parasite/pathogens of these hosts

Question
What are the possible ways of predicting gene-to-gene interactions or gene regulatory networks between hosts and parasites?

About what kind of interactions do you think? Transcription factors from parasites that influence the host?

thanks for the question. at the simplest level an interaction would involve binding, e.g. gene A that expresses a transcription factor that represses gene B via binding it's promoter sequence would be considered an interaction between gene A and gene B.

there is no way by which you can predict genetic interactions based on sequence alone.. You need more information such as protein-DNA interactions, expression correlation, protein-protein interaction etc

exactly! which is why i am asking the question i suppose, you hinted at some ideas there thank you - could you expand on them?


text:
The Assumption of Weak Selection?
I was reading this question and I failed to fully understand the introductory part of it.
The OP (@Artem Kaznatcheev) says:

Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection.

I don't fully understand it. Can you help me making sense of why assuming weak selection allows one to Taylor expand the selection function. I am hoping someone would answer by presenting a mathematical model that at first does not assume weak selection and show why assuming weak selection allows the use of a Taylor series to linearize the function. I'd like to understand which terms fall down and which terms left with this assumption.

This is my take in this, without experience of using the Taylor series to analyse evolutionary game theory problems.
As you know the Taylor series expansion of $f(x)$ at point $a$ can be written as:
$f(x)= f'(a)(x-a) + \frac{f''(a)}{2!}(x-a)^2 + \frac{f^{(3)}(a)}{3!}(x-a)^3 + ... + \frac{f^{(n)}(a)}{n!}(x-a)^n + ...$
Often factors above second order are dropped as a simplification. However, to use the Taylor expansion, the function must be differentiable at point $a$, and to be differentiable it must be continuous.
As @Artem Kaznatcheev writes in his question, "...with weak selection meaning the game modifies overall fitness only slightly..." and "... it is typical to model organisms as having a base fitness that is modified slightly by the game interaction...". These statements imply that the overall fitness function/surface can be assumed to be relatively smooth and continuous (i.e. the payoff is negligible), which means that the Taylor series expansion can be used. If the game payoffs for a single game would determine a large proportion of the overall fitness, the fitness surface would be discontinuous.
An example where a Taylor series expansion is used to simplify the fitness function under weak selection is given in Andre & Godelle (2006) (see equation 20 ff).
You might also find this supplement to Nowak et al (2010) interesting (a rather controversial paper), especially page 8.

thank you! I know what is a Taylor expansion and understand how it can be used to drop polynomials of higher degree in order linearize a function. But I still don't understand what function we linearize and why it is useful to do so. I haven't read your links yet though! For example, I would love having a mathematical model that gets much more easier to interpret or to solve using the assumption of weak selection. So that I can see what function is linearized and for what purpose. I'll have a look to the links, thank you.

@Remi.b It's the fitness function that is Taylor expanded, and how the fitness function is defined naturally depends on the game being modelled. There are a lot of papers out there, but I've included one example now (haven't checked it closely though). Overall, this is a quite technical body of litterature.

I think at @fileunderwater provides a good explanation of the basics math behind it, and some good references. I would like to go more into detail about the modeling decisions and benefits of assuming weak selection and why it is done in the literature.
When you are making evolutionary models, especially one in evolutionary game theory, the first place is to start with a differential equations model of inviscid populations (this usually means that you assume very large population size). These models often result in dynamics of the form $\dot{x}_i = x_if_i(\vec{x})$ where $f_i$ is a non-linear function corresponding to the relative fitness but where the non-linearity depends on the strength of selection. Making a weak-selection argument, often allows you to come close to linearizing $f_i$ using Taylor expansion. This reducese your equations to a form like $\frac{dx_i}{dt} = x_i(\vec{c}_i^T\vec{x} - \phi)$ where $\phi$ is an average fitness. Although the transients of this dynamic are still complicated, the equilibrium is usually relatively easy to analyze and reduces to looking at the matrix $C = [\vec{c}_i^T]_{1 \leq i \leq n}$ with its columns given by your linearization of the $f_i$s.
Of course, this is only a first step, and the current trend in the literature is to move to a setting where you have spatial structure. Here, weak selection gives you a further bonus because you can use it to separate the timescales of local (dominated by the constant term) and global (dominated by first-order in $w$ -- the selection strength) network dynamics. This allows you to use the powerful pair-approximation technique. A great example of its use is Ohtsuki & Nowak's (2006) solution to the evolutionary dynamics of games on $k$-regular random graphs (you can find a brief overview here).
The final settings where this is useful is for studying the interaction of mutation and selection in finite populations. In this case, weak selection allows you to look at the selective force as a small perturbation of the mutator-balanced steady state. In the setting of EGT this rquires you to define some new solution concepts for what it means for one strategy to be "better" than another but then some interesting connections (see Antal, Nowak, & Traulsen (2009) for more) and very general analysis of the mutation-selection equilibrium can be done (Antal et al., 2009).


text:
Counterintuitive action of Vitamin D?
Vitamin D acts in a way which to me is counterintuitive. It functionally supplemets Parathormone. It in the intestinal tract steps up calcium absorption by altering nuclear gene expression and also prevents calcium excretion in kidneys. All of this is understandable. But it also, like parathormone, steps up osteoclast action in bone (actually steps up both osteoclast and osteoblast, but the osteoclast action is increased more to result in net bone resorption). This means that Vitamin D increases blood calcium level by increasing bone resorption.
Then how does Vitamin D help in improving bone density, bone strength and prevent rickets or osteoporosis? All of these would require bone deposition rather than resorption.

yes there are some colflicting theories.. This article says that Vit-D actually inhibits osteoclastogenesis. What I can say about it is that the action of Vit-D should be studied in a systems perspective. It may be the effect of dynamics. It allows calcium absorption, and its deficiency would cause reduced calcium leading to reduced bone-mineralization as seen in rickets. However, it also affects resorption and active modeling of the bone. It is important to take other factors (hormones etc) into consideration.

There are two pieces to this question:
a) How does bone resorption (movement of Ca/Phos out of bone into the blood) result in net improvement in bone structure?
Bones are constantly remodeling, primarily in response to mechanical stressors. Although you clearly already realize this, I will make it explicit: osteoblasts are the cells that create new bone; osteoclasts break down (resorb) bone.
Quoting Harrison’s Internal Medicine1:

Radioisotope studies indicate that as much as 18% of the total skeletal calcium is deposited and removed each year. Thus, bone is an active metabolizing tissue.…The cycle of bone resorption and formation is a highly orchestrated process carried out by the basic multicellular unit, which is composed of a group of osteoclasts and osteoblasts

Bone mineral density (BMD) can not be equated with bone quality. (This is the difference between osteoporosis – deficient bone density – and rickets – poor bone architecture.) Thus, vitamin D’s stimulation of both osteoblast and osteoclast activity is beneficial to bone structure.
b) How does vitamin D lead to overall increased bone density?
In addition to the effects above, you mentioned that vitamin D increases serum calcium by several mechanisms. This is true. Both this increased serum calcium as well as the direct effects of Vitamin D on the parathyroid gland suppress PTH production.* As PTH has powerful actions to increase bone resorption by mobilizing calcium and phosphorus to move from the bone into the blood, the suppression on its excretion applied both directly and indirectly by Vitamin D results in a net increase in bone density.
Thus, both by its effects on bone quality and quantity, vitamin D is a net boon for the bones.

*Parathyroid hormone, a.k.a. parathormone. There is a paradox here, because drugs such as teriparatide (a.k.a. Forteo, recombinant PTH) are anabolic for bone and are used to treat osteoporosis. Although the mechanism is unresolved, intermittent administration (as in the case of drug treatment) increases BMD while chronic sustained elevations decrease BMD.2

References

1. Bringhurst F, Demay M.B., Krane S.M., Kronenberg H.M. (2012). Chapter 352. Bone and Mineral Metabolism in Health and Disease. In Longo D.L., Fauci A.S., Kasper D.L., Hauser S.L., Jameson J, Loscalzo J (Eds), Harrison's Principles of Internal Medicine, 18e.

2. Rosen CJ. The cellular and clinical parameters of anabolic therapy for osteoporosis. Crit Rev Eukaryot Gene Expr. 2003;13(1):25.

Nice answer, but I still am unclear about how suppressing parathormone will help out bone density. Since functionally, Vit D and Parathormone are complimentary, will not suppressing PTH be equivalent to negative feedback control, valid for most hormone systems?

@SatwikPasani Thank you for the feedback. I have added some additional explanation. This system is more complicated than a straightforward negative feedback loop, and the two hormones, while complimentary, do not have identical functions. Hopefully my addition and the reference to the pieces that remain unresolved gets at what you're asking.


text:
Are B Cells unique to an individual's immune system?
I was wondering how the body "remembers" viruses after having once overcome them, and while reading this article on the immune system (page 14, Vaccinations), I read:

There are many diseases that, if you catch them once, you will never catch again. Measles is a good example, as is chicken pox. What happens with these diseases is that they make it into your body and start reproducing. The immune system gears up to eliminate them. In your body you already have B cells that can recognize the virus and produce antibodies for it. However, there are only a few of these cells for each antibody. Once a particular disease is recognized by these few specific B cells, the B cells turn into plasma cells, clone themselves and start pumping out antibodies. This process takes time, but the disease runs it course and is eventually eliminated. However, while it is being eliminated, other B cells for the disease clone themselves but do not generate antibodies. This second set of B cells remains in your body for years, so if the disease reappears your body is able to eliminate it immediately before it can do anything to you.

Which made me wonder, instead of vaccinating people with weakened forms of the disease, getting their B cells to activate as described, what would be wrong with growing large colonies of B cells for a given virus and injecting them into someone who has never had the disease so that one can go straight to the last sentence of that paragraph, having many of those B cells in place before the virus is ever experienced?

the problem is transplantation rejection - the body will reject the injected cells as foreign...

There is no other way than vaccination (besides the infection) to bring these B-cells in place.

That's essentially what the vaccines do ! In vivo !

Remember first that the human body nearly always, although there are exceptions, rejects any non-genetically identical graft placed into it, and therefore one cannot prepare a general colony of B-cells to confer immunity to the population at large. However, in principle, there is no impediment to removing B-cell progenitors in an individual, conditioning them to produce antibodies (which would be an artificial analogue of the natural process of 'Clonal Selection'), and re-injecting these differentiated B-cells into the patient. To my knowledge this process is currently beyond the capacity of our current cell culture techniques, as B-cell differentiation is controlled by an elaborate cell-signaling process, and even if it was feasible, it would remain impractical for several reasons. First, since the B-cell products, antibodies, can be transferred humorally, and should be tolerated by the general population, many existing treatments simply involve injecting antibodies into the patient's bloodstream. Examples of antibodies taken from volunteers' sera are the RhoGam preparations as well as IgG mixtures used to treat certain forms of immunodeficiency. There is a means of growing B-cells in culture to produce antibodies of precise specificity (i.e. monoclonal antibodies - note that clonal selection occurs in a living host for this technique, the B-cells are subsequently harvested then immortalized in culture). Adalimumab is a therapeutic monoclonal antibody.
There is however, very promising work being conducted involving T-cell vaccination, which is technically similar to what you described. The advantage in using T-cells is that these leukocytes can orchestrate an immune response, mobilizing the several, diverse elements of the immune system to respond to a specific antigen. These techniques are being principally researched as cancer treatment regimens.

And to clarify, the T-cells are coming from the pt, or in more extreme cases HLA matched donors, not just generic T-cells from a cell line or pool.

@AtlLED - Presumably. It is essentially adoptive immunity, which by definition would seem to indicate histocompatibility. Being an experimental procedure, there are several methodologies explored to produce these cells. I will try to keep an eye out for a good review article on the preparation methods. A promising aspect of this therapy is that in addition to inducing immunity, the possibility of producing T-regulatory cells may enable us to effectively treat autoimmune diseases and allergies.

@J.AlfredPrufrock When we have vaccines available, do you think what the author of the post describes is necessary ?

@biogirllajja - Direct antibody injection is currently more technically feasible and easier to control. However, there may be niche applications for B-cell adoptive immunity, perhaps if one needed antibody against a very specific epitope. Otherwise I believe T-cell adoptive immunity would initiate a more natural immune response. I have not seen an article that employs the method of B-cell adoptive transfer. I would presume that even if the clone of interest could be isolated, it would be difficult to ensure its proliferation in vivo.

Biogirl hit the nail on the head. Vaccines are one of the most beneficial medicines ever invented - in large part this is because they take advantage of a well evolved immune system rather than re-inventing the wheel.

There is also some work with programming a patients own stem cells to become long lived plasma blasts for broadly neutralizing antibodies against HIV (and other diseases I assume). Although you are essentially asking what is harder...eliciting these broadly neutralizing antibodies with traditional vaccine approaches (difficult), or working out the complex cell signalling pathways to get from stem cell to long lived plasma blast. Even the pathway from memory b-cell to plasma blast is still not entirely understood, so we are several years away from this approach.
It is so appealing though for so many reasons. Once you have a plasma cell secreting a broadly neutralizing antibody, you have it forever (or at least many many years). This circumvents the extremely expensive antibody therapeutic approach as large quantities of these proteins are indeed just expensive to make as with all protein therapeutics.


text:
How long can a bee surive in a jar?
So, some people and I encountered an adventure game where you have a bee in a jar and need to move it from place to place before it suffocates, and someone tried to find out how long a bee would actually survive in the jar. We've found three relevant papers:

Oxygen consumption in the foraging honeybee depends on the reward rate at the food source [1]
Oxygen consumption and body temperature of active and resting
honeybees [2]
Physiological Correlates of Foraging Efforts in Honey-Bees: Oxygen
Consumption and Nectar
Load [3]

which has given us what we think is a good high-end guess of 40µl of oxygen per minute consumed.
However, we don't know at what point the oxygen level would get too low for the bee, or if carbon dioxide poisoning  would occur. Does anyone have a source for the minimum oxygen levels a bee needs to survive, or the point at which CO₂ toxicity becomes a problem?

visit this link you get some ideas dude
https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CC0QFjAA&url=http%3A%2F%2Fwww.beesource.com%2Fforums%2Fshowthread.php%3F262439-keeping-bees-alive-in-a-jar&ei=On3WUrGEE4ulrQf9hIDQDQ&usg=AFQjCNG12br-dEdUZpGLSGmgoEH_0t3ywA&bvm=bv.59378465,d.bmk&cad=rja

@gopinath First thing they talk about is air holes.

As an amateur beekeeper, I think I can work up an answer for you in the next few days. The answer will be regarding the typical honeybee. Is that acceptable? Just to be sure, the question you want answered is "What is the minimum level of oxygen for a bee to survive?" On a side note, I think it is a horrible game if it requires that a creature suffocate to determine a winner.

@fredsbend In the game you have to transport a bee from place to place in a sealed jar, to protect it from a toxic atmosphere. However, the bee runs out of oxygen and dies very, very quickly, limiting where you can take it. We thought this was unrealistic, and wanted to work out what what the actual time was.

@Canageek Well, I was going to mention that oxygen may not be the limiting factor. Bees are quite susceptible to high temperatures, and in a sealed jar there is no ventilation to cool the bee. Put the jar in the sun and that bee will die in under 15 minutes. The average bee's body temperature cannot stand anything much hotter than 110 for longer than a minute or two.

@fredsbend The scenario in question takes place on Mars, so I'd be more worried about the opposite situation, but that is good to know.

Assuming the jar is airtight--
I think your oxygen consumption rate may be too high and that 40$\mu l$ per hour$^1$ might be closer but since it's a high figure anyway we can use it. 40 $\mu l$ per minute would be about 2400 $\mu l $/hr.
A 12-ounce jar is about 0.355 liters. At sea level, air contains about 20% oxygen so the volume of oxygen in the jar is about 0.0709 liters.
At altitudes which are considered high for humans (17000 feet or higher) the percentage of oxygen falls to about 15%. If a bee is able to get 2400 $ \mu l$ of oxygen per hour from a jar, the volume of oxygen will fall to about 13% after ten hours.$^2$
Based on oxygen consumption alone I think a bee would be stressed at this level, especially at temperatures exceeding 32C. I would guess the bee would be stressed well before this, maybe after 5 hours (16.6% oxygen). If we factor in the likelihood that the bee's respiration is up due to the agitation of confinement I think we can shave another hour off.
Depending on the age, size, species, variety, temperature, location, etc. I think an outside limit of 4 hours in an airtight jar is a good guess.
Toxicity from CO$_2$ may be a problem but bees have a much higher tolerance for CO$_2$ than humans, according to one set of entomology notes. At 0.04% the concentration will only increase marginally due to a drop in oxygen alone but the bee itself will produce CO$_2$ and in far greater quantities under stress. A chart here shows production of CO$_2$ in reaction to a light being turned on. 400 ppm is 0.04% but in this case it is due to the bee. If the bee during respiration returns CO$_2$ as quickly as it consumes oxygen the jar could reach 7% CO$_2$ in four hours, a level that may be toxic for humans. But we have already suggested the bee is under stress from oxygen depletion at that point.
There are many assumptions in this note. A conservative estimate might be an hour in an airtight jar. I would not bet on more. There are probably other issues I haven't thought of. Bees are very fragile and the chart linked above suggests they would not fare will in such an environment.
$^1$ Respiration of Worker Honeybees of Different Ages and at Different Temperatures, Allen, 1958, J. Experimental Biology 36, 92-101. At page 97 Allen gives a chart showing log $\mu l$ $O_2$/mg body weight/hr. For a 14-23 day old bee at 32C he appears to give about .5 which means 1.65/mg/hr or about 115 $\mu l$ per hour for a 70mg bee. It may be a typo or perhaps I am misreading the chart. Also the study uses an older method of measuring respiration.
$^2$ This is a simplification. The bee will start breathing a mixture containing falling oxygen levels and this may slow the oxygen depletion a little. But if we say the bee needs what it needs this saves us a differential equation.

@WYSIWYG: "bodyweight" is not in Webster's. To edit an answer as opposed to a question is a little much, especially if the OP accepted it without comment. I usually offer proposed corrections in comments. Form for footnotes changes every few years as journals revise their style guidelines. I find this style easy to read.

Ok.. I am sorry.. Point taken.. I was trying to replace TeX code with Unicode wherever possible. Sorry that I altered the post.

@WYSIWYG: no problem and I do prefer the unicode version for microliter I'll change that back to your version when I get a chance. For CO2 I think it's easier in Latex but maybe I'm just used to it.


text:
The Origin of Mitochondria
For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were "engulfed" by another cell which acted like it's host. This is the endosymbiotic hypothesis.

"The endosymbiotic hypothesis suggests mitochondria were originally
  prokaryotic cells, capable of implementing oxidative mechanisms that
  were not possible to eukaryotic cells; they became endosymbionts
  living inside the eukaryote."

However, recently I looked at the wiki entry on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous.

"In the autogenous hypothesis, mitochondria were born by splitting off
  a portion of DNA from the nucleus of the eukaryotic cell at the time
  of divergence with the prokaryotes; this DNA portion would have been
  enclosed by membranes, which could not be crossed by proteins."

It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (This question here deals with some aspects of multiple-occurence/convergent endosymbiosis).
My questions are;

How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis?
Further, are there any other (plausible) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?

This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called Power Sex and Suicide. You would be interested to read it.
There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example:

There are no microfossil records for the evolutionary intermediates
Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously

So to answer how it exactly happened is quite difficult.
As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check this post.
There are eukaryotic cells that lack mitochondria (eg. Entamoeba histolytica ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner.
There is one more evidence to support the endosymbiosis theory:
There is this observation that organelles that are less numerous in a cell have retained more of their genome compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the Limited Transfer Window Hypothesis which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles.
This article suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (I need some time to mine up the reference. Read it a while back) but these are not the the ancestors of eukaryotes.

Just to follow up: "it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without ... mitochondria" -  how do we know that an early form of mitochondria didn't evolve which allowed the cell to become the larger eukaryotic cell we see today? (It is a bit of a chicken or the egg argument from me there [prokaryote-> prokaryote with mitochondria-> eukaryote, versus, prokaryote-> eukaryote-> eukaryote with mitochondria], and I don't necessarily believe that the early mitochondria came first, just playing devils advocate).

@GriffinEvo: yes definitely.. I didn't say that prokaryote with mitochondria is the precursor of eukaryote. The available information suggests that the eukaryotic ancestor got all its eukaryotedness in a relatively short span of time. It suggests that perhaps there was some non-ubiquitous microenvironment which promoted it.
The argument is that a large eukaryotic cell carrying out the mitochondrial function without having a dedicated organelle cannot thrive because of high energy expenditure.

@WYSIWYG I think you are talking about secondary endosymbiosis, but maybe I'm wrong.

@AtlLED.. I am aware of secondary endosymbiosis but I am not talking about it here.

authors: عبدالرحمن المغربي


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Can antibiotic resistant bacteria compete with normal one in an antibiotic free environment?
The question is based on an intuition that antibiotic resistance can't come along. This mutation will probably make bacteria less tenacious. Is there any research how AR bacteria compete with normal one in an antibiotic free environment? Because if them generally lose to normal bacteria then AR bacteria is not a big threat and they can't spread to much.

They CAN spread like wild fire when an antibiotic is introduced in their environment.

The antibiotic resistance adds to growth cost. In an antibiotic free medium the antibiotic-susceptible strains will outgrow the resistant ones. See this

So it is a myth that antibiotic resistant bacteria is somehow dangerous? You will not catch this AR infection if you are not using antibiotic. Normal bacteria will outgrow it.

Well..no.. Your immune system acts as a barrier to both strains (both are pathogenic)... Then you take antibiotics to control the infection. In this condition the resistant ones thrive.

AR bacteria is less viable it will not be present if I didn't use antibiotic. Both this infections fight not only with immune system but also with eachother and AR lose.

We are talking about the condition in which the immune system requires drug supplementation. For example in the case of tuberculosis.. The drug resistant strains are a major issue of concern

I am interesting how AR strains are able to spread. If they can't compete with normal bacteria then worst possible scenario is to ban antibiotics worldwide for a year. Wait while AR bacteria instinct in a competition with normal one and remove the ban. Or better to switch between two types of antibiotics on odd and even years. If AR bacteria really lose to normal one then the issue is not as bad as it depicted in mass media.

It is not that easy as it seems. Indiscriminate use of antibiotics should be controlled to prevent evolution of resistant strains. However, infections which evade immune system naturally are a matter of concern and the technique that you suggest wont work.

@ZAB Before a century, antibiotics were not used but the AR bacteria WERE present. So, even if we stop use of antibiotics there will be certain bacteria which have resistance to it. One more thing, DO NOT take this thing so LIGHTLY. Antibiotic resistance IS creating problems. If there were an easy and feasible way to tackle it, agencies like CDC would definitely have implemented it.

In general, antibiotic resistant strains may be a little less fit than sensitive strains in the absence of the antibiotic.  But that doesn't mean they are at all times and places instantly competed out of existence.  Once you apply the antibiotic, the resistant organisms grow from resistant organisms that were in the population to start with.
Ad of course once you have a large number of resistant organisms in the population, selection might encourage the increase in organisms bearing compensatory mutations, such that the growth of those organisms is closer to the growth level of sensitive organisms.
Your premise is a little weird.  Resistant organisms are out there.  XDR tuberculosis, MSRA Staph...why would you assert that those can't be problems when empirically, they obviously are?

Totally agree with the last sentence. They ARE there and they ARE bad.

How long will XDR tuberculosis and MSRA Staph last if we ban antibiotics or if we will globally alter one antibiotic with another once in a decade? That is a question. If resistant stains are less fit then normal stains then they will extinct.

Ban all antibiotics all together?  Do you understand that the idea is for people to not die from infectious diseases?  Sitting back and watching someone die from a drug-sensitive strain because you are banned from using antibiotics is not an improvement over watching someone die because you don't have a useful antibiotic to use.

You do not listen. Ban penicillin worldwide and treat people with metronidazole. Then switch. Stain resistant to both of them will not survive in competition. After a year of penicillin treatment all metronidazole resistant stains will extinct. And so on.

You can't treat everything with one antibiotic.  For one thing, there are people who are allergic to penicililn.  And I'm sorry, but there are such things as compensatory mutations, it certainly is possible for resistant organism to compete with sensitive ones.  Just repeating over and over again that that's not true isn't helpful.

In short, yes. Perhaps the best way of thinking about antibiotic resistance is not to think of there being 'antibiotic resistance' genes at all, but rather ordinary alleles that are vertically transferred in the typical fashion until at a certain time a deleterious chemical agent is introduced and one specific allele just happens to mitigate the effects of that chemical. It is less a matter of competition than it is of blind chance. Now of course, in principle, the lucky genetic element that will ensure survival may come with an increased energy cost as opposed to the 'wild-type' genome expression, but considering the general mechanisms of antibiotic resistance, one or two extra gene products, maybe a slightly less active enzyme, an extra membrane transporter, the cost is typically not excessive. In culture, antibiotic-resistant bacterial strains grow essentially as fast as non-resistant strains.
Now concerning the retaining of the resistance after removal of the antibiotic, if the gene is integrated into the genome with the proper regulatory apparatus, it can remain in the species essentially forever. In the case of plasmids or other mobile genetic elements, bacteria do tend to lose these through random processes between divisions, however, many of these elements do have mechanisms to preserve (plasmid addiction) and propagate themselves (horizontal gene transfer).
The most important thing to remember about resistance, however, is that only an infinitesimally small proportion of the population actually needs the resistance genetic element to actually start a new resistant population upon antibiotic introduction.

" In culture, antibiotic-resistant bacterial strains grow essentially as fast as non-resistant strains.".. Antibiotic resistance does pose and additional cost on growth.. It might be difficult to observe it in a gross scale.. However it is true that that resistant strains must have optimized the protein synthesis machinery as much as possible to minimize cost.


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Citing species in a biology article
My question concern the abbreviation of the genus of a species.
I talk about two species: Amphiprion clarkii and Amphiprion perideraion.
Question 1
Let's assume I haven't said a word about these species in my article yet. Should I say:

Amphiprion perideraion is a small fish and Amphiprion clarkii is a big fish

or

Amphiprion perideraion is a small fish and A. clarkii is a big fish

Question 2
If I talk about these two species in the abstract, should I use the abreviation the first time I cite them in the introduction or not?

I would use the long form for the first citation in the main text end after that the short form. You also wouldn't put references into an abstract, so this is repeated later (even if its part of an abstract) and then correctly referenced.

To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in the title (if relevant) and once in the body text (which includes the abstract), so you can abbreviate after the abstract. However, this is really only a space issue, and you can use the full name at all instances (you may abbreviate, but don't have to), unless of course journal style prohibits this. I find it useful to write the name in full both in the abstract and once in the main text.
See The International Code of Zoological Nomenclature (Appendix B: General Recommendations) for a reference. To be picky, technically, authorship and year of species names should also be included at least once in each paper (e.g. Amphiprion clarkii Bennett, 1830), to clarify exactly what definition of a name you are using. However, this is often not done in practice (in fields outside taxonomy/systematics). What you often see is that people refer to a authoritative source, e.g. "... all species names used in the study follow Doe et al. (2008)."


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Effect of single nucleotide deletion or insertion on primer annealing
How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ?
Imagine a primer like this:  GCGTCATAAAGGGGACGTG (primer)   and the corresponding part of template DNA has one G missing, so it looks like this:  GCGTCATAAAGGGACGTG (template).
The possible pairing could be
GCGTCATAAAGGGGACGTG primer
GCGTCATAAA_GGGACGTG template
or
GCGTCATAAAGGGGACGTG primer
GCGTCATAAAGGG_ACGTG template
 or anything in between.
Is it possible that amplification with such primer would be completely disrupted in normal real time PCR at 60°C annealing? Could this completely disrupt the amplification?
If the mismatch was substitution-like, I would be pretty confident, the primer would be still functional and amplification would occur. In the extreme case, it would be at least residual amplification at late Ct. There are a lot of data, how substitution mismatches affect primers and I also have a lot of personal experience with that.
Unfortunately, the deletion mismatches are less studied plus googleproof. The only indication I have found is this work:
Lipsky RH, Mazzanti CM, Rudolph JG, Xu K, Vyas G, Bozak D, et al. DNA melting analysis for detection of single nucleotide polymorphisms. Clin Chem. 2001;47:635-44.
In that work, single nucleotide deletion had similar or lower affect on melting temperature than substitution mismatch. But it was about longer oligos.  Examples:
Effect of deletion:
133 bp fragment, 67 % GC, deletion SNP at position 43, delta Tm (homo-hetero duplex) = 1.2°C
Effects of substitutions:
152 bp fragment, 43 % GC, substitution T to C at position 68, delta Tm (homo-hetero duplex) = 0.9°C
100 bp fragment, 41 % GC, substitution T to C at position 42, delta Tm (homo-hetero duplex) = 1.4°C
163 bp fragment, 60 % GC, substitution C to T at position 86, delta Tm (homo-hetero duplex) = 2.2°C
110 bp fragment, 59 % GC, substitution G to A at position 66, delta Tm (homo-hetero duplex) = 3.8°C
Questions:
1. Can you recommend me literature about how deletion mismatches inside (not at the very end of !!!) primers affect annealing and PCR ?
2. Would You guess the primer in my example would be still functional , at least partly, or would You expect no amplification at all ?

EDIT after your inputs:
This online application " mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting " thinks, deletion mismatches are more destabilising than substitutions, at least for short primers. For my own example, it calculated delta Tm (homo-hetero duplex) = 12.9°C .
If I try substitution mismatches instead, delta Tm (homo-hetero duplex) is in interval 3,8°C to 5,7°C.
New question  If you have experience as similar as possible to my case, which is 19 nt long primer with single nucleotide deletion in the comlementary template at position cca 6 - 9 from 3' primer end, annealing temperature used at 60°C, please let me know if You achieved amplification or not.  Please, give me a respective reference, if you have it, so I will quote it in my review :-) .
Also, I am still interested in general info, as long as the topic is narrow enough to be about single nucleotide deletions or insertions in primers. (Not substitution mismatches).

primers would be functional as long as the 3'ends match properly and the mismatch is not huge. You can calculate the changed melting temperature using UNAfold DNA-DNA hybridization server.

Very neat application, thanks ! For the benefit of others - I have found where exactly one enters the sequences at the server: http://mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting

Similar to @Chris, I've used longer, even ultra-mers to cause deletions.  I've been curious about how small I could make the primers, but I've always had the luxury of being able to make them pretty long without worrisome 2ndary structures.  Have you considered trying this on a test template to see how it goes?  Wouldn't be too costly to test (I've considered it).

We used this kind of primers to generate out of frame mutations or to add additional bases. In my experience your PCR will work (probably a a lower efficiency) and you will get a product with an additional base. We used primers with bigger differences in PCR based site directed mutagenesis of plasmids, there up to 10 bases didn't match but the primers where also longer. For single nucleotide mismatches (either + or - one base) we used primers around this size.
Regarding the literature, this publications might be useful:

A guide to the design and use of mismatched and degenerate
primers
Effects of primer-template mismatches on the polymerase chain
reaction: Human immunodeficiency virus type 1 model studies
The Effects of Internal Primer-Template Mismatches on RT-PCR: HIV-1
Model Studies
Effect of primer mismatch, annealing temperature and PCR cycle number
on 16S rRNA gene-targetting bacterial community analysis

Especially the first publication contains a lot of other interestings references.

If you do not wory about your identity, would you mind sending me a reference for your publication, where there was primer of this size (cca 19 nt), had a single nucleotide deletion or insertion, and still worked ? ( Iknow I am probably too demanding, because you have sent me 4 publications already. It would just be convenient to have reference for this specific example right away).

No big deal: Look at this paper, the sequences are in the supplemental data. The shortest primer pairs are 25mers. The length is dictated by the surrounding sequence.

@Barbara What I forgot: I recently used sligtly shorter primers (21 and 22mers) but this results are not published yet.

@ Chris: Thanks, at least I have assurance, it can work this way. But if by chance you'll remember you have a poster presentation where those short primers are mentioned, please, let me know.

@ Chris again: The articles you listed say nothing about single nucleotide deletions, with the exception of Kwok 2014, which says minimum. (Kwok says, the primers can be used to indtroduce indel SNP and that they should be placed in the middle of 24 - 36 base oligo.) Your own article mentions only long (46 nt) oligos spanning 3nt indel. Am I overlooking something ?

Yes, you do. In the supplemental document there are 25mers documented.

@ Chris  The only 25 nt long primers are N278D-F and N278D-R. Blasting them against nrnt database shows, that N278D-F has a central G, where most mice have A. N278D-R has a central C, where most mice have T. It looks like substitution mismatches, not indels. (Limiting blast to Homo sapiens does not give good primer matches). In which primer is an indel mismatch and which template should I blast it against to see the indel myself ?

I never talked about indels, for this purpose you will need longer oligos. This short primer was used to introduce a point mutation. Which worked quite well according to our sequencing results.

@ Chris  Where does the information come from, that (single nucleotide) indels are more destabilising to annealing than substitutions ? (Maybe we use different definition of indel and point mutation. What I was talking about are single nucleotide insertions or deletions. But not substitutions)

what do you mean by indels ? In your vocabulary, is single nucleotide deletion or insertion a subtype of indel ?

I name this small changes point mutations (when we only change one nucleotide to another to express a different amino acid). Otherwise I stick to the definition of indel, that you find in the Wikipedia: "In germline and somatic mutation studies, indel describes a special mutation class, defined as a mutation resulting in both an insertion of nucleotides and a deletion nucleotides which results in a net change in the total number of nucleotides, where both changes are nearby on the DNA."

Your answer confuses me further. For clarity, let us just speak about frame shift mutations caused by only one nucleotide insertion or deletion. Do you have citation about 25 nucleotide long (or shorter) primer, which harbors single nucleotide-based frameshift mutation in the middle ?

I haven't done frame shift mutations since this doesn't occur in the transcription factor would analyze (it would be embryonical lethal). What we have done is to introduce point mutations (exchanging single nucleotides against others) and here relatively short primers can work (the N278D mutation in the paper mentioned above is done with a 25mer).

Thanks. Now, which part of Your main answer (not comments) pertains to single nucleotide-based frameshift mutation ? Did you previously work with cca 19-22 nucleotide long primer with single nucleotide-based frameshift mutation in the middle ?

Adding another reference. This group looks at the effect of different mismatches (e.g. A>T vs A>G) and also looks at positional effects.

Our results show that single mismatches instigate a broad variety of
  effects, ranging from minor (<1.5 cycle threshold, eg, A–C, C–A, T–G,
  G–T) to severe impact (>7.0 cycle threshold, eg, A–A, G–A, A–G, C–C)
  on PCR amplification. A clear relationship between specific mismatch
  types, position, and impact was found.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797725/

I was interested in deletions, not substitutions. No matter how much stress this out, people keep sending me info about substitutions in every forum ever.


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Are there any good reviews on the mouse and human conservation in coding and gene regulatory module regions?
I was looking for reviews that deal with conservation between mouse and human of proteins, noncoding RNAs, gene regulatory module (such as promoters and enhancers), gene regulatory networks post the mouse genome sequencing era

you can look at the conservation tracks in UCSC genome browser.. or download latest MAF file from there.. You can do the analysis yourself.. You wont find reviews on this specific question.


text:
How are Raunkiær's plant life forms viewed today?
At the beginning of the 20th century, Raunkiær proposed a typology of plant life-forms based on where they bear their buds, roughly as:
cryptophytes: belowground
hemicryptophytes: at the surface
chamaephytes: close to the surface
phanerophytes: projected above the surface
Are these still held to be useful / biologically meaningful categories? Is there a different typology preferred (eg. tree/shrub/subshrub)? Or are people moving toward gradients of quantified traits instead of typologies (eg. measuring plant height, specific leaf area, etc.)?

Oreotrephes, it all depends on the needs. Reproductive schemas don't exclude shape schemas. There has been, however, a shift to cladistics in classification, which means to give scientific names ONLY to monophyletic groups, i.e. groups that include all the descendants of a single ancestor - and only its descendants. But we still use tree/shrub distinction and epiphytes, for instance, but that's to describe the ecology of species, helping identify them, not to classify them on these grounds alone.