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Why aren't organelles considered alive?
I'm taking a 3-week Bio I summer course, and my textbook says the cell is the smallest/basic unit of life. I asked my professor why organelles aren't a living unit, and her reply was that they aren't self-sufficient. But it seems that cells in multi-cellular organisms need other cells with different specializations in order to survive. You can't just (or can't always) pluck a cell out of a larger organism and leave it to fend for itself outside of it. Same with an organelle. She said only the entire cell fits all the requirements for life, referring me to the textbook, but I couldn't find an actual description of these requirements. So, what is the relevant difference between an organelle and a cell such that only the entire cell is considered alive?

Proptoplasam is the only living organelle present inside the entire cell

The definition of life is a controversy in itself, and as it is simply a word that can be understood by everyone however they wish, there is no "correct" definition. It is thus not really possible to give a "correct" answer to your question, but here are a list of things you may want to consider:

Replication of DNA is probably the most agreed common feature to all life on earth. Most organelles do not contain their own DNA but are simply lipid and protein constructs.
Independence is a difficult criterion of life, as parasites require a host for reproduction. However, while the organism may require a host, its cells individually can replicate without a host.
Cells are able to replicate when removed from the body - under the right conditions. (We are getting better and better at culturing all sorts of cell types, for example to avoid having to use animals for research.) Most organelles are not able to replicate under any conditions.
In nature, there are single living cells. In fact, the majority of organisms on earth consist of one cell only. There are no organelles living in nature.

Mitochondria and plastids make a complicated exception to these, as they are originally derived from bacteria themselves. It is indeed debatable whether they could be considered alive, as they possess DNA and it is replicated in order for them to divide, like individual cells do. However, the machinery required is not produced by themselves but rather by their "host" cell, making them subject of a similar argument as viruses.

Neither Mitochondria nor Plasmids could maintain or replicate themselves outside of a cell because both have passed the genes that encode for key proteins over to the host cell.

Which genes exactly are you referring to? As far as I'm aware, mitochondria (I don't know about plastids) replicate their genome themselves and perform a process similar to binary fission themselves as well; but under regulation of the "host" cell.

In human cells, mitochondrial DNA codes for just 37 genes. All other genes required for mitochondrial function have been transfered to the nuclear DNA. Specifically the POLG and POLG2 genes that are involved in mitochondrial DNA replication are now located on chromosomes 15 and 17, so without being present in the host cell they could not replicate. The replication itself occurs in the mitochondria but the proteins needed are synthesised by the host machinery.

So very much alike viruses in regards to their being alive or not then. Thanks :)


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How are our senses dimmed during sleep?
Our senses are not as sensitive during sleep compared to wake. There is an arousal threshold during sleep that only when it is overcome will it wake a person up. My question is how is this arousal threshold lowered as sleep progresses? And how it is raised again during the latter stages of sleep?

At night several changes occur in the body due to absence of sunlight and other surrounding changes. The biological clock inside the body performs certain function in a healthy body whenever changes are sensed.
There are many receptors in our body located on cell membrane. They are made up of proteins and their function is to receive information from neurotransmitters. This information will be sent to specific part of the brain. If we take sensory information then it is Parietal lobe. This lobe receives the sensory information from all over the body and responds to it when body is active. During sleep, the senses that go through the thalamus, are shut down by gating either in the Nucleus Reticularis Thalami (NRT) or in the Thalamus itself. GABAergic inhibition of the thalamus, most likely deriving from the NRT is probably a part of the reason that sensory stimuli doesn't penetrate during sleep.
This is also influenced by release of hormones in the body whose level when rises in the blood causes certain changes in the concentration at some regions such as receptors which gets blocked temporarily and stops signaling the brain. There is a study on how muscle relaxes when we sleep can be found here Muscle sleep. So it is all the neurotransmitters job at the receptors which stops signals going into brain but internal to the brain it will be active controlling other routine works which it has to do when we are asleep.
The main thing to note here is the 5 different stages of sleep such as non-REM and REM sleep. During those stages several changes take place in the body. The below website gives an excellent insight into different changes happening inside the body when body takes rest at night.
Please refer to "What happens to your body while you are asleep".

When you're awake; the sensations around you as well as your mental will, keep your mind active. How the air smells and what needs to be done all contribute to your day. In order to sleep your brain must weaken these receptors significantly, though not enough that if we heard something too loud or unfamiliar (such as a predator), we overlap those boundaries that keep us resting and wake. Now of course i am talking about the middle of the night. As morning arrives the amount of stimuli needed to overcome the wall that is sleep is diminished, allowing something such as the crowing of a rooster to wake us up.

That's a common theory, but the question is how? How are these 'receptors' weakened? What it is that controls both these receptors and sleep?

Another lead are sleep spindles, closely related to the RTN as mentioned before. Basically the thalamus enters a state of high-frequency firing to a low-frequency synchronous one, thereby taking the cortex with it. Sleep spindles are slow-wave potentials as apparent on the EEG that block out the normal flow of peripheral sensory information from thalamus to cortex. Basically this leads to a loss of consciousness as one is unaware of its environment. A similar thing occurs during absence epileptic seizures, where patients temporarily loose consciousness as marked by paroxysmal slow-wave EEG activity interrupting the high-frequency EEG associated with consciousness Kostopaulus (2000). Hope this helps.

source: Stack Exchange

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

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What are ways to compare the "costs" and "gains" of food production systems?
I'm looking for methodologies to compare the costs a food production requires with the gains it delivers (not in economic terms).
I'm aware of energy returned on investment. Are there other methods used in literature (also including qualitative approaches)?
To be a bit more precise (or rather unprecise?): Costs may include the input of fuel, feed, energy in general or - for me most interesting - the environmental burden to our environment (for example the carbon footprint) while gains should refer to the nutritional output of the product (energy, protein content, other (rare) nutrients).
The purpose is to link (or discuss) the burden of food production chains to their benefits but to find a unit that is quantitative comparable (except the pure energy content) doesn't seem so trivial - so I'm very happy with suggestions how to approach that - in the best case with a link to studies that employed the method.

This is called "Life cycle analysis"

@David Thank you. I'm fully aware of that :) I'm rather looking for factors that have a comparable unit when they enter and leave a food production system. Sure, there is for example the output of CO2 linked to the consumption of fossil fuels but I wonder if there are some that are more obviously linked, also speaking in terms of being easier to understand.

Calories and dollars are the most obvious and straightforward, but including additional variables complicates the accounting. . A great paper that used energy has been updated in a more recent publication. Emergy is an interesting alternative.
Current work includes the Natural Captial project that "aims to integrate the values of nature into all major decisions affecting the environment and human well-being". Of course, this approach exchanges a simple currency for a more comprehensive one.
Climate regulating value is also a relatively straightforward and relevant currency that can be used to compare the value of food production systems.

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


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How is transport of glucose into prokaryotic cells different from transport into eukaryotic cells?
I was reading page 92 of Fundamentals of Microbiology, 4th edition, which states

In facilitated diffusion, the substance (glucose, for example) to be transported combines with a plasma membrane protein called a transporter.

The section of text that says this is in a section describing prokaryotic cell anatomy. As far as I understand human biology, (just to use one example) that facilitated diffusion is regulated by insulin, which, to use less than perfect language simply to streamline my question, uses insulin to "unlock" the plasma membrane proteins.
What's the difference when prokaryotic cells aren't dependent upon insulin to get glucose in?

In prokaryotes the glucose transporter is always present in the cell membrane; in cells whose glucose uptake is insulin-regulated the transporter is only present in the plama membrane when hormone levels are high.
GLUT4 is the isulin-regulated glucose transporter found in muscle and adipose tissue. When insulin levels are low the GLUT4 protein is in the membrane of small vesicles inside the cell. The appearance of insulin signals the fusion of these vesicles with the plasma membrane. In this way the number of GLUT4 molecules in the plasma membrane is increased, raising the capacity of the cell for glucose transport. GLUT4 transports glucose into the cell by facilitated diffusion.
More information about the GLUT family of glucose transporters can be found here.

Interestingly, bacterial and eukaryotic glucose transporters are similar in structure, though bacteria do not have insulin. http://www.ncbi.nlm.nih.gov/pubmed/23075985


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Why does it hurt more when you touch a nerve directly?
I am not a biologist nor know much about biology (so please explain in layman's terms) however I have always been curious as to why this is.
What causes the difference in pain between touching an open wound and pushing down on your skin? In both circumstances you are applying pressure to the nerves except one is a foreign object touching the nerve and the other is the nerve's natural surroundings in your body.
Why is it that a foreign object causes so much more pain?

see this post. Similar kind of question

I answered the other question and it is similar. However, this one is different enough that I will give a slightly more simple explanation.
Nerves transmit messages using electrical current, more specifically the flow of sodium and potassium. Just remember that it's electricity. When you have any sort of cut or damage, your body recruits white blood cells which protect you from any bacteria that might enter. They also cause inflammation to prevent those bacteria from spreading (and to warn other cells that they may become infected). It is also important that we feel pain, so we know something is wrong (because we have the ability to do something about it). That's why inflammation causes pain. It does this by lowering our threshold so our nerves are more sensitive. In other words, it takes less damage, pressure etc. to cause our nerves to send the pain signal. Normally, it is set higher, so we don't suffer too much pain. Naturally if you want clarification on anything just ask.


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What effect do oligosaccharides, like those found in legumes, have on the composition of intestinal flora in humans and if so how so?
I know that intestinal flora metabolising oligosaccharides, like those found in legumes, is the cause for the well known fact that legumes cause flatulence, but does an oligosaccharide-rich intestine change the composition (i.e. which specific bacteria make it up) of intestinal flora in humans?

The answer to this is fairly complex, and it depends on whether you are talking about short-term or long-term changes to the microbiota.
When talking about short-term changes, the answer is almost certainly a resounding yes. Any ingested nutrient will lead to an increase in the growth rates of bacteria capable of metabolising that nutrient, and will therefore lead to a change in the composition of the intestinal microbiota.
This is, unfortunately, difficult to observe, as most studies of the intestinal microbiota use fecal samples to look at intestinal microbial composition. Since stool represents an average of what happens between two bowel movements, it is difficult to draw inferences about short-term changes in the microbial composition of the bowel. However, there is evidence from Pythons that suggests extensive remodelling of the microbial composition does indeed occur, at least in animals with less regular feeding schedules.
In the case of long-term changes, there is strong evidence that specific oligosaccharides contained in human milk specifically select for certain strains of Bifidobacterium and Lactobacillus. Apart from this very specific set of oligosaccharides however, there is a paucity of studies dealing with the effects of diet on the gut microbiota, and even fewer looking at specific nutrients.
The premise that long-term changes to the gut microbiota can be made with diets is the foundation on which the entire prebiotics industry is built. The most popular prebiotics are fructo-oligosaccharide, inulin, galacto-oligosaccharide and lactulose. These are said to encourage the growth of beneficial strains of Bifidobacterium and Lactobacillus. However, there is currently no consensus on the long-term effects of these oligosaccharides on the microbiota.


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Are humans more aggressive during a full moon?
Is it true that we are more agressive during the night when there is a full moon?
If true, could this be a remnant from times where we needed to hunt for our food and so could see more at night when there was a full moon?
Source of question: article

Umm, what gives you that idea? Could you provide a reference?

added an article

newspapers say such things all the time.. there is not much credibility..

thats why I asked if it was a myth or true story :D

This is more fit for Skeptics and has already been asked there. http://skeptics.stackexchange.com/questions/948/are-more-crimes-committed-during-a-full-moon/949#949

This seems to be a piece of pseudoscience commonly seen these days. The truth is that this effect has never been statistically observed.
From the Skeptics Stack Exchange site:

Ivan Kelly, James Rotton and Roger Culver (1996) examined over 100 studies on lunar effects and concluded that the studies have failed to show a reliable and significant correlation (i.e., one not likely due to chance) between the full moon, or any other phase of the moon, and each of the following: The homicide rate, traffic accidents, crisis calls to police or fire stations, domestic violence, assassinations, kidnappings, aggression by professional hockey players, violence in prisons, assaults, gunshot wounds, stabbings

... and many more seen here.


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Knockdown of long noncoding RNA (lncRNA) - how is it done?
I don't work at the wet lab and don't know all the details about the knockdown techniques.
My question is:
How lncRNA knockdown is done?
For example - you have lncRNA that is functional in the nucleus. How is it possible to do knockdown using iRNA if interference happens only in the cytoplasm?
Sorry if there is biology related misconception in my question.

Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.
UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found this paper to quote:

Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).

Reference or it didn't happen :)

I added a reference

Nuclear RNAi happens.. check these articles:
http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html
http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr891.full
Also there is some evidence that Ago2 binds to lncRNAs.
However, you can employ other techniques to knock down lncRNAs for e.g. ribozymes.

This is controversial, but most groups in the field have concluded that RNAi does not work in the nucleus despite the presence of Ago.  When lncRNA have been KD'd with RNAi, they are usually shown to be present in both the nucleus and cytoplasm, and the KD is thought to occur in the cytoplasm, not nucleus.  Of course as always in biology it is possible that nuclear RNAi does occur in some cell types or under some special conditions.  Gapmer oligonucleotides acting via RNAseH are usually an excellent way to KD a nuclear lncRNA, but I would add that you should be prepared to test say 6 or more different oligos, as the efficacy is unpredictable, and in contrast to RNAi, there are no great generally available algorithms for antisense oligo design.


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General undergraduate zoology textbook recommendation?
I am very interested in zoology,and I want to study zoology in my spare time.
Any undergraduate level zoology text book recommendation?

This is a rather broad question. In an attempt to narrow things down: Are there specific areas of zoology in which you are interested?  Are there specific types of textbooks that you like more than others (or what do you not enjoy in a textbook)?

@dd3 general introductory level zoology textbook

I used Zoology by Miller and Harley in my undergraduate years and I found it to be an engaging, informative text book.

LIFE : The Science of Biology by Sadava & Hills & Hellar & Berenbaum


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What is the purpose of Y-shaped adapters in Illumina sequencing?
Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.
The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.
What are the advantages of this?
My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that:
-Upon primer annealing, the primer in turn would bind to the start AND end of the DNA fragment, and thus not allow synthesis to continue to until the end. Therefore, the next primer would not have a template to bind at the start of the fragment...
Y-shaped adapters also allow for paired-end sequencing. Fragments have a unique sequence on either end, which allows for the first "run" to sequence one side of all molecules, then synthesize the reverse and sequence that.
Am I on the right track?

This looks like a nice explanation.

Normally, when you need two unique adapters, say A & B, on either end of unknown insert sequences, cohesive-end ligation is difficult because the insert sequences are "unknown". So you have to do blunt-end adapter ligation, in a reaction containing Unknown Inserts + adapter A + adapter B. This can result in 3 possible versions of insert-ligated product: A-insert-A, B-insert-B and A-insert-B, among which only A-insert-B is the only desired product.
1) Ligation of A-tailed inserts with Y-adapters gives you 100% A-insert-B.
2) Lets now assign a directionality to the insert - say from base 1 to base 400. Following Y-adapter ligation, you will have 2 kinds of insert-ligated products per insert: A-Insert (1-->400)-B and A-Insert(400-->1)-B, both of which are very useful. Each will create a separate clonal cluster and you will get sequence information starting at both base 1 and base 400 of the insert, since in single-read sequencing, the instrument always sequences from Adapter A. However, to know that both these sequences belong to the same insert, one will need to do paired-end sequencing.


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Why do neurones use chemical signalling at synaptic junctions?
When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical Brownian diffusion signalling with receptor surface proteins is relatively slow and is often exploited by venoms and susceptible to toxins (on the plus side it's the reason a lot of medical drugs work). It seems flawed for evolution to have selected for this rather than some alternative quicker and more direct electrical interface.
Question. Why are chemical synaptic interfaces used in higher organisms at the synaptic junction?

This is the coolest part. Those synapses are the reason the brain is so complex! Basically you've got the first part right, the neurones are quicker and they transmit messages from one end to the other. The other thing you have to do is analyse and calculate. Signals from multiple neurones feed into a single neurone using a chemical synapse. Similarly the converse is true, a single neurone can feed multiple synapses. So when we for example walk, receptors monitoring our balance can feed this to our conscious and unconscious mind, but I'm grossly simplifying this. What our brain does is take hundreds and thousands of ports of information, with where the chemical synapse is and the type of synapse and the receptors and a million other things just slightly changing the information until it's perfect and then send that information a million ways however it likes.
The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude, however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc. Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.
Does that make sense?

I think I understand the principle, but would it not be more efficient to have interlocking physical connections that could carry a voltage?

The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc.
Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.

If it still doesn't make sense or there's anything else just ask :)

I hadn't thought about it in terms of an analogue signal. I think that's they key bit I was missing.

No problem :) updated the original answer to everything so far.

There are both chemical and electrical synapses in many organisms.  The electrical synapses are called gap junctions.
As you point out, the primary advantage of gap junctions is their speed, and they are commonly used in systems involving defensive reflexes.
However, as AndroidPenguin indicates, chemical synapses allow for greater computational abilities (changing the gain, integrating multiple inputs, etc).  Gap junctions are also disadvantageous because they often (but not always) transmit signals in both directions; chemical synapses tend to be more unidirectional (of course, there's always backpropagation).

There are indeed 'gap junctions' which pass current directly from one cell to the next. So what advantages do we get out of chemical synapses that gap junctions do not provide?

Asymmetry. Synapses do not operate in reverse, thus the postsynaptic cell cannot generate currents in the presynaptic terminal (although there are secondary forms of communication which may operate in the reverse direction).
Ion Selectivity. A synapse allows one set of ionic currents to be transformed into any other set. Thus sodium and calcium influx at the presynaptic terminal might translate to chloride influx to make the synapse inhibitory. Furthermore, the ability of the postsynaptic cell to control calcium levels is critical for plasticity mechanisms.
Insulation. Gap junctions increase the conductance of the cell membrane, which can reduce the fidelity of signals as they propagate along the dendrite. In contrast, an inactive synapse might have virtually no effect on the postsynaptic cell--it does not pass currents.
Kinetics. Because chemical synapses generate their own ionic currents, they are also free to modify the speed of those currents (how quickly they rise and fall). This is much more difficult to achieve with gap junctions.

There is a very long list of functionality provided only by synapses which I have not listed here, but I think most of those are things which could, in principle, also be achieved with gap junctions (for example: amplitude control, metabolic responses, short- and long-term plasticity).


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Primer design for Gibson assembly
I'm trying to design a primer for Gibson assembly.  My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid.
I am unsure how to design my primers for PCR. I know that I need 2 sets of primers (4 total).

Backward and forward primer to copy my gene out of the plasmid that holds it.
Backward and forward primer to copy the plasmid.

I also know that I need to create complementary regions of overlap between my gene and the plasmid I want to put it in.  How do I do this?
Here is the plasmid and the gene. I want to place the gene in between the biobrick prefix and suffix.
Here is what primers I think I need:
For the plasmid I want to put the gene in, my primers should be

Forward: ATTCGCGGCCGCTTCTAGAG
Reverse: CTGACGCGGCCGCTACTAGTA

Primers to copy gene and add overlap

Reverse: ATCATTTCAAATTCGTCCATCTCTAGAAGCGGCCGCGAAT
Forward: AATTAGAAAGAGATTATAATACTAGTAGCGGCCGCTGCA

Here is the gene

IodoY TyrRs

Here is the plasmid I want to put it in. I am using geneious, but I think for this purpose, word works just fine.

your gene is 5kb long.. you cant assemble it with 4 primers..
BTW.. why do you need to assemble it ? you can do a normal PCR.. easier

@WYSIWYG the TyrRs gene is just 1920 bp of the plasmid in the linked file.

@AlanBoyd.. that would still require more than 4 primers to assemble it.. To assemble a ~320bp fragment I used four 90mers..

Marco... I think what you want to do is a nested PCR.. in gibson assembly you assemble the entire DNA fragment using several small oligos..

Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two 20 bp segments of each 40mer.

Here is a good overview of primer design considerations when using Gibson assembly.
http://j5.jbei.org/j5manual/pages/22.html

it says can linearize the plasmid by cutting it and so you'd only need 2 primers to clone the insert.  what advantage is there clone the vector as well?  I guess it saves a miniprep, but 2 oligos cost more than a miniprep does..

Well the downside to cutting the vector is that a restriction site must already exist at the junction. This is a major limitation that Gibson overcomes. The potential downsides of using PCR to amplify the backbone: you might have problems getting PCR to work (always a potential problem), and there is a minimal risk of introducing mutations during PCR (but phusion polymerase should give very few mutations).

Most vectors do have convenient cut sites, but I can see that this is convenient in a lot of ways and it would be quick to order new oligos for the vector.  i really want to try this in the lab...

@MarkB would you be able to [edit] your post to summarise some of the content of that link in case it is not around in the future?

This link helps to answer the question, but on Stack Exchange we prefer answers which don't depend entirely on a link to another website


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What's seen when stress echocardiography shows ischaemia? Can this happen without angina?
What can be seen on the screen when stress echocardiography (a pair of heart ultrasounds before and after exercise) suggests ischaemia? Can this happen without chest pain?
Illustration from Wikipedia:

A number of things can be seen. Ischaemia is typically caused by the narrowing of blood vessels that prevents perfusion (blood flow) to the heart or other organs. When the heart muscle doesn't get enough oxygen, the walls of the heart might not "beat" (i.e. contract) properly. We observe this and thus can tell if a coronary artery is reduced or blocked or fine. It doesn't give absolute numbers of how blocked it is, although observation of the way the muscle moves can give some indication. Contrast can further allow us to visualise the wall with more detail, giving a clearer indication of coronary artery disease in the vessels that supply this part of the heart.
Pain is caused when the heart muscle is really suffering, which doesn't occur unless the vessels are seriously blocked. They're so great that even if about 70% of the artery is blocked there is almost no effect including chest pain. In fact it is silent, which is quite worrying also. However, when the heart is most stressed, we can potentially detect decrease in perfusion from small changes in the contraction of the heart.

Many thanks for the answer. Is injecting a dye a usual part of standard stress echocardiography? Or is a dye injected during stress echocardiography under some special conditions?

Your answer makes me think me that ischaemia should be visible with plain echocardiography. Is the second echocardiography after exercise important?

You answered that in stress echocardiography we "see how it responds to increased exercise (does the blood flow increase by the same amount everywhere?)". 10 days ago Xaqron answered "echocardiography [was] not sensitive enough to do so". Was Xaqron wrong?

You can't visualise it directly. Basically you compare the baseline (at rest) to the stressed heart. What you specifically compare is the motion of the walls. The important word here is "compare". Without a baseline you can't see as much. Contrast (i.e. the dye) enhances visualisation where it is difficult to see wall thickening.

I've updated the answer to make it more clearer. You can't tell the flow difference directly, but you can indirectly by measuring the differences in the way the heart contracts. As there's a lot of other factors at play (oxygen concentration of the blood, anaemia etc.) you can't simply equate flow and the observations on an echo. As you are keeping most of these variables constant by doing a before and after, the only thing really affected is flow which is decreased dramatically by thickening of the blood vessels, which you can thus measure.


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Writing methods section on PCR amplication in a paper
Considering that I am writing a paper for a journal, could the following phrase be understood? or should I put the 'step-by-step' way by giving numbers?
PCR Amplification and sequencing
PCR reaction for sequencing with universal primer  ITS5: F: (5’TCCTCCGCTTATTGATATGC3’ and ITS4:R: (5'TCCGTAGGTGAACCTGCG
C3'), including 5,8S rDNA region (White et al 1990). Amplification condition  was performed in a 25 ml reaction volume and consisting of 10 µL nuclease free water, 12.5 µL Tag green master mix, 0,5 µL forward primer, 0,5 µL reverse primer, 0,5 µLDMSO, 1 µL template. Mixture solution  was amplified by PCR machine (Biorad). Thermal cycle programmed for 90 seconds at 95°C as initial denaturation, followed by 35 cycles of 30 sec at 95°C for denaturation, 30 sec at 55 °C as annealing, 90 sec at 72 °C for extension, and final extension at 72 °C for 5 min. PCR products were examined by electrophoresis  at 100 V for 30 minutes in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker used DNA ladder 1 kb.  Electrophoresis gel was soaked in ethidium bromide for 30 minutes then visualized in UV light.

You should change your "Amplification..." sentence to remove the word "condition" and change 25 ml to 25 µL, but other than that it looks okay. Also, maybe spell out "Forward" and "Reverse" when listing your primers.

Is Tag meant to be Taq?

@AlanBoyd Is there any reference as a guidance for writing a journal; cases like 'mins should be min' and 'secs should s', and other abbreviation in (micro)biology term.  Should I only learn from the previous reviews/journals? Thanks.

@Des-microbiology this site looks like a reasonable place to start.

@des: according to the SI (which is the reference for these matters) the abbreviation for seconds is s not sec.

@AlanBoyd what is the abbreviation of diameter? dia Or diam? The references in my hand do not provide it. The context is: Phomopsis sp (3).
Cultural characteristic: Colony of  2-3-1-B2 isolate on potato dextrose agar after 7 d, fast growing fungus, abundant with aeral mycelium, cotton-like, white colour, 51 mm diam, serrated edges colony.

@des There isn't a "correct" abbreviation for diameter - it isn't a physical unit in the same way that seconds or minutes are. However specific journals probably have their own rules - check their Style Guide.

Here's my take, just a few minor changes which are shown in bold (I have also changed ,to . for decimal numbers and added a few spaces where needed):

PCR Amplification and sequencing
A PCR reaction for sequencing was performed using universal primers ITS5: F:
  (5’TCCTCCGCTTATTGATATGC3’) and ITS4:R: (5'TCCGTAGGTGAACCTGCG C3'),
  including 5.8 S rRNA region (White et al. 1990). Amplification condition
  was performed in a 25 ml reaction volume and consisting of 10 µL
  nuclease free water, 12.5 µL Taq green master mix, 0.5 µL forward
  primer, 0.5 µL reverse primer, 0.5 µL DMSO, 1µL template. PCR was performed using a Biorad PCR machine. The thermal cycle was
  programmed for 90 s at 95 °C for initial denaturation, followed by
  35 cycles of 30 s at 95 °C for denaturation, 30 s at 55 °C for
  annealing, 90 s at 72 °C for extension, and 5 min at 72 °C for the final extension.
  PCR products were examined by electrophoresis at 100 V for
  30 min in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker
  used a 1 kb DNA ladder. The electrophoresis gel was soaked in ethidium
  bromide for 30 min then examined in UV light.

The first sentence is not a sentence.

@terdon or even better, use the correct abbreviation for seconds which is s, not sec(s). And use min for minutes (never mins)

@AlanBoyd thanks! It's 22:00 here and I'm still in my lab writing a report for a grant I received, so my mind is not at its best. I knew that sec bothered me but I couldn't put my finger on it. WHile absolutely correct, your comment about min is nicely ironic given that what I read is: "@terdon or even better, use the correct abbreviation for seconds which is s, not sec(s). And use min for minutes (not mins) – Alan Boyd 4 mins ago". :)

@kmm indeed it was not.

Tag should probably be Taq...

@terdon I use rDNA not rRNA.


text:
By what mechanism is Streptococcus bovis acting as a risk factor for colorectal cancer?
Streptococcus bovis bacteremia/endocarditis is considered a risk factor for colorectal cancer. What pathophysiological mechanism may link the two together?

As you probably know, there is a lot of literature on the correlation between Streptococcus bovis and colorectal cancer, but very little on possible mechanisms.
In an editorial (Streptococcus bovis: Causal or incidental involvement in cancer of the colon? in the International Journal of Cancer 119(9):xi-xii), Harald zur Hausen referring to this paper:

Biarc J, Nguyen IS, Pini A, Gosse F, Richert S, Thierse D, van Dorsselaer A, Leize-Wagner E, Raul F, Klein JP, Scholler-Guinard M. (2004) Carcinogenic properties of proteins with proinflammatory activity from Streptococcus infantarius (formerly S. bovis). Carcinogenesis 25: 1477–84.

comments:

...used a partially purified S. bovis S300 fraction representing 12 different proteins and triggered the synthesis of proinflammatory proteins (human interleukin-8 and prostaglandin E2, correlated with the in vitro overexpression of cyclooxygenase-2 [Cox-2]) in human colon carcinoma cells (Caco-2) and in rat colonic mucosa. These data could point to a role of oxygen radicals in colon carcinogenesis induced by a chronic infection with S. bovis. The mechanism could be similar to the one suspected for the development of gastric carcinomas after persisting Helicobacter pylori infections. Presently it would still be important to know whether the increased presence of S. bovis in colonic cancers and polyps results from the preferential bacterial colonization of these cancers and their precursors or whether S. bovis represents a carcinogen that is causally involved in colon cancer.

The last sentence summarises the ongoing debate: does the bacterium promote the cancer, or does the cancer promote the bacterial infection?


text:
What is the disadvantage of having no anticoagulation after pulmonary embolism?
Is chronic anticoagulation always given after pulmonary embolism?
What are the risks or disadvantages

if anticoagulation is not given?
if terminated early?

Not always, however typically it is given for at least a few months. Lack of anticoagulation therapy would greatly heighten the risk of having another PE or related cardiovascular events. At the worst side this could cause death or permanent disability, and PE related deaths are quite common. However this depends on the nature of the PE and risk factors. For example, obesity, cancer and the pill are all risk factors and if these were reduced then it is likely the person wouldn't have another PE despite not being on long term anticoagulation therapy. However, if there is an underlying cause even despite anticoagulation therapy a person may suffer a PE.
The problem with anticoagulation therapy is of course it stops your blood clotting. Thus haemorrhages are more common and also more severe. However in an individual receiving anticoagulation therapy, they typically have increased clotting so this may be balanced out by therapy.
Finally anticoagulation therapy is typically warfarin in the long term. Warfarin interacts with so many drugs including even antibiotics, it is teratogenic and quite sensitive to diet (any changes in Vitamin K will directly affect the effectivity of warfarin) thus frequent monitoring is required. This is annoying for the patient as they have to report for frequent blood tests as well as watch their diet etc.

It should be noted that the teratogenicity should not be too great of an issue as those trying to conceive can be switched to low molecular weight heparin

I summarize that specifically addresses my questions: Anticoagulation is typically given. Not giving anticoagulation risks another PE or related cardiovascular events, in the worst (not rare) case leading to death or permanent disability. -- Would the second PE be somehow triggered by the first one? Or by the same factors triggering the first one?

The latter, same triggers


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Has medical progress stopped human evolution?
We can cure many diseases nowadays, and thus the natural selection is very limited.
Plus, mankind spent the whole beginning of its existence in almost the same hostile environment, and that's where he evolved the most, whereas our environment is changing very quickly. So, can we say that mankind froze, if not stopped, its own evolution ?

As long as some individuals reproduce more often than others then there will be evolution.

Not at all.

Mutations accumulate independent of medical progress. In fact harmful mutations which would otherwise cause an individual to die can now be "cured" thus if anything increasing the gene pool.
Typically medical progress extends our lives when we are much older, thus we have already passed mutations on to our children before a bottleneck in evolution could occur
We are getting taller, less hairy and women are getting more attractive which is another form of evolution
As new diseases develop the selective pressures on humans are ever changing. HIV which was never as widespread is now pushing certain immunogenetic traits to be favourable, the same is true for malaria (HLA 5701) and many others

In conclusion, whilst there are fewer and fewer strong selective pressures forcing extreme evolution, our bodies are designed to evolve slowly unlike viruses like HIV. Our mutation rates are around 1 in 10^9, allowing us to always slowly evolve as there will always be traits which are slightly more advantageous.

Women are getting more attractive?! Could you please elaborate?

Women that are going to have children pass their traits on. Some people believe that the women who are more likely to get married and have multiple children are those that are most attractive. Other theories suggest that the most attractive women do not have children. Either way a certain trait, whatever it is, is the one more prevalent in women bearing children and thus this is the one that is passed on.

It doesn't sound like there is a testable hypothesis in any of this. Do you have a cite or two?

here's a post if not the primary reference.  This sounds reasonable to me, though i'm sure its not completely proven.  http://www.abc.net.au/news/2009-07-29/evolution-makes-women-more-attractive/1371676

Evolution is not entirely progressive - look up the 'red queen' on wikpedia.  Competition changes traits by selection, but there is constant competition from the outside that reinforces change only for change's sake - it doesn't necessarily make the traits stronger. If you get the most masculine man and the most feminine woman, will the children have both extreme traits when and where you want them?  Many exceptional trait combinations are not reproduced in offspring - they are as much coincidence as they are the product of selection. Look at pictures of Schwarzenegger Sons - not that big.

All this is not a simple question well tastes in what is attractive also changes.  I'd say our appearance does and has changed over time, and this is because of sexual selection to a great extent.  its a viable hypothesis, and there's evidence, but there are also definitely other forces in play here.

As an example that we do change with evolution and a further Arnold reference, you can see that Neanderthals definitely were physically quite different from us.  "Modern man a 'wimp'" :  http://www.independent.co.uk/news/science/modern-man-a-wimp-says-anthropologist-1802501.html

Keep in mind that most people live in environments where antibiotics are of limited availability and hygiene is not as rigorous as in the "western" world. Combine this with high population densities and you get, if anything, more natural selection due to the spread/proliferation of pathogens and the subsequent mortality of the patient.
Also, don't confuse natural selection for evolution. Natural selection is one of only five causes of (micro-) evolution. Mutations will continue to occur. Sexual selection continues unabated, and migration is more important now than ever. The only evolutionary factor I'd argue is being diminished is genetic drift since there are so many people today.

authors: άθλια βδέλυγμα


text:
How difficult is to renature a protein?
I know of Anfinsen's experiments and I'm aware that some denatured enzymes may regain their lost activity through the removal of the denaturant agent. What I'm unaware of is how rare is it for a protein to be able to renature? Can all proteins do that? If not all of them can do it then how rare or common is it to find a protein which can be renatured?
P.S. To avoid answers like "depend on your denaturation process" let us assume that a protein can be renatured if it has been shown to renature in at least one experimental setup.

This is a very difficult question, and I doubt the answer is known to any satisfying degree of certainty.  The best suggestion I have is to look at proteins requiring chaperones to fold.  Even that I couldn't find any numbers on, but there might be some papers out there addressing it.

The answer is more like "It depends on the protein, and the renaturation (or refolding) process." There are a lot of factors that contribute to an individual protein's ability to refold, including size, sequence, secondary structure, amount and type of inter-amino acid links like disulfide bonds, number of subunits, the presence of chaperones/heat shock proteins, and, yes, how it was denatured in the first place (sorry, I couldn't resist). Smaller proteins will refold more easily than larger ones. Hydrophilic proteins tend to refold better than more hydrophobic ones, especially membrane-bound proteins. Multi-subunit proteins/complexes tend to need some help to properly reassemble. Adding in chaperones/heat shock proteins will almost certainly help the process along for all but the smallest and hardiest samples, and will give you better results than just dialyzing all the salts/detergents/chaotropic agents away into PBS. Finally, if you denature by boiling in Laemmli buffer, you're going to have a very difficult time refolding most things, while going from Guanidine HCl to PBS isn't always that bad, depending on what you're looking at.
So, unfortunately the answer is "it depends." You have to remember that the intracellular environment is very complex, and is designed to correctly fold proteins after they're made, and break down misfolded proteins before they can aggregate or cause other damage. There are hundreds of thousands of proteins just in humans, so it is rather difficult to make blanket statements, but for the sake of resistance to damage, many smaller, single-subunit proteins can likely be at least partly to mostly refolded and regain some or all of their original activity. As complexity grows, however, the likelihood of successfully regaining function decreases.

my impression has been that only relatively small proteins (~10kDa) are readily renatured and used in protein folding kinetics experiments.  Its pretty unlikely that anything larger will be useful.  Do you have any specific examples of a larger protein that has been refolded by any means, and if so do you think this is a typical result?

@shigeta - I was specifically thinking of antibodies (150 kDa, 4 subunits disulfide-bonded to each other). At my previous job we experimented with purifying antibodies by eluting them from an antigen column with varying concentrations of guanidine, then dialyzing directly into PBS. We didn't do any biophysical characterization to look at the extent of denaturation, but in our functional assays they performed similarly to those eluted by the standard (pH-dependent) method.

those antibodies would not be fully denatured. just enough chaotropic agent probably to disrupt protein-protein interactions to get the antibodies off the column.  Antibodies have one of the more stable folds and will not usually denature under such conditions.  if you did I would be surprised if you could reconstitute a functionally folded protein... imho


text:
What kind of arthropod/animal is this?

Can anyone identify this strange creature? I live in a very urban part of Montreal, Canada. It wasn't moving (seemed dead) and although the image is huge, it wasn't as big as it seems (a couple of centimeters).

It's a type of centipede.
Based on the long legs, I would bet on something like that:
http://en.wikipedia.org/wiki/Scutigera_coleoptrata
Or at least a Scutigeromorpha http://en.wikipedia.org/wiki/Scutigeromorpha#Scutigeromorpha

I live in Japan and here they are called "gejigeji". As mentioned, they are a member of the centipede family and are as creepy as hell. I live in a newly-built house, so thankfully there are no cockroaches, but every now and again one of these little blighters will scurry across my floor in my peripheral vision and scare the bejesus out of me.
They are not dangerous (at least not to humans). I have been told they eat the larvae of other insects, like cockroaches so they are not so bad really. Also, and I assume this is just a Japanese myth, but it's said they hunt in pairs.

It is a common house centipede. Apparently they're everywhere but I've never seen one before.


text:
How to use mechanical microstrainer to extract tissue proteins from human?
Background:
There are many methods to extract proteins form human tissues out there. The majority of them use an extraction buffer containing variable concentrations of detergents and protease inhibitors to preserve the extracted proteins as much as possible and keep them functional until being analyzed by downstream applications, like western blot, ELISA, etc. One drawback of this chemical extraction is the interaction of the buffer components with antigen-antibody binding in the analysis. The interaction is sometimes difficult to predict, therefore, validation of the sample matrix is necessary before going into the real analysis, e.g., for ELISA, spike-and-recovery, linearity-of-dilution are two known validation assays to this effect. For more info about these two assay you may find this answer useful.
One optimal way would be to avoid such interaction by avoiding the use of extraction buffer altogether and using mechanical methods plus protease inhibitors, instead. I don't know the drawback of this method, but one may be it is not as effective to get cytokines out their vesicles to be accessible by assay analysis.
Questions:

How to use Microstrainer as a mechanical substitute for protein extraction in human gastric tissue?
What are the pros and cons of using the Microstrainer?
How effective is it to measure human cytokines from tissues?

what is a micro strainer?  is this an idea you have or a reference to a specific piece of equipment?   several methods of the sort you have described may be used, but i've not heard of a microstrainer...

@shigeta, it is some sort of milli-pore filter that would disrupt tissue by vortexing. I have never used it, here  you can find a reference that used it.

thanks - never used it so can't comment - sounds cleaner and more $$$ than a hydraulic press, a bead beater or other similar methods.. :)


text:
TCGA data, and bioinformatics design questions for SNP/ mirna analysis
It's my first time posting to this forum but was looking for some help on the data aspects of this project.
My tools of choice would be in python/R .
Goal: I'm looking to create a disease specific profile of just SNPs and SNPs in miRNAs and miRNA target sites.
PART 1: TCGA
My first step is using TCGA data which lists a ton of harmful mutations in a LOH .txt format. I'd like to be able to map those mutations to SNPs or genes or miRNAs  (whatever entities they belong to). The TCGA datasheet is here.
Example data is here. for breast cancer. I guess I can use this miRNA and mRNA data as well.
Questions here:

How to decipher the LOH data to figure out if it's meaningful and where it maps?
Which Tools to use for mapping and what formats for final data ? Fasta ?

miRNA/Targets and SNPs
Next up is getting cancer specific miRNAs and mRNAs and mapping SNPs to them?
I'm assuming using dbSNP or Sanger miRNA databases to get miRNA/targets and seed sequences.
I'm a bit lost as how to combine all these pieces of information, what formats to use for output (linked to individual pieces) and which tools if any to use to gather all this data using python. This tool is useful tool mirdsnp.

I think you might be missing a few links - I don't see your TCGA datasheet and I can't tell whether the last sentence is meant to have a link or not.

Hi I edited it.
I believe I was only allowed one link so hopefully it's fixed.. here is the data sheet
I guess my issue is understanding how to make sense of the LOH data and how to map it in a meaningful way.. The second is how to incorporate the miR and miRsnp related data.
Thanks for catching the missing links. If I wasn't clear enough or didn't provide enough information let me know and i'll clarify as much as I can

I can't comment on the science, but as far as the analysis goes, Biopython has great tools for working with FASTA-formatted data: see SeqRecord

You can take a look at this tutorial to understand TCGA MAF files. And you can find a list of TCGA MAF files containing mutations mapped to genes and miRNA at https://www.synapse.org/#!Search:syn1710680

Thanks for the answers. @dd3 I was planning on using SeqRecord. Though I'm not sure how to add features to SNPs to link them to associated miRNAs or targets etc..

those are great links. How did you deduce the MAF. I'm looking at SNP and expression miRNA profiling for level 3 [https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp data]. for where I found that information and it mentions LOH and MAGE-TAB. Here is another [http://www.broadinstitute.org/collaboration/gcc/data/data-types link] .. So i guess for this particular part I'm confused about data format, and meaning of the data :) . For the rest it's how to manipulate miRNAs and then batch search with python/biopython. Thanks again.

Affter finding this [https://wiki.nci.nih.gov/display/TCGA/Accessing+MAF+files link] it seems to me that level 2 files are MAF files. Level three are .txt something else.

@prussiap: I'm not familiar with the file formats, but could you use Python dictionaries, using SNP IDs as keys?

That is the method I am using so far. This does remove duplicates but I still would like to do a mass download of positions and annotations for each SNP.

@prussiap: Level 2 is processed data and Level 3 is interpreted/validated data. Check the TCGA Data Level Classification page for more details.


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Endophytic Xylariaceae: diversity and taxonomy inferred from rDNA sequence analyses
"Thailand is considered as one of the areas containing a high percentage of unknown taxa of Xylariaceae (Rogers 2000).  In Thailand, several studies on endophytic fungi have been documented, namely, from several bamboos (Luyong et al. 2000), banana (Musa acuminata) (Photita et al. 2001), monkeypod/rain tree (Samanea saman) (Chareprasert et al. 2006), and several xylariaceous endophytes were also reported from those plants."
Review quoted from Izumi okane, Prasert Srikitikulchai, Kyoko Toyama, Thomas Laessoe etc. Full Paper; Study of endophytic Xylariaceae in Thailand: diversity and taxonomy inferred from rDNA sequence analyses with saprobes forming fruit bodies in the field.
Have any of you known the similar cases (the high percentage of Xylariaceae) in the USA, France, or UK, proved by reference(s)?

Are you looking for areas that high a high percentage of Xylariaceae as compared with total fungi species richness? Or for areas that have a high percentage of unknown taxa of Xylariaceae compared with total Xylariaceae taxa?

@Oreotrephes: The high percentage of Xylariaceae in the USA, France, or UK, proved by reference(s), thanks.


text:
What medical and commercial proteins are made using genetically modified animals?
Recombinant technologies in micro-organisms being used to produce commercial and medically useful proteins like insulin are fairly common.
However some proteins are still produced commercially in genetically modified animals. Why are animals a better choice than microorganisms, and which are the most common proteins produced this way?

Transgenic animals are not used for commercial activities as of now.

The rationale for the choice of higher organisms as the producing source is based on costs and biological activity.

Biological activity. In their active forms, various proteins have
post-translational modifications (i.e. glycosylation) which are
difficult to reproduce in bacteria. Alan's answer is already
exhaustive.
Costs. Mammalian cell lines are easier to generate and maintain but
suffer from genetic and epigenetic instability (the transgene can be
lost or inactivated). Contrarywise, transgenic animals require more
investment but once established that the transgene is present in the
germline and breed through, the protein can be produced in larger
quantities with ~1/10 of the costs required to setup a
GMP-bioreactor. This is particularly appealing for small
pharmaceutical niches, i.e. drugs targeting rare diseases: if the
market is small, farming few goats can be more profitable than
building and maintaining sterile bioreactors. Downstream purification
facilities are however required for both cellular and animal farms.
That's why animal models that produce high levels of the therapeutic
protein in secreted matrices (i.e. milk, egg white) are preferred:
this facilitates bulk storage of unpurified protein prior to
purification.
A good and recent review comparing models and strategies is from Wang
et al., Expression Systems and Species Used for Transgenic Animal
Bioreactors (doi:10.1155/2013/580463).

To stay updated on recombinant proteins from transgenic farms entering the market, the official reference would probably be the FDA section on Biologics. Two companies actively working on transgenic farms are GTC Biotherapeutics and Synageva.

GTC Biotherapeutics produces human antithrombin alfa (ATryn) in the milk of transgenic goats, for use in patients with hereditary antithrombin deficiency (HD). Quoting the ATryn executive report:

Antithrombin III (recombinant) is a highly purified, well
  characterized recombinant glycoprotein consisting of432 amino acids, 3
  disulphide bridges between cysteine residues and 4-N linked
  glycosylation sites, identical to human plasma-derived antithrombin.
  Recombinant human antithrombin is produced in the milk of transgenic
  goats. For expression of rhAT, the DNA construct contained a goat beta
  casein promoter with the cDNA coding region for human antithrombin
  (hAT). The DNA construct was microinjected into fertilized one-cell
  goat embryos, which were transFerred to female recipients. Kids born
  from the recipients were tested for presence of the transgene and
  expression of the human protein. A founder transgenic goat was
  selected from which subsequent offspring were generated by natural
  breeding to give rise to a production herd of hAT transgenic goats,
  which are milked to provide the source material for downstream
  purification.

Synageva produces Sebelipase alfa (SBC-102) in the egg white of transgenic hens, for use as an enzyme replacement for Lysosomal Acid
Lipase (LAL) Deficiency. I think they are in clinical phase 2/3 (not
yet on the market). According to their 2012 Annual Report:

Our proprietary vectors allow incorporation of the gene of interest
  into the genome of normal cells of an avian (Gallus) with selective
  expression of the resulting protein in the oviduct tissues and
  secretion into EW. The importance of this cellular environment for
  therapeutic protein expression is highlighted by the tight consistency
  of post-translational modification, including glycosylation, seen in
  proteins manufactured using our platform compared to cell culture
  produced material. Furthermore, our expression system yields
  consistent expression levels and quality of protein within production
  lines and through multiple generations.

ATryn is a human antithrombin produced in the milk of transgenic goats by GTC Biotherapeutics. It has FDA approval and I believe that it is available for prescription in the USA.
Added later, after the emphasis of the question changed somewhat.
Proteins produced in a mammalian system are more likely to have post-translational modifications that are much closer to those found on the human protein. Antithrombin, for example, has four disulphide bonds and four glycosylation sites. Although it is reasonable to assume that the disulphide bonds would be correctly formed in a eukaryotic microorganism, the same isn't true of the glycosylation: microbial glycans differ from mammalian glycans, and these differences could affect the stability of the protein in the mammalian bloodstream, or the response of the mammalian immune system to the protein. Mammalian cells in culture could be used but are, of course, quite fastidious. So the holy grail of recombinant protein production has always been to get the protein secreted into an animal's milk, allowing the use of very cheap feedstocks and the easy harvest of the protein over a period of years, notwithstanding @shigeta's remarks.

might well be right that this is the only current case.  Transgenic animals are really expensive compared to transgenic bacteria - its very expensive to make a transgenic goat and the ability to produce the transgenic product often doesn't breed through - making you start all over again from scratch when the goats die.


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Is Schoons Hard Shell muskmelon a hybrid?
Would Schoon's Hard Shell muskmelon be considered a hybrid as I have read it was a cross between a Bender's Surprise and a Honey Rock.

Do you have a reference for where you read it?

Goldman surmises that Schoon's Hard Shell is a variant of the Bender, so would have been bred from the Surprise, Irondequoit, and Tip Top, all of which were from the Sill's Hybrid.
In that sense, I suppose it's a hybrid. I'm guessing that you're asking because you want to know if you can save the seed; that is, if Schoon's Hard Shell will breed true or will lose its characters in subsequent generations.
I can't find any specific detail on that, but given that it's sold by Seed Savers Exchange, I'd guess that it is a good candidate for seed saving, as long as you make sure it's not crossing with related species in your garden. Seed to Seed has detailed info on melon seed saving.

Goldman A. 2002. Melons. Artisan Books (p. 76)

Whealy K. 2012. Seed to Seed. Chelsea Green Publishing (p. 103)


text:
Diffusion across cell membranes
I got this question and don't really understand the difference between the answers.
Diffusion is (in cell membrane):
a) passive by nature, no metabolic energy is needed
b) driven process by pressure or voltage

Diffusion is always a passive process that doesn't require energy.  Therefore it would seem that A is correct, B doesn't really make a whole lot of sense.  In the case of the cell membrane diffusion will often be in the form of 'facilitated diffusion' through carrier proteins, however the transport is still not active.

Diffusion relies on the fact particles move randomly in whatever they're in. If they are concentrated (I.e. there are lots of them in one place) they will fill out the whole place. With respect to cell membranes, anything that can diffuse freely will be the same concentration inside and outside the cell. It doesn't require metabolic energy as the cell doesn't need to do a thing. Thus the answer is A.
Facilitated diffusion is where the cell puts protein channels on its membrane to allow diffusion of things that can't pass through the cell membrane normally or do so really slowly. This can be driven by a voltage or by pressure, which "facilitate" or help the diffusion. Glucose for example moves like this into the cell. It uses the fact that there's a high concentration of sodium outside the cell that "wants" to move in because of the cell inside being negative and low concentration inside. So glucose hops onto a sodium ion whilst it is moving in.

AndroidPenguin's answer has really muddied the water, but I can't fit my response into a comment.
When a glucose molecule moves from the blood into, for example, a muscle cell, it is indeed diffusing down a concentration gradient, and the GLUT transporter protein acts to facilitate this process by providing a route for the polar glucose molecule to get across the membrane. This is facilitated diffusion. The movement of the glucose molecules requires no input of metabolic energy. That part of AP's answer is ok, and really that's all that the OP was about.
In direct contrast to this, enterocytes can transport glucose from the gut lumen into their cytosol even though the gradient of glucose concentration is in the other direction. They do this by linking the inwards movement of the glucose molecule to the outwards movement of Na+ ions, down the electrochemical gradient for these ions. This Na+ gradient is, in turn, generated by a pump which uses ATP to move Na+ out and K+ in. So in this example the energy derived from ATP hydrolysis is 'stored' in a gradient of Na+ concentration, and this gradient is tapped as a source of energy to power movement of glucose. This is NOT an example of facilitated diffusion. The ATP-powered movement of ions is an example of primary active transport, and the action of the Na+/glucose transporter is an example of secondary active transport. Note also that the glucose and the Na+ move in opposite directions (antiport) so there is no question of a direct interaction between the ion and the glucose.


text:
Immunity during pregnancy
I have learnt that our immune system distinguishes self from non-self by using MHC. So a mother during pregnancy should also develop antibodies against the fetus as it is also a genetically different individual. Answering by saying that antibodies won't cross the placental barrier seems wrong as there is so much research going on this thing that such a simple explanation wouldn't suffice.
Why doesn't the mother reject the baby?

Perhaps an equally interesting question is why the immune system doesn't attack sperm. I've seen the answer before (but don't have a reference handy) and if I remember correctly, there's some special hard-coded marker, which is actually pretty scary. In any case, I think the mechanism is quite different from the one involved in your question.

In fact antibodies do cross the placental barrier:  there is active transplacental transport of maternal IgG into the foetal circulation.

Actually her body can reject the embryo. That can be one cause of infertility, and a mild immunosuppressant can help...

Awesome question! The immune system detects the presence of non-self using MHC and T cells and the lack of self using NK cells. The placenta first of all doesn't display MHC so T cells can't detect it, and expresses NK inhibitory receptors which stop NK cells killing it. Furthermore, the immune system isn't able to get to the foetus so it isn't able to activate against these antigens nor produce the antibodies which require T cells to be activated first, which then activate B cells. This is because the placenta is a syncitium, thus no spaces between cells for immune cells to slip through (a mechanism used by viruses). The placenta also secretes Neurokinin B, this makes it hard for the immune system to see the baby, and is a mechanism used by parasites. There are T reg cells which act to supress an immune response.

thank u so much for answering . Your explanation seems quite plausible but I read in a book (Campbell Biology 9th edition) that still research is going on for finding explanation. So why is your answer not actual "answer" ?

I would imagine because it isn't the complete picture. I would imagine (but am not sure) that investigating the above features doesn't sufficiently depress the immune system preventing rejection of the foetus.

I think the research is far from complete in this topic. Afaik. there can be cells from the children in the mother and these cells are tolerated by the immune system.

http://www.ncbi.nlm.nih.gov/pubmed/23049819

@inf3rno yeah... microchimerism..


text:
Can proteins move outside cells?
I am trying to learn about basic cell biology, and have what is probably an extremely simple question.
So this is how I understand it so far:
Proteins are made from amino acids. This process is called protein biosynthesis, which is carried out by the ribosomes. So proteins are made by the ribosomes in every single cell.
So are the proteins made by the ribosomes to stay in the cell? Or can a protein move to other cells, and if so, what's the reason behind it?

Yes. All proteins actually begin to get synthesized on cytoplasmic ribosomes but if they are going to be used for extracellular purposes, they are tagged and whole ribosome is taken to ER where protein synthesis is completed. The proteins are exocytosed with help of Golgi body, the post office tagging and packaging organelle (the Golgi body packages these proteins into the vesicles that fuse with the plasma membrane).
Examples of this process are: the pancreas secreting insulin for blood sugar control, digestive enzymes for digestion, the immune system telling the body there's a bacterium we must fight it and calls more immune cells (cytokines). Most proteins of course stay in the cell, and are necessary to make the cell or carry out metabolism or DNA transcription.

Extremely good answer which really helped. Thanks!

My pleasure Lars!

Thanks Alan :) how did I forget Adrenaline is a steroid hormone...

Other examples are neuropeptides produced by neurons in the brain (e.g. endogenous opioids, various neurohormones such as GnRH, GHRH, vasopressin, oxytocin etc etc)

Collagen and elastin are other examples of extracellular proteins.

I would like to complement dd3's answer a bit. It is about bacteria

Bacteria secret enzymes outside. The bacterial membrane has import size limits and it is necessary for them to chop the big molecule into smaller pieces before import. Examples are glycoside hydrolases and protease. Bacteria take part in the clean-up after the annual algal and jellyfish bloom. It is especially important for the jellyfish because they have few predators and if it were not for the bacteria, their gelatinous body will pile up at our sea bottoms.
Bacteria release protein toxin, either to defend, or use to recognize the host if they are symbionts.
Gram-positive bacteria use peptide as autoinducer to do quorum sensing.
Last but not least, bacteria sometimes form aggregates. The glue among them is chemically very complex (in other words, we don't know exactly what it is). It is believed sugars are there and, proteins too.


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Transplantation of stem cells
During the autologous transplantation of stems cells from bone marrow to produce new blood cells why all the other stem cells other than the one obtained are destroyed?

Autologous stem cell transplants are used to treat individuals who have had their bone marrow destroyed or damaged by diseases such as lymphomas or by irradiation or cancer treatments. As they are damaged and potentially cancerous, they are removed. They are then replaced in the transplant. The whole idea is to destroy all the cells before transplanting the marrow back.

thank you
So the stem cell is obtained from another part of the body and transplanted into the bone marrow and not obtained from the bone marrow itself?

or to make it simple where is the stem cell obtained from ?

Although most of these stem cells are in the bone marrow, there are also some in the blood and these are collected in order to perform an autologous transplant.

What Alan said is not always true, they can be taken from the blood or bone. Certain chemicals can cause the cells to leave the bone marrow to collect them in the blood. They are collected when you are in remission or free of any disease and stored, frozen. Then if the disease comes back, every cell is destroyed (hopefully killing every cancer cell) then the frozen stem cells are transplanted back to reconstitute the immune system. This can be repeated but typically shouldn't need to be.


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Why does the sweat of children not smell like adults?
My kids sweat plenty in this hot heat, but they don't smell afterward. I on the other hand need all kinds of deodorant. Why doesn't kid sweat smell?

There are two types of sweat glands: (1) eccrine sweat glands and (2) apocrine sweat glands.

Eccrine sweat glands are present from birth in humans and secrete sweat that is mostly water and functions in evaporative cooling.
Apocrine sweat glands are found in the armpits and groin regions and become active in humans at puberty (although the distribution appears to be broader fetally). These sweat glands secrete an oily substance containing lipids and proteins that through interactions with bacteria on the skin (e.g., bacteria digesting lipids), lead to the "smelliness" of adults (including body odor).

So it's not really the sweat that smells, it's the action of bacteria on apocrine sweat that becomes prevalent after puberty.

Excellent, thank you! I did know that the smell comes from bacteria, not the sweat, but I didn't know we had two kinds of sweat glands. Darn those apocrine glands!

Which leads to the natural question, why are those second category of glands active only after puberty?


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Reverse complement of reconstruction model for assembling reads
One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this problem is the reconstruction model, which calculates the minimal edit distance between a possible superstring (that contains all fragments) and each one of the fragments. What I don't understand yet is the fact that when calculating the edit distance for a given fragment, it's necessary to calculate the edit distance for the reverse complement of that fragment. An example of a fragment and its reverse complement could be:
 ACTGTCC fragment
 TGACAGG complement (the complementary strand as we know)
 GGACAGT reverse complement
According to the book I'm reading the ideia behind it is to find a superstring as short as possible that either the given fragment or its reverse complement must be an approximate substring of the superstring. I know that many mathematical/computational models don't have a biological sense for their way of soluting a biological problem, but this recontruction model I could think it's biologically reasonable to find a string that contains all the fragments of a certain region of a DNA sequence, and all the complement fragments, after all when assembling we can find both strand sequence. But a reverse complement is not something that exist for a given sequence, unless it has suffered some kind of break-recombination event, which is something not expected, mainly when talking about conserved regions. Do you any idea why this model takes into account the reverse complements ? Thanks in advance.

Isn't this just a case of keeping everything straight with respect to 5'>3' direction? If a read matched "TGACAGG" this would not correspond to either strand of your example, because writing it like that implies that it is 5'-TGACAGG-3' unless it is made explicitly clear that it is the bottom strand of a duplex.

So you're saying that in fact the model see every fragment in 5'->3' direction? It doesn't consider the real existence of a reverse complement, but simply uses it because the reverse complement is a way of seeing the complementary strand of a given fragment with 5'3'direction? I'm sorry about the slow reasoning.

Yes, if you have a read (which will be by convention 5'>3') then you can search for it directly on the top strand of the target (also 5'>3'). If you need to look for it on the other strand of the target you can't simply search on the complementary because this is 3'>5', so you derive the reverse complement. It's just the equivalent of turning the dsDNA sequence (on the page) through 180 degrees.

Nice! Thank you very much, Alan. You helped me a lot.

"But a reverse complement is not something that exist for a given sequence, unless it has suffered some kind of break-recombination event" I am not sure that I understand what that means. Why wouldn't a reverse complement exist? If your DNA is double-stranded then it must exist!


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Cat purring: What are some possible underlying mechanisms behind purring and bone remodeling and formation?
http://www.scientificamerican.com/article.cfm?id=why-do-cats-purr
The article above says that cats purr mostly when they're wounded or under duress. They hypothesis that cats purring leads to increases in bone density and bone healing. How is this possible? What are some physiological possibilities for something like this to occur?
I don't see any journal articles backing up any of these claims. Is it similar to how ultrasound in clinical trials works?
Is the cat purring affect formation of osteoblasts? What is possibly happening microscopically?

The author is likely referring to the mechanosensory behavior of bone (reviewed in Huang and Ogawa, 2010; lots of Google Scholar citations). Bone loading produces very tiny mechanical deflections (strain) which are translated into biochemical signals that promote bone growth through the action of osteoblasts. Burger and Klein-Nuland (1999) review possible mechanisms.
The low frequency soundwaves produced during purring overlap the frequencies that have been shown experimentally to induce bone formation (1-50Hz; e.g., Castillo et al., 2006; Xie at al. 2006). Although an interesting hypothesis, I don't think that osteogenesis in response to purring has ever been experimentally shown in cats.
Huang C, Ogawa R. 2010 FASEB J. 2010 Mechanotransduction in bone repair and regeneration. 24(10):3625-3632.
Burger EH, Klein-Nulend. 1999. Mechanotransduction in bone--role of the lacuno-canalicular network. FASEB J 13(Suppl):S101-S112.
Castillo AB, et al. 2006 Low-amplitude, broad-frequency vibration effects on cortical bone formation in mice. Bone 39:1087-1096.
Xie L, et al. 2006. Low-level mechanical vibrations can influence bone resorption and bone formation in the growing skeleton. Bone 39:1059-1066.


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How did the activities of protocells become inheritable?
I have learned that first a protocell came to exist and its characteristics came to be passed on by genetic material. So how come genes for all the activities come to incorporate into genetic material? Did genetic material come first and random sequences made random proteins that were used to make cells ?

another side of the argument, which Richard Dawkins made is that replicators are necessary for selection.  Sure other metabolizing and energy utilizing systems might have shown up, but those which replicate are the only ones you will see over time.

I dont want to debate what came first. I want to know how RNA or DNA or whatever genetic material came first began to be " genetic material " . How did it "know" that this particular polypeptide ( for example ) will be coded by this particular sequence ?

The reason I mentioned the 'replicator' is that it posits that while the primordial chemical soup probably contained many millions of kinds of molecules, the nucleotide bases which were capable of reproducing themselves would win out very quickly.  it sounds a little circular, but that is how it 'knew' if you make 100s of billions of millions of RNA molecules, only those who replicate will quickly be the only ones you see.  we don't know much more detail than that.  the people looking at RNAworld research are trying to get a handle on that.

Well.. This is a tough question (Something that has bugged me for years and still doing so). I don't fully agree that replicative potential came first. This is just my opinion based on some reasoning and I dont really have any reference.
If you compare a nucleotide and a protein, the likelihood of formation of protein is much higher because:-

Amino acids are simpler molecules and simplest of them did appear in the famous Urey-Miller experiment. Nucleotides on the other hand are much more complex
Peptide/amide bond formation is a well known phenomenon even in non-biological chemistries whereas Phosporic esters cant be called common compounds.

In my opinion function evolved first and then its codification. Initially the cell division must have been just like a huge drop dividing into two. I would like to differ from mgkrebbs on this. Lipids are simple molecules and they can spontaneously form compartments such as miscelles based on simple principles of thermodynamics. If miscelles get huge they can divide.
I still cannot understand whether it is chemical reproduction that came fist or sustained multispecies chemical reactions. I tend to believe the second with relatively more confidence.
The popular RNA world hypothesis is justified by certain observations and fits nicely in the Darwinian scheme of biology that we are so used to believe in all the time. But it doesn't answer the previously mentioned thermodynamic perspective. Also I fail to understand why an ancient RNA would code a protein. What advantage would it have to code a protein in the first place. So to conclude I don't have a doubt that proteins came first. The initial soup and the basic functionalities were provided by them. Then nucleotides evolved parallely and they became catalysts of protein synthesis. So the reactants came before the catalysts and the better catalyst got selected.
I again iterate that this is just my opinion which you may consider pondering over along with the answers that others have provided.

The sequence is believed to be opposite of that implied by the phrasing of the question: the inheritance of structures supporting inheritance came before protocells.  The important point is that you need a system of reproduction before building more complicated structures (such as a cell).  Without replication (reproduction), a cell would be little more than a soap bubble, and would disappear without a trace before long.
The initial (or very early) form of replication is thought to be based on a simple form of RNA. The reason for this is that (1) RNA does encode genetic information in a way that is replicatable, and (2) RNA can take on shapes and chemical structures that act as an enzyme (called a ribozyme) that catalyze chemical reactions.  The hypothesis is that an RNA molecule formed that catalyzed assembly of copies of RNA chains, including itself.
After such replication was established, probably some kind of enclosure like the cell membrane evolved to contain the chemicals, making the reactions more efficient.  After (or maybe before) this, RNA catalyzing assembly of simple protein-like molecules whose sequence was encoded by RNA sequences evolved, leading to protein-based cellular machinery.  This mechanism is still evident in life today in that protein assembly uses a ribozyme-based molecule assembly (the ribosome) to translate messenger-RNA into proteins.

The general theory is RNA came first, then DNA. Both are able to replicate with simple changes in temperature (see polymerase chain reaction). So if we imagine a world with nucleotides making RNA, the idea is the survival of the fittest RNA. RNA for example that also had enzymatic activity was "fitter" than RNA that did not. Then go further down the line where RNA that made a certain protein was more "fitter" as thus it's concentration increased. Keep going down the line as this continues, whatever was favourable in the surrounding environment increased until we have what we have today.
Of course this is widely disputed.

AndroidPenguin and mgkrebbs both gave excellent answers to this. There are currently several ideas about the first life on Earth. Data for these methods are pretty useless because we can argue for what is the most probable and what can be modeled in the lab, but we can't (as yet) look for any fossil remains of molecules to see what really happened.
One of the most satisfying hypotheses is that protocells and self-replicating molecules (like RNA) probably came about independently, but in the same location. If the self-replicating molecule found a way to hide out in the protocell, this might be the beginning of something like what we call life.
A good talk on this topic is Martin Hanczyc's TED talk.

Can you give some references to support what you are saying?


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Mapping a mutation to known SNP, 3' UTR, miR
I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information.
The ssm is in the following format:
['Gene name', 'Ensembl Gene ID', 'Chromosome', 'Chromosome start', 'Cancer Type']
['NTRK1', 'ENSG00000198400', '1','156849827', 'Prostate Adenocarcinoma (TCGA, US)']

From there I would like to grab each mutation and :

Map the chromosomal position to a known SNP (rs something output).
See if this snp is found in a 3'UTR
See if this snp is found in a miRNA
Missense or sense mutation
Any relevant genbank etc.. ids

I'd like to do this Python (I think BioPython is suited for this) for downstream applications.

What is the question? It would also help if you gave the format of the file you would like to process.

I've already parse the format for this:
code   ['Gene name', 'Ensembl Gene ID', 'Chromosome', 'Chromosome start', 'Cancer Type'] ['NTRK1', 'ENSG00000198400','1', '156849827', 'Prostate Adenocarcinoma (TCGA, US)'] code
First line is features, second is an example of what's in it. aka. gene name, ensemble gene id, chromosome position and cancer type..
I would like to use this information (any or all) to locate if these SNPs occur in any miRNAs or any 3'UTRs predominantly.

You can also post on biostars.org for bioinformatics related questions.

In order:

Unfortunately, there's no easy way to batch query with only location. You could look up SNPs within genes here.  (You could find the gene a SNP is located in by searching an annotated human genome file for the position.)
You can figure out whether it's in 3'UTR by comparing to a list of human 3' UTRs. The UCSC genome browser page here will help: change the region to "genome", output format to "BED", click "get output", and then filter for 3' UTRs.
You can figure out if it's in a miRNA by comparing chr/start positions to the database available here.
You could use the chromosomal locations and compare to the human genome sequence.  There is probably a better way to do this, but the FASTA for each chromosome is available here.
You could use the SNP IDs to map to Genbank accessions, as per the instructions here.

You don't need BioPython for the first three steps, since it's just parsing each line and comparing values. BioPython is useful for working with FASTA files (so part 4).  All in all, this is mostly reduced to a programming question with all of these resources (basically, you need split each string to get the appropriate numbers/IDs and then compare).

So I've managed to wrangle mutations and their corresponding 3'UTRs . I still don't see a way to determine if that mutation in the UTR is in a miRNA target site ? Are there any thoughts on this?

@prussiap: your original question asked to find if a mutation was in miR -- to find if a mutation is a target of a miR, the best I know is DIANA. Unfortunately, the lookup goes the other way: if you look up a miR, you can find predicted target sites: http://diana.cslab.ece.ntua.gr/


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cell uptake prediction
I'm generating random molecules I would like to know if they are able to pass through the cell membrane. Are there any ways (preferably computational) to predict cellular uptake of an organic molecule which is about 55 atoms?

If it's polar, it's not going through. If it's non-polar, there's a good chance it will diffuse through...

cLogP? I would imagine that's a fast dirty way to get an estimate. http://en.wikipedia.org/wiki/Partition_coefficient

Absorption, distribution, metabolism, excretion, and toxicity ADMET can be somewhat computationally defined but is largely secretive due to the money involved in drug discovery. FAF-Drugs2 will do basic ADMET. The Schordinger Suit provides a more indepth ADMET for a fee.


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What's food mode?
I've been watching a The Crocodile Hunter episode about Komodo dragons, and Steve Irwin kept speaking about the animals being in "food mode", in which they apparently change their behavior to one of a killing machine. He said if bark falls of a tree when they're in food mode, they'll snap it.
Is it for real? I googled "food mode" but nothing interesting came up. Which animals have a food mode like this? Is it restricted to reptiles? Does it have a scientific name? Can I read about it somewhere?

I suspect he just meant "when they are hungry" and likely was playing it up for TV.
According to the San Diego Zoo, they only manage to eat about once a month, and spend a few days digesting their prey.

Adults spend an average of 26 days searching for prey. 10-20 minutes eating. (A 50 kg female was observed to swallow a 31 kg boar in 17 minutes). 3-6 days is spent in digestive pause.
Ingestion rate may be as much as 2.5 kg/min - higher than any other predator except large snakes.
High digestive efficiency (70-90%) Time is dependent upon temperature (about 26 hours at normal body temperature) Cool nights can delay to almost 5 days. Stress can slow or even stop digestion (defecation of partially digested prey may occur)

http://library.sandiegozoo.org/factsheets/komodo_dragon/komodo.htm


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Excretion and metabolic waste?
I know there is a difference between digestive and metabolic waste, but which one is called excretion? And what's the other one called? Thanks!

Egestion is the expulsion of undigested food which occurs typically via the anus. Although, interestingly or maybe just gross, flatworms must use their mouth has they have no anus. This is the non-metabolised material.
Excretion is the transfer of any metabolised material to the environment, including urine or carbon dioxide.


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copper spiral birth control not toxic?
I Always thought that copper was toxic to the human body.
So how can it be safe to place a copper object (birth control spiral) into a uterus for a duration of 5 years?

It is toxic enough to disrupt reproduction which is relatively sensitive, but not enough to kill anyone.  Still there are side effects that show up often.

Copper is toxic, however from a copper device insufficient levels enter the bloodstream to cause any harm. The released copper is however toxic to sperm. Nevertheless at the site of insertion, they can cause inflammation (especially in the first 21 days and during menstruation) and thus they also recruit white blood cells and the increase in levels of prostaglandins. However, this isn't that common.


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How does the immune system distinguish own and foreign antibodies?
Therapeutic antibodies, for example Rituximab which recognises CD20 on B lymphoma cells, can cause adverse effects (e.g. http://www.ncbi.nlm.nih.gov/pubmed/19399690)
One reason behind these adverse effects could of course be an over-response of immune cells stimulated by the Fc region of antibodies attached to lymphona cells.
However, it could also be thinkable that the immune system launches a response against the antibody itself, recognising it as foreign. Does this occur? If so, what part of the injected antibody acts as the epitope recognised by immune cells as foreign?

The short answer is that antibodies are proteins like any other, and if an antibody from a foreign source is injected it can result in an immune response. This is, of course, exploited in the production of secondary antibodies for use in research (e.g. goat anti-rabbit IgG is a goat  antibody that recognises rabbit IgG).
Because of this, therapeutic antibodies are "humanised" and this is the case with Rituximab which is derived from a mouse monoclonal IgG:

Rituxan is a genetically engineered chimeric murine/human monoclonal antibody directed against the CD20 antigen found on the surface of normal and malignant B lymphocytes. The antibody is an IgG1 kappa immunoglobulin containing murine light- and heavy-chain variable region sequences and human constant region sequences. Rituximab is composed of two heavy chains of 451 amino acids and two light chains of 213 amino acids

Presumably it would be possible for the remaining mouse-derived variable regions to be recognised as foreign by the human immune system, and this possibility is hinted at in the abstract of an early paper on rituximab (McLaughlin et al. (1998) Rituximab chimeric anti-CD20 monoclonal antibody therapy for relapsed indolent lymphoma: half of patients respond to a four-dose treatment program. J Clin Oncol.16:2825-33.) My emphasis...

A chimeric monoclonal antibody more effectively mediates host effector functions and is itself less immunogenic than are murine antibodies.

However, I'm not aware of any evidence that simple immune responses to Rituximab actually occur.

You are correct that it is possible for the human immune system to detect remaining traces of "mouse-ness" in the variable regions of this particular monoclonal, as the humanization process was rather unsophisticated. Nowadays it is possible to take sequences from the mouse CDRs that are actually responsible for antigen binding and put them in a more human variable domain scaffold that is less likely to be antigenic to the host.

In this case the real question would be, do foreign antibodies trigger an innate or a specific immune response, or both? If innate, what sort of pathogen pattern do they match? If specific, how are B and T lymphocytes specific to own Abs removed during negative selection (especially seeing as their specific sites could be specific to parts of an Ab antigen binding site)?

It is unlikely that an antibody would bind another antibody within just the human species. Human antibodies which bind to the human Fc portion cannot exist as they would be filtered by self tolerance mechanisms (as these B cells would be chronically activated or would the T cells that would be required for costimulatory help allowing the B cells to class switch and make the antibodies). Antibodies that bind to other portions are possible but unlikely because they wouldn't be pathogenic thus wouldn't cause an inflammatory response so wouldn't be presented with the relevant danger signals to instruct T cells and B cells to respond. If they were CD8 T cells would rapidly destroy these B cells by binding to these B cells so again, no B cell antibodies recognising self antibodies.
There must be mechanisms to prevent this as if there weren't as B cell survival is dependent on its cognate antigen, if its cognate antigen were itself or other antibodies we would be in for deep trouble: namely a lymphoproliferative disorder is assume. But all this is off the top of my head, so guys correct me if I'm wrong.
I don't say there aren't B cells that can recognise antibodies, I just say they'll be deleted.


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Reflexes & Pathologies including the Vagus Nerve
I only know the vasovagal reflex. I would really appreciate if someone could inform me about the other ones.
About the pathologies, I already know the effects of direct nerve damage. I am talking about more sparse and indirect ones, for example so far I found Roemheld syndrome, which is a gastrocardiac syndrome.
Actually, any subtle clinical presentation including the vagus nerve could be really helpful!

One pathology affecting the vagus nerve is autonomic neuropathy which can be secondary to several causes-one of the most commonly acquired cause is diabetes mellitus. It can manifest with various symptoms such as resting tachycardia (heart beating fast without exercise), exercise intolerance, orthostatic hypotension, constipation, gastroparesis (delayed gastric emptying), etc.
If you'd like to read more-http://care.diabetesjournals.org/content/26/5/1553.full
Hope its helpful.

I know the vagus nerve is linked to ulcerative colitis, which could have serious effects on the brain due to body-wide inflammation. You could probably search "vagus nerve" "colitis" and "neuroinflammation" and get some good papers on pubmed.


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Is there any source for raw data of SNP genotype frequency?
On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares it with SNP frequency to find rare SNPs that the user possesses. I'm thinking that the only way to do this might be to scrape it from a SNP database. Is there anywhere you know of that makes this information available in a more accessible format, ideally preformatted for parsing?

I found what would be a good source, but the links are dead: http://snp.cshl.org/downloads/index.html.en

Here's another, but it's about as clear as mud: http://useast.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles

There was also the Frequency Finder, but the NIH mirror and so is the UChicago mirror (which Google suggests was hacked): http://bioinformatics.oxfordjournals.org/content/20/3/439.full.pdf

I encountered the same problem about a year ago.  After digging through several databases, the only answer I could come up with was the 1000 genomes project. That's when I let the dream die, but would certainly be interested if you decided to tackle it.

You might be able to get some raw data on SNP frequency by batch querying the dbSNP database.  I have not used it myself, though.

This is one of the reasons the 1000 genomes project was created.

Have you looked at ALFRED (The ALlele FREquency Database)?  The data is from 2011, but seems extensive and has downloadable zip files at http://alfred.med.yale.edu/alfred/alfredDataDownload.asp