neuroscience - Do taller people have larger somatosensory cortices than short people?

I would say no.

Your question somehow implies that somatosensory cortex is equally distributed among the different sensory areas of the body, whereas in the reality this is the known "cortical homunculus" concept of how this distribution looks:

If you look at this representation you'll see that chest and legs take only about one third to one fourth of the cortex, thus the changes between short and tall people don't seem to have noticeable contribution to the overall cortex size.

If we just walk away from cortex size and discuss the amount of nerve cells in these areas I would say that these numbers should correlate with the number of peripherial receptor cells that provide input for them, and since there is no known changes in receptor density among different body sizes, even the amount of nerve cells seems to be more or less same.

What is a good Non Fluorescent DNA Dye?

Can anyone suggest a dye which specifically targets DNA, but is not fluorescent?

(We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak Signal even a low emission would disturb the reading)

Any tips would be much appreciated.

immunology - Organ cloning - possible to make a non-antigenic organ?

From a J. Neil Schulman article on Organ Cloning:

Cannibalizing organs from other people also entails the risk of
rejection because of incompatibilities, not only for tissue-typing but
also for gross anatomical mismatches. Cloning organs [...] has the
potential of taking a human being's own genetic material and growing
perfect replacement organs which are fully compatible with their
genetic makeup.

The reason for using a person's own DNA, is obviously to avoid an allergic reaction to the antigen markers on a strange organ. But in the blood typing system, there exist types which don't have any trouble-making antigens (such as type O-negative, called a "Universal Donor").

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Would it be possible to grow an analogous "universal" internal organ, which didn't have any antigens indicating it was a foreign body? (By editing a DNA sample to remove certain expressed proteins, then growing it into an organ.)

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I realize this is technically a science-fiction question :) But - A: it may not be in the near future, and B: I can rephrase it to remove the SF component:

In the blood-typing system, the AB antigens don't appear necessary for proper functioning of red blood cells - are the antigens on a person's own cells, actually needed for any essential functions, or could they be removed, without affecting that person's health?

How do you break up cell clumps when passaging?

In some protocols for setting up primary cultures (for example from mouse bone marrow or rat endometrium), there is a step that requires pushing cell suspension through a large needle to get rid of clumps. Of course, this carries a high risk of damaging the cells, so sometimes collagenase is used instead.

It might also be helpful to wash your cells with PBS without ions before passaging and use tripsin with EDTA. That should get rid of at least some calcium from the plate, so that action of adhesion proteins would be inhibited.

cellular respiration - What effect does ambient temperature have on the cardiovascular system?

I am sorry if this is not appropriate for this site, but I think it fits so I am asking it here:

I went for a run yesterday, and it was about -8⁰C. I was wearing a couple pairs of shorts, a t-shirt and a long sleeved shirt, which is not that much, so I went with the idea that I would warm up a lot while running. After running for a while, I found that I was tired and out of breath much earlier on then I would normally be. It raised the question:

How does decreasing the ambient temperature affect the cardiovascular system?

There were two things I could think of that might directly affect it. (1) The fact that my body's metabolism has to work to heat itself, and this takes energy. However I am not sure how much of a role this plays since running warms you up anyway. (2) The air being so cold, and entering the lungs, I imagine my body has to work much harder in some way to deal with it. What exactly happens here, and how is the process different from breathing at 25⁰C?

Also, how much faster would we expect a runner to be able to finish a 10km run when it is 25⁰C outside versus -5⁰C outside?

human biology - Is there such thing as a generic "metabolic type"?

A while ago I picked up a book called "Eat right for your metabolic type". The book discussed the effects of the endocrine system on the overall shape and the speed of metabolism.

The book outlined few major metabolic types:

• Adrenal


• Thyroid (hypo/hyper)


• Muscular

The book proceeded to discuss the overall shape of the body, including shape of fingers to help identify the metabolic type and give suggestions on which foods to avoid for a particular type.

The book then gave examples of effects of foods on metabolic types - for example an Adrenal type who eats too much sugar would crash and compensate for this by sleeping.

Since I can no longer find that book in print, I'm interested if there's really such a thing as a metabolic type that can be easily identified ? Are there indeed some foods that people should avoid eating?

biochemistry - How do plants 'tell time' for circadian rhythms based on a ~24 cycle?

I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously this is done in order to synchronize with the sun, but many such plants continue to perform these actions even when left it constant darkness or light. It follows that this is the result of some sort of biochemical pathway, but whatever internal 'clock' is used is also independent of temperature.

How can these plants perform certain actions every 24 hours at different temperatures when the chemical reactions most biochemical pathways use are temperature dependent?

It would seem like the length of the cycle should vary widely according to the temperature as it affected the reactions involved, but instead it stays at a very constant length very close to 24 hours. How can this be?

(This is in my textbook, but unfortunately the book doesn't cite any studies. I would greatly appreciate it if anyone could help me find one to link to so I can improve the question. :)

biochemistry - What are the limitations to current nucleotide sequencing technologies?

It seems like you answered your own question,the signal from a few molecules running through an enzyme or a polymerase tend to fall out of synch after a few hundred bases. If an enzyme for sequencing was more rigorously in time step that could help for instance. The machines read traces in four channels with nice bumps for each base. See this article for a nice example. You can see that if there are too many of the same base consecutively it gets hard to tell how many bases there are there. Over time all four traces will start to smear out and you cant tell Adam from Thelma if you take my meaning.

But there are other bottlenecks.

The sequencers currently put out such a high volume of data that the analysis of the meaning of the output data can't be analyzed fast enough. This follows the trend in biotech over the past 12 years or so - more sequence data, micro array data, more mutation data, more genomes than people who can actually use it to understand the biology. There is a bit of an analysis bottleneck now.

So some of these sequencers have greater read lengths, which can make it easier to assemble a sequence. These sequencers generally cost more. For instance if you have a library to sequence a little fungal or algal genome - you will get the answer back in a day or less now. In the form of 1 Tb of reads maybe 50 to 200 bp long. It might take quite a bit of time to put that together into a novel genome sequence, still more to find the genes, build the gene networks from a template of pathways etc. Just imagine a thousand sequencers pumping out day and night and you get the picture I'm trying to paint here.

About cost. Ion Torrent and the new oxford nanopore sequencers are really cheap - $50k to perhaps $900 for Oxford Nanopore's USB sequencer. Most other systems cost hundreds of thousands of dollars. Ion torrent and Nanopore have more disposables - you throw away a chip or even the entire sequencer - at a cost of hundreds of dollars a sample.

human biology - Is the 'fluttering feeling' when under stress neurological or physical?

If you want to find out about the the relationship of this response to romance in particular, there's a pretty comprehensive research paper called Love is more than just a kiss: a neurobiological perspective on love and affection[1] which reviews a lot of the work done in this area. This is pretty good as it discusses all the different stages including breakup.

Essentially, there seems to be a lot factors at play which elicits various responses through different stages of love.

In terms of anxiety and stress, initially, there's a large increase in levels of cortisol[2] and a marked drop in serotonin. Depletion of serotonin is found in many psychiatric conditions such as depression, anxiety and panic disorder. There's even been evidence that these levels at early stages of love are similar to those suffering with OCD. Obviously, the 'symptoms' of early love are quite similar to these conditions so it's hypothesised that this, at least in part contributes to those feelings.[1]. It was found that these levels are back to normal in 12-24 months.

The elevated levels of cortisol contribute to the feelings of stress but this hormone has also been shown to promote attachment.[2].

There are also changes in activity of the amygdala. Responsible for regulating a lot of emotions such as fear and sexual drive, the amygdala can activate autonomic nervous system responses through the mechanisms which Kevin described.

There are a bunch of other things at play here including dopamine, oxytocin, vasopressin, nerve growth factor (NGF), testosterone, increased activity in the hypothalamic-pituitary-axis (HPA) and variations in activity in other areas of the brain.

Again, that first reference gives a pretty comprehensive overview of the mechanisms involved.

To answer the actual question about the fluttering feeling, as Kevin mentioned, it's hypothesised that this is caused by reduced peristalsis in the intestines as a result of sympathetic stimulation. I don't have an academic reference for this but there are plenty of non-academic sources that talk about it (a quick Google of butterflies in stomach and physiology will probably show them).

A lot of the mechanisms noted above can contribute to, sensitise for or cause sympathetic activation. For example, panic attacks and anxiety, mentioned earlier with the serotonin relationship, can cause the same feeling.

1. Boer, et al. Love is more than just a kiss: a neurobiological perspective on love and affection. Neuroscience. 2012. 201:114-124.




2. Marazziti, et al. Hormonal changes when falling in love.
   Psychoneuroendocrinology. 2004. 29(7):931-936.




3. Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.

Alternatives to TBE buffer for denaturing polyacrylamide gel electrophoresis of DNA and RNA?

I just stumbled upon an article promoting 10 mM sodium borate as an alternative to the well-known TAE and TBE buffers for agarose gel electrophoresis of DNA (Brody & Kern, 2004). They claim that sodium borate outperforms TBE and TAE at high-voltage conditions due to the significantly lower heat development.

I'm currently using TBE buffer and gels with 7M urea for my denaturing PAA gels, and I'm wondering if there are similar alternative conditions for those denaturing PAA gels of nucleic acids?

I couldn't find anything on using sodium borate for denaturing PAA gels, so I'm wondering if it should work the same as for the agarose gels or if it just isn't a good buffer for that kind of gel.

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Brody, J. R. & Kern, S. E. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36, 214–216 (2004).

biochemistry - Are there any plants that fix their own nitrogen?

As far as I know, all biotic nitrogen fixation is performed by prokaryotic organisms such as Rhizobium. I don't know of any plants which can carry out this function on their own.

Plants can't use atmospheric N₂ because it is held essentially inert by the nitrogen triple bond. The process of reducing N₂ to NH₃ which is usable by plants can be summarized:

N₂ + 8e^- + 8 H⁺ + 16 ATP -> 2 NH₃ + H₂ + 16 ADP + 16 P_i

(where P_i is a phosphate group)

Nitrogenase catalyses the reaction reducing N₂ to NH₃ by adding H⁺ and electrons. The whole process requires 8 ATP and is therefore energy intense.

In order to perform this coversion, bacteria require sufficent carbohydrates from decaying matter or plant vascular tissues (this is how Rhizobium derives energy from the host plant).

However, I should add that bacteria often have a mutualistic relation with the plant to perform this function, so in this sense you could say that plants can fix their own nitrogen.

There are also "free living" ammonifying bacteria in soils.

Ref

Science and the Garden, eds. Ingram, D.S., Gregory, P.J., Blackwell, 2008