text:
Do any cells change in size or mass as mammals grow?
That is to say, are there cells that, between infancy and adulthood, get larger?  Or is all growth done entirely via cell division?  I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.

I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.

Not exactly.  When a tissue is put under stress, it can respond in four main ways:

Hypertrophy - individual cells get larger.  E.g. stressed muscle cells get bigger.
Atrophy - invidivual cells get smaller.  E.g. naturally in the thymus during development.
Hyperplasia - increased cell division to produce more cells.  E.g. mammary gland cells in pregnancy
Metaplasia - one type of specialised cell is replaced with another, usually more durable one, E.g. columnar epithelium in the respiratory tract of a smoker being replaced with squamous epithelium.

The first three responses to stress can change both cell size (auxetic response) and number (multiplicative response), meaning you can't really say that cells per unit mass stays constant throughout life.
Muscle tissue grows predominantly by hypertrophy, meaning that the muscle gains during puberty are likely to be more as a result of cells getting larger than the development of new ones.
Both auxetic and multiplicative growth occurs as the body develops.  In addition to this, accretionary growth also occurs - where connective tissues such as bone and cartilage increase in size.

This is not my field so I am sure there are other examples, but certain neurons will definitely be larger in adulthood than in infancy. There are motor neurons that connect the spine to, for example, the toes. These will grow in length as an animal grows. So, in a human infant they will be a few centimeters long and can reach lengths of over a meter in an adult.


text:
How can I compare rates of evolution for two sets of proteins?
I have a list of candidate proteins as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidates are evolving faster or slower than the rest of the proteins in my dataset.
Now, I know how to do this manually by building multi species alignments for each of my proteins and calculating ka/ks ratios for each set of alignments. This, however, is not a trivial process and I really do not want to do this manually for my ~1500 candidates.
Can anyone suggest a tool that will take two lists of proteins and return an estimate of evolutionary rate for each one?
I am primarily interested in human but also mouse, yeast, fly and worm. Ideally, I would need a tool that can take a list of proteins, assign them to an orthologous group and return a value representing the rate of evolution for that group.

I think you'll have to build the MSA regardless of the strategy that you use. You could try faster tree-based methods.

are you working on species that have already been sequenced (for which you might info in databases), or do you have novel sequencing data?

@MichaelKuhn definately sequenced. I am working on human primarily. There should be a database around that can give me this information right?

The eggNOG database also contains alignments for protein families, but these are on the amino acid level. So you would still somehow have to go back to a nucleotide alignment, which I'm not quite sure how to do. :-/ Might be a good question to ask on BioStar with its larger bioinf audience.

@MichaelKuhn, protein data is fine, I just realized my original question was not clear enough and have updated it. I said genes in the original because I thought it would be easier to find a relevant tool. My bad.

@terdon: if you want to compute ka/ks ratios, you need to look at the nucleotide sequences, no?

@MichaelKuhn, yup, that's why I had said genes in my original question. Since you suggested a protein database, i wanted to make it clear that protein data is fine. It does not necessarily need to be ka/ks, any metric of evolutionary change will do. There could, for example, be a database out here that has calculated homology scores for protein families, that would be fine for me.

If protein alignments are sufficient for you, I suggest that you look at the eggNOG database. There you can download mappings from proteins to protein families, and for the families you can also download pre-computed multiple (protein) sequence alignments.
I guess depending on the type of analysis you want to do you would have to trim the alignments to get only homologous regions (for example, see this recent paper[1]).

Wu M, Chatterji S, Eisen JA. 2012. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288, doi:10.1371/journal.pone.0030288.

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text:
Cell growth conditions for preparing electrocompetent cells
Usually the protocol for preparing electrocompetent E. coli cells calls for growing the cells at 37deg and 225rpms until they reach OD of 0.3. I was wondering, is there any reason they should grow at optimal conditions for growth, instead of at suboptimal, for example at 30 degrees? Also, what is the physiological/epigenetic difference between a culture of OD 0.2 vs 03. vs 0.3?

I don't know for sure, so I won't post as a formal answer, but my guess is that you want to maximize cell health and viability. Transformation of electro competent cells kills a lot of them, and you want to maximize the chance some of them survive.

I'm new so I can't make this a comment, and I don't think the other commenter addressed your questions so here it goes: I don't think there will be much difference, if any, between 0.2 and 0.3 OD. Once you get higher and the cells start transitioning into a stationary phase is a different story. Did you mean to ask about 0.03 OD as well (you wrote 03.)? I'm not an expert in E. Coli, but they would probably be less likely to produce proteins that are contact inhibited. Sub-optimal temperatures may have a minor effect on growth, but I don't believe this will initiate much change or induce production of large amounts of cold shock proteins.

I did electroporation of E.coli before using common protocol "growth at 37oc until OD 0.4-0.6, and pellet cell and dowstream works at cold condition". Recently, some publications gave different protocols with much higher efficiency. Briefly, (i) they growth E.coli at 18oC and did the same procedure; or (ii) they growth E.coli at 37oC and pellet cell, transformed at 24oC..
The references tittles are shown: "Growth of E.coli at low temperature dramatically increases the transformation frequency by electroporation" and "Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency"
You may try and find out protocol suited to your works.

Welcome & thanks for your answer. Can you add those references?

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How efficient is the sodium-potassium pump ?
I am reading about transportation of ions in a cell. It is necessary to transport sodium back out and potassium back in, against their electrochemical gradient. This task is carried out by sodium-potassium pump, which transports three sodium ions out across the cell membrane for every two potassium ions carried inward. The source of energy for this transport process was hydrolysis of ATP.
My question is the order of the efficiency of a sodium-potassium pump.

The efficiency of a pump is equal to the work done by that pump divided by the energy that an ATP gave to pump and transform to ADP.

I couldn’t find a value for this but I have calculated an efficiency of 84 %.
Caution: this seems too high to me, so I show below my calculation, fully dissected, in case anyone can spot an error.
First of all the parameters. Ion concentrations are:
internal Na+  = 12 mM;
external Na+ = 140 mM;
internal K+   = 140 mM;
external K+   = 5 mM;
and membrane potential = -60 mV (negative inside the cell)
I use these values for constants:
gas constant R = 2 cal mol-1 K-1
Faraday constant F= 23,062 cal mol-1 V-1
and I’ll assume that the temperature, T, is 37℃ = 310 K
The Na+/K+ pump uses 1 molecule of ATP to move 3 Na+ out of the cell and 2 K+ into the cell.
The efficiency of the pump is therefore energy required to move these ions/energy released by ATP hydrolysis.
How much energy is needed to move the ions? In each case there is a contribution from the fact that the ions are moved along a concentration gradient (the chemical component) and from the movement along a gradient of electrical potential (because of the membrane potential). In considering these components we have to think about whether energy needs to be used when the ions move, or whether it is released.
For the chemical component we can use
ΔG = RTln(ratio of concentration, inside and outside), where ln = natural logarithm
The sign of this ΔG will depend upon how the ratio is expressed (in/out or out/in) but the absolute value will be the same. So I calculate an absolute value and then deduce the sign of the free energy change.
For Na+ ΔG = modulus(2 x 310 x ln(12/140)) = 1,523 cal mol-1
Since Na+ is being moved up a concentration gradient, work must be done so the free energy change is positive.
Applying the same formula and logic for the movement of K+:
ΔG = 2,065 cal mol-1.
(This value is greater than that for Na+ because the concentration gradient is steeper.)
Next I calculate the electrical components using:
ΔG = zFμ, where z is the charge on the ion = 1 in both cases, and μ is the membrane potential (in volts).
So for both Na+ and K+ the absolute ΔG value is 1,383 cal mol-1.
However, in this case Na+ is moving out, against the membrane potential while K+  is moving in with the membrane potential. Thus the value of ΔG is positive for Na+ but negative for K+.
Now I combine the chemical and electrical components to get the net free energy change per mole of ions moved:
Na+ ΔG = 1,523 + 1,383 = 2,906 cal mol-1
K+ ΔG = 2,065 -1,383 = 682 cal mol-1
Now I consider how to combine these two values. Each cycle of the pump uses 1 ATP to move 3 Na+ and 2 K+. Therefore each mole of ATP moves 3 moles of Na+ and 2 moles of K+.
Energy from 1 mole ATP that is used to move ions = (3 x 2,906) + (2 x 682)
= 10,082 cal
= 10.1 kcal
How much energy is released from hydrolysis of 1 mol of ATP? Estimates vary but a commonly accepted value seems to be 12 kcal mol-1
Thus efficiency of the pump = 100*(10.1/12) = 84%.
I think the free energy of ATP hydrolysis depends on ATP concentration, pH, and the amount of Mg present. For a well-fed brain, this is around 14 kcal/mol (see Journal Of Physical Chemistry B, 114 (49), (2010). 16137-16146). This gives an efficiency of around 70%, still too high but better...


text:
Are tongues red because they contain blood?
Many animals have red tongues, though not all of them - blue-tongued skinks and giraffes come to mind. Are they red because of the blood (and therefore haemoglobin) in them?
It sounds plausible, but it also sounds like a post-hoc explanation.
I'd be especially curious about any other species having blue blood, like horseshoe crabs, but still having red tongues, unlike horseshoe crabs, which apparently don't even have tongues.

i would think so, but if a tongue is not red, its probably because there are other colored molecules in the tongue besides iron globins - it wouldn't necessarily mean the blue tongues have less red coloring.

The tongue is just a huge muscle, so it should have its colour from the same source as other muscles - which to my knowledge is blood. Unless it is pigmentated in its skin :) Human tongue I'm pretty sure is due to blood.

Mammalian tongues are red because of haemoglobin. Blue/black colouration is due to the additional presence of melanin.

At the boundary between the epidermis and dermis are melanophores, cells that contain melanin. This brown pigment absorbs ultraviolet radiation from the sun that might otherwise damage the underlying dermal tissue. Melanin in the dark tongues of giraffes (Giraffa camelopardalis) protects the tissue from sunburn as the animals lift their heads into the top branches of trees to forage for leaves. In humans, synthesis of melanin increases upon exposure to sunlight and produces tanning. Extensions of melanophores reach into the epidermis where they inject their pigments into developing hair cells. In a few cases, such as the bright ischial callosities of baboons, pigmented patches of skin are used as visual signals. The blue and red coloration on the scrotum and perineal region of male vervets (Chlorocebus aethiops) is used in dominance displays.

From: Mammalogy: Adaptation, Diversity, Ecology by George A. Feldhamer, Lee C. Drickamer, Stephen H. Vessey and Joseph F. Merritt (2007) p 97 The Johns Hopkins University Press; 3rd edition edition


text:
What measures are commonly used for the complexity of an organism?
I'm aware of measures like number of distinct cell types being used as a measurement of complexity in biology, for example in the G-value paradox. But this doesn't really help for unicellular organisms. Is it possible to define a unit of complexity to make comparisons between different organisms?

This is a very interesting question. Not sure if there is any way to answer without specifying a definition for complexity.
It is clear that everything is made of only the same few elements, so complexity must involve more than that. Do the number and position of identical molecules matter? If so, size matters and we would label a large jelly-fish as more complex than a cat and the air in a large hot-air ballon as more complex than any single living organism (assuming it is bigger).
I think it is clear that this is not what is meant by biological complexity. Molecules acting identically should not count multiple times; the number of different molecules matters more than the mere number of molecules. But are immune cells really more complex simply because of a relatively minor difference that allows them to generate a wide variety of genetic variants?
What about the variable coat color of a calico cat. Does the complex and non-repeatable (even with cloning) pattern mean it is complex, or does the fact that a simple genetic process underlies it mean it is simple.
The difference in complexity of different representation of the same thing is a classic problem in information theory (see Kolmogorov complexity). The ratio of the circumference of a circle to its diameter requires an infinite number of decimal digits to describe, but it is just a single geometric concept and it can be represented with one or two characters, as pi or π. This applies to the problem of using phenotypes to measure complexity -- the language and definitions we use to describe or to differentiate phenotypes determines what is complex and what is simple.
Moving beyond a simple static snapshot case, biological complexity involves time-dependent evolution. The "game of life" demonstrates how simple rules + initial conditions yield apparent complex behaviors, and the beauty of fractals arises the same way. Many apparently complex organisms grow from small seeds plus time-evolved exposure to simple things like water and light and CO2. Are trees only as complex as the seed they grow from?
Finally, what about higher order complexity? One human brain is very similar in general makeup to another, but the concepts and memories stored seem complex and very different. Comparing the complexity of stored information between two people is the whole complexity problem over again.
It seems to me that complexity can only be cleanly measured within a specific context, and then only relatively. One can measure the relative genomic complexity of two organism as the edit distance between the alphabetic sequences representing their genomes. The relative regulatory complexity can be measured as mentioned above by @user1682. Each of these says something about an organisms complexity. But what if organism A has higher genomic complexity and organism B has higher regulatory complexity? It might be possible to derive something like a principle component "basis set" from several of these kinds of measurements using a training set and a list of organisms with predefined complexity values. Applying this "standard" scoring metric to another organism would allow ranking it on a "standard" scale, but it would be difficult to generate and obtain consensus on the initial "expert" ranked organism scale. Such a standard might have some value, but is not really theoretically satisfying in that it describe an organisms complexity in the same way that the average of a small sample describes the distribution of a large population.

I think your answer raises a few deficencies in the question, so I think I'll have to address them in another question. Thanks.

I don't know if it is helpful for your problem, but I measured complexity in gen regulatory networks by parsing them into boolean networks. Then you can initiate all nodes with a random boolean value and update the network until it reaches an attractor. For a hand full of initial states you can compute the average entropy and mutual information. Additionally the topology (scale free, small world [Barabasi]) and count of reached and cycle lengths as well as robustness (reaching same attractor by flipping a randomly chosen node in the trajectory) can give you information about the complexity. To compute all attractors by all possible initial states of the boolean network can be done with a sat solver [Dubrova].
regards

The OP is asking about organism complexity, not gene network complexity. One can argue that the two are connected but this is not an answer to the question.

Any references to published work defining or estimating these complexity measures for gene networks or the like?


text:
Why is Paracetamol so great?
Every time I get ill (cold, flu etc) I take a couple of these wonderful tablets for up to 4 times a day and I, eventually, get better.  What exactly is paracetamol?  Why is it so effective and is it really not harmful as my doctor would have me believe?

If your doctor seriously tells you that taking paracetamol (or any other drug) liberally is not harmful you should really think of changing doctor...

Sachin didn't say the doctor said taking the drug liberally is not harmful.  I think the doctor would have said taking the drug when Sachin has a cold, flu etc. is not harmful.  Would it be ok if a doctor said drinking water isn't harmful?  Of course.  But if you drink too much water you'll die.  Remember the reason people go to physicians is for individual advice, not general advice.  That's why anyone asking for individual advice is encouraged to seek a physician.  Therefore I don't think you can judge the doctor, since you don't know the individual circumstances.

Paracetamol is a pain killer, it does not treat the cause of your illness, it only alleviates the symptoms. From its wikipedia page:

Paracetamol [...], chemically named
N-acetyl-p-aminophenol, is a widely used over-the-counter analgesic
(pain reliever) and antipyretic (fever reducer).

So, paracetamol does not make you better. Your immune system makes you better. Paracetamol just makes you feel better while you are waiting for your immune system to get an infection under control.
You should be aware that it is only safe in small doses and a toxic dose is not that much more than the recommended one (source):

Risk of severe liver damage (ie a peak ALT more than 1000 IU/L)
Based on the dose of paracetamol ingested (mg/kg body weight):
Less than 150 mg/kg - unlikely
More than 250 mg/kg - likely
More than 12 g total - potentially fatal

Again from wikipedia:

While generally safe for use at recommended doses (1,000 mg per single
dose and up to 4,000 mg per day for adults),[6] acute overdoses of
paracetamol can cause potentially fatal liver damage and, in rare
individuals, a normal dose can do the same; the risk may be heightened
by chronic alcohol abuse, though it is lessened by contemporary
alcohol consumption. Paracetamol toxicity is the foremost cause of
acute liver failure in the Western world, and accounts for most drug
overdoses in the United States, the United Kingdom, Australia and New
Zealand.

I am sure someone else can explain the pharmacokinetics and details of action of paracetamol. I just wanted to point out that paracetamol can be dangerous and should be treated with respect.

Over-the-counter paracetamol pills are usually 500mg. Therefore, the 150 mg/kg figure you listed for acute liver damage in a 60kg adult would be 60*150/500 = 18 pills in the span of a day or so. Cumulative damage can occur at lower doses but I think this is only seen in people who take it to control chronic pain.

The mechanism lies within the production of the messenger molecule Prostaglandin and COX-2 inhibitor. (Graham & Scott 2005, Mechanism of Action of Paracetamol, wikipedia: COX-2_inhibitor & Prostaglandin). Thinking back to my school days, these are involved in the transmission of signals in neurones related to pain. Paracetamol reduces how much is produced making reducing signalling activity. I am by no means an expert on this and hope someone can expand on this further, hopefully this will prompt people! Also, please don't try to work out how many you can "safely" take, tolerances vary greatly

Paracetamol, also known as acetominophen and Tylenol is a Non Steroidal Anti Inflammatory Drug (NSAID).  Other NSAIDs include aspirin and ibuprofen (Advil).
NSAIDs all help with inflammation, reduce fever, but each has its own effect. Aspirin tends to thin the blood more than Paracetomol.  Paracetomol also has less effect on inflammation, but acts to reduce fever (antipyretic) and reduce pain (analgesic).  Your doctor has probably chosen this prescription because your needs fit better to this drug's properties.
Ibuprofen for instance probably causes more problems more frequently when it's used frequently, one of the most common being ulcers because ibuprofen inhibits generation of stomach acid, but cancer and a slew of other problems can crop up.
While it is true that Paracetamol is the leading cause of pharmaceutical liver damage in North America, its toxicity as a drug is fairly moderate and the high number of cases is due to the fact that it is sold as an over the counter drug (with no prescription required) and is taken millions of times a day. The FDA has recently lowered the dose of Paracetamol to four 300 mg doses a day - but that's still 1.2 g a day.
Its important to watch to see if you are one of those people who have an adverse reaction or if your liver is under stress.  You should not use this drug beyond its expiration date - it really does matter in this case.
Still, all told, you probably could just take a handful of aspirin and feel just as good, but this prescription should get you feeling a little better a little faster, especially if you have pain or fever.
It's true what @terdon says that acetominophen is not curing you, but drugs really mostly balance the body - healing never comes from pharmaceuticals, they often just let the body heal with fewer obstacles or discomfort.  I know I feel that when my fever comes down that I'm on the  mend - though thats not necessarily the case.

I thought that paracetamol was not traditionally classified as an NSAID, because it is not an anti inflammatory drug? Its effect on fever appears to be related to a central influence on temperature regulation via prostaglandines. Additionaly, it is to my knowledge not known for any influence on coagulation processes, while NSAIDS  do have that characteristic.


text:
How do neurons form new connections in brain plasticity?
I've been reading about brain plasticity and how the brain can "rewire" itself.
One of the things that is not clear to me - how neurons can establish new connections. Does this rewiring mean that neurons can "disconnect" from other neurons to reuse existing dendrites?  Or do neurons grow new dendrites to make these new connections, adding to existing ones?
Thank you for your input!

Related (almost a duplicate): http://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form

I haven't read anything particularly about dendrites being reshaped, though I would expect them to be as flexible as other parts of the cells.
The more commonly discussed topic (in my literary experience) is reshaping of the axon's branches before forming synaptic terminals. These branches are not fixed even in adults - neurons can grow new and retract old branches, attaching (synapsing) to other cells in new places and removing old connections (see Wikipedia: Synaptogenesis).
Additionally to this actual change in the number of synapses, individual synapses can be regulated in their signal strength by adjusting the number of neurotransmitter receptors in the postsynaptic membrane (Gerrow&Triller, 2010, also see Wikipedia: Synaptic plasticity)

There is actually quite a lot of literature on changes dendritic branching.

Must be because my "reading" is mostly that suggested by lecturers and syntactic elasticity was a topic in lessons but dendritic wasn't :)

Take for instance this (but there are many other examples) Chronic Psychosocial Stress Causes Apical Dendritic Atrophy of Hippocampal CA3 Pyramidal Neurons in Subordinate Tree Shrews

Like @nico says, there is a lot of literature on dendritic "reshaping" (see, for instance, http://biology.stackexchange.com/q/8/72). I'd say that dendritic reshaping is discussed with about as much frequency as axonal reshaping.

Under conditions where the sensory input to the cortex has been altered, large-scale changes in dendritic branching have been observed after enriched environment experience (e.g. Greenough and Volkmar, 1973) and sensory deprivation (e.g. Tailby et al. 2005). However there is a discrepancy between those post-mortem studies and more modern in vivo studies, where only small-scale changes of the dendritic tips have been observed (Schubert et al. 2013). Large-scale axonal re-arrangements have been also implicated in post-mortem studies after sensory deprivation (e.g. Darian-Smith and Gilbert, 1994) but no such effects have been convincingly described in living animals.
These somewhat different results may be due to several technical limitations: 1) post-mortem studies have utilized injectable tracers and their uptake and/or expression levels may contribute in part to the observed results, 2) in vivo studies have been confined to superficial dendrites due to optical access limitations. Furthermore, these manipulations of the animal's experience are relatively crude ways of probing cortical circuits and do not necessarily reflect the processes that the brain may use under more physiological conditions.
By far the most well described processes under enriched environment experience, sensory deprivation and sensory stimulation, and learning paradigms are microscopic changes at the level of individual synapses. These include increased synaptic turnover (Trachtenberg et al. 2002, Xu et al. 2009), synaptic stabilization (Holtmaat et al. 2006), and synaptic strength changes (Hofer et al. 2009). These microscopic changes provide a very economical way, in comparison to large-scale dendritic or axonal re-arrangements, in which neuronal circuits can be extensively rewired given the enormous potential of dendritic spines and boutons to sample different synaptic partners (Stepanyants et al. 2002).

References
Darian-Smith, C., & Gilbert, C. D. (1994). Axonal sprouting accompanies functional reorganization in adult cat striate cortex. Nature, 368(6473), 737–740. https://doi.org/10.1038/368737a0
Greenough, W. T., & Volkmar, F. R. (1973). Pattern of dendritic branching in occipital cortex of rats reared in complex environments. Experimental Neurology, 40(2), 491–504. https://doi.org/10.1016/0014-4886(73)90090-3
Hofer, S. B., Mrsic-Flogel, T. D., Bonhoeffer, T., & Hübener, M. (2009). Experience leaves a lasting structural trace in cortical circuits. Nature, 457(7227), 313–317. https://doi.org/10.1038/nature07487
Holtmaat, A., Wilbrecht, L., Knott, G. W., Welker, E., & Svoboda, K. (2006). Experience-dependent and cell-type-specific spine growth in the neocortex. Nature, 441(7096), 979–983. https://doi.org/10.1038/nature04783
Schubert, V., Lebrecht, D., & Holtmaat,  a. (2013). Peripheral Deafferentation-Driven Functional Somatosensory Map Shifts Are Associated with Local, Not Large-Scale Dendritic Structural Plasticity. Journal of Neuroscience, 33(22), 9474–9487. https://doi.org/10.1523/JNEUROSCI.1032-13.2013
Stepanyants, A., Hof, P. R., & Chklovskii, D. B. (2002). Geometry and structural plasticity of synaptic connectivity. Neuron, 34(2), 275–88. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11970869
Tailby, C., Wright, L. L., Metha, A. B., & Calford, M. B. (2005). Activity-dependent maintenance and growth of dendrites in adult cortex. Proceedings of the National Academy of Sciences, 102(12), 4631–4636. https://doi.org/10.1073/pnas.0402747102
Trachtenberg, J. T., Chen, B. E., Knott, G. W., Feng, G., Sanes, J. R., Welker, E., & Svoboda, K. (2002). Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex. Nature, 420(6917), 788–94. https://doi.org/10.1038/nature01273
Xu, T., Yu, X., Perlik, A. J., Tobin, W. F., Zweig, J. a, Tennant, K., … Zuo, Y. (2009). Rapid formation and selective stabilization of synapses for enduring motor memories. Nature, 462(7275), 915–9. https://doi.org/10.1038/nature08389


text:
Does the entire surface of the earth contain organisms?
Does the entire surface of the earth contain organisms?
My teacher mentioned that in some parts of the earth, there aren't any organism. Is this true?
Thanks in advance.

have you questioned their claims? can they tell you where these places are? Obvious place to start checking is hostile places, but there are a lot bacteria & other unicellular organisms that can withstand extremes, e.g. Thermophilic bacteria live in very hot places such as black smokers

That will depend on many things. How do you define surface? Is one meter underground still "surface"? How about a kilometer?
Also, how large an area are we talking about? You could probably find a square millimeter in, for example, Antarctica that has no organisms. I don't think you would find a square kilometer with no organisms though.
There are organisms (called extremophiles) that thrive in the most hostile environments we know, they can survive extreme heat, cold, acidity, salinity etc. I found this very nice list:

Cold – The McMurdo Dry Valleys in Antarctica are some of the coldest, driest deserts on Earth, with average annual temperatures of
  -20oC (-4oF) and less than 10 centimeters (4 inches) of precipitation a year. Scientists have found bacteria in liquid water pockets
  embedded about twelve feet deep in “solid” lake ice. Some of these
  bacteria use chemical nutrients from particles of dirt in the ice and
  use energy from sunlight for photosynthesis.
Hot – Large concentrations of microbes thrive in Yellowstone National Park’s Grand Prismatic Springs, a hot spring with water
  temperatures up to 90oC (188oF). Other hot springs in Yellowstone are
  extremely acidic, yet are home to many different kinds of bacteria and
  microbes. Many of these microbes use chemical nutrients in the waters
  and energy from sunlight for photosynthesis. Deep underground –
  Scientists have discovered bacteria living in ground- water 5
  kilometers below the surface in deep gold mines of the Witwatersrand
  Basin in South Africa. These microbes thrive in cavities and cracks in
  rocks. Scientists are also are investigating life within and below
  permafrost in north- ern Canada.
Bottom of the sea – Scientists have found abundant life clustered around hydro- thermal vents on the ocean floor, including bacteria,
  mussels, clams, shrimp, and giant tubeworms that can reach ten feet in
  length. Water pouring out of the vents in the complete darkness
  thousands of feet under the surface of the sea can reach temperatures
  of 113-120oC (235-248oF). The high pressures keep the water from
  boiling. Bacteria use chemicals in the vent’s water, primarily
  hydrogen sulfide, as their energy source instead of sunlight. Other
  creatures survive by eating the bacte- ria or each other.
High Acidity – The water in the Rio Tinto in southwestern Spain is very acidic, a result of chemical reactions between the water, and
  iron and sulfur minerals in the ground. The river has a deep red
  color, like wine, because of iron dissolved in the water. Microbes
  living in the water use chemical reac- tions with iron and sulfur
  minerals to generate the energy they need. Products from these
  metabolic reactions contribute to the low pH in the environment. Many
  algae and fungi also live in the acidic waters.

As far as I know, there is no evidence of life in molten lava. Apart from that though, just about every habitat you can find on the earth has been colonized by life. Ask your teacher what parts of the earth she is talking about, and report back here.
UPDATE:
MCM's very interesting answer prompted me to do some more research. It seems that life has now been found even in the Atacama (taken from Azua-Bustos
et al):

For a long time it was thought that regions of the Atacama could not
  uphold any type of life forms. However, recent culture-independent
  methods (metagenomics, transcriptomics, in situ hybridization, etc.)
  have improved the sensitivity for life detection. Thus, microorganisms
  have been found even in the driest areas of this desert, which makes
  scientists wonder about the true limit of water availability needed to
  sustain life as we know it. In this review, we summarize the efforts
  devoted to the characterization of microbial life in the Atacama
  Desert.

So, it seems that life can exist even in the Atacama. That leaves only molten lava...
Reference
Azua-Bustos et al, Life at the dry edge: microorganisms of the Atacama Desert, FEBS Lett. 2012 Aug 31;586(18):2939-45

The bottom of the sea is (relatively) crowded with life, even away from hydrothermal vents. http://en.wikipedia.org/wiki/Whale_fall

@JeremyKemball of course it is, my point was that an underground volcano spewing sulfuric acid and with the pressure found at half a kilometer underwater is hardly an environment that kends itself to life.

A fair point. I've gotten so used to hydrothermal vent = oasis I kind of forgot that they're toxic pressure cookers.

Barring the very obvious surfaces (the pits of active volcanoes), the only place I'm aware of that might not contain life is the Atacama Desert near the Andes Mountains in Chile and Brazil.
Whereas other places that seem inhospitable - Antarctic, Hot Springs, regular deserts, extremely high altitudes, etc. - the basic necessities for life still exist (carbon, water, nitrogen). In the Atacama, though:

The average rainfall in the Chilean region of Antofagasta is just 1 millimetre (0.04 in) per year. Some weather stations in the Atacama have never received rain. Evidence suggests that the Atacama may not have had any significant rainfall from 1570 to 1971...  Studies by a group of British scientists have suggested that some river beds have been dry for 120,000 years.

It's the driest place on the planet. It's drier than every other desert by a long shot, and is so dry that NASA occasionally uses it to simulate Mars.

In 2003, a team of researchers published a report in the journal Science titled "Mars-like Soils in the Atacama Desert, Chile, and the Dry Limit of Microbial Life" in which they duplicated the tests used by the Viking 1 and Viking 2 Mars landers to detect life, and were unable to detect any signs in Atacama Desert soil. The region may be unique on Earth in this regard and is being used by NASA to test instruments for future Mars missions. The team duplicated the Viking tests in Mars-like Earth environments and found that they missed present signs of life in soil samples from Antarctic dry valleys, the Atacama Desert of Chile and Peru, and other locales.

So while life might exist in the Atacama (signs of life do not always point towards currently-existing life), it's hiding extremely well. Probably beneath the topsoil, where no multicellular organisms have ever been spotted and unicellular organisms may not exist at all.
Ultimately your teacher is correct, although whether they meant the Atacama or erroneously considered other places on the planet you'll have to ask them.

A fascinating place - still I'd be suprised if a ribosomal rna PCR reaction showed up nothing - bacterial spores and simple animals like rotifers can survive for decades without water.  the volcano caldera and maybe the tops of mountains like K2 are good ideas though!

Heh, nice, +1. However, recent research has found life in the Atacama. See my updated answer.

@shigeta and terdon -  Yeah, I doubt there's any place on the planet that hasn't seem at least some biproducts or spores on it through dispersal and human activity, but as far as actively growing and consuming resources I don't think anything has been confirmed in some parts of the Atacama (though edges of it saw enough rainfall to briefly support wildflowers in 2011).

Sterile! Lake Vostok’s microbes elusive in first measurements of surface water
A first analysis of the ice that froze onto the drillbit used in last
  February’s landmark drilling to a pristine Antarctic lake shows no
  native microbes came up with the lake water, according to Sergey Bulat
  of Petersburg Nuclear Physics Institute (Russia). The very uppermost
  layer of Lake Vostok appears to be “lifeless” so far, says Bulat, but
  that doesn’t mean the rest of it is.   Bulat reported what he calls
  his team’s “very preliminary results” on Tuesday, at the 12th European
  Workshop on Astrobiology (ENEA 2012), in Stockholm, Sweden, at the
  AlbaNova University Center. Bulat and his colleagues counted the
  microbes present in the ice sample and checked their genetic makeup to
  figure out the phylotypes. They counted fewer than 10 microbes/ml —
  about the same magnitude they would expect to find in the background
  in their clean room. And three of the four phylotypes they identified
  matched contaminants from the drilling oil, with the fourth unknown
  but also most likely from the lubricant.   Bulat hopes to get clean
  samples from the ice frozen in the borehole below where the drill bit
  stopped. That won’t be until next May (2013), if all goes well after
  the next Russian drilling expedition in December-January. Even if the
  top of the lake ends up being empty, Bulat suspects microbes will come
  from lower water depths, or from sediment samples at the bottom of the
  lake.   Lake Vostok is a stand-in for icy bodies that might harbor
  life, like Jupiter’s moon Europa. Gerda Horneck of the German
  Aerospace Center (DLR) said that any result from Lake Vostok is
  important for astrobiology, and the search for extremophiles that
  could give hints of what life could be like elsewhere. “Let’s see what
  comes out next round,” she told me at the end of the meeting on
  Wednesday.

http://www.scoop.it/t/amazing-science/p/3031509753/sterile-lake-vostok-s-microbes-elusive-in-first-measurements-of-surface-water

More info on Lake Vostok:
http://earthsci.org/education/Lake_Vostok/vostok.html

Welcome to Bio.SE! It's always a good idea to check that you're using quotes to support your answer rather than to write one :)


text:
How does a single-stranded RNA bind to a double-stranded DNA to form a "triplex structure"?
If you have a single-stranded RNA that is complementary to a double-stranded DNA, how do they interact to form what my prof. calls a "triplex structure"?
e.g.
    UGCUGAUAGCUACG
ACGTACGACTA
TGCATGCTGAT

I don't understand how the DNA can form 2 bonds there?

None of those sequences are RNA. I assume it's the one at the top that is supposed to be?

Sorry I fixed that, yes the one on top is RNA

DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.
rCCCCCC
dGGGGGGGGGGGGGG
dCCCCCCCCCCCCCC

rUUUUUU
dAAAAAAAAAAAAA
dTTTTTTTTTTTTT

but it is now known to occur in more complex sequences. One of the best studied examples is in the promoter of the human DHFR gene:

Gee, J. E. et al.(1992) Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J. Biol. Chem. 267, 11163–11167

In this work the oligonucleotide GR19 was shown to bind in a triple helix to SpI binding site I in the DHFR promoter (CR19 was used as a control). Triplex formation was detected by gel shift, and the specificity was confirmed by DNase I footprinting.
This effect is part  of the regulation of DHFR - the transcript from a minor upstream promoter binds to the major promoter, see:

Martianov, I. et al. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670

The structure of these triple helices involves a combination of Watson-Crick base pairing in the DNA duplex together with Hoogsteen base pairing in the RNA-DNA interaction:

Figure taken from:

Morgan, A. R. & Wells, R. D. (1968) Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 37, 63–80


text:
Good book on Origin of Life
What is a book that goes into reasonable detail (but isn't textbook-level technical) about the origin of earth and in particular the origin of life on earth? Something intended for a broad audience, but that still covers the biology/geology and does not completely gloss over the sicence.

I think this may be way too broad.  Are you able to narrow down your interests any further?

I would recommend The selfish gene by Richard Dawkins. It is targeted at a scientifically interested audience, but well written and recognized by the scientific community.
http://amzn.com/0199291152

I think this book (The Story of Life, Southwood) would be just what you are looking for - it was one of my modules during my undergrad in Evolution and I think it touches on the basic geology too. It is quite an easy ready but covers the material pretty well, it also has good reviews on Amazon etc.

This book by Steven Rose is supposed to be an update of the original for a modern audience:
http://www.amazon.co.uk/Almost-Like-Whale-Species-Updated/dp/055299958X

I think you mean Steve Jones. Steven Rose wrote The Chemistry of Life.


text:
Would exposure to a strong magnetic field have deleterious effect on the human?
This article states of a 25T magnet, ".. If are ever caught in one of these devices, let’s just say you probably won’t live to tell the tale."
Is the above statement in order? What effect would exposure to such a high magnetic field have on the exposed human?

That article contains some blatanly wrong statements, I woulnd't consider it trustworthy at all. 25 Tesla is not the strongest magnet in existence (see e.g. a 45 Tesla hybrid magnet built in 1999). Those high-field magnets usually have a very small bore, so you can't put a human into the maximal magnetic field of the magnet, as there's just not enough space inside.

@MadScientist: Thanks, the question is updated to be more to-the-point now

I don't think you need to remove that part, I just wanted to point out the errors in the linked article

First thing comes to my mind is the Hall effect. Any directional ion or electron flow will experience a force (depending on the orientation with respect to the magnetic field). So if the magnet is very strong, I think some of the ion channels for action potential generation and propagation would malfunction. (11 mT stopped action potentials for a while but recovered in mouse as reported here.)
However, according to these papers static magnetic fields has little biological effect, and it seems to be reversible. But, this reports genotoxicity in 4.5T (in vitro), and developmental disorders in 1.5T (in vivo, mouse). Contradictory reports indicate we do not know the full answer yet as usual.

"Strong" is en entirely relative term, but given the number of MRI's performed, its pretty clear that fields several orders of magnitude larger than the Earth's background 0.5 gauss are at least "mostly harmless" with an exposure of limited duration.
From an FDA publication regarding MRI scanners:

There are no known harmful side-effects associated with temporary exposure to the strong magnetic field used by MRI scanners. However, there are important safety concerns to consider before performing or undergoing an MRI scan.

This article describes human brain imaging with a 9.4T instrument, although this is about 10x larger than the strength of most MRIs. Note that "no detrimental effects" does not mean zero effects, but this is starting to get into the range of the 25T described above. There are 20T+ MRI machines avaialble, but I could not find an article describing use on live organisms. There is just this one on dead mice parts.


text:
Is territoriality only the domain of the male of a species?
Is territoriality (recognizing a geographic location, and challenging another member of the same species and gender) only in the domain of the male of a species? Are there any species out there where the female of the species identifies, defines, and protects her territory? What about any species where territoriality is gender neutral (tic humans excluded!)?
I thought of bees, but that is a community affair - even if it is a matriarchial society.

From personal observation: house sparrows "stake a claim" at a bird feeder, and both males and females chase away competitors

Absolutely not.  In many spiders and insects, the female holds the territory.  Many spiders for instance have much larger females than males - in these species the female can be > 10x bigger than the male and the male may not even eat during its lifetime.
Ordinary garden orb weaving spiders are this sort of animal.  Only the females even spin webs.
Another example is the Australian red back spider.
Quite often males are the 'disposable sex'.

Both sexes of red squirrels defend exclusive year round territories.
See Smith 1968 or Steele 1998.

The elephant matriarch (in Africa) leads her followers where they go for food and water.


text:
Functionality of vitamin A, Bx, C, D, E, K as used in cosmetics for the skin?
I was wondering if someone can compare the functionality of vitamin A, Bx (x means numbers, such as 1, 2, 3, ...), C, D, E, K in the skin?  They are used in cosmetics but what is their actual effect?
If there is some source that compares between them in particular, I think it will help me understand some important basics.
Some products:
GNC Vitamin C Moisturizing Cream
GNC Vitamins E, A & D Moisturizing Cream
Reviva™ Labs Alpha Lipoic Acid Vitamin C Ester & DMAE Cream
Reviva™ Labs Vitamin K Cream

I added a section to your question to ask for the effect the vitamins have on skin in general separating it out from their presence in cosmetics.  Feel free to re-edit if I've missed your point.

Bx and C are water-soluble so unless there are special uptake systems that I'm not aware of, they should have 0 effect if you rub them on the skin...

@Armatus: Perhaps I was not accurate enough. There are cosmetic products with ingredients of Bx and C derivatives.

Yes, my guess was that using those vitamins would probably be purely for marketing purposes, not for any actual effect :) Except for hair products maybe, but your question is about skin.

@Armatus (1) Why different for hair and skin? (2) How about their various derivatives, some of which may be more stable, soluble in water or oil, and therefore used for skin products? Such as L-Ascorbic Acid (a derivative of VC) has been used as antioxidant, VB3 and VB5 have been used for anti-aging.

@Tim (1) Skin is a protective tissue with the special purpose of keeping things out. Hydrophilic substances have no way of getting past it other than wounds, but lipophilic substances can dissolve through the cell membranes. Hair is a collection of dead cells and protein as far as I know and vitamins may have effects on them in some way. (2) As I said, there might be uptake systems of the skin that I don't know about which could be exploited by modifying the vitamins. Anti-aging is a disputed concept as far as I know.

I think this question is too broad to encompass all known vitamins.

Vitamin A: One study conducted in the 60's claims that vitamin A acid prevents formation of comedones in Acne Vulgaris [1]. Another one conducted in the 70's found no significant improvement of plantar warts when vitamin A acid was applied topically [2].
Vitamin D: Agents like calcipotriene associated with topical steroids are effective against psoriazis [3]. They inhibit keratinocyte proliferation, normalize differentiation and modulate the activity of immune cells [4]. Active form of vitamin D is also effective against vitiligo [5].
Vitamin E: It reduces skin damage induced by UV [6, 8], but it shouldn't be applied on scars [7].
Vitamin K: It prevents bruising after laser treatment and reduces the severity of eventual bruising [9, 10].
Vitamin B12: It is an effective treatment for atopic dermatitis [11] and children with eczema [12]. It could also potentially improve olfactory function when associated with corticosteroids [13].
Vitamin B1: It doesn't protect you from mosquitoes [14].
Vitamin B3: It improves fine lines/wrinkles, hyperpigmentation spots, texture, red blotchiness and sallowness [15, 16].
Vitamin C: It improves wrinkling by new collagen formation [17]. It is useful in sun-induced skin ageing [18, 19] where it increases density of dermal papillae [20].
And here are the results of a study [21] which assessed multiple vitamins:

Vitamins A, C, E, and B3 have been shown to have potent antioxidant and anti-inflammatory properties, but to achieve optimal effectiveness, products must be delivered in appropriate formulations. Products containing alpha-tocopherol (vitamin E), L-ascorbic acid (vitamin C), retinol (vitamin A), and niacinamide (vitamin B3), are effective for the treatment of photoaging. These compounds have also shown effectiveness in the treatment of inflammatory dermatoses, acne, and pigmentation disorders and wound healing.

The same study [21] also concludes that combinations are better:

There is emerging evidence that combinations of vitamins have additive effects that provide enhanced efficacy compared with individual compounds.

References:

Kligman AM, Fulton JE, Jr., Plewig G. Topical Vitamin A Acid in Acne Vulgaris. Arch Dermatol. 1969;99(4):469-476. doi:10.1001/archderm.1969.01610220097017.
de Bersaques J. Vitamin A acid in the topic treament of plantar warts. Dermatologica. 1976;150(6):369-71. PubMed PMID: 1201813.
Devaux S, Castela A, Archier E, Gallini A, Joly P, Misery L, Aractingi S, Aubin F, Bachelez H, Cribier B, Jullien D, Le Maître M, Richard MA, Ortonne JP, Paul C. Topical vitamin D analogues alone or in association with topical steroids for psoriasis: a systematic review. J Eur Acad Dermatol Venereol. 2012 May;26 Suppl 3:52-60. doi: 10.1111/j.1468-3083.2012.04524.x. PubMed PMID: 22512681.
Tanghetti EA. The role of topical vitamin D modulators in psoriasis therapy. J Drugs Dermatol. 2009 Aug;8(8 Suppl):s4-8. PubMed PMID: 19702030.
Gorman S, Judge MA, Hart PH. Immune-modifying properties of topical vitamin D: Focus on dendritic cells and T cells. J. Steroid Biochem. Mol. Biol. 2010 Jul;121(1-2):247-9. doi: 10.1016/j.jsbmb.2010.02.034. PubMed PMID: 20211255.
Burke KE, Clive J, Combs GF, Commisso J, Keen CL, Nakamura RM. Effects of topical and oral vitamin E on pigmentation and skin cancer induced by ultraviolet irradiation in Skh:2 hairless mice. Nutr Cancer. 2001;38(1):87-97. doi: 10.1207/S15327914NC381_13. PubMed PMID: 11341050.
Baumann LS, Spencer J. The effects of topical vitamin E on the cosmetic appearance of scars. Dermatol Surg. 1999 Apr;25(4):311-5. PubMed PMID: 10417589.
Krol ES, Kramer-Stickland KA, Liebler DC. Photoprotective actions of topically applied vitamin E. Drug Metab. Rev. 2001;32(3-4):413-20. doi: 10.1081/DMR-100102343. PubMed PMID: 11139138.
Shah NS, Lazarus MC, Bugdodel R, Hsia SL, He J, Duncan R, Baumann L. The effects of topical vitamin K on bruising after laser treatment. J. Am. Acad. Dermatol. 2002 Aug;47(2):241-4. PubMed PMID: 12140470.
Cohen JL, Bhatia AC. The role of topical vitamin K oxide gel in the resolution of postprocedural purpura. J Drugs Dermatol. 2009 Nov;8(11):1020-4. PubMed PMID: 19894369.
Stücker M, Pieck C, Stoerb C, Niedner R, Hartung J, Altmeyer P. Topical vitamin B12--a new therapeutic approach in atopic dermatitis-evaluation of efficacy and tolerability in a randomized placebo-controlled multicentre clinical trial. Br. J. Dermatol. 2004 May;150(5):977-83. doi: 10.1111/j.1365-2133.2004.05866.x. PubMed PMID: 15149512.
Januchowski R. Evaluation of topical vitamin B(12) for the treatment of childhood eczema. J Altern Complement Med. 2009 Apr;15(4):387-9. doi: 10.1089/acm.2008.0497. PubMed PMID: 19368512.
Heilmann S, Just T, Göktas O, Hauswald B, Hüttenbrink KB, Hummel T. [Effects of systemic or topical administration of corticosteroids and vitamin B in patients with olfactory loss]. Laryngorhinootologie. 2004 Nov;83(11):729-34. doi: 10.1055/s-2004-825676. PubMed PMID: 15538662.
Holzer RB. [Protection against biting mosquitoes]. Ther Umsch. 2001 Jun;58(6):341-6. PubMed PMID: 11441693.
Bissett DL, Miyamoto K, Sun P, Li J, Berge CA. Topical niacinamide reduces yellowing, wrinkling, red blotchiness, and hyperpigmented spots in aging facial skin. Int J Cosmet Sci. 2004 Oct;26(5):231-8. doi: 10.1111/j.1467-2494.2004.00228.x. PubMed PMID: 18492135.
Bissett DL, Oblong JE, Berge CA. Niacinamide: A B vitamin that improves aging facial skin appearance. Dermatol Surg. 2005 Jul;31(7 Pt 2):860-5; discussion 865. PubMed PMID: 16029679.
Fitzpatrick RE, Rostan EF. Double-blind, half-face study comparing topical vitamin C and vehicle for rejuvenation of photodamage. Dermatol Surg. 2002 Mar;28(3):231-6. PubMed PMID: 11896774.
Humbert PG, Haftek M, Creidi P, Lapière C, Nusgens B, Richard A, Schmitt D, Rougier A, Zahouani H. Topical ascorbic acid on photoaged skin. Clinical, topographical and ultrastructural evaluation: double-blind study vs. placebo. Exp. Dermatol. 2003 Jun;12(3):237-44. PubMed PMID: 12823436.
Farris PK. Topical vitamin C: a useful agent for treating photoaging and other dermatologic conditions. Dermatol Surg. 2005 Jul;31(7 Pt 2):814-7; discussion 818. PubMed PMID: 16029672.
Sauermann K, Jaspers S, Koop U, Wenck H. Topically applied vitamin C increases the density of dermal papillae in aged human skin. BMC Dermatol. 2004 Sep 29;4(1):13. doi: 10.1186/1471-5945-4-13. PubMed PMID: 15456516.
Burgess C. Topical vitamins. J Drugs Dermatol. 2008 Jul;7(7 Suppl):s2-6. PubMed PMID: 18681152.


text:
Which part of oranges contain fiber?
I think it's pith, but here (non-english country) many chef suggest orange's vascular veins which look "fibrous" and have similar translated word with "fiber" itself.
Please enlighten me which?

Cellulose is one of the most common sources of fiber in the nutritional sense. Because oranges are plants, their cells have cell walls, made out of cellulose, so some of the fiber in an orange is surrounding each individual cell. Both vascular cells and pith cells tend to have particularly thick cell walls, so they are probably higher in fiber (this article also suggests that the pith is particularly high in fiber - vascular tissue is probably not mentioned because it is less prominent).


text:
Is there any complex organism that is both autotroph and heterotroph?
Possibility also include "adaptation mode" if such exist. I don't discern whether autotrophic/heterotrophic part play only minor role either.

Does "complex" mean multicellular here? Or something more? Plants are usually autotrophs - do they count as complex?

yes multicellular at least

For example sundews are plants (so autotrophic), but they "hunt" for insects to get additional nutrients, e.g. nitrogen. As far as I remember the nitrogen is the main reason for eating other organisms but they also use other substances, including carbohydrates, from their prey.

To add to this: Those which are both are called photoheterotrophs or chemoheterotrophs. They get their energy from the sun/chemicals (via oxidation of electron donors) respectively but do not get all of their carbon from carbon dioxide, it is subsidised by the consumption of other matter.

@jkadlubowska: OK, but it make sundews ambiguous to fungi or other parasitic plants. I'm expecting more extreme case, maybe invertebrate?

@dhubris could you make what you actually want clearer? in the question it says "complex organism" then in the comments you define that as "multicellular at least" and now here you set the bar higher and want invertebrates, clarity will get the best answers. There are some cases of symbiosis between chemoautotrophs and invertebrates almost exclusively in deep sea environments (http://www.geology.wisc.edu/~wiscsims/pdfs/Dattagupta_ISME2009.pdf). However, in the definition of the animal kingdom it states that all animals are heterotrophs (http://www.windows2universe.org/earth/Life/animalia.html)

I think the concept of autotrophy and heterotrophy is narrower than the one you are using here. They refer to the source of carbon and not just source of matter. If we accept that sundews are auto- and hetero- troph, then we'll have to accept that we (human) are also hetero- and auto- trophs as we are mining for salt.

Just look up kleptoplasty
http://en.wikipedia.org/wiki/Kleptoplasty
The slugs who most frequently employ it would fit your more restrictive definition. Now, if we're getting technical, they aren't born that way. They steal the chloroplasts, but you didn't say, so I guess you need to revise your expectations again. ;)

now that is a cool symbiosis!

Do these slugs use inorganic carbon? Do they have a Calvin cycle of carbon fixation? If not, they only get energy from light, meaning that they are photoheterotroph and not autotroph.


text:
Do humans have chemosensors for nutrients or chemicals?
I'm reading about chemoreceptors on Wikipedia, and see that the typical ones are mentioned: taste, smell, CO₂.  I would like to learn more about the other kinds of chemoreceptors that humans may possess. I'm particularly interested if these can detect chemical compounds, or lack of thereof in food.
Here's an example:
Do omnivore mammals vary food preferences based on dietary needs?

There's "rapid recognition of Indispensible Amino Acid(IAA) depletion in the rat brain's IAA chemosensor, the anterior piriform cortex (APC)"

Reading the article above, it appears that at least rats and birds can develop aversion to food that does not contain indispensable amino acids. This is done through chemosensors in the brain. Do humans possess any similar chemosensors?
Thank you for your input!

The answer to this question would fill books. Take Pheromones, for example, this is a very complicated story by itself! Could you be a bit more specific in which particular field you're interested in?

I'm interested in digestion - are there any chemicals or chemical imbalances that can be detected in food?

Isn't our sense of smell basically from a large number of chemosensors in the nose? Am I missing something?

@Qubei You are right, it is the pattern of activation of 100+ olfactory receptors that provokes smell.

I vote to close this question. This would indeed require to write a book...


text:
Is a minimum size/complexity necessary for an organism to exhibit territoriality?
A follow-up to Is territoriality only the domain of the male of a species?
I've seen a large butterfly chase a different kind of butterfly around - it may, or may not have been territoriality. Is there a minimum scale of size, sentience(?) an organism must attain to exhibit territoriality?

With some bacteria (e.g.. Bacillus subtilis) when food gets scarce they will start trying to kill their neighbors. (See this arstechnica article) This appears to be a fight to the death between children and parents. That's a kind of territorial behavior, selectively applied only when there are not enough resources to go around. As there is no "recognition" of a specific territory being defended, just wherever the bacteria is currently, this might not meet a strict definition of territorial behavior. But the only thing simpler than bacteria are viruses.
Come to think of it, I bet there are viruses that, once they infect a host cell, will change the cell's membrane or metabolism in a way that reduces its chance of being infected again by a similar virus. Such 'behavior' could be compared to defending a breeding ground. Can't find any examples though.

+1 for the viruses. http://www.pnas.org/content/109/44/18078 ;)... But I don't really think that article is really an example of territoriality.

Without some selective defense of something, I don't see any indication that the small virus behaves territorially. But a virus that infects a virus is still a pretty neat thing.

This is pretty cool; I've +1'ed it for now. If another answer doesn't come through in a day let me then flag this as correct.


text:
Is it more likely to develop a throat-ache at night?
I have noticed that I rarely develop phlemmy throat-aches in the daytime, but often notice them after I have been sleeping.  Is this a recognised phenomenon?  Could it be because viruses or bacteria aren't being flushed out by food, water and vibration of the throat from speaking or that one's immune system is lower at night? If it is the latter, why is this?

It's because your mouth and tongue are stationary at night, so you don't move the slowly-drying saliva around to lubricate tissues. The mucous tissues dry out, resulting in greater friction with muscle movements (like swallowing), and your body is slightly dehydrated after 6-10 hours without water. If you've ever undergone surgery where they intubated you (stuck a tube down your throat to ensure air supply), afterwards it's a very similar feeling to waking up with a soar throat because your throat dries up and the anesthesia prevents muscle movements.
Your immune system actually works better at night and requires rest to work efficiently. Bacteria and viruses don't really care about the time of day, although the muscles of the larynx do ensure that the mucous layer is continuously circulated. The continual circulation helps prevent debris and bacteria/virii from establishing themselves, although the magnitude of the effect isn't on the same scale of other tactics taken by your body.
Several factors can affect mucous/phlegm/saliva production - including infections, hydration levels, environmental temperature, smoking habits, diet, environmental humidity, and lots more. If it's a constant trouble, you can try drinking more water during the day, a steam humidifier, or talking to your doctor.


text:
How does the body measure dehydration?
What, physically, does the body do to measure it? I assume it's measured by how how turgid or plasmolysed certain 'sample cells' are, or water concentration in the blood,

What is the way they use to measure it?
What do the receptor cells that do the measuring actually do that is variable with water concentration, etc.

This article reviews the subject but I can't access it. http://www.nature.com/nrn/journal/v9/n7/full/nrn2400.html perhaps someone has access to nature neuroscience and can relay the details, good luck!

From Wikipedia entry on thirst:

In the mammalian brain, the posterior surface of the hypothalamus
  forms the front wall of the third ventricle (a cerebrospinal
  fluid-filled cavity) and clusters of cells (osmoreceptors) on this
  surface, notably in the organum vasculosum of the lamina terminalis
  (OVLT) and subfornical organ (SFO), signal this cellular dehydration
  to other parts of the brain, and thirst is experienced. Destruction of
  this part of the hypothalamus in humans and other animals results in
  partial or total loss of desire to drink even with extremely high salt
  concentration in the extracellular fluids.1

The entry on osmoreceptor says in part:

When the osmotic pressure of blood changes (i.e. it is more or less
  dilute), water diffusion into and out of the osmoreceptor cells
  changes. That is, they expand when the blood plasma is more dilute and
  contract with higher concentration.

It also describes how the kidney measures chlorine anion flow through some nephrons, which triggers a cascade of messenger molecules resulting in increased blood levels of the hormone angiotensin, which also results in thirst messages originating in the hypothalamus.
1Derek A. Denton (8 June 2006). The primordial emotions: the dawning of consciousness. Oxford University Press. pp. 118–19. ISBN 978-0-19-920314-7.
2Walter F., PhD. Boron (2005). Medical Physiology: A Cellular And Molecular Approach. Elsevier/Saunders. ISBN 1-4160-2328-3. Page 872

How do osmoreceptors work? That is, how and by what is the 'swollenness' of the osmoreceptors measured, and how does this turn into an electrical signal?

Dehydration results in decreased blood volume (hypovolemia) and in slight decrease of blood pressure. The body recognises dehydration by these ways:

Baroreceptors in the aorta detect the drop of blood pressure - this results in activation of the sympathetic nerves and the release of adrenaline from the adrenal medulla - this leads to constriction of the arteries ad increased heart rate.
Volume receptors in the heart atria detect hypovolemia - this result in the secretion of the antidiuretic hormone from the pituitary gland - this results in water retention in the kidneys.
Osmoreceptors in the hypothalamus detect increased blood osmolality - this triggers the release of the hormone ADH.
Juxtaglomerular apparatus in the kidneys detect decreased perfusion, what results in the renin-angiotensin-aldosterone release cascade, which results in water retention in the kidneys.

All these mechanisms are activated in the compensated hypovolemic shock.


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3D models of adult male brain in the Blender software? Any open-sourced version for research?
I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would like to use some open-sourced candidate so anyone could preview things. So does there exist 3D models of brains in Blender?

I am interested in this as well

...this movie under cc3 and some brain model: http://mango.blender.org/gallery/

A side note, for those interested in mouse brain anatomy: you may want to have a look at the Allen Brain Atlas website, particularly to Brain Explorer

Am I the only one who initially (mis)read "adult male brain in a blender"? :)

There is a model of an adult, male, real human brain here:
http://brainder.org/download/brain-for-blender/
It can be imported into Blender or any other 3D application that can read Wavefront OBJ or Stanford PLY formats.

http://www.turbosquid.com/3d-models/max-human-brain/580672
That one is only 30 which really isn't bad for a model. You will have trouble finding an  anatomically correct model for free.
I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? And if you would like to elaborate, I am curious about what end product you are looking for.
Side note: Autodesk has 'student' license version of software --in case you want to try learning Maya or 3Ds max, the latter has Retopology tools.
You can download from here:
https://students.autodesk.com/?nd=download_center
ITKsnap is a program you could use to get 3d data from ct or mri scans
http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.Downloads
MRI and CT data can be found here:
http://www.osirix-viewer.com/Downloads.html
I know you just wanted a free model, but the above are the steps to get to one at least.

Academia is mostly against the photo electricity of brains with mammals https://twitter.com/heoalov/status/274090762524848128 -- just curious: placebo or some other effect with led-tosslink-in-ear?

Err photosensitivity -- still requiring placebo test, easy trials: get cheap toslinks and different intensity light. Can you detect it? Does skin-senses become different after some use or just placebo? I cannot understand if not placebo, how does it work? If LEDs were UV, then D vitamin? Otherwise what is the physiological reaction? I do not know but pretty curious so investigating brains and ears etc

I think all models are too generic out there.
Radiological models you can find in imaios.com's e-Anatomy where the Premium access gives you some RTG, CT and MRI videos which you can combine to form some 3D models.
I am working with the visualization of CNS lymphatic vessels here where I would like to create thin membranes to visualize how deep the lymphatic circulation goes.


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How are epigenetic marks transmitted during cell division?
As far as I know, this is one of the biggest questions in the epigenetic field: how are the epigenetic marks like histone modifications propagated through cell division? A lot is already known about DNA methylation (e.g. as in How does “inheritance of methylation” of DNA and/or histones work?), but very little about histone modifications. What is the current state of knowledge?

I know this could probably fill a whole thesis, but a brief overview for someone who has an "advanced beginner" knowledge of genetics would be perfect.

As far as I understand Alberts, after dissociation from DNA at the replication fork, histones will randomly reassociate with the copy and the original, so half of the marked histones will associate with the copy in the region which was just replicated. Then you get HP1 and such propagating the modifications all the way to the ominous "boundary element".

I can get the ball rolling..
Found a nice paper which looks at this phenomenon in yeast.
So as a primer, 8 histone proteins come together to make a spool of sorts which DNA wraps around:

Histone proteins have many sequence variants, and each one of them can be covalently modified with methyl, acyl, phospho, SUMO, adp and many other sorts of chemical groups via a chemical bond.  Although its not yet clear exactly how it works its clear that these modifications can change the behavior of the histones which prevent transcription of the gene when they have the chromosomal DNA all wrapped up.
So as to the question a pattern of inheritance of modified histone patterns is indeed seen and has epigenetic effects.  (that is, it modifies the genetic phenotype of daughter cells which retain the histone modifications of the parent cells).  In this paper, newly synthesized (and labelled) yeast histone can be found incorporated into certain segments of the genome, which demonstrates that large segments of the histones are carried forward from the parent cell.
They also found a particular case of histone epigenetic labeling carried forward through division:

Furthermore, if the heterochromatin-binding protein Sir3 is unavailable during DNA replication, histone H3-K4

So there's evidence that histone configurations are transmitted epigenetically, In this 2011 paper, the author support a 'conservative distribution model' and compare it to a 'semi-conservative' model:

The conservative distribution model proposes that newly synthesized histone molecules form nucleosomes that are randomly inserted among preexisting parental nucleosomes.
The semi-conservative distribution model proposes that a hybrid nucleosome that contains both newly synthesized and parental histone H3-H4 dimers is formed, which facilitates the transmission of epigenetic information within the basic nucleosome unit.

They go on to say that a conservative model of histone inheritance allows for strong epigenetic inheritance as the remaining parent histones will tend to attract similarly labelled histones as the new histones incorporate themselves among the parental histones on the daughter chromosome.
Its still being worked out though...


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Action Potential Distribution On Synapses
This is a biology+physics question. Since there is no biology section, I am asking here.
In brain, when a neuron reaches to threshold value, it fires an action potential. In most graphics, that is shown as 40 mV. An example is

Neuron's this potential reaches to all synapses where this neuron is connected to, and chemically transferred to other neuron and transformed into electric charge again.
My question is, because in artificial models not shown, if that whole 40 mV is distributed to those synapses according to synapse strengths, or do all synapses take a total 40 mV which is like creating a potential while it is not there?
Another small question is if the collected potential is stored in neuron if it cannot reach to threshold value like a capacitor in circuit?

I'm migrating this because you probably would've posted on [biology.se] first if you'd known about it, and it doesn't look like you're going to get the answer you're looking for here.

Can you revise your question? I am not sure what you mean when you say the "whole 40 mV is distributed" versus "a total 40 mV" which is "not there."

Well, it is about electron movements actually. That's the reason I have written it is biology+physics question. Normally, in an electric circuit, if you have 40 mV in circuit, this voltage is divided according to resistance in parallel wires. I mean electrons are divided, but with resistance it can be defined as voltage. Anyway, neurons send their signals to other neurons by both electric charge on axon and chemical at synapses. My question was if that electric charge is shared when the active potential reaches to where axon starts making branches to axon terminals.

I think you are really wondering how axonal morphology affects the voltage along the axon. The short answer to your question is that each synaptic terminal sees the same voltage because that voltage is generated "fresh" at each site. This has nothing to do with synaptic strength, which determines the amount of voltage deflection in the postsynaptic terminal but not in the presynaptic terminal.
The axon has two major properties that allow for this even activation across its branches. First, as @Armatus said, the axon is an active structure, meaning that the action potential (AP) regenerates as it travels along the axon. This means that there is essentially no decay of the voltage as the AP propagates.
Second, the axonal geometry appears to be carefully regulated. As you seem to have guessed, there has to be sufficient current flow to activate an action potential in the neighbouring patches of membrane or else there is a propagation failure and the AP stops. This is a problem at axonal branch points (see Box 1 in Debanne, 2004), where the diameters of daughter branches have to be correctly sized so that there is little or no extra electrical load. (For instance, if one branch stays the same size as the mother, the other branch is an extra load that will "steal" current and leave less current travelling down the mother branch). Recent work using voltage-sensitive dyes have shown that in mammalian neurons, in practice, propagation failures are rare (Foust et al, 2010). This suggests that there is fine regulation to ensure that the geometry is "just right." (Those "just right" rules are basically governed by cable theory, which I've previously described here.)
To your last question, yes, there is time-dependent decay of subthreshold potentials because the membrane is a capacitor (~1 uF / cm^2). I wouldn't call this "storage" exactly, but it does work just like a capacitor in a circuit. Many people think of the membrane as a capacitor and a resistor in parallel.

Debanne, D., 2004. Information processing in the axon. Nature Reviews Neuroscience 5, 304–316.
Foust, A., Popovic, M., Zecevic, D., McCormick, D.A., 2010. Action Potentials Initiate in the Axon Initial Segment and Propagate through Axon Collaterals Reliably in Cerebellar Purkinje Neurons. J. Neurosci. 30, 6891–6902.

Action potentials are governed by the ion concentrations on different sides of the membranes. When an AP is triggered locally, it spreads because the ions which travel across the membrane during the AP spike diffuse to neighbouring regions and trigger the same response in the ion channels there.
Hence, it is irrelevant where an AP is, it is always the same voltage. The 40mV are not "distributed" at all - they diffuse and cause new depolarisations around them, triggering new 40mV potentials until they reach the neuron terminals. So in a way, yes, the AP propagates by "creating a potential while it is not there". All terminals will have the same 40mV potential (the exact voltage of course may be different between cell types).
Potentials which do not reach the threshold value are stored to some extent. This is in the sense that potentials around neurons are always established by ion gradients - a potential in your sense means a change in concentrations from the resting state. Until the concentrations are normalised again by the various transport mechanisms for ions across the membrane, the potential across the membrane will remain changed and it may be closer or further away from the AP threshold.

I need to get my essay in by thursday so I can't spare much more time right now, but if someone bumps this on thursday night I can gather some further reading :)

I liked your answer. As far as I understand, there is no connection between strengths of different synapses of same axon also. This has collapsed all the theory I was telling myself. Anyway, I want to ask one last question. Is it discovered that what kind of events change the value of threshold, or maybe is it fixed for all neurons?

I would make the guess that the voltages (resting potential, AP, threshold) are characteristic for each neuron type, but can be changed for individual cells according to circumstances, like most things about neurons.

Threshold is not fixed, even within a single neuron over short periods of time. Fundamentally, threshold is reached when enough voltage-gated sodium channels open so that a rapid depolarization occurs--that is, when inward current is much greater than outward current. When this occurs is a complicated function of membrane resistance, leak currents, the recent history of the membrane, other inward currents present, the kinetics and voltage-dependence of outward currents, etc., etc.

@Armatus, the ions that flow in through ion channels during the action potential are almost certainly not the same ions that carry current axially to depolarize adjacent sites. The charge travels (that's what current is) but the ion fluxes are local.

Both of you guys have given quite good information. I appreciate it. I have one little question. This is the last one I think about this topic. Is it possible that when 40 mV reaches to axon terminal, it is raised let's say 45 mV? Technically speaking, can I say min and max transferred potential everytime between -40mV and +40mV according to excitatory or inhibitory effect?

Here is a pretty good animation of neurotransmission:
google:Neurotransmitter action potential
What they don't show there very well is that the action potential signal does not travel like a voltage on a wire, but as a propagating chemical condition.
At the synapse, how strongly the connection is made to the next neuron is addressed in the 'long term potentiation' module.

I have read these documents before. But no matter how the potential is carried, I think the potential must be divided in its circuitry. But unfortunately, I have never seen any information about this yet. Either it is not discovered or no body cared. Maybe it was better I asked this question to biology section.

Each discrete Na/K pump contributes to the action potential, but it isn't until a threshold is met that the action propagates. It's closer to fluid dynamics than electronics: When a pump opens, the ions exchange and equalize, then recover. It's not circuitry, it's concentration gradients that maintain the Voltage and propagate the action potential. In circuits, electrons move freely on a metal surface, in neurons Ions move towards equilibrium.

@MCM: don't have the time to reply now, but just wanted to say that Na/K pump does not contribute to the generation of AP, but rather to the mainteinance of the resting membrane potential

@nico - Yeah, I worded that oddly. Thanks for clearing that up.


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Comparative cost of RNA-seq vs sequencing full length cDNAs
I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data (high coverage for reasonable cost, error rates notwithstanding), but another benefit of RNA-seq data in particular is that they can be used in multiple ways. For example, I am mapping the RNA-seq reads to the genome to estimate transcript abundances and do some differential expression analysis, but I have also assembled the RNA-seq reads de novo to use as evidence for genome annotation.
There are, however, limitations to using RNA-seq-derived transcripts for annotation. Full-length cDNAs would facilitate much more reliable annotation. However, I have no intuition for the relative cost, time commitment, or complexity of extracting and sequencing full-length cDNAs vs next-gen sequencing. Can anyone here comment on this?

What kind of organism? Splicing makes using RNA more difficult. Is there a good existing reference genome for you organism (if lacking in annotation)? Do you have a specific goal, such as biofuels, drug production  fighting pathogenic or parasitic organism, or do you have X amount of money and want to do the best basic research? The type and depth of sequencing that is most cost efficient will vary with your goals.

"What kind of organism?" It's eukaryotic, a social insect to be precise. "Is there a good existing reference genome for you organism?" As I said, this is a non-model species, so I am the one assembling the genome. I don't know what your criteria are for a "good" genome: no physical mapping, gap filling, etc has been done yet, but the assembled sequence is close to the expected genome size and preliminary annotations have identified about the number of genes we would expect (perhaps a little bit less).

"Do you have a specific goal?" The PI of this genome project is primarily interested in the intersection of evolution, genomics, and behavior, and uses several species of social insects as model organisms for these subjects.

IMO you should do a full length cDNA sequencing (sanger) only for the doubtful cases (Small contigs/ contigs mapping with gaps/ low depth)

I would comment on this instead of an answer but I don't have the reputation to comment yet. So RNAseq is actually done on cDNA. Specifically after selecting for mRNA before making a cDNA library by its poly A tail etc... It sounds like you are thinking that RNAseq is on actual RNA molecules? Or is your question more about long sequencing of full length cDNA from RNA instead of fragmented? That comes down to an increased error rate from sequencing longer sequences (of DNA). There shouldn't be any loss of de-novo information, transcript abundance, as well as isoform abundance from alternative s

Does your organism have scaffold information on ncbi? In that case you may find the gnomon predicted cds on ncbi as well


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What is a good list of unsolved protein structures?
I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein.
Things that I've been able to think of are low producing transcription factors and novel fusion proteins.

You can build it yourself by comparing protein names (of the species of your choice) and PDB records. UniProt flat files have PDB accessions for some, not all proteins. Extracting the entries with no PDB should be a good starting point. Let me know if this interests you and I can write up an answer with the details.

@terdon, that pretty much sounds like what I'm looking for. Unfortunately, there might be a significant number of proteins that have analogs in other species but essentially the same structure. Probably the safe test would be to look at the unsolved structures in ecoli.

Pick a protein, any protein. You are likely to pick one that does not have a solved crystal structure. Also, you'll need to find evidence that the protein is not disordered if you want your structure to mean anything.

@leonardo, well that seems to be a challenge.

There are some funded projects and analyses available just for this purpose.
Structural genomics or high throughput structure projects take all available peptide sequences group them into families and make sure sequence families pointing to most likely novel folds were available.
Here are the status and target list for the joint center for structural genomics. This list is filtered by species as well as by project status.
Their analysis is availble for us to browse through.  http://www1.jcsg.org/prod/newscripts/psca/help/document.cgi
Sorry this isn't so thorough.  Nature also hosts Target Track, which allows several high throughput structure centers to coordinate their efforts.  Each might have resources which could do your work for you.

This is how I would do it:

Download the UniProt/SWISSPROT flat file for bacteria from here.
After decompressing the files, extract the E. coli protein IDs for which there is no PDB annotation in the file (I am giving you a command line that will work on *ix systems (Linux/Unix/OSX etc)):
zcat uniprot_sprot_bacteria.dat.gz | gawk '{if($1~/ID/){if($2~/_ECOLI/){id=$2; frag=0; eco=1; want=1}else{eco=0}}  if($1~/DE/ && $0~/Flags: Fragment/){frag=1;}if($1~/DR/ && $2~/PDB/){want=0; } if($1~/\/\// && want==1 && eco==1 && frag==0){print id}}' > no_pdbs.txt

Explaining the details of this command line is clearly off topic here :). Suffice it to say that it will print those UniProt IDs from the flat file
whose name ends in _ECOLI and for which there is no PDB annotation in the file. It also ignores protein fragments. If you need help understanding it, let me know and we can chat or something.

The result of this quick and dirty analysis is a list of 2694 E.coli proteins with no PDB annotations in the UniProt flat files.
CAVEATS:

These are only the curated SWISSPROT proteins, you may want to also get the UniProt/TrEMBL proteins from here. I would recommend you stick to SWISSPROT though.
As others have pointed out, you should filter this list for homology to other known structures.
The fact that there is no PDB annotation in the flat file does not necessarily mean that there is no known structure.

So, this is not perfect but it should serve as a starting point. Good luck!

You can also filter for different protein model databases like "ProteinModelPortal" to get rid of proteins that can be modelled based on homology.

Try looking at structure homology databases - the sequences that they have no annotation for are likely the kind of sequences that you are seeking.
SUPERFAMILY has a comprehensive annotation across almost 2500 fully sequenced cellular genomes. this would be a good place to start ...


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Low temperature PCR
We're trying to do emulsion PCR using HA-coated polystyrene beads and we're noticing that the beads are seeing drastic issues with thermal degradation above 90C. As PCR has an unfortunate requirement of requiring a high temperature, I was curious about what options are out there to reduce the temperature during PCR denaturation or to stabilize the beads.

Unfortunately melting temperature of nucleic acid is an intrinsic property of the molecule. Do you need to use polystyrene as a substrate? Perhaps silicon or glass are better suited for this in situ PCR.

Well you can change the melting temperature using additives like DMSO and betaine. Unfortunately, the beads have to be coated and the polystyrene seems to be the best for the downstream steps so we would prefer to stick with polystyrene before re-optimizing everything else.

That's true, but there is a diminishing return on additives (at least DMSO) in which after a certain threshold either the polymerase will no longer function or the reaction will shift towards non-specific priming.

If there was an easy solution, I wouldn't be asking it on SE.

I've seen PCR melt temps as low as 92 C. It's too low a temp to melt, but do they become fluid > 90 C?

Perhaps isothermal amplification is possible (NASBA)?
Amplification of DNA also seems possible (NASBA at biomerieux).

Look at chemical hydrogen bond breakers.  Guanadine hydrochloride is included in the buffer conventionally to compete with the the hydrogen bonds that form the double helix.  Other hydrogen bonders like Propionamide and 2-Pyrrolidone can weaken the helix and I would think lower the melting point of the bonds.
How much the Tm is affected would depend on the concentration of the breaker in the buffer.  It might not be possible to lower the temperature this much and you may loose specificity - you might be able to squeeze a few more degrees if the oligos can't get any shorter.

Doesn't this accomplish the same thing as DMSO?

i think a few molar salt will also do it, or just amping up the Gu in the solution, but the paper also tries to estimate specificity and fidelity of the PCR reaction with different compounds so that you don't get as much error with increased bond breaking.  In the extreme concentrations of adding bond breakers, you get no double helix formation at all.

Update (21/09/17) as the answers are a little outdated by now:
Isothermal amplification methods are fairly well established by now and commercially available. They tend to amplify DNA at temperatures of around 56°C.

Wikipedia entry on Loop-mediated isothermal amplification.
For the more tech-savvy, an open research article on
loop-mediated isothermal amplification in Nucleic Acids Research.
Link to a commercially available product using isothermal amplification: ANSR (Disclaimer: I work for this company)


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Is nicotine toxic to humans?
More specifically, is nicotine in the concentrations that smokers receive when smoking cigarettes toxic? I know that in great enough concentrations it can be toxic (but then, so can just about anything else, including oxygen) and I know that in plants it is used as a defense against insects and can even be used as an insecticide. However, it has always been my understanding that nicotine is irrelevant as far as the harmful effects of smoking go.
I recently had a conversation with another biologist who had just quit smoking and had done quite a bit of research on the subject. He said that nicotine itself is in fact bad for you and, therefore, that tobacco-less alternatives to cigarettes (such as electronic cigarettes) are still harmful because of the nicotine alone.
Does anyone have any more information on this? Perhaps some references? Or, even better, a detailed explanation of the pathways involved? Again, I stress, not about nicotine's toxicity in general but about its harmful effects on vertebrates (preferably human) at the kinds of concentrations one could expect to ingest when smoking.

This would be such a perfect chance for me to revise our recent lecture on nicotine. I'm under deadline pressure though so just a quick one: Nicotine is a stimulant and next to its effects on the brain (reward cycles, addiction etc) it upregulates the sympathetic autonomous nervous system. This can lead to problems mainly with the cardiovascular (CV) system due to raised blood pressure and cardiac activity. Essentially this shows itself like CV disease. It also raises metabolic rate and decreases appetite. And it protects from Alzheimer & Parkinson. Still not as bad as other stuff in smoke :)

@Armatus, yes it protects from Alzheimer's, but you never remember where you've left your cigarettes :). Joking aside, please take the chance and revise, or at least post some juicy references. This smoker would very much appreciate it.

I think its useful to say that nicotine is not very toxic to humans - cells don't die or get sick for typical smoking habits.  Secondary health effects are possible, but here is a toxicological profiles.
Nicotine is a toxin in large enough quantities and nicotine has an LD50 (lethal dose for 50% of individuals) of 0.5-1 mg Nicotine / kg of body weight.  So even a small spill on your skin of the chemical can be life threatening, but for smokers the nicotine itself is not dangerous.
Individuals who smoke intake about 1 mg per cigarette smoked.  So a small adult (110 lbs) can smoke 25 cigarettes in a short period of time (or all at once!) and just barely get to the bottom end of that limit.  Nicotine is water soluble and clears out through the urine at a fast rate though - half of the nicotine from a cigarette is cleared from  your system within 2 hours, which means that 4-5 pack a day smokers are not really killing themselves (from nicotine).
That being said, children are about 5-10 times more sensitive than adults, so even 5-6 cigarettes in an hour can be toxic.  That's quite a bit of smoking though.
Not all animals have the same relationship to the nicotinic acetylcholine receptors as humans do.  Nicotine is toxic to insects and will kill an insect in a matter of minutes or hours. Rats are about 50x less sensitive than people.
I think its comparable to the question of whether caffeine is harmful to people.  In the amount we consume it, sometimes up to grams a day, there is no obvious common side effect, but you figure that decades later it will show up as a problem - a difficult connection to prove.

I do recall this being used as a method for murder in the novel Random

Nicotine acts as a ligand for nicotinic acetycholine receptors (nAChRs), which are ligand-gated ion channels normally activated by acetylcholine. This family of receptors is expressed in every mammalian cell (Schuller, 2009). A priori, at least to me, I'd suggest that it's a bad idea to chronically introduce a foreign substance that mimics the activity of an essential signaling molecule like acetylcholine.
Directly to your question of toxicity, nicotine appears to be linked to many forms of cancer (Schuller, 2009). Cancer promoting signaling pathways are stimulated as a result of calcium entry through nAChRs. Also, interactions of nAChRs with other signalling systems, such as those based on stress hormones, GABA, and dopamine, can lead to cancer.
Nicotine also has important effects in the brain. Chronic exposure to nicotine induces a homeostatic mechanism that upregulates nAChR expression in the brain to maintain responsiveness to endogenous acetylcholine. This effect partially underlies nicotine addiction (Penton and Lester, 2009). As @Armatus notes, nicotine appears to have some neuroprotective properties against neurodegenerative diseases like Parkinson's (Quik, M., Wonnacott, S., 2011) and Alzheimer's (Mehta et al, 2012).

Schuller, H.M., 2009. Is cancer triggered by altered signalling of nicotinic acetylcholine receptors? Nature Reviews Cancer 9, 195–205.
Penton, R.E., Lester, R.A.J., 2009. Cellular events in nicotine addiction. Seminars in Cell & Developmental Biology 20, 418–431.
Quik, M., Wonnacott, S., 2011. α6β2* and α4β2* nicotinic acetylcholine receptors as drug targets for Parkinson’s disease. Pharmacol. Rev. 63, 938–966.
Mehta, M., Adem, A., Kahlon, M.S., Sabbagh, M.N., 2012. The nicotinic acetylcholine receptor: smoking and Alzheimer’s disease revisited. Front Biosci (Elite Ed) 4, 169–180.

When exploring whether nicotine is toxic to humans, the discussion isn't complete without the inclusion of non-adult humans / humans-in-development. Nicotine is toxic to humans beginning at conception. Nicotine has adverse effects on sperm, making them malformed, less likely to fertilize eggs, and making the embryos they do create less likely to survive. Mohamad Eid Hammadeh, PhD, professor of obstetrics and gynecology a the University of the Saarland, Homburg/Saar, Germany, in an interview with WebMD, is quoted as saying,
"The DNA alphabet of these sperm has one or two letters missing. And this cannot be repaired. When we inject these damaged sperm into an egg cell, the sperm is not capable of fertilizing the cell. And even if it does, the [miscarriage] rate is very high."
This paper talks about the abnormalities seen in sperm exposed to nicotine, whether sperm can recover, and after how long.
This paper links the nicotine consumption of fathers to their children's likelihood of developing childhood cancer, citing one possible explanation that smoking causes genetic damage to sperm cells. The sperm cell mutations then become inborn cancer-causing mutations in the offspring.
They jury may be out on the extremity of nicotine's impact on adult health, but it's clear that it's deleterious to the next generation.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3880486/
Suggesting that the LD50 is an oral LD50 of 6.5–13 mg/kg.

Hi and welcome to the site. While this might indeed be relevant, it isn't considered a useful answer here. Please [edit] your answer and explain the relevant points of the paper here as well as how they answer the specific question asked. For instance, a suggested LD50 is irrelevant unless you also discuss the amount that would be ingested while smoking and what part of that LD50 it represents.