Mitochondrial inner membrane I know that the cristae of the inner membrane can be tubular or vesicular but I would like to know what are the functions of each .

There is a reasonable speculation. That is to get more areas where ATP synthases are localized in order to produce ATP. But this doesn't tell why the structure has to be the exactly that shape.

As the review Ilan show, the shape seems to be determined by ATP synthase dimerizetion. The shap may be just a consequence of ATP synthase dimerizetion, although it successfully enlarges the area where ATP synthase is localized.


Structures of cyclodextrin complexed with small ligands For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could only find on the PDB database some proteins complexed with cyclodextrin, but no structure of cyclodextrin with small ligands, could you help me?

I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including:

  Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170

  Ali et al (2012) Structure determination of fexofenadine-a-cyclodextrin complex by quantitative 2D ROESY analysis and molecular mechanics studies. Magnetic Resonance in Chemistry 50:299-304

  Lula et al (2012) Interaction between bradykinin potentiating nonapeptide (BPP9a) and beta-cyclodextrin: A structural and thermodynamic study. Materials Science & Engineering C 32: 244-253

I looked at some of the papers but I didn't find any specific case where a structure has been deposited in a database. There were, however, several mentions of the Cambridge Crystallographic Data Centre  as a source of small molecule structures.


Is cysteine deficiency possible? Is there such a thing as cysteine deficiency in humans or other mammals?

What effects would such a deficiency have?

As I understand it, most cysteine for humans comes from dietary sources, though it can be biosynthesized in humans.

Cysteine deficiencies are possible, and one cause is the genetic disorder homocystinuria. Cysteine can be produced from methionine through a homocysteine intermediate, and defective genes for the enzymes involved can prevent proper cysteine production and cause a buildup of homocysteine. Patients have to eat a very carefully controlled diet with very low amounts of protein. This prevents homocysteine buildup by avoiding methionine exposure, but also requires that the patient take vitamin B6 and  B12 supplements and betaine. They might need to take cysteine supplements as well. The symptoms affect many organ systems, including the brain, nerves, and blood vessels, with about 25% of patients dying due to blood clots by age 30.


Does octopus eye presents the equivalent of fovea in primates? I'm working on a simple computational model of Primate eye:  as we know, it presents a central part, the fovea, that is very rich of receptors in comparison with eye periphery. I'm wondering if other species eye, like octopus, present a similar structure: a central fovea.
Thanks

Yes, they do have an area of densely packed receptors, although not point-like as the human fovea.

Talbot and Marshall (2011) performed a retinal topography analysis in three species of cephalopods: a cuttlefish, a squid and an octopus.

According to the authors:

  It was found that all species possessed an increase in photoreceptor density in a horizontal streak approximately placed at the position of a potential horizon in the habitat.

Here is an image from the same paper:

The retinal topography of each of the three species in this study: (a) S. plangon and (b) O. cyanea show a prominent, horizontally orientated band of increased photoreceptor density across the horizontal equator of the retina; (c) S. lessoniana shows a more centrally positioned area of increased photoreceptor density.

Source: Talbot, C. and Marshall, J. (2011). The retinal topography of three species of coleoid cephalopod: significance for perception of polarized light. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1565), pp.724-733.


Difference between medicinal caffeine and regular caffeine There are some OTC paracetamol tablets, some with caffeine. Is this caffeine the same as the regular caffeine (found in a coffee)? Does it perform better than it in any way?

From a pharmacology point of view, there is no difference between caffeine in caffeine pills and in a cup of coffee. It doesn't matter, how a chemical substance (in this case caffeine) is made, the effect of the substance is the same. What can make a difference is the presence of secondary plant ingredients.

For pure caffeine there are two possible sources: By chemical synthesis ("A Novel Method of Caffeine Synthesis from Uracil") and as a byproduct of the decaffeination process when producing decaffeinated coffee.

What is also different is the amount of caffeine. While pills contain standardized amounts of caffeine, the amount for caffeine in brewed coffee varies between different kinds of coffee beans as well as for different brewing methods. See this figure (from here):


PDB file for Osteopontin (SPP1) I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself.
Thanks

There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised.

Osteopontin is hypothesized to assume an elongated and flexible structure (Sodek et al., 2000). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed or stabilized in some way. I'm not a crystallographer, but this protein doesn't look like it can be crystallized in the full form.

For NMR it is a bit on the large side, a full structure would likely be not feasible.

It also has extensive posttranslational modifications, which makes it much harder to produce in large amounts as needed for crystallography, and extremely expensive for NMR where you would have to isotope-label the protein as well.


Examples of Vestigial Genes I consider the existence of a broken GULO gene in humans to be the clearest evidence for human evolution - just what else is it doing there otherwise?

Are there any other examples of vestigial genes in the Human genome? Or perhaps vestigial proteins?

Genes that were once functional but no longer are are called pseudogenes (as Corvus pointed out in the comments).

Many genes that are similar today (homologs) are hypothesized to have come from duplication events in the past.  In most cases, these duplicates diverge.  The divergence can happen in several ways:
1) one retains the original function while the other obtains a novel function
2) a dosage response occurs where both (keeping the original function) become necessary for that function
3) one retains its function while the other loses all functionality.

This third group are the pseudogenes.  This isn't the only way pseudogenes come to be, but it is probably the most well-characterized.

There are several resources for lists of these.  I'll just point you in that direction.  I assume you are interested in a particular group (i.e. genes important in development or patterning), so that you can dig more deeply into:

http://seqanswers.com/forums/showthread.php?t=32054
http://www.genomebiology.com/2012/13/9/r51


How are the paranasal sinuses linked with the capillaries in the ear canals? Sinus congestion often seems to be accompanied by excess pressure on the outer ears (as anyone who has shared a transcontinental flight with an infant can attest to) or fluid buildup in the canals.  An increase the capillary pressure within the ear canals would explain the pressure, but what is the physiological connection between the sinus pressure and pressure in the ears?

The most obvious answer I can think of is that any direct drainage from the sinuses would cause a backup of fluid into the Eustachian tubes.  This would only explain pressure coming from the other side of the eardrum, but is such pressure simply relieved by blood pressure transfer to the capillaries in the ear canal, or is there a non-trivial mechanism by, e.g., a vagal circuit which governs the relationship between the sinuses and the outer ear?

There is no direct link between the capillaries in the sinuses and the ear.

The Eustachian tubes drain the middle ear (between the eardrum and the inner ear) into the nasopharynx, the part of the throat that is just behind the nose.

The para-nasal sinuses drain into the nasal passages themselves at different points. The sinuses and middle ear constantly produce some fluid, which is either reabsorbed or drained.

Often what happens is that in the case of a common cold or other upper respiratory tract infection, the nasopharynx and nasal mucosa are both infected. The inflammation causes swelling and blocks off the Eustachian tubes and the drainage pathways of the sinuses and the trapped fluid itself causes sinus & ear pain and can get infected causing sinusitis and otitis media. Alternatively a viral infection can also go up into the middle ear and sinuses causing direct infection.

The process that occurs when you go on a plane is slightly different. The Eustachian tubes and sinus openings collapse due to pressure and thus the natural fluid that is produced accumulates as well as there being an inability to neutralise the internal and external pressure (thus why making your ears 'pop' works- you force the Eustachian tubes open via positive pressure)

Regarding blood supply of the paranasal sinuses and the ear:

The ear is supplied by the posterior auricular and superficial temporal arteries of the external carotid artery.

The paranasal sinuses are supplied by various branches of the internal and external carotid artery including the maxillary artery, anterior and posterior ethmoidal arteries, ophthalmic artery, supraorbital and supratrochlear arteries


Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin? I recently found out that red kidney beans contain a relatively high amount of the toxic lectin, phytohaemagglutinin.
An article on phytohaemagglutinin on the FDA website states:

Several outbreaks have been associated with "slow cookers" or crock pots, or in casseroles which had not reached a high enough internal temperature to destroy the glycoprotein lectin.
It has been shown that heating to 80°C may potentiate the toxicity five-fold, so that these beans are more toxic than if eaten raw.

What I do not understand is how the toxicity could increase if the beans are cooked at lower temperatures in a crock pot. I would understand if the toxicity remained the same (that is, not be deactivated), but I thought a toxin is nonliving (i.e., unable to grow and reproduce) since it is not a bacteria?
I know nothing about biology, so I am utterly confused.

I am a Snr lecturer and a PhD candidate. Currently, I am putting my theses together. My research area involve in part the kinetic degradation of lectins in neglected and underutilized legumes. I  also looked at the possibility of using irradiation to produce complexed degraded starches  to inactivate lectins during low temperature extruder cooking.I observed in some of the extruded samples that lectins have actually potentiated up to about 50%. I was confused. I know lectins are proteins so they are supposed to denature when heated. I was looking around to see whether someone has made similar observation and I saw that indeed somebody has reported similar observation. I was so over joyed but it was short lived-no explanations were offered.  I now offer a possible explanation. Yes, lectins are proteins(or glycoproteins) and like most proteins their tertiary and quaternary structures are 3D. So the 3D forms have a couple of smaller subunits, woven together into the giant super structure(lectin). In the 3D form, most of the binding sites are "buried" or not fully exposed. It is possible that these smaller units have binding sites for carbs and are best positioned to present their ligands for  exposure and maximal binding when the 3D structure begins to "melt down". This melt down occurs at low temperature when denaturation has actually started.  Thus, the greater the exposure  number of subunits bearing the binding sites, the greater the potentiation. My work used low temperature extrusion cooking and the observation occurred in the extrusion cooking.

I just hope this suggestion is adequate. That is indeed the explanation I am going to offer for my observation anyway. Wish me best of luck!

Bye!


Can you build muscles from watching point of view videos of people weightlifting? According to this, "new research has found that viewing other people exercise actually increases your heart rate and other physiological measures, just as if you were working out yourself".

This got me thinking, can muscles be developed to be stronger and bigger from simply watching videos of people weightlifting from the point of view of the weightlifter?

That is highly unlikely.

The article to which you linked specifically states:

  While watching other people exercise may increase your heart rate and have other physiological effects, nothing can replace the health benefits of getting off the couch.

With proper nutrition, muscle is built through exercise by

  adding sarcomeres [to muscle cells which is] physiologically determined by the degree of force a muscle can generate that is in turn dependent on the degree of overlap of the thick and thin filaments. Thus, the amount of tension would control the number of in-series sarcomeres in a single muscle fiber.[1]

Watching a show about cooking might stimulate hunger, but it won't put food into your stomach. Watching something that evokes a sympathetic response (fear, fighting, an attractive person exercising vigorously, an athlete in a competitive event, etc.) will elevate heart rate, sweat production, and resting muscle tension, but there is not enough tension to produce muscle growth.

In addition, there might be small deleterious effects to watching emotionally charged movies which elicit a sympathetic response: they cause stress. An effective horror film will elicit tension and maybe even a startle response - making you jump in your seat - but it will also elevate your blood pressure, etc.

Exercise is good for you physiologically. Simple stress without exercise is much less so.[2]

[1] Muscle growth and exercise
[2] The Physiology of Stress: Cortisol and the Hypothalamic-Pituitary-Adrenal Axis (simplified but relevant)


Can we influence evolution by teaching primates to control fire? Should we? Most people with a strong interest in biology will have heard of Kanzi the Bonobo, the ape that has the wherewithal to collect fuel for a campfire and play pac-man.

But is it conceivable to influence the course of their evolution so that it becomes more likely they gain the intelligence to support a civilization in the distant future?

Let's face it: it's easy to imagine that Bonobos are looking superficially like early human ancestors.  They have been forced to become more peaceable and social because they are polyamourous (which is why the human phallus is shaped the way it is).

If we are willing to genetically modify them, we would have to do so so heavily the depend on the genetic modifications, or they might just get bred out again - intelligence may be delicate.

In conclusion, is it conceivable to "enlighten" some groups of primates and send them into the wild, in the hopes they (much) later evolve intelligence?  Their existence would serve as an "insurance policy" on intelligent life in the not unlikely event we destroy ourselves.

Is it conceivable to influence the course of their evolution so that it becomes more likely they gain the intelligence to support a civilization in the distant future?

No, I don't think so, based on what is known about evolution.

Your idea is in keeping with the opening of Kubrick's 2001: A Space Odessey, where the monolith inspires one of the primates to see a femur as a weapon. He picks it up, hits an opponent with it, and the idea catches on within his group; the implication is that this inspired male's (female's?) group goes on to domination and are the progenitors of the human race.

In real life, that's not how intelligence is passed on. You can teach a gifted bonobo how to build a fire, but if he's not into roasted meat, or really cold, or trying to scare away predators (or if he doesn't realize that's what fire is good for), all you have is one bonobo who can start fires. It doesn't influence his genes.

To actually influence evolution of bonobos, I imagine it would look like this: You capture 4/5ths of all the bonobos in the world (leave the 1/5 for genetic pool variation). You test them for basics of quick-wittedness. Kill all the bonobos that fall below a certain threshold, and release. Repeat several generations later. Keep doing so for 50 cycles. What you will have are a race of quick-witted bonobos - maybe. Because if the quick-wittedness you selected for doesn't provide them with a survival advantage, it (and they) will die out. What if the smarter bonobos all want to be alphas, and all that fun cuddling and sex-as-peacekeeping were to disappear? They might not survive the bonobo-chimpanzee wars, because they won't live in large, peaceful, cooperative groups any more. Maybe you can teach the bonobos to plant crops, assuring a food source. Will they irrigate, too? What would this decrease in roaming mean for pygmies who hunt bonobos for food?

My point is, we can't control evolution very much unless we also control the total environment they live in. That's one way we have been able to have such an impact on a rather extraordinary species: dogs. But in the end, a dog, whether it's a sheep-herding or rat-catching or boar-hunting or bull-baiting or duck-fetching breed, is still only a dog. Invaluable helpers, but after all that selective breeding, they're just dogs. The smartest dog in the world still likes to play fetch more than anything in the world. Even eating, if she's anything like my two Border Collies.


Have skeletons of "failed" animals been found yet? I don't know what the correct term for "failed animals" is, but I mean those animals which wheren't able to survive due to their "failed" evolution process. Because evolution, as we see it today, has gone through a lot of "this doesn't work" and "this does work" - so the "good" outcomes of mutation have survived and the others haven't.

This is for some an argument against evolution, but just because they don't know really why nothing has been found or that something has been found.

So I want to ask if skeletons of any of those "failed animals" have been found or not. So is there any evidence of animals who had a "really bad" mutation (not illness, but mutation) and haven't survived in the process of evolution?

Short answer
The dodo and Irish Elk, both going extinct relatively recently, are examples of species that have yielded skeletons and went extinct, at least partly, due to maladaptations.

Background
Extinct animals are an example of an answer to your question, barred those species did not go extinct through a cataclysmic event of course. No species can evolve into a meteor-resistant species. The term you are looking for is, I think, maladaptation.

For example, the Irish elk (Fig. 1) has been proposed to have gone extinct at least partly through a maladaptation. The male Irish elk was grew the biggest antlers ever recorded, (over 10ft (3 m) wide. Irish elk became extinct 10,600 years ago, and the male antlers have been proposed as a possible reason, although this is debated (source: Wikipedia). For example, males might have suffered because they got entangled in thickets. The climate changed at the end of the last Ice Age, causing the woodlands in which elk live to shrink. And food shortage might have resulted in a lack of nutritional support for the hefty antlers. However, extinction of an entire species is always caused by a multitude of cooperative factors, so the antlers alone can't be blamed (source: Love Nature, Wikipedia).

Also the dodo (Fig. 2) can be an example of an answer to your question. While not caused by a natural phenomenon, some animals simply become maladapted due to human influences. The dodo is the classic example. The dodo went extinct in the 1600's. It was adapted to life without ground-dwelling predators, as it nested on the ground and couldn't fly. The plump, slow, flightless birds were unable to escape from the sailors and their dogs, rats and pigs who landed on Mauritius (sources: Smithsonian, Love Nature).

Fig. 1. Skeleton of Irish Elk. source: Love Nature

Fig. 2. Dodo skeleton. source: Physiology

Sources
- Love Nature
- Smithsonian
- Wikipedia page on Irish Elk


Bicoid regulation of hunchback I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? In other words, does the level of bicoid directly govern the expression of hunchback, or are there steps in between?

These two papers[1] [2] argue that bcd is a direct activator of hb, although be aware that this does not rule out downstream events feeding back to further activate  hb. (In fact, given the complexity of the embryonic gene network, it is likely that both mechanisms have a role.)

Struhl G, Struhl K, Macdonald PM. 1989. The gradient morphogen bicoid is a concentration-dependent transcriptional activator. Cell, 57(7): 1259-1273, doi:10.1016/0092-8674(89)90062-7.
Driever W, Nüsslein-Volhard C. 1989. The bicoid protin is a positive regulator of hunchback transcription in the early Drosophila embryo. Nature, 337: 138-143.


Why are there relatively more predators on the land than in the oceans? Our biology teacher told us that among worse conditions one of the reason that intelligent life had actually evolved on land is that there is a more important selective pressure due to the bigger number of predators.

Is there really relatively fewer predators (in numbers) on the land? What is the cause of this phenomenon?

I wouldn't say conditions on land are poorer... just more unstable, less predictable over a span of a million years. And an unstable environment appears to be one of the factors in the evolution of human intelligence. ie the environment changes faster than evolution can adapt the body... so one solution is to adapt the animal's behavior which requires intelligence.

That said, dolphins too are plenty intelligent. Octopus also are quite good puzzle solvers.. but are short lived.

As for predator -prey ratio https://www.mcgill.ca/newsroom/channels/news/why-arent-there-more-lions-254873 Here is something to read. Predator-prey ratio appear to be govern by the rate of growth of prey items

And prey in the ocean has a faster turn around in the ocean.. so there are more predators in the ocean than on land. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4240998/.


Is the motor cortex identical to the sensorimotor cortex? As far as I understand, the primary motor cortex (M1) and primary sensorimotor (SM1) are notations for the same cortical area in the brain. Am I right that there is no dedicated motor cortex, and that M1 actually processes both sensation and movement functions?

The primary somatosensory and primary motor cortices are distinct cortical areas. According to the structural classification of Brodmann, the primary somatosensory cortex is referred to as Brodmann's areas 1,2 and 3 (BA1, BA2 and BA3). The primary motor cortex is referred to as Brodmann's area 4 (BA4). The primary sensory cortex is sometimes denoted by S1, and primary motor cortex by M1.

Source: My Brain Notes

The primary somatosensory cortex is concerned with the processing of somatosensory input, such as tactile stimuli coming from the skin. The motor cortex is concerned with executing movements and hence with motor output. As such, there is a functional as well as structural distinction between the two areas.

Within the primary somatosensory cortex, basic processing of somatosensory information takes place in BA3, while more advanced processing takes place in BA1 and 2. Neurons in the somatosensory cortex project to adjacent regions, including the motor cortex (Kendal et al., 2000).

Because the primary sensory and motor cortices are four strips of cortex closely situated together, and because they are functionally coupled at the physiological level, they are sometimes collectively referred to as the sensorimotor cortex.

Reference
Kendal et al. 2000. Principles of Neural Science


How do chameleons signal cells to change color? I have read about how they can change color, but is there literature about the chemical signaling process they use to do so?  I read that it could be some combination of hormones and neurotransmitters, but I couldn't find specific information on the receptors or chemical mechanisms.

As said by @dblyons, there has not been a lot of research (biochemical) on chameleons. So, the exact part of mechanism that you're looking for is still not understood. However, we have recently caught the broad end of the stick. Chameleons don't have special cells for color, their complete skin has a layer of pigments (dermal iridophores) which helps them in changing color. See this (or this) article:

  Chameleon skin has a superficial layer which contains pigments, and under the layer are cells with guanine crystals. Chameleons change color by changing the space between the guanine crystals, which changes the wavelength of light reflected off the crystals which changes the color of the skin.

These guanine crystals are actually like colorless mirrors, but by changing the distance between these crystals, wavelength of light absorbed (and reflected) can be changed. It is quite similar to how the color of ozone changes from pale blue in gas to violet-black in solid form. However, how chameleons trigger this change in distance of crystals, is not yet known.

This is how these crystal lattice works:
sourcesource

This is what a guanine crystal looks like ((a) is guanine):

You can also see a nice real-time video of guanine crystals changing color of chameleon here.

The color changing portion of skin has 3 main layers:

superficial s-iridophores which help in changing color in visible region rapdily.
deep d-iridophores which reflect light in infrared refion and are thought to provide thermal protection to chameleon.
layer of melanin which is actually yellow in color, making chameleons naturally yellow(!) in color. When the guanine crystals come closer, they reflect the blue portion of visible spectrum. This blue light, along with the natural yellow color of melanin, becomes green which gives green color to chameleon. So, the actual color visible to us is a combination of color reflected by guanine crystal and yellow color of melanin.

As I said already, the exact biochemical signalling process behind this process is not known yet. It could be complex hormonal or neurotransmitter signals. However, hormones are considered as the main triggers because chameleons have been shown to change color due to changes in mood instead of environmental protection.

  Cephalopods such as the octopus have complex chromatophore organs controlled by muscles to achieve this, whereas vertebrates such as chameleons generate a similar effect by cell signalling. Such signals can be hormones or neurotransmitters and may be initiated by changes in mood, temperature, stress or visible changes in the local environment.


Will plants accumulate toxins from soil contaminated by toxic substances like paint thinner/lead paint? After my grandfather died, demolition crews dumped garbage from the house onto his huge vegetable garden, including lead-painted windows, aluminum, asbestos tiles and more.  Much of it got burned in a few bonfires, which I assume released the toxins into the soil.

I've cleaned out every object I can see from that pile, but I'm wondering if the vegetables grown in that soil will be toxic?  It's been about three years since the demolition.

Also, to avoid the possible toxins from that area, we created a raised container garden using soil from a different location.  Yesterday, 3 Tablespoons of paint thinner mixed with water was dumped accidentally on one of the plants. We hosed it down, and it's still alive, but I'm thinking that the squash it will eventually produce is now toxic too, right?

Thanks in advance. We're new to gardening and really want to understand how this works.

You could use other plants to extract harmful substances from the soil. There are plants which are called hyperaccumulators which absorb high amounts of contaminants from the soil.
Have a look at at Phytoremediation where the process of phytoextraction is described in detail.

Normally phyotextraction needs several generations of plants to be grown in order to be effective. Consequently you could just plant your vegetables as usual but take samples and test them for heavy metals or other contaminants of concern.


How do you dilute forward and reverse primers for a master mix? I apologize for the very naive question, but I'm just starting out in a high school biology lab and I am very confused.
If I have stocks of 100μM for forward and reverse primers separately, I can dilute them to 10μM very easily. But what if I want to make a master mix? I have 1000μL of 10μM for each primer, forward and reverse (not mixed). Would I just add 500μL of my forward primer and 500μL of my reverse primer for a mix of 1000μL in  which both concentrations are still 10μM?

Would I just add 500μL of my forward primer and 500μL of my reverse
  primer for a mix of 1000μL in which both concentrations are still
  10μM?

No.  Diluting your 10μM solution in half will half the concentration.  Mixing equal parts of 10μM primer will make a master mix where each primer is 5μM

But in general, primers are added to these reactions in great excess, so 5μM of primer might be okay.


What are the consequences of voluntary total celibacy? Psychologically this might be a tough question, but in means of biology, what are the effects of total celibacy on the gonads and the nervous system concerning both man and woman in short and long term? Has there any research made in medical terms and as a bonus question, is there anything similar on other animal kingdom like deliberate celibacy?

I was told in my undergraduate degree that males produce sperm all the time, and that under conditions of no sexual stimulation, that sperm is excreted involuntarily every 15-16 days, at night, while dreaming. I was also told that the renewal rate of sperm is higher under regular sexual stimulation, which increases the fertility of the sperm that is excreted.


Does modern theory of evolution include modification of physical environment? Does any branch of modern evolution theories include aspects of evolving organisms modifying the physical environment?

An example from the evolution of life could be early stage introduction of oxygen and carbon dioxide to the atmosphere from single cell bacterial growth, thereby establishing a basis for growth of more complex organisms.

See also somewhat related question: https://physics.stackexchange.com/questions/22771/does-the-universe-follow-a-general-physical-and-computational-principle-of-evolu

Yes, such processes are considered but there is still a lot of work to be done in this field.

Because the question is open-ended I will just define two concepts of interest and let you go through papers if you want to understand how such processes are modelled.

Niche Construction

Niche construction is the process in which an organism alters its own environment. Sometimes, niche construction takes a broad definition and it then refers more globally to any environment change that is induced by an organism regardless of whether the individual/lineage experiencing the environment is the same one than the one causing the modification. Under this broad definition, niche construction has the meaning as ecological engineering to my understanding.

Some obvious examples are bird nests, beaver's dam and humans's houses. The process of niche construction gets really interesting when the niche is inherited by future generations.

Ecosystem engineering

Ecosystem engineering is the process in which an organism alters the its environment and the environment of other lineages/species. Ecological facilitation is one class of examples.

Ecosystem engineering vs Niche Construction

To my understanding, the term niche construction is more often used in the evolutionary ecology literature, while the term ecosystem engineering is more often used in the ecology literature. Note again that (in my understanding) niche construction in its broad sense takes the same definition as ecosystem engineering but not in its narrow sense.

Models of niche construction in evolutionary biology

There are a number of models of niche construction in evolutionary biology. I am not expert in this field and am not able to make a good summary (would take a while even for an expert anyway). Here are a few papers (that I haven't fully read) that you may want to consider

Niche construction - Odling-Smee et al. 1996
The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory - Laland et al. 1996
Evolutionary consequences of niche construction and their implications for ecology - Laland et al. 1998
Macroevolution of ecosystem engineering, niche construction and diversity - Erwin 2008

Note that depending on your level of understanding of evolutionary biology, these papers may be a bit complicated to fully understand.


Can drinking caffeine, alcohol and other diuretics be part of a good drinking regime? Tea, Coffee, Beer, Coke etc…

I wonder if the benefit from amount of fluid we get from them is bigger or smaller then the handicap of dehydration. In other words it is worth to drink them if we want to have a good drinking regime?

Opening on the recommendation from this question.

A PlOS One study notes drinking moderate amounts of coffee (aka moderate caffeine intake) doesn't necessarily lead to dehydration. They note coffee has hydrating qualities akin to water. Further empirical studies found no substantial fluid loss in caffeinated beverages.

EDIT: Make note we're talking normal doses and moderate intake, though source 2 goes into diminishing effect of caffeine-mediated fluid loss in heavy/prolonged uptake.

The issue therein is with alcohol, which tends to inhibit vasopressin and the kidneys are constantly permeable to fluids.


What are the different ways an exon gets spliced? Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.

There are several ways splicing can occur, which depends on the RNA molecule to be spliced and the catalyst that performs the splicing:

mRNA splicing is carried out by spliceosome, which consists of small nuclear RNAs. There are sequences at the end of the introns and branch sties which indicate the splice sites. The so called lariat structure is formed when the 2'OH group of an adenosine residue in the branch site attacks the 5' splice site.
self-splicing of ribosomal RNA precursor - it is performed with the absence of spliceosome.
tRNA splicing - it requires three enzymes and ATP hydrolysis.

References:

Biochemistry, L. Stryer, 5th eddition

J. Abelson. tRNA Splicing


What is meant by 'proteolytic activation' of a virus? Noob biologist here. I suspect that at the first stage this means 'activating the virus by lysis of a surface/spike protein'? Seems kind of obvious, but I put it here in case 'proteolytic activation' is not in fact merely a subset of 'virus activation', and means something slightly different.
Second, if the above interpretation is correct, what precisely do we mean by virus activation? Is it the release of viral RNA into the host cell cytosol? This would be my guess, as it is necessary (sufficient?) for replication of viral RNA to commence, and viral replication to occur. Another idea is that 'virus entering host cell' is enough to constitute viral activation, though I suspect some viruses can enter cells and remain dormant there. Hardly seems like activation to me.
Would really appreciate clarification of this terminology so I don't have misconceptions when reading literature.

Viruses all have some mechanism to enter cells' lipid membranes, and these need to be prevented from activating prematurely. Often this means the virus is in an inert state while it is assembled and trafficked out of the host cell, then activated by some chemical signal such as the low pH of inner endosomes. So "activation" is usually going to refer to a chemical change that removes the barriers to cell entry.
For example; in flaviviruses such as Zika or Dengue, the E glycoprotein that handles most of the host entry functions is assembled while bound to prM protein. Once virions are assembled with E in an inert arrangement, prM is proteolytically cleaved. When the new host cell absorbs the virion into an endosome and lowers the pH to digest it, the E glycoproteins rearrange into spikes that can penetrate the endosomal membrane and induce fusion with the viral membrane. If prM isn't cleaved, the virus can't infect cells. Here's a recent paper that discusses this process, with high resolution structures. For these viruses there are two rounds of activation, and only the first one is proteolytic.


Can a viable embryo develop from the fusion of two egg cells? For a zygote to form, two haploid gametes undergo meiosis and fuse during fertilisation. Since two egg cells (or even two sperm cells) are both haploid, is it theoretically possible for them to make an embryo (via experimental manipulation)?
I’m guessing that if such a thing were possible, the two egg cells could each come from the same organism or two different sources.
Would there be any side effects, such as persistence of mutant alleles due to a lack of genetic variation if both egg cells originate from the same organism?

Yes, it is possible to make a zygote from two ovules. Other more complex scenarios are possible as well. You might want to read this cbc article. If the two ovules came from the same organism, then the baby will very likely suffer from a number of diseases due to very low heterozygosity (same mechanism that is causing inbreeding depression and problems of consanguinity).

It is likely not possible to get a zygote from two spermatozoids though because you would lack mitochondrial DNA (mtDNA). There is a little bit of mtDNA in spermatozoids but they are generally not transmitted. Through experimental setup I imagine it might be possible. Also, spermatozoids are very small and would lack many of the ressources necessary to start a zygote.


What is the scientific name of this tree? The tree flowers prior to the monsoon season and sheds it's leaves in Winter and regrow them in Spring and Summer.
I have seen three different colours of the flower (growing in my neighbourhood): pink, violet and white.
Place-India, Kolkata, West Bengal. Season - Monsoon.

It is Lagerstroemia, perhaps Lagerstroemia indica, the common crape myrtle.

https://en.wikipedia.org/wiki/Lagerstroemia

Myrtle in french means blueberry: "From Medieval Latin myrtillus, diminutive of Latin myrtus (“myrtle”), from Semitic: Arabic مُرّ (murr, “bitter”), Hebrew מֹר (mor, “bitterness") ." Myrtle is an unrelated family with tough spicy seed pods which are used as a condiment including eucalyptus.

Crape, refers to the frilly flowers, from Latin Crispus, Crispy: frilly, crèpe is often used to refer to frilly fabric and it also means pancake in french, which is a chapatti with butter and milk and an egg from the bible.

Because you said it is common, I checked google images for "india frilled pink flower tree", it was about 20 images in. There should be a Hindi/Indian script of the wiki page, with the Indian derived name.


What can cause the bloating in high protein diet of Whey proteins? I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins.
Liver does breaks those proteins to branched chain amino acids (BCAA), which can cause this swelling.

However, I am not sure if this is the reason.
It may be the carbohydrates which are broken to enable this BCAA synthesis.
If you take the protein diet with carbohydrates, there seem to be less swelling.
So apparently easier energy for BCAA synthesis.

The combination of proteins, carbohydrates and lipids seem to be important.
Creatine should also be mentioned.
Fat burner thing is also important here, I think.

What can cause the swelling of gastrointestinal system after high protein diet of Whey proteins?

The cause of the swelling is lack of lymphatic carriage capability of proteins to the muscles, because of systemic conditions affecting the circulation of proteins through your lymphatic system.
There will be edema extracellularly because of insufficient carriage of proteins through lymphatic system.

My schematic drawing about the fluid movement between these spaces

I started to think why some people do not observe so much swelling.
I discussed with a few and come to conclusion that the main difference between those people who did not have noticeable swelling was that that they did lymphatic system massage by maximising abdominal breathing after taking whey proteins (before training and after training).
I think it sounds sensible to some extent.
Those people also included lymphatic system massage in their recovery after training.
One video here Lymphatic Drainage for Abdomen and Trunk.
So another reason what may cause the swelling is insufficient drainage of lymphatic system.

The swelling does not happen to the same extent in all people.
Some people swell much after one intake of protein drink.
Some people also do not have to do lymphatic massage.

My conjecture: The reason to this is most probably one glue-gene-group.
Those people who have this genome have other systemic diseases that causes the lymphatic drainage have high proportion of proteins already:

for instance, uncontrolled asthma patients, who are circulating lysed DNAs of lymphocytes from small bronchial tree through the lymphatic circulation

Lymphatic circulation is the system which circulates the proteins to the muscles.
After absorption from the digestive tract, lymphatic circulation carries proteins systemically.
However, since there is already a high proportion of proteins, lymphatic circulation cannot take much more proteins to carry.
Our body has to remove toxic wastes before it can build new materials.
Catabolism then conquers anabolism in some situations.


How does the immune system "learn" from a vaccine? According to Wikipedia:

  A vaccine typically contains an agent that resembles a disease-causing
  microorganism, and is often made from weakened or killed forms of the
  microbe, its toxins or one of its surface proteins. The agent
  stimulates the body's immune system to recognize the agent as foreign,
  destroy it, and "remember" it, so that the immune system can more
  easily recognize and destroy any of these microorganisms that it later
  encounters.

Question:  How does the immune system ""remember"" a foreign agent introduced via a vaccine?  And how does it learn how to deal with subsequent encounters?

Vaccines work by introducing an attenuated strain of the pathogen (or alternatively the antigens that are normally present on the pathogens surface) into the body, whereupon the body mounts an immune response.  As this will (hopefully) be the first time that the body has encountered the antigens on the pseudo-pathogen's surface, the response is called the primary response.

This consists of two main divisions: the cell mediated pathway and the humoral pathway.  In vaccination it is the humoral pathway that is important.  This is where a division of white blood cells (B-Cells) produce antibodies that are complementary to the antigens on the pathogen surface, causing a negative effect to the pathogen (death, inability to reproduce, de-activation of toxins, etc.).  However as each B-Cell produces a different antibody, there needs to be a mechanism to select the correct one:

Antigen Presentation (technically part of the cell-mediated-response) - a phagocyte engulfs the pathogen and displays the pathogenic antigens on its own surface.
Clonal Selection - B-Cells that are attracted to the invasion site attempt to bind their antibodies onto the pathogen's antigens.  It takes time for this to occur successfully as you are essentially waiting for the correct mutation to happen.
Clonal Expansion - Once a complementary antibody producing B-Cell has been found it is then activated with the help of a T-Helper cell.  This causes it to divide rapidly whereupon these cloned specific B cells can secrete their antibodies which will cause detriment to the pathogen.

It's at this point that I can start to answer your specific question.  The large clone of B cells will then sub-divide into two types.  Plasma Cells remain in the blood and produce antibodies to fight the infection.  The other type, much smaller in proportion, are called Memory Cells.  These cells have a very long lifetime and move to lymph nodes across the body (including the spleen), where they remain dormant until the same pathogen is found again.

When this is the case, the memory cells are activated by T-helpers so that they can divide into massive numbers of plasma cells to fight the infection the second time.  This secondary response is a much faster as the clonal selection stage does not have to wait for the right mutation - they are already waiting in the lymph nodes.  The response is also much stronger as each memory cell can produce large numbers of plasma cells - i.e. you can start with multiple activated B-cells (as many as you have memory cells) rather than just the one that has mutated into a complementary shape in the primary immune response.

The aim of the vaccine is for the secondary response to be so quick that potentially life threatening symptoms do not occur; the body has time to find and store the correct antigen in a safe environment as the pathogen has been deactivated.


Please identify this bone found on the beach I've found it on the beach in Çanakkale, Turkey. Width 7.5 cm, height 5 cm. Inner hole dimensions are 2.5 cm x 3 cm.

It's an atlas vertebra from a large herbivore, a goat, a young horse, a deer. Also know as the C1 vertebra it's probably a sheep from a mechoui party.


Can bacterial RNA be degraded at -80⁰C in a SDS solution? I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded.

Comes from a pellet of pure liquid culture.

I think it is relatively unlikely that the RNA will degrade under these conditions. For the future, I would handle this differently:

You can centrifuge the cells and snap freeze them in an appropriate
buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing.
Alternatively, you centrifuge them, break them up with Trizol (or whatever you use for this purpose) and freeze them in this solution. This will be
safer as it completely denatures all proteins including all nucleases.

I would choose (and have done this already several times with cell samples that I couldn't process without problems) the second method.


Nerves, Neurons, Axons and Dendrites by Example Here is a simple diagram of a neuron:

A few (very closely related) questions:

Where are receptors located (for pain, pressure, temperature, etc.): in the axon terminals or the dendrite tree?
Please confirm: for sensory nerves, signals travel from axon terminal to dendrite tree, yes?
According to Wikipedia, axons communicate with each other across synapses, and nerves are chained bundles of axons (basically forming a cable with each other). However, if sensory signals travel from axon to dendrite, then how can axons be chained together? In other words, if axons are a "male" recepticle, and dendrites are a "female" recepticle, then how can you have a chain of all-male recepticles?
Please confirm: a nerve is just the cabling that houses bundles of long, individual strands of neurons, yes?

Receptors are typically not located in a neuron. Instead, receptors generally synapse onto a primary neuron, and specifically on the primary neuron's dendrite;
Within the neuron physiological signals are received in the dendrite and are transmitted uni-directionally via the axon to the axon terminal. Between neurons the signal is transmitted from axon to dendrite via the synapse (see figure).
Although axo-axonal communication exists, it is not the typical way of neural communication (they are regulatory in nature and do not convey information as such). Typically, axons synapse onto another neuron via the dendrite of that second neuron.

The typical connection is the following:

Nerves typically do not contain cell bodies, only the elongated parts of neurons, i.e. the axons. A nerve is a bundle of axons that contain closely related signals from closely related structures in the body.


What are the differences between insects and spiders? I have always been told that a spider is not an insect, since the former has 8 legs and the latter 6 legs.

Is it just a matter of definition and spiders could have been defined as "8-legged insects"? Or are there more fundamental differences between the two kinds of animals and the distinction makes sense from the viewpoint of biology and evolution?

Spiders and Insects have been separate independent linages of animals for 500 million years. Spiders have two body parts (cephalothorax and abdomen), while insects have 3 (head, thorax and abdomen). Besides the differences in number of legs, spiders and insects have different forms of respiration, different mouthparts, and different exoskeletons. Insects have antennae, while spiders don't. In short, spiders and insects are more different from one another than mice are from sharks.


Do chromosomes change with time? An offspring is 23 chromosomes of mother and 23 of father, if one of the mate learns say music after the birth of their first child— will their second offspring have better music skills than former? about my knowledge of biology, so far I read about DNA, Genome, chromosomes and genetic engineering, I am an engineer by profession.

Short Answer: Probably, at least a little, much research still needs to be done.  For a great paper on this see here.

Your question can be answered in two parts:

Can Epigenetics be inherited - The answer to the simple question in your title, do chromosomes change with time, is yes.  There are copying errors, and carcinogenic mutations that can permanently change cells' genomes.  Less permanent is epigenetics, which are temporary chemical modifications to the DNA which changes how it is expressed. The epigenetics of the cell may change for various reasons from the cell undergoing mitosis to a wildly changing diet.  However, when sperm and egg cells are formed these epigentic modifications are typically wiped from the genome in order to remove any possible damaging marks.  However, there is a growing body of literature which states that some marks escape the purge and change the characteristics of the progeny.  Studies include scare-treating mice, 1836 famine, fatty rats, human psychological changes.  While the exact genes causing the change is unknown, there is clearly a strong correlation
Can Music Skill be Captured in Epigenetics - Music skill is to difficult to measure biologically, but likely has some links in speech skills, which would be captured in the brain, and muscle skills.  While there is some evidence for there being an muscle epi-memory, brain epigenetic inheritance is more tenuous (although see this exciting paper on RNA causing memory changes through epigenetics).  I would say the general scientific consensus is that there is some relation between epigentics, and memory, and music skill - there is a great deal of work still to be done.


Using DTNP to find free thiol groups on a protein I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA).

After measuring the absorbance, finding the concentration of TNB and calculating the concentration of the BSA, I've come out with a result of around 0.4 free thiol groups per molecule of BSA, which seems unlikely! There is either a free group or there isn't!

Yet, the implication from the demonstrator is that is is the correct result!

How can this be? Is it possible to get a value of less than one in an experiment like this?

This is a perfectly reasonable result. Remember that you are measuring an average value for a very large population of BSA molecules. Essentially what the 0.4 means is that at any one time, about 40% of the BSA molecules have a free thiol, while the rest of the cysteine residues are disulfide-bonded.


What is the minimum number of chemical elements required for life on earth? Does it vary between kingdoms? As a non-biologist, I assume that there are certain elements that occur in all life forms as we know them. Examples might be carbon, hydrogen, oxygen and so forth. There are also elements that are rarely, if  ever, required for life on earth. My question is not about what elements might be required for life (although such information might be interesting for me and other readers). Rather it is about what the minimum possible number of elements that any life form on earth has, if we know the answer to that question. Also, if it is known, (how) does this differ between the plant, animal and other kingdoms?

You are far more likely than me to know what tags might be appropriate here. Please feel free to edit.

If we change the question to "what is the minimum number of elements common to every form of life?", my lists would be as follows. (I am not considering either viruses or prions to be 'alive').
The following elements are surely common to all forms of life (List 1):

H (1), C (6), N (7), 0 (8), Mg (12), P (15), S (16) [#7].

In addition, the following elements are very likely to be common to all forms of life (List 2):

Na (11), Cl (17), K (19), Ca (20), Fe (26), Cu (29), Zn (30) [#7].

If we broaden things to include elements occurring in any form of life I would add (List 3):

B (5), F (9), Si (14) [!Seemingly], V (23), Cr (24), Mn (25), Co (27), Ni (28), Se (34), Mo (42), Cd (48), Sn (50) [!Maybe], I (53) , W  (74) [#14].

No element in either list has an atomic number greater than 74 (Tungsten). (In the list given by Frieden (1972), the highest is I (53)).

For List One (and as pointed out by @bob1), H (1), C (6), N (7), 0 (8), S (16) are all present in proteins. P (15) is present in ATP and NAD. We must surely also include Mg (12), as the true substrate of almost all ATP-requiring enzymes is a complex of Mg++ and ATP. I can't see that any element can be removed from this list, but it could be argued that we need to add some from List 2.

For List 2, Fe (26) is present as haem in haemoglobin and the cytochromes, and (not necessarily complexed to heme) in other components of the electron transport chain. It might be possible that anaerobic life is possible without iron, in which case Fe (26) needs to be demoted to List 3 (but I doubt it). Zn (30) occurs in many enzymes (including yeast and liver alcohol dehydrogenase). It might be possible for a life form to exist without requiring Zn, but I don't know of any examples.

If we restrict consideration to plants, then Mn (25) needs to be promoted to List 1 (Mn is an essential component of Photosystem II, the enzymic system responsible for the 'splitting' of water in photosynthesis). As life as we know it would be impossible without PS, Mn (25) should possibly be in List 1 without qualification.

List 3 will probably always be contentious, but here are my thoughts:

B (5) is present in boromycin the only naturally-occurring compound containing Boron (as far as I am aware). It has long been considered essential for some plants, but this is contentious. See The importance of boron in biological systems and Boron: the essential element for vascular plants that never was
Edit B (5). @john has pointed out that B is required by some cyanobacteria, and has provided the following reference: Boron Requirement in Cyanobacteria. Its Possible Role in the Early Evolution of Photosynthetic Organisms.
The authors (Bonilla et al.) point out that B is a trace element that "although required in higher plants, has no role in animals or fungi". They suggest that B (possibly as boric acid?) can stabilize membranes by forming cis-diols with glycolipid -OH groups, a role previously suggested to account for B requirement in plants. (References to the original plant research may be found in Bonilla et al.).

This, I think, justifies B being included in List 3: required for some forms of life (but not a minimum requirement for life).

F (9) occurs in fluroacetate (See also The natural production of chlorinated compounds by G W Gribble)

Si (14). A paper in Science in 1972 suggests that Silicon is an essential element for the chick (news to me!). Frieden (quoted below) has this to say: "Possible structural unit of diatoms; recently shown to be essential in chicks. "

V (23). Occurs in haloperoxidases (See Coordination environment changes of the vanadium in vanadium-dependent haloperoxidase enzymes.  The vanadate ion is very similar to phosphate. See The role of vanadium in biology)

Cr (24) Whether Chromium is an essential trace element is controversial. It may play a role in insulin action (see Wikipedia) but this is not universally accepted (the Wikipedia article gives a good summary of the current position). Some bacterial can reduce chromium but this seems to be a detoxification mechanism (See also Chromium: is it essential, pharmacologically relevant, or toxic?). Frieden states "Essential in higher animals; related to action of insulin." but this, it appears, is still controversial. Possibly Cr (24) needs to be deleted from List 3.

Co (27) is a component of Vitamin B12

Nickel (28). Urease, the first enzyme crystallized (by Sumner in 1926), an accomplishment that played an essential role in establishing that enzymes are proteins, was shown in 1984 to contain Nickel (see Urease (Wikipedia))

Se (34) Selenium (as selenocysteine) is directly incorporated on the ribosome into some enzymes (SelenoCys is considered "the twenty-first amino acid")

Mo (42) is a component of quite a number of enzymes, including xanthine oxidase and is often associated with a pteridine cofactor.  See Molybdenum and Molybdenum-Containing Enzymes

Cd (48) A carbonic anhydrase from the marine diatom Thalassiosira weissflogii contains cadmium. It is thought that in oceans depleted of Zn, diatoms can use Cd as a zinc substitute. (See Biochemistry: a cadmium enzyme from a marine diatom and
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms)

Sn (50) There have been some reports that Tin is an essential trace element for rats and humans (see Case study: bioavailability of tin and tin compounds and Frieden (quoted below)), but the evidence appears to be very scanty. Tin probably should be deleted from List 3.

I (53). Iodine is known to be a component of the thyroid hormones

W (74) Tungsten The first enzyme to require tungsten, a NADP-linked formate dehydrogenase from Clostridium thermoaceticum was purified and characterized in 1983. Since then a number  of tungstoenzymes (at least ten) have been identified, including acetylene hydratase. In many cases (and in a similar fashion to molybdoenzymes), W is often bound to a pterin cofactor. (See Tungsten in biological systems)

I think The chemical elements of life by E.Frieden, published in Scientific American in 1972, is still relevant, and I have relied heavily on the table on p55 of this publication in compiling the above lists
I haven't considered Sr (38), Nb (41), Ba (56) or Ta (73) but from Tungsten in biological systems  it appears that there is a case for these elements to be included in List 3


What factors govern the variable age of onset in Huntington's Disease? "Huntington's disease (HD) is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and psychiatric problems." As we all know, this genetic disease exhibits a generally late age of onset. It has been shown that a increase in the number of CAG repeats in the hungtingtin gene is negatively correlated to the age of onset of the disease. However, patients having a  particular number of CAG repeats still have an extremely variable age of onset, which leads to believe that other factors are contributing to the Huntington phenotype.(reference)

 (reference)

What other genetic or environmental factors have been shown to vary the age of onset of Huntington's disease?

References

Andrew, S. E. et al. The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington’s disease. Nature Genetics 4, 398–403 (1993).

There is quite a bit of data available from Venezuelan HD families, but they haven't identified the factors themselves. From the abstract of the paper, emphasis mine:

  Analysis of the 83 kindreds that comprise the Venezuelan HD kindreds
  demonstrates that residual variability in age of onset has both
  genetic and environmental components. We created a residual age of
  onset phenotype from a regression analysis of the log of age of onset
  on repeat length. Familial correlations (correlation +/- SE) were
  estimated for sibling (0.40 +/- 0.09), parent-offspring (0.10 +/-
  0.11), avuncular (0.07 +/- 0.11), and cousin (0.15 +/- 0.10) pairs, suggesting a familial origin for the residual variance in onset*. By
  using a variance-components approach with all available familial
  relationships, the additive genetic heritability of this residual age
  of onset trait is 38%. A model, including shared sibling environmental
  effects, estimated the components of additive genetic (0.37), shared
  environment (0.22), and nonshared environment (0.41) variances,
  confirming that approximately 40% of the variance remaining in onset
  age is attributable to genes other than the HD gene and 60% is
  environmental.

*This paper also suggests the same, with a smaller (but different) samples.

A recent study of an Italian sample suggests that a polymorphism in Atg7 (autophagy-related gene) is a modifier of age-of-onset, but this result does not generalize to a European cohort.

What is apparently not linked to age of onset in HD? β-defensin copy number variation.

Also, CTCF doesn't appear to be linked to the CAG repeat instability (mutations in CTCF have previously implicated in triplet repeat instability).

Mutations in PGC-1α, mitochondrial regulator, were previously associated with age of onset, but a more recent study suggests that this might have been due to stratification of the sample.

Similarly, a polymorphism in HAP-1 was previously associated with age of onset, but a subsequent study found no evidence of association.

Altogether, these results suggest that population stratification needs to be taken into account when evaluating associations between age of onset and genetic polymorphisms.  It is also possible that there are population-specific genetic factors that affect age of onset.


Clonality of tumour cells Does all cancer cells come from a single clone of cells or are there evidences of polyclonal cancer cells too?

Most tumors are probably not strictly clonal; all cancer cells in a tumor seldom have the exact same set of mutations. Tumors tend to be subclonal, with all cancer cells having a single common ancestor but with later evolution resulting in some mutations shared among all cancer cells but others restricted to sub-populations of cancer cells. This fact and its implications for therapy were noted 40 years ago by Nowell (Science 194:23-28, 1976), and verified by much recent work as reviewed for example by McGranahan and Swanton (Cancer Cell 27:15-26, 2015).

A tumor might need to have a billion ($10^9$) or so cancer cells to be clinically detectable. Thus many years and many cell divisions have passed since the time that a single cell developed the set of mutations originally needed to produce the invasive tumor. With a probability of some uncorrected mutation at each cell division, particularly in cancer cells that often have defects in DNA replication and repair and in chromosome separation, it is essentially impossible for all of the billion cancer cells in the tumor to have identical sets of mutations. See, for example, the work of Bozic et al (eLife 2: e000747,2013). So although there is a clonal origin of the tumor, the tumor is typically a collection of related but genetically distinct populations best considered to be subclones.

Differences among subclones present a major barrier to traditional cytotoxic therapies, to more modern targeted therapies, and to the immunotherapies that presently receive so much attention. Even if most of the tumor is sensitive and responds, a subclone whose mutations somehow provide resistance to the therapy will be able to repopulate the tumor thereafter. Bozic and Nowak (PNAS 111:15964-8, 2014) estimated that a clinically detectable tumor may have 10 or more subclones resistant to any targeted therapy, due to mutations accumulated during the subclinical growth of the tumor.

As examples from immunotherapy for cancer, McGranahan et al recently showed (Science 351:1463-1469, 2016) that responses to immune checkpoint inhibition in melanoma and non-small cell lung cancer were best in patients with clonal rather than subclonal tumor neoantigens for the immune system to attack. Zaretzky et al (New Engl J Med 2016, epub ahead of print) identified subclonal mutations in interferon-receptor signaling and antigen presentation in some patients, mutations enriched in the recurrent tumors following immune checkpoint inhibition and thus likely accounting for relapse following that therapy.

It is possible in principle for a single physical tumor to have multiple cells of origin. Tumors often develop from a region of tissue that has been subject to field cancerization, where carcinogenic challenges have produced many cells with mutations that lead to dysregulated but not invasive behavior. This can lead to multiple independent cancers arising from the same general location, as individual cells later develop the full complement of mutations needed for an invasive tumor. In principle, such multiple cancers might coalesce into a single tumor mass so that the tumor is polyclonal, but I'm not aware of any well documented cases. So it seems that tumors are seldom truly polyclonal with multiple independent cells of origin.


Optimizing Gel Electrophoresis: Ampere, Volts and Buffer concentrations I am a master student in biochemistry, and I have used gel electrophoresis many times before. What I want to know is how one should adjust the mA (mAmpere) compared to the voltage and the buffer one uses.

Normally I used 1xTAE buffer (run at 90V) or 1x sodium borate buffer (run at 110V). I know that if I adjust the voltage up, the buffer heats up faster, the samples travel faster, but the "picture" of the gel becomes more blurry. This is however all I know about adjust the parameter.

So my questions can be summarized as the following:

How should I adjust the ampere, is there a range I should be in
compared to the buffer or sample I am running?
Does the ampere effect the travel speed if adjusted up or down?
Can I adjust the concentration of the buffer to run sample at a
higher voltage, what effects will this have (to increase or decrease
concentration)?
Is there a relationship between the ampere and the voltage which I
can manipulate, in this case: how and why?

As far as I know you can either adjust the ampere or the voltage as
both is dependent of the resistance from the buffer. Which means that
I would suggest you to let the voltage as it is.
As the ampere = voltage / resistance and voltage = resistance *
ampere and as you can see that the voltage has to get higher if the
ampere is increased and the ampere has to get higher if the voltage
is increased (at least if I understand it correctly) the travel speed
should be increased the higher the ampere is set.
I would neither decrease nor increase the concentration of the buffer. Maybe easily using another kind of buffer would help you. But this depends on the different samples you are running. Maybe that could help you:
Brody, J.R., and Kern, S.E. (2004). History and principles of conductive media for standard DNA electrophoresis. Analytical Biochemistry 333, 1–13.
The resistance is more or less given. Therefore as far as I know: No.


What does "regulatory genomics" mean? I have read about basics of molecular genetics ,although its not a thorough in-depth knowledge. I would like to know about "regulatory genomics". What is it actually?

The genome may be divided into two classes of sequences - those that code for proteins and those that do not. Those that do not code for proteins may be again divided into classes consisting of actively transcribed sequences that have biological activity (such as long noncoding RNA, microRNA, competing endogenous RNA and so on) and those that aren't.

These untranscribed noncoding regions may be involved in regulating the activity of protein coding and actively transcribed regions by binding to transcription factors or transcriptional coactivators/corepressors that control whether certain genes are expressed or not - this can happen close to the start of the gene (i.e, promoters) or far away (at enhancers). Distant enhancers can still affect gene expression because they and the genes they affect can be close together in three-dimensional space (The genome is folded in cells!).

Regulatory genomics is, simply put, the study of these regions, which are called genomic "features" and how they regulate genes. A great example of studies in this area are offered by papers published as part of the ENCODE project http://www.nature.com/encode/#/threads


What really causes cancer? A lot of things are claimed to cause cancer, eating red meat, eggs, smoking, using phones, deodorant, breathing.

Surely these can't all actually significantly contribute to the development of cancer.

I've heard smoking is a big one to lung cancer, with someone--I can't recall--saying that most patients with this cancer are smokers.

What kind of activities/foods are sure to, or have high chances to, lead to the development of cancerous cells and how do they cause them, at a molecular level?

Cancer is caused by the mutations in cells.

Cancer exists because of the failure of cell cycle checks which could actually allow cells to survive with erratic genomes. However, that alone does not cause cancer.

Cancer is the uncontrolled proliferation of cells. That only happens when cells have accumulated enough errors during cell division and each cell division goes undetected to the point that cells refuse to commit apoptosis; they are no longer receptive to the body's control mechanisms.

Cancer cells are also malignant. That means that cancer cells cannot be called cancer cells until they are invasive. That means a few cancerous cells cannot be caused cancer because they don't take nutrients from the body . Also, tumour  suppressor  genes can also cause cancer when they turn proto-oncogenes into oncogenes.


How many generations between the first lifeform and humans are there? I expect very large error bars, but what's the number of generations between the very first lifeform (that can be described as evolving in generations) and humans? Is it closer to a quadrillion or a trillion?

A related answer estimates that there were around 300,000 generations between us and the chimp/human common ancestor.

The generations that preceded multicellular life will so vastly dominate the answer that the last 500,000,000 years don't even matter. So life is 3.5 billion years old, and for most of this time, life was prokaryotic, dividing every 20 minutes or so. Thats 26,000 generations per year. Multiply that by 3.5 billion and you get 9 trillion generations. That is likely an overestimate, based on optimal growing conditions of bacterial in exponential growth. But it is unlikely to be orders of magnitude off.


Does evolution head to some optimum? Currently we have many species which are "good enough" for current environment, some species emerge, another die. So let's say that they could be close to some local optima. Does the evolution head to some optimum that in future we will have only one species which will be superior to all other extinct form of life?

An issue in the question that I will ignore

You say

  Does the evolution head to some optimum that in future we will have only one species which will be superior to all other extinct form of life?

Firstly, it is a little bit weirdly phrased. By "superior" I suppose you would refer to a species that could outcompete all the other. This sounds very impossible to me firstly for simple ecological reasons. However, it would be a long answer to fully address this point and I don't feel like addressing (I might not be very much able to) in addition to the other questions.

Evolution vs Natural Selection

Just for a start. Evolution is way more than just Natural selection. There are plenty of other absolutely essential processes such as mutation and drift that are important to understand.

What is Natural Selection?

Natural selection is the process by which most fit individuals end up being at higher frequency in the population as a result of reproducing more and surviving better. Natural selection does not necessarily diminish the probability of a species to get extinct. It will not necessarily increase the ability of a species to compete another. It will not necessarily increase the rate of increase in the number of individuals in the species.

local vs global optima

Reading you post you seem to understand the concept of local vs global optimum (from algorithmic maybe). If selection alone was acting in the population and if mutations were feeding genetic variation to this population at a low enough rate, then population will ultimately reach a local optimum and will get stuck there forever. They would never reach a potential higher local optimum somewhere else. Drift may allow for such switch though, it is refer to "shifting balance theory".

Envrionmental change

The environment changes much faster at a local scale that you seem to think. When talking about environmental change for a lineage, we are not only talking about important ice age or current days global warming but we are talking about more subtle and more frequent changes. Imagine a species of unicellular living in a 50 cubic centimeter puddle. For them environmental change are drastic and frequent. So do population really have time to achieve any equilibrium. It is here a general question that comes in many field of evolutionary biology and also outside biology. Are the system that we study expected to be at equilibrium (in regards at some variables at least) in nature or are they never given the time to reach any equilibrium?

Mutations and drift

Mutation and drift are stochastic processes in evolutionary biology (among others). Mutations is the ultimate production of genetic variation. Most mutations are deleterious but not all are. The exact mutation (and mutational effects) and number of mutations that will occur in a population in a given amount of time is a stochastic process. Genetic drift refers to the random sampling of individuals that are chosen to survive. Drift is inversely proportional to the population size and you may want to have a look at this post to get some intuition for why this is the case.

How much fitness is lost du to ever occurring mutations?

As mutations are always occuring we might wonder how far is a population from its optimum due to these deleterious mutations.

Let's consider a very simple model.

Let $p$ be the frequency of the wild-type (not mutant) allele, $s$ be the deleterious effect of the mutation in the homozygote mutant and $h\cdot s$ be the deleterious effect in the heterozygote. The mean relative fitness in the population is

$$\bar w =  1 - 2 p (1-p) h s - (1-p)^2s$$

Let's define the mutation load $L$ as $1-\bar w$. As a consequence

$$L = 2 p (1-p) h s - (1-p)^2s$$

At selection-drift equilibrium the expected frequency of $p$ is $p=\frac{\mu}{hs}$, where $\mu$ is the mutation rate. As a consequence the

$$L = 2\mu$$
and
$$\bar w = 1- 2\mu$$

Let's assume that fitness effect at different loci are multiplicative (no epistasis). As a consequence an individual carrying $n$ deleterious mutations has a fitness of

$$\prod_{i=1}^n 1-s_i $$.

Let's further assume that all mutations have the same deleterious effect on fitness, that is $s_1=s_2=...=s_n=s$. Let $l$ be the number of nucleotides on which deleterious mutations can occur. Coming back to $w=1-2\mu$, we can say that over all loci in the genome the fitness is

$$\bar w = \prod (1-2\mu) ≈ e^{-\sum_{i=0}^l 2 \mu} = e^{-2\mu l} = e^{-U}$$

, where $U=2\mu l$ is the genome-wide deleterious mutation rate. According to best estimates, in humans $U≈2.2$ and therefore our load is $L = 1-e^{-2.2} ≈ 0.9$.

From this simple model, we would expect that 90% of the mean fitness of a population is lost due to ever recurring deleterious mutations. This sounds pretty big and suggest that we'll always be pretty far way from an actual optimum.


How does the brain instinctively know the math behind Newtonian Physics? A 10 year old child does not have the intellectual power to accurately calculate the energy required to throw a ball an arbitrary distance. Yet they are able to accurately throw a ball at a distinctive target.

Similarily, we often "instinctively" know an approximation of the amount of energy and force required to accomplish certain tasks, even considering that many of us have minimal knowledge of the mathematical complexity behind the tasks.

How does the human brain know the values of force, energy etc. required when accomplishing certain tasks, while being ignorant of the mathematics behind the Newtonian Physics of the task? Is it just a game of "guess and check"?

Trial and error.

The CNS is very much a living, changing organ system - much more so before you are an adult. While you are a child your neurons fire, muscles contract, and force is exerted on objects - then your CNS modifies itself (either through redistribution of neural contacts or growth of new neurons spurned by chemical changes) to account for the results.

This is why "practice makes perfect." As you continuously perform a task, like throwing a ball, your body is keeping track of the results. Did X muscle fibers contracting in Y muscles overshoot your buddy? You register the failure and compensate by utilizing X-N muscle fibers that contract in Y muscles until you consistently satisfy your goal.

Your CNS is keeping track of everything, all the time. There isn't a single instant in your life - asleep or awake - that's not being monitored, so your body has copious amounts of data to work with when making its estimates.

This is also why simulations take time to adapt to, even if the person is fully aware of the basics behind the physics involved.


Why doesn't G-actin concentration fall once microfilament polymerization begins? I don't really understand why the monomer concentration on this graph will stay flat when the monomer concentration is above the Cc.

The critical concentration is better defined as the "equilibrium concentration of the pool of unassembled subunits"1.

An analogy that might be helpful is thinking about a NaCl (table salt) solution — once you add enough salt some will start to precipitate, but the amount in solution will remain the same.

You can think of the solution as having the capacity to support a certain concentration of molecules (or ions) — below that concentration subunits will separate from the polymerized form faster than it can accumulate new subunits, above that concentration the subunits will stick together faster than they "fall off" the polymer.

For more a detailed molecular understanding of why this is so, you probably need to read up on chemical equilibria — for example Chemistry or even Khan Academy might be helpful.

Reference:

1: Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., & Darnell, J. (2000). Section 18.2 — The dynamics of actin assembly. Molecular Cell Biology.


What is the subcellular location of synthesis of non-essential amino-acids? What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this?

I thought the whole point of DNA is coding for how to synthesize proteins and that it is the mechanism of genes expression. Triplets of nucleotides are codes of amino acids and that is the granularity that cell works with.

Now it turns out cells knows how to synthesize more than half of the 20 amino acids, in humans, and I do not see, in the web, good texts of how it is done, where, and how that is coded.

Thank you for helping to shed some light.

There are several enzymes involved in amino acid biosynthesis. These some of thse enzymes are encoded in the human genome. You can check out KEGG for a detailed pathway in different organisms.

The green arrows denote reactions (and enzymes) that are present in a given organism (Homo sapiens, in this case). If you click on the arrows you can know the details about the enzyme.

These enzymes are present in the cytoplasm as well as in mitochondria. Moreover, the reactants for synthesis of certain amino acids are produced in mitochondria (TCA cycle intermediates). See this article on the role of mitochondria in amino acid metabolism.

  Overview of the amino acid metabolic network in human mitochondria. Shaded areas represent the cytoplasmic segments of the pathways.


how to culture mc38 cells I work at a start up company in a vivarium. My boss would like me to start working with MC38 Cells. I bought all of the equipment (recommended by a colleague) and should be ready for the cells. Could anyone recommend a good place to learn how to do this fast? He has surprised me and already ordered the cells. I do have some knowledge on the subject ( from bachelors degree in Biology), but it is not enough. I need somewhere that can teach me even the little steps. I have tried looking at scientific papers, but they typically skip over much of the steps that are common knowledge (to most).

Edit: Similar questions have been asked before: Textbook/lab manual for mammalian cell culture
Cell culture reagent/consumables suppliers can have good step by step recommendations for how to use their products. For example Thermo has some guidelines that you may find helpful. Specifically, cell culture maintenance would seem to be helpful.
These folks also have what superficially look like good resources.
Reviewing MC38 culture requirements is also always a good idea.
Good luck!


What are the functions of disulphide bonds? What are the functions of disulphide bonds between amino acids in proteins or peptides?

Disulphide bonds occur in proteins, not amino acids, although they involve a covalent bond between two amino acids (both cysteine).

The received wisdom is that disulphides are used as extra stabilisation of the structure of proteins which are secreted, or which have an extracellular domain. It's important to get hold of the idea that they do not occur in the cytoplasm, but are only formed in proteins which pass through the secretory pathway: they are formed in the endoplasmic reticulum (ER), and there are resident ER proteins (protein disulphide isomerases) whose function is to assist in their formation.

Classical examples of disulphide-bonded proteins are insulin (where the A and B chains are linked by disulphides) and immunoglobulin G where each Ig domain has an intradomain disulphide, and where the heavy chains are linked by disulphides. There are, of course, many others.

Cells also contain the tripeptide glutathione which includes a cysteine residue. the ratio of oxidised (disulphide bonded dimers) to reduced (monomers) glutathione helps to set the redox state of the cytoplasm and the lumen of the endoplasmic reticulum.


Did we evolve from monkeys? Since I was young, I always understood that evolution taught that we descended from monkeys (or apes, not too sure a distinction was ever made). However, someone recently told me that this isn't correct, and that we actually share a common ancestor, but not a direct line of evolution.

Can anyone clarify which approach (if either) is correct?

Assuming the latter is correct, doesn't it raise problems of missing fossils? If we descended from monkeys, there is less of a gap to fill, but if we share a common ancestor, we would need to fill a much bigger gap, right the way back to the point where our family trees diverged.

As I said, I don't know much about this, and find most of the online material too technical to understand. If anyone could explain this in simple terms, I would be very grateful.

Welcome to Biology.SE.

About your post

It is a very standard question and a common source of misunderstanding from the general public. If you just google do we descend from monkeys you will get tons of hits that will answer your question.

Because this question is introductory and has already received a lot of answers online, there is therefore no point for me to make a long and extensive answer here. I will just state the essentials and let you investigate it further through the multiple online sources that exists.

Note by the way, that if you want to get some introductory knowledge in evolutionary biology, you might want to have a look at a few course on Understanding Evolution by UC Berkley

The actual answer

In short, It makes no sense to say of any species that it descends from any other extant species. Two extant species share a common ancestor though. The Most Recent Common Ancestor (MRCA) is of particular interest. Following this logic, humans do NOT descend from modern days chimpanzee, but humans and chimpanzee have a common ancestor. Their MRCA was another ape, but not an ape that exists today (even though it may look like one).


Predators faking to be not hungry? I believe that there are predator/prey combinations where the prey can easily spot that the predator is not hungry and will not try to flee from it. I’m thinking, for example, of gazelles who will happily graze in sight of sleeping lions. (Please correct me if this is already wrong.)

It seems to be sensible (in an evolutionary sense) for the predator to not put unnecessary stress on the prey. First question: Are there predator who actively signal that they are not hungry, e.g. by a certain sound?

And my second question: Is there such a combination where the predator will, in times of severe hunger, pretend not to be hungry in order to more easily catch a prey?

I would suggest that the behaviour of the gazelles you are citing is perhaps over simplified. There will likely be temporal and spatial dynamics in their behaviour... Prey will probably spend more time concentrating on observation when they know there are predators around. There will also be likely peak times during which hunting occurs (in savannah systems it tends to be dawn and dusk) and prey would be more cautious at these times.

It seems to me that the prey would not be judging the hunger of the predators but instead they learn the consistent patterns in the level of risk associated with being near predators. This could be genetic in its cause. If there is a gene (or genes) which determine when a prey individual is most likely to be out in the open grazing then the higher probability of predation at certain times would reduce the frequency of the genes which cause that choice.

There could also be fluctuations over time as the predators learn that the prey have become less cautious, which then causes predators to take advantage of unsuspecting prey, which you might be interpreting as the "faking" behaviour... it is not a deliberate fake, more taking advantage of the risk taking behaviour of the prey (as time passes without attack they will become more brazen). To the best of my knowledge there are no examples of the deliberate fake but predator prey dynamics are not my specialism.

Overall, I think you are asking a question based on learning and information use of repetitive patterns in behaviour of predators by prey, and have interpreted these behaviours in an over complex way (see Occams Razor).


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

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.


What would happen if you slowly crushed a live brain? In a hypothetical scenario, if you cut open a person's skull to show the live brain, and then you slowly start to crush it..

At what point would the person loose consciousness?

What would the person be feeling all this time?

Would it cause pain?

It seems there's way too many variables here.  Crushing can occur in a number of ways, leading to different primary damage in different regions first and different people have a different level of system failure thresholds.

Technically, there are no pain sensors on the brain, so you wouldn't feel any pain in the classical sense.  However, it's hard to determine how you would affect the pain interpretation circuits (again, "crushing" can occur a number of different ways); you could inadvertently cause pain signals.

Losing consciousness would also depend on when what region of brian is crushed.  And how it's crushed.  Most of our higher processing regions associated with consciousness are on the very outer surface of our brain.  In one scenario, if it just gets compressed, and damage tend to accumulate in the center of the brain first, it would be a different outcome than if it was some kind of shear crushing force that damaged outer brian first.


Average Nucleus size of human skeletal muscle cell I’ve been struggling the last couple of days to find reliable data on the average nucleus size of a human skeletal muscle cell. If I deduce it from pictures it should be in the range of 20 micrometers long and 3 micrometers in diameter but I need reliable data and a proper source.

Could anyone help me with this?

The average "length" for normal human myonuclei is 11.75 µm according to the abstract for:

Watkins, S. C., & Culien, M. J. (1988). A quantitative study of myonuclear and satellite cell nuclear size in Duchenne's muscular dystrophy, polymyositis and normal human skeletal muscle. The Anatomical Record, 222(1), 6-11.

If you can get access to this paper it should have more information for you.


How might one determine if bacteria are nitrogen fixing or not? If you had an isolate bacteria sample how would you determine if they were nitrogen fixing?

Never mind found the answer myself you can use the acetylene reduction assay.