qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
17,057 | <blockquote>
<p>Also, transplants from one identical twin to another are <strong>almost never</strong> rejected.<br />
<sub>[ Source: <a href="http://www.nlm.nih.gov/medlineplus/ency/article/000815.htm" rel="nofollow noreferrer">Medline Plus</a> ]</sub></p>
</blockquote>
<p>Why can a tissue from an <em>identical</em> twin be rejected ?</p>
| [
{
"answer_id": 17068,
"pm_score": 2,
"text": "<p>MattDMo, I think you're right on. Also remember the <a href=\"http://en.wikipedia.org/wiki/Thymus\" rel=\"nofollow\">thymus</a> is where T-cell recombination and maturation occurs during fetal development, and rates are highest during neonatal period thr... | [
{
"answer_id": 17059,
"pm_score": 2,
"text": "<p>This was too long for a comment, but I have absolutely no evidence for what I'm about to say :)</p>\n\n<p>It looks like that sentence was a little bit of hand-waving, as the author didn't want to categorically state that identical twin tissue would <stron... |
17,065 | <p>In math, there are special numbers, like Pi (3.14159...) and e (2.71828...). In chemistry, there's numbers like avogadro's number (6.0221413e+23). For example a circle can be defined in terms of 2 * Pi.</p>
<p><strong>Are there any significant constant numbers in biology that define the shape of an organism</strong> (ex: mammal)? I'm talking about stuff like shoulder to hip ratio or length of an organism, etc? </p>
<p>Here's an example that came to mind - different fetuses developing into different organisms. Is there any constant that is the same for these at some stage of development? Like the ratio of head to tail?</p>
<p><img src="https://i.stack.imgur.com/Zc2Lj.gif" alt="enter image description here"></p>
| [
{
"answer_id": 17067,
"pm_score": 4,
"text": "<p>I don't know if this is what you mean, but take a look at <a href=\"http://bionumbers.hms.harvard.edu/\" rel=\"nofollow\">BioNumbers</a>.</p>\n\n<p>Also, mathematical constants like pi are different from physical constants. Mathematical constants are true... | [
{
"answer_id": 17088,
"pm_score": 2,
"text": "<p>I think you have the direction of causality reversed. Due to either physical, chemical or dynamical properties of cells and organisms, it would certainly be possible to see patterns of constants emerge when making some measurements. I don't think you can ... |
17,081 | <p>In his song <a href="https://www.youtube.com/watch?v=ESFANzZTdYM" rel="nofollow">Lullaby</a>, Tim Minchin <a href="https://www.youtube.com/watch?v=ESFANzZTdYM?t=57s" rel="nofollow">sings</a>:</p>
<blockquote>
<p>Your nappy is dry and your tummy is full<br>
Of enough antihistamine to chill out a bull<br>
Yet still all this gringing</p>
</blockquote>
<p>According to Wikipedia, antihistamines are used against allergies.</p>
<p>So, why is there antihistamine in his baby's tummy and why is it supposed to make her sleepy?</p>
| [
{
"answer_id": 17083,
"pm_score": 4,
"text": "<p>This song most likely refers to an <strong>off-label</strong> (<em>and usually <strong>inappropriate</em></strong>) use for certain antihistamines like <strong>Benadryl</strong>. They are sometimes used by parents to <strong>sedate their children</strong>... | [
{
"answer_id": 17082,
"pm_score": 2,
"text": "<p>This is not only happening in babies...\nIn short (I will look for some references later and edit the post) the antihistamines are effective in the whole body and block the histamines there. The antihistamines which cross the blood-brain barrier do the sa... |
17,104 | <p>I recently read about an experiment where they removed the dendrites and axons from rat neurons and placed them on a grid. After a while they started reconnecting and were able to learn things.</p>
<p>Since I'm trying to create a model simulating this, I'd like to know (as much as is needed to make it look at least a little bit realistic) how they reconnected. As far as I know some molecules are secreted attracting or repelling axon growth cones.</p>
<p>I think I can model that part, but the problem is that the axons can easily grow back to where they came from, so how do the axons in a brain 'know' they are not growing back to the neuron they originated from.</p>
| [
{
"answer_id": 17291,
"pm_score": 4,
"text": "<p>I think I can partially answer you question. As far as I'm aware, there are many surface receptor molecules such as ephrins that are responsible for axonal guidance and dendritic repulsion in developing organisms such as flies (Drosophila). As you can tel... | [
{
"answer_id": 17302,
"pm_score": 3,
"text": "<p>In cases of severe head injury where a large portion of neurons and their connections get shredded. I don't think a neuron would be very choosy when presented with quite a few axons and lots of intracellular fluid </p>\n\n<p>There are coup and the contra... |
17,159 | <p>What is the difference between transformation and transfection? How do both of these methods work?</p>
| [
{
"answer_id": 17161,
"pm_score": 4,
"text": "<p>If you are interested in the history of molecular biology this is an interesting question. </p>\n\n<p>Basically transformation came to be used to describe experiments in which the phenotype of an organism was changed by the uptake of DNA, and because of t... | [
{
"answer_id": 17160,
"pm_score": 2,
"text": "<p>As far as I know (and I haven't found no evidence against it) this is mostly a semantic difference. Both processes describe the addition of genetic material into cells using various techniques. </p>\n\n<p>Transformation is here mostly used for bacterial w... |
17,170 | <p>I am trying to determine the "translated" meanings (not seeking the common names) of different insects, (presently some bees and wasps). Does anyone know of a printed or internet resource that defines the various names. I have one for plants, but not for animals. Knowing the (English) meaning of the Latin / Greek/ etc. is often very informative -- IF I can find it. </p>
<p>I can give more specifics if you want.</p>
<p>Thanks.</p>
<p>Glen B
Olympia WA, USA</p>
| [
{
"answer_id": 17161,
"pm_score": 4,
"text": "<p>If you are interested in the history of molecular biology this is an interesting question. </p>\n\n<p>Basically transformation came to be used to describe experiments in which the phenotype of an organism was changed by the uptake of DNA, and because of t... | [
{
"answer_id": 17160,
"pm_score": 2,
"text": "<p>As far as I know (and I haven't found no evidence against it) this is mostly a semantic difference. Both processes describe the addition of genetic material into cells using various techniques. </p>\n\n<p>Transformation is here mostly used for bacterial w... |
17,185 | <p>I need to draw simple, phylogenetic tree for kids lecture. </p>
<p>I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should be based on how close those organisms are (I don't need genome alignments).</p>
<p>Similar figure producing tool would be perfect.
<img src="https://i.stack.imgur.com/rSi0A.jpg" alt="## Heading ##"></p>
| [
{
"answer_id": 20273,
"pm_score": 4,
"text": "<p>As per your requirements I will suggest:</p>\n\n<p><a href=\"http://www.onezoom.org/\" rel=\"nofollow noreferrer\">http://www.onezoom.org/</a></p>\n\n<p><img src=\"https://i.stack.imgur.com/4IXP7.jpg\" alt=\"\"></p>\n"
}
] | [
{
"answer_id": 20271,
"pm_score": 2,
"text": "<p>I don't know what background you have given the kids or what level, but here's something we do in a non-majors freshman level biology course that could easily be adjusted. First, to get them thinking about trees and relationships, give them a simple famil... |
17,186 | <p>What are the functions of disulphide bonds between amino acids in proteins or peptides?</p>
| [
{
"answer_id": 20273,
"pm_score": 4,
"text": "<p>As per your requirements I will suggest:</p>\n\n<p><a href=\"http://www.onezoom.org/\" rel=\"nofollow noreferrer\">http://www.onezoom.org/</a></p>\n\n<p><img src=\"https://i.stack.imgur.com/4IXP7.jpg\" alt=\"\"></p>\n"
}
] | [
{
"answer_id": 20271,
"pm_score": 2,
"text": "<p>I don't know what background you have given the kids or what level, but here's something we do in a non-majors freshman level biology course that could easily be adjusted. First, to get them thinking about trees and relationships, give them a simple famil... |
17,207 | <p>I was at the park lying on the grass and its the third time I have seen them, I used to think they were parasites when I was like 7. It is the very small brown worm on the green leaf. It moves by squiggling. It comes in different colors but same size.</p>
<p><a href="http://postimg.org/image/ea3x2nw95/" rel="nofollow">http://postimg.org/image/ea3x2nw95/</a>
<a href="http://postimg.org/image/zfawh9pr1/" rel="nofollow">http://postimg.org/image/zfawh9pr1/</a></p>
| [
{
"answer_id": 35153,
"pm_score": 2,
"text": "<p>For me it looks like an <a href=\"http://en.wikipedia.org/wiki/Geometer_moth\" rel=\"nofollow noreferrer\">inchworms</a> which are the larvae of geometer moth or Geometridae.</p>\n\n<p>By your picture it is almost impossible to see of which type it is.</p... | [
{
"answer_id": 17379,
"pm_score": 2,
"text": "<p>Is this what you mean? </p>\n\n<p><img src=\"https://i.stack.imgur.com/popbq.png\" alt=\"wireworm\"></p>\n\n<p>It's pretty hard to tell from this photo, and I'm no entemologist, but to me, it looks like it may be a <strong>wireworm</strong>, a larvae of a... |
17,213 | <p>There's undoubtedly more than one way to do this, but if a DIY biologist were to attempt to detect food fraud (e.g. as done by students from <a href="http://conservationmagazine.org/2008/09/impostor-fish/" rel="nofollow">Stanford University</a> and <a href="http://www.nytimes.com/2008/08/22/science/22fish.html?_r=0" rel="nofollow">Trinity School, Manhattan</a> with respect to fish samples from markets and sushi restaurants), then what would be the minimum steps and equipment?</p>
<p><em>(I know barely anything about molecular genetics, but have been reading about DremelFuge, OpenPCR, and Blue Transilluminator, and wondered whether they - or things like them - might get such an investigator some of the way towards the goal above; and what else would be required.)</em></p>
| [
{
"answer_id": 17221,
"pm_score": 4,
"text": "<p>There are several ways you could go about identifying species through DNA. If you want to do everything yourself, the simplest option in terms of equipment needed consists of evaluating fragment lengths observed during gel electrophoresis after amplifying... | [
{
"answer_id": 17267,
"pm_score": 1,
"text": "<p>This can in principle be done at least partly with DIY methods, by using PCR followed by gel electrophoresis. The DremelFuge, OpenPCR, and Blue Transilluminator would be the primary tools, along with pipettes, test tubes, autoclave (or equivalent), etc.</... |
17,245 | <p>If a person's head was cleanly and rapidly decapitated by a sharp blade slicing through the neck, such as would happen on the guillotine, could that person remain conscious? If so for how long? Long enough to be aware of (the head) falling down and hitting the ground? </p>
<p>Obviously it would be brief due to lack of blood supply, but it seems plausible that it could be a few seconds.</p>
<p>Or is there some inherent neurological shock due to the severing the top of the spinal cord that would cause near instantaneous loss of conciousness?</p>
<p>Could Marie Antoinette have seen her own severed neck from the basket below the blade?</p>
| [
{
"answer_id": 17247,
"pm_score": 4,
"text": "<p>According to <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029360/\">this</a>, in rats it takes about 17 seconds after decapitation for the EEG to become iso-electric. But there is no known correlation between EEG and consciousness. Also at 50-80... | [
{
"answer_id": 17263,
"pm_score": 0,
"text": "<p>I remember reading that during the French Revolution Antoine Lavoisier arranged with his assistant condemned to death to blink after the cut off if he still had conscience (Lavoisier was to call his name first to limit automatisms). He reported a possibil... |
17,246 | <p>It is obviously very onerous to generate heat at all, although it has advantages. We don't have to lie on the sun like a crocodile to get warmer. And we avoid the freezing of our body water by out own means. But wouldn't just a little of heat be enough? </p>
<p>Why do humans go as far as 37 C? Couldn't we just have a temperature of 10 C to avoid freezing but stay at it?</p>
| [
{
"answer_id": 17247,
"pm_score": 4,
"text": "<p>According to <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029360/\">this</a>, in rats it takes about 17 seconds after decapitation for the EEG to become iso-electric. But there is no known correlation between EEG and consciousness. Also at 50-80... | [
{
"answer_id": 17263,
"pm_score": 0,
"text": "<p>I remember reading that during the French Revolution Antoine Lavoisier arranged with his assistant condemned to death to blink after the cut off if he still had conscience (Lavoisier was to call his name first to limit automatisms). He reported a possibil... |
17,264 | <p>I couldn't seem to find one elsewhere, at least not with a scientific source.</p>
<p>It would seem as it's quite a striking feature there would be an advantage it would infer.</p>
| [
{
"answer_id": 17287,
"pm_score": 4,
"text": "<p>As your commenters have suggested, no.</p>\n\n<p>In order for an explanation to be a <strong>good</strong> evolutionary explanation, it needs to have a testable hypothesis and a mechanism to test it. </p>\n\n<p>The most common mechanism for testing the cr... | [
{
"answer_id": 17417,
"pm_score": 0,
"text": "<p>I quite like the explanation I found on the website of \"Exploring the BioEdge\". Robin and Honeybadger explain the black and white colouration as follows: To minimize the risk of being attacked by the tiger, the colouration of the giant panda is aposemat... |
17,276 | <p>There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a experiment through which we would be able to identify specific Gs or Gi proteins in cell lines?</p>
| [
{
"answer_id": 17414,
"pm_score": 3,
"text": "<p>Bez experiments are too difficult and costly you don't need to do that.</p>\n\n<p>Take, label samples then apply ligands and sustenance. The inhibitory will have have a slower rate of <strong><em>growth</em></strong> not death and use a control with repli... | [
{
"answer_id": 17337,
"pm_score": 2,
"text": "<p>EDITED ANSWER</p>\n\n<p>Based on comments and responses my original answer to this question received I have decided to edit the answer and respond to some questions.</p>\n\n<p>Since I work on proteins, I tend to favour protein based approaches specially w... |
17,320 | <p>I thought that the definition of a definitive host was that the parasite had to sexually reproduce in that particular host. </p>
<p>I've been told that mosquitoes are the definitive host for the plasmodium parasite, but I thought that the fertilization (and thus the sexual reproduction) takes place in the human?</p>
| [
{
"answer_id": 17321,
"pm_score": 4,
"text": "<p><em>Plasmodium falciparum</em> (the main causative agent of malaria) and other <em>Plasmodium</em> species have a very complex life cycle, with stages in the female host <a href=\"http://en.wikipedia.org/wiki/Anopheles\" rel=\"nofollow noreferrer\"><em>An... | [
{
"answer_id": 56874,
"pm_score": 0,
"text": "<p>The answer contains a lot of information, some incorrect, and does not answer the question.</p>\n\n<p>The mosquito is the definite host of plasmodium, despite the humanocentric way this parasite is always looked at.</p>\n\n<p>What happens in the human is ... |
17,370 | <p>An <a href="https://pets.stackexchange.com/questions/3159/what-is-an-acceptable-flea-treatment-for-kittens/3176#3176">answer at Pets</a> suggested using dawn dish soap to kill fleas. I did a little looking around, and found several references supporting the idea. Most of what I found was in 'selfhelp' and 'save a dime' type books and web sites. So while it seems to be a popular idea, I am unsure if it is an effective idea.</p>
<p>Is there any reliable science supporting the use of dish soap to kill fleas and/or ticks? If so what points in the life cycle would it be effective? If it does work, how often would I need to use it to be relatively sure all the fleas/ticks have been through the appropriate life cycle and are dead?</p>
| [
{
"answer_id": 17477,
"pm_score": 5,
"text": "<p>First part of the answer - Yes fleas (Siphonaptera) can be drowned. But not as easily as the internet would lead you to believe.</p>\n\n<p>There are many claims on the internet (and printed works) expounding on how simple it is to drown fleas. The best s... | [
{
"answer_id": 37134,
"pm_score": 2,
"text": "<p>You have to use Lemon Dawn specifically because they have <a href=\"https://en.m.wikipedia.org/wiki/Limonene\" rel=\"nofollow noreferrer\">Limonene</a> and <a href=\"https://en.m.wikipedia.org/wiki/Linalool\" rel=\"nofollow noreferrer\">Linalool</a> from ... |
17,441 | <p>It is said that genes define how we look physically and psychologically; so for example if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female, and a finite total available. Could there be people identical in appearance if the same genetic combinations recur?</p>
<p>Also we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?</p>
<p>Please correct my biology and share the possiblity of having genetically identical people across different geographic locations.</p>
| [
{
"answer_id": 17478,
"pm_score": 3,
"text": "<p>For ease of explanation let me first tell you that the \"genetic makeup\" is called \"genotype\" and that \"how we look physically and psychologically\" is known as \"phenotype\". These are not complete definitions of the terms but this should help you un... | [
{
"answer_id": 17475,
"pm_score": 1,
"text": "<blockquote>\n <p>It is said that genes define how we look physically and psychologically</p>\n</blockquote>\n\n<p>I would be skeptical of anyone saying this. Nature vs. nurture is far from settled, especially in psychology. The trend seems to be that many ... |
17,498 | <p>I am wondering exactly what a-fib is (causes and symptoms).
<p>
I would really appreciate having a sample of an EKG with it (because in my limited research, I have found it nearly impossible to find just a sample piece of an EKG that has a-fib on it) with your answer, so I can actually get an idea of what it looks like. With the sample EKG, I would love to have a normal one beside it so I can kind of analyze the differences between the two.</p>
<p><strong>Note:</strong> This is not and never was a homework question! </p>
| [
{
"answer_id": 17555,
"pm_score": 4,
"text": "<p>A human heart can be viewed as 2 hearts, the left and the right heart, each consisting of an atrium and a ventricle. The atrium's function is to fill the ventricle with as much blood as it can and the ventricle then pump the blood away. Also there is a sy... | [
{
"answer_id": 27565,
"pm_score": 2,
"text": "<p>Remember that except for the concluding pathway through the A-V bundle, the atrial muscle mass is separated from the ventricular muscle mass by fibrous tissue. Therefore, ventricular fibrillation.</p>\n\n<p>The mechanism of atrial fibrillation, except tha... |
17,532 | <p>The Price equation describes mathematically the evolution of a population of units from one generation to the next. </p>
<blockquote>
<p>$\bar{w}\Delta \bar{z}$ = $Cov (w_i,z_i) $+$ E(w_i\Delta z_i)$</p>
</blockquote>
<p>I would like to know how to actually employ the equation to some data. Perhaps a simple online "walk-through" type guide of the Price equation would help. It should simply show the calculation of the Price equation using numbers from an example population. For example, I'd like to see how the Price equation is applied to the following scenario:</p>
<blockquote>
<p>A population, $P$, of 5 individuals reproduces to produce population
$P'$. </p>
<p>The trait value of the $i^{th}$ individual is $z_{i}$ where $z_1$,
$z_2$ and $z_3$ all = 1 and where $z_4$ and $z_5$ both = 2 and $\bar{z}$ = 1.4. </p>
<p>Absolute fitness is $w_i$ for the $i^{th}$ individual where $w_1$,
$w_2$ and $w_3$ all = 1, and $w_4$ and $w_5$ both = 5. </p>
<p>Relative fitnesses, $\omega_i$, are $\omega_{z=1}$ = 0.077, and $\omega_{z=2}$ = 0.385.</p>
<p>Thus the population $P'$ has $n$ = 13, with 3 individuals where $z$ = 1
and 10 individuals where $z$ = 2 and $\bar{z}'$ = 1.769. </p>
<p>$\Delta z $ is the transmission bias and is equal to 0 in this case
(perfect transmission of the trait score $z$)</p>
<p>The value $\Delta \bar{z}$ = $Cov (w,z)/ \bar{w}$ = ....</p>
</blockquote>
<p>Here's an R script to create the above information:</p>
<pre><code># Define two trait values:
z1 = 1
z2 = 2
# Define two fitness values:
w1 = 1
w2 = 5
# Set number of units possesing each trait in P population:
n1 = 3
n2 = 2
# Create data
df = data.frame(c(rep(z1,n1),rep(z2,n2)),c(rep(w1,n1),rep(w2,n2)))
colnames(df) = c("z","w")
df$omega = df$w / sum(df$w)
n_P = length(df$z)
n_O = sum(df$w)
z_P_bar = mean(df$z)
z_O_bar = sum(df$w*df$z) / sum(df$w)
omega_z1 = mean(df$omega[df$z==z1])
omega_z2 = mean(df$omega[df$z==z2])
# Parental population size:
n_P
# Offspring population size:
n_O
# Parental mean trait:
z_P_bar
# Offspring mean trait:
z_O_bar
# Realtive fitnesses:
omega_z1
omega_z2
</code></pre>
| [
{
"answer_id": 17560,
"pm_score": 3,
"text": "<p>Here is a simple example using your data in which both terms of the Price equation are needed, since the value of the character for $z_2 $ changes in the second generation. I used your suggested change $z_2'=(9\\cdot 2 + 1\\cdot 3)/10 = 2.1$. </p>\n\n<p>T... | [
{
"answer_id": 17533,
"pm_score": 2,
"text": "<p>This is a nice numerical walk-through and explanation, see this <a href=\"http://www.tedpavlic.com/post_price_equation.php\" rel=\"nofollow noreferrer\">webpage</a>.</p>\n<p>As requested I've sketched out a solution to the specific case above.</p>\n<p>A n... |
17,539 | <p>I fail to see how natural selection can build any kind of new functionality.</p>
<p>New functionality in a design requires sacrificing a complex series of meanwhile useless steps before the new functionality works and becomes advantageous.</p>
<p>For example, if I want to upgrade a stationary chair to a wheelchair, there are many intermediate steps that must be done (which are not advantageous) before the added functionality becomes advantageous.</p>
<p>If a human being sits there and tries to intelligently assemble the wheelchair in such a way that it will be advantageous at each step, he will not be able to do it. it just doesn't work like this.</p>
<p>Can someone fill me in as to how this works and whether there have been experiments that demonstrate this, for example, having someone assemble a simple functional design with the limitation that every few step adds advantageous functionality.</p>
| [
{
"answer_id": 17560,
"pm_score": 3,
"text": "<p>Here is a simple example using your data in which both terms of the Price equation are needed, since the value of the character for $z_2 $ changes in the second generation. I used your suggested change $z_2'=(9\\cdot 2 + 1\\cdot 3)/10 = 2.1$. </p>\n\n<p>T... | [
{
"answer_id": 17533,
"pm_score": 2,
"text": "<p>This is a nice numerical walk-through and explanation, see this <a href=\"http://www.tedpavlic.com/post_price_equation.php\" rel=\"nofollow noreferrer\">webpage</a>.</p>\n<p>As requested I've sketched out a solution to the specific case above.</p>\n<p>A n... |
17,541 | <p>I'm planning to scale up a PCR reaction, and I'm wondering if filling the PCR tubes to the maximum volume of 200 ul would be a problem. It would mean a lot less pipetting as I would only need 1/4 of the tubes.</p>
<p>The typical protocols I've seen always use 50 ul for a PCR reaction, I'm wondering if there are any issues with larger volumes, e.g. differences in heat transfer, that could cause issues if I scale up the volume in one tube.</p>
<p>Is scaling up the volume problematic? Any specific aspects I should consider?</p>
| [
{
"answer_id": 17560,
"pm_score": 3,
"text": "<p>Here is a simple example using your data in which both terms of the Price equation are needed, since the value of the character for $z_2 $ changes in the second generation. I used your suggested change $z_2'=(9\\cdot 2 + 1\\cdot 3)/10 = 2.1$. </p>\n\n<p>T... | [
{
"answer_id": 17533,
"pm_score": 2,
"text": "<p>This is a nice numerical walk-through and explanation, see this <a href=\"http://www.tedpavlic.com/post_price_equation.php\" rel=\"nofollow noreferrer\">webpage</a>.</p>\n<p>As requested I've sketched out a solution to the specific case above.</p>\n<p>A n... |
17,565 | <p>I am a bit confused with the notion that "<strong>walking after meals helps you in digestion</strong> ", </p>
<p>Some say that it helps, whereas others oppose it. Can someone come up with a valid explanation for this?</p>
| [
{
"answer_id": 17566,
"pm_score": 4,
"text": "<p>apparently walking helps in the movement of food into the stomach and improves digestion. Also helps in decreasing blood sugar after meals, which decreases cardiovascular risk and potential signal diabetes by helping muscles absorb glucose in the blood. H... | [
{
"answer_id": 35432,
"pm_score": 2,
"text": "<p>Well it depends what you mean by helping digestion. </p>\n\n<p>This <a href=\"https://skeptics.stackexchange.com/posts/11169/edit\">answer</a> in skeptics may shade some light:</p>\n\n<blockquote>\n <p><b>a walk after my lunch [is] a healthy habit that h... |
17,568 | <p>To what extent do brains (e.g. of humans) contain <a href="http://en.wikipedia.org/wiki/Recurrent_neural_network">recurrent </a> connections? </p>
<p>I am studying artificial neuronal networks and frequently encountered the statement, that recurrent neural networks are closer to biological neuronal networks than for example <a href="http://en.wikipedia.org/wiki/Feedforward_neural_networks">feed forward networks</a>. But I didn't find information on the question if feed forward or recurrent architectures dominate the brain architecture.</p>
| [
{
"answer_id": 17569,
"pm_score": 4,
"text": "<p>The recurrent patterns of connections in a network are known as network motifs.</p>\n\n<p>You can check <a href=\"http://www.sciencemag.org/content/298/5594/824.full\">this</a> paper out. They have identified common network motifs in different types of re... | [
{
"answer_id": 20766,
"pm_score": 2,
"text": "<p>Ok, let's talk about mammalian neocortex rather than about the entire central nervous system.</p>\n\n<p>The vast majority of synapses within the cortex are formed between neurons within the same cortical area (<a href=\"http://dx.doi.org/10.1523/JNEUROSCI... |
17,591 | <p>If the squamous (top) layer of epidermis, or skin, is burned or damaged in another way, will it then be replaced by the next layer of below?</p>
<p>Also, from where does the basal membrane originate? Does it regenerate from a different layer of cells? </p>
| [
{
"answer_id": 17654,
"pm_score": 3,
"text": "<p>The epidermis is a four- or five-layered epithelium. The top layers are squamous whereas the bottom ones are more columnar (<a href=\"http://en.wikipedia.org/wiki/Epidermis_(skin)\" rel=\"nofollow noreferrer\">http://en.wikipedia.org/wiki/Epidermis_(skin)... | [
{
"answer_id": 17655,
"pm_score": 2,
"text": "<p>It would first be good to look at the <a href=\"http://www.webmd.com/skin-problems-and-treatments/picture-of-the-skin\" rel=\"nofollow noreferrer\">different layers within the skin </a> as you mentioned in your question. </p>\n\n<blockquote>\n <p>The sk... |
17,597 | <p>Quoting from : Scientific American July 1975 <em>The Manipulation of genes</em> by Stanley Cohen :</p>
<blockquote>
<p>Restriction endonucleases (and modification methylases) are widespread
in microorganisms; genes for <strong>making</strong> them were found on <strong>viral
chromosomes</strong> and extrachromosomal plasmid DNA as well as on many
bacterial chromosomes.</p>
</blockquote>
<p>Why would the genes for making RE be found on viral chromosomes ? Also, could you give some examples where they are found on plasmids ?</p>
| [
{
"answer_id": 17654,
"pm_score": 3,
"text": "<p>The epidermis is a four- or five-layered epithelium. The top layers are squamous whereas the bottom ones are more columnar (<a href=\"http://en.wikipedia.org/wiki/Epidermis_(skin)\" rel=\"nofollow noreferrer\">http://en.wikipedia.org/wiki/Epidermis_(skin)... | [
{
"answer_id": 17655,
"pm_score": 2,
"text": "<p>It would first be good to look at the <a href=\"http://www.webmd.com/skin-problems-and-treatments/picture-of-the-skin\" rel=\"nofollow noreferrer\">different layers within the skin </a> as you mentioned in your question. </p>\n\n<blockquote>\n <p>The sk... |
17,599 | <p>I'd appreciate some help identifying these three corvids I photographed in Austria during the Summer:</p>
<p><a href="https://i.stack.imgur.com/AIyuO.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/AIyuO.jpg" alt="corvids"></a></p>
<p>I know identifying corvids can be difficult and I'm not an ornithologist -- just an amateur bird watcher. After looking through many images of various crow species and their hybrids, I've tentatively identified these as:</p>
<ol>
<li>Carrion crow (<em>Corvus corone</em>)</li>
<li>Carrion crow × Hooded crow (<em>Corvus corone × Corvus cornix</em>)</li>
<li>Carrion crow × Hooded crow (<em>Corvus corone × Corvus cornix</em>)<br>
I initially believed this to be a Hooded crow (<em>Corvus cornix</em>), but the broken coloration on the wings made me think it might actually be a hybrid as well.</li>
</ol>
<p>Can someone here either confirm my identification or provide a more informed identification?</p>
| [
{
"answer_id": 60503,
"pm_score": 4,
"text": "<h1>1. <strong>Carrion crow</strong> (<a href=\"https://en.wikipedia.org/wiki/Carrion_crow\" rel=\"noreferrer\"><em><strong>Corvus corone</strong></em></a>)</h1>\n<p><a href=\"https://i.stack.imgur.com/fl9tJm.jpg\" rel=\"noreferrer\"><img src=\"https://i.sta... | [
{
"answer_id": 21355,
"pm_score": 3,
"text": "<p>The first 2 are correct.\nThe third one is actually a hooded crow. The different color of the wing depends on the generation of feathers. Feathers of different generations (changed during different time) are abraded (used) in a different way. The wing fea... |
17,629 | <p>For maggot therapy, how are maggots disinfected? I'd imagine there's a limited scope of measurements that can be taken to sterilize the maggots - i.e. we don't want to sterilize them and kill them too. </p>
| [
{
"answer_id": 17793,
"pm_score": 5,
"text": "<p><strong>History</strong></p>\n<p><a href=\"http://en.wikipedia.org/wiki/Ambroise_Par%C3%A9\" rel=\"noreferrer\">Ambroise Paré</a> is credited with being the first to note his observations on <a href=\"http://en.wikipedia.org/wiki/Maggot_therapy\" rel=\"no... | [
{
"answer_id": 17792,
"pm_score": 3,
"text": "<p>There is an interesting and authoritative paper on rearing of larvae of blue bottle flies for debridement purposes, cited below. </p>\n\n<blockquote>\n <p>Essentially the eggs are disinfected (rinsed) using .25 % chloramine solution (NH2Cl), then the lar... |
17,631 | <p>I have been wondering why would insects in general, not be scared when important changes happen on your monitor where they have landed...</p>
<p>If you move even just a finger, they are <em>scared to death</em> and fly away, but anything on my monitor and they remain completely placid.</p>
| [
{
"answer_id": 28251,
"pm_score": 5,
"text": "<p>Flies see motion. When the monitor screen changes, the visible spectrum of the pixel is changing and nothing is moving.</p>\n\n<blockquote>\n <p>Flies have limited color vision. Each color has its own wave frequency, but flies have only two kinds of colo... | [
{
"answer_id": 50671,
"pm_score": 1,
"text": "<p>Flies monitor the space above them:</p>\n\n<p>Flies have a very strong innervation of the back of the head, which contacts the surface ( <a href=\"http://flybase.org/reports/FBim0000875.html\" rel=\"nofollow\">http://flybase.org/reports/FBim0000875.html</... |
17,741 | <p>Wikipedia says Caliciviridae Family.
My notes say that Norovirus includes the following</p>
<p>Noroviruses</p>
<ul>
<li>Norwalk-like viruses</li>
<li>Caliciviruses</li>
<li>Astroviruses and some small gastroenteroviruses</li>
</ul>
<p>which is a larger definition including at least two families than the Wikipedia definition.
I think </p>
<ul>
<li>Caliciviruses $\subset$ Caliciviridae </li>
<li>Astroviruses and some small gastroenteroviruses $\subset$ astroviridae</li>
</ul>
<p>so the note is taking subsets among different families and classifying them into abstract class called <strong>Noroviruses</strong>.</p>
<p><strong>Extension based by Chris' excellent <a href="https://biology.stackexchange.com/a/17744/86">answer</a>.</strong></p>
<p>Criteria of Noroviruses</p>
<ul>
<li>(+)sense ssRNA viruses</li>
<li>Structure and replication:
<ul>
<li>1) only (+)sense ssRNA, </li>
<li>2) simple nucleocapsid viruses, </li>
<li>3) only viruses transmitted by fecal-oral route, </li>
<li>4) size about 30 nm in diameter. </li>
</ul></li>
</ul>
<p>and then final classification of Noroviruses by these criteria</p>
<p>Noroviruses</p>
<ul>
<li><strong>Noroviruses</strong> $\subset$ Norwalk-like viruses ($\subset$ F. Caliciviruses)</li>
<li>Some Astroviruses ($\subset$ F. astroviridae) and some small gastroenteroviruses (what?)</li>
</ul>
<p>which, however, does not make sense since Caliciviridae $\not\subset$ Astroviridae.
I do not understand what is the point of referring to the viruses by the sentence</p>
<blockquote>
<p>Astroviruses and some other round/small gastroenteris viruses</p>
</blockquote>
<p>which are not part of Astroviridae.</p>
<p><strong>Which viruses of Caliciviridae are similar to <em>Astroviruses that are apparently round and small gastroenteritis viruses</em>?</strong></p>
| [
{
"answer_id": 17744,
"pm_score": 4,
"text": "<p>You are mixing different things here: Virus are grouped based on their genetic material (dsDNA, ssDNA ssRNA and so on) into several groups (see <a href=\"http://en.wikipedia.org/wiki/Virus_classification\">here</a> for details), then grouped into families... | [
{
"answer_id": 17752,
"pm_score": 1,
"text": "<p>I take <a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi\" rel=\"nofollow\">NCBI's taxonomy</a> any day over what wikipedia says. According to NCBI Caliciviridae includes Lagovirus, Nebovirus, Norovirus, Recovirus, Sapovirus, Vesivirus, Se... |
17,742 | <p>Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is the problem of infering the original protein from its constituent peptides.
Why is this digestion step needed when you have to go back to protein level ? Is it just technological limitation? </p>
| [
{
"answer_id": 19139,
"pm_score": 1,
"text": "<p>I found the answer to my own question\nIt was formulated in a Nature publication by Mathias Mann (Title: The ABC's (and XYZ's) of peptide sequencing), a pope in Proteomics:</p>\n<blockquote>\n<p>Why are peptides, and not proteins, sequenced?</p>\n<p>After... | [
{
"answer_id": 17743,
"pm_score": 2,
"text": "<p>This is going to be a very long answer but to give a short response.</p>\n\n<p>You have to consider that MS for peptide detection works on the bases/principle of mass to charge (m/z) to detect an AA molecule, which is then normalised and analysed etc etc ... |
17,799 | <p><strong>Background</strong></p>
<p>The standard definition of species refers to the concept of <a href="http://simple.wikipedia.org/wiki/Reproductive_isolation" rel="nofollow noreferrer">reproductive isolation</a>. If two lineages are found to be reproductively isolated, then we consider these two lineages to belong to different species. My question concerns evolved reproductive isolation in Drosophila sp. following labs due to experimental evolution.</p>
<p><strong>Question</strong></p>
<p>Have we ever demonstrated that two Drosophila sp. lineages that could initially interbreed (in nature or in labs) evolved through artificial selection (and drift and mutations) in labs to finally not be able to interbreed anymore either due pre- or post- zygotic isolation (see <a href="http://en.wikipedia.org/wiki/Reproductive_isolation" rel="nofollow noreferrer">wiki</a>)? Or, in other words, have we ever demonstrated that two drosophila lineages evolved to become different species (reproductive isolation definition) in labs experiments?</p>
<p>If not, have we ever observed some partial reproductive isolation such as inbreeding depression for example?</p>
<hr>
<p>Note: This question is motivated by @LotusBiology that could not receive the answers she/he was waiting for because he/she failed to ask questions that are possibly answerable! So I wanted to ask this question that somehow addresses <a href="https://biology.stackexchange.com/questions/17736/if-evolution-is-true-how-would-you-explain-the-fruit-fly-experimentations">this</a> question he/she asked (now on-hold)</p>
<p>For more information about the concept of species, please have a look at <a href="https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species">How could humans have interbred with Neanderthals if we're a different species?</a></p>
| [
{
"answer_id": 17801,
"pm_score": 5,
"text": "<p>Rice and Salt$^1$ bred fruit flies for 35 generations and from one line of flies created two groups that were isolated from each other reproductively. They could not interbreed because they no longer bred in the same environment. Depending on one's defini... | [
{
"answer_id": 17819,
"pm_score": 3,
"text": "<p>Diane Dodd's experiments on Drosophila pseudoobscura would be another example of lab-based speciation. </p>\n\n<p><a href=\"http://www.jstor.org/stable/2409365?__redirected\" rel=\"noreferrer\">http://www.jstor.org/stable/2409365?__redirected</a></p>\n\n<... |
17,823 | <p>I read about this <a href="http://www.instructables.com/id/Mosquito-trap-mosquito-abortion-clinic-or-source-t/">idea for a mosquito trap</a> (with a rather tactless name) where the idea seems to be that because the water available for the mosquito eggs is so shallow, they will die somehow or not be viable. Mosquitos are pretty small though, wouldn't they not need much water for the eggs to hatch?</p>
| [
{
"answer_id": 17824,
"pm_score": 4,
"text": "<p>Many mosquitoes, such as Culex quinquefasciatus, lay their eggs on the surface of fresh or stagnant water. The water may be in tin cans, barrels, horse troughs, ornamental ponds, swimming pools, puddles, creeks, ditches, catch basins or marshy areas. Mosq... | [
{
"answer_id": 77062,
"pm_score": 0,
"text": "<p>I have them in my property breeding in my containers all the time. From a few inches gets the best results (more mosquitoes) but I’ve gotten colonies in water up to 2-3’ deep. </p>\n"
}
] |
17,840 | <p>In the resting membrane potential of neurons the inside of membrane is kept negative and outside of membrane is kept positive by the utilization of energy through Na-K Atpase pump, While during action membrane potential through the opening of specific gated ion channels inside of membrane is made positive while outside is made negative, What is the significance of specific charges across the membrane, does these specific charges across the membrane play any role in the passage of neurotransmitters ? or these charges are just arbitrary ?does this can happen that during resting membrane potential the inside will become positive and outside will become negative and vice versa, I want to know that what is the significance of these specific charges across the membrane ..?</p>
| [
{
"answer_id": 17824,
"pm_score": 4,
"text": "<p>Many mosquitoes, such as Culex quinquefasciatus, lay their eggs on the surface of fresh or stagnant water. The water may be in tin cans, barrels, horse troughs, ornamental ponds, swimming pools, puddles, creeks, ditches, catch basins or marshy areas. Mosq... | [
{
"answer_id": 77062,
"pm_score": 0,
"text": "<p>I have them in my property breeding in my containers all the time. From a few inches gets the best results (more mosquitoes) but I’ve gotten colonies in water up to 2-3’ deep. </p>\n"
}
] |
17,845 | <p>There are many combination vaccines available but I've noticed that there don't seem to be any with both live and non-live components, e.g. DTaP/IPV/MMR. Such combinations could be useful in some cases, since most developed countries give a second dose of MMR (or MMRV) at the same time as DTaP/IPV. Is there a biological reason that this is difficult?</p>
| [
{
"answer_id": 20110,
"pm_score": 4,
"text": "<p>First let me point out that for the US, I'm not knowledgeable enough to speak for the rest of the world, you are correct.</p>\n\n<hr>\n\n<p><strong>There are no approved live attenuated vaccines mixed with componet/subunit/inactivated vaccines.</strong></... | [
{
"answer_id": 20059,
"pm_score": 3,
"text": "<p>The major reason for this are differences in the preparation methods. <a href=\"http://en.wikipedia.org/wiki/Attenuated_vaccine\">Live (attenuated) vaccines</a> need permanent cooling, which makes their use in third world countries difficult. </p>\n\n<p><... |
17,899 | <p>Some <em>Aspergillus</em> species appear to like walnuts. My question concerns the association of <em>Penicillium</em> and <em>Aspergillus</em>. No sooner does <em>Aspergillus</em> colonize a walnut (or some other challenging carbon source) than <em>Penicillium</em> seems to move in, eventually killing the <em>Aspergillus</em> colony.</p>
<p>A totally unscientific guess is that <em>Aspergillus</em> is a good colonizer and <em>Penicillium</em> a good opportunist and that this is a common pattern with these two species. Is there any science in this direction? I do recall a sort of well-known picture from an old text in which <em>Penicillium</em> is shown more or less strangling a species of <em>Aspergillus</em>. I didn't think about it much at the time. </p>
<p>The image attached is not very incriminating but the theme is the same. <em>Penicillium</em> are the green hand-like structures strewn about the clover-like <em>Aspergillus.</em> Foot-cell of the latter cropped. </p>
<p>This seems like a simple question but a quick search doesn't reveal a lot, I think in part because this would generally come up as a contamination issue. </p>
<p><img src="https://i.stack.imgur.com/hJwq7.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 17901,
"pm_score": 4,
"text": "<p>It is hard to find any articles on the <em>association</em> between <em>Penicillium</em> and <em>Aspergillus</em> species, although they are both considered <a href=\"http://www.jiaci.org/issues/vol18issue3/2.pdf\" rel=\"noreferrer\">two of the most commo... | [
{
"answer_id": 40652,
"pm_score": 2,
"text": "<p>A year after the fact I found a short passage in Thom and Raper's 1945 text, <em>Manual of the Aspergilli.</em> At page 59 the authors relate that <em>Aspergillus niger</em> colonies are commonly overrun with <em>Penicillium rugulosum</em> which \"winds i... |
17,902 | <p>Some peppers, such as the <a href="https://en.wikipedia.org/wiki/Habanero_chili">habanero</a> or <a href="https://en.wikipedia.org/wiki/Carolina_Reaper">Carolina reaper</a> are extremely spicy, and when eaten in larger amounts than one is accustomed to, can cause some discomfort.</p>
<p>I've also heard anecdotes claiming that pepper spray, if applied with sufficient intensity, can cause death.</p>
<p>What if you were to eat as many spicy peppers as possible, despite the noxious taste? Is it possible to commit suicide in this way (and what would the cause of death)? Would you faint from excessive mouth pain? Would uncontrollable vomiting prevent you from consuming further peppers?</p>
| [
{
"answer_id": 17903,
"pm_score": 5,
"text": "<p>The more "dangerous" properties of spicy peppers are chiefly due to capsaicin.</p>\n<p>Sigma-Aldrich sells <a href=\"http://www.sigmaaldrich.com/catalog/product/sigma/m2028?lang=en&region=US\" rel=\"noreferrer\">purified capsaicin</a>, for w... | [
{
"answer_id": 17910,
"pm_score": -1,
"text": "<p>If you have cardiovascular problems, then it should be quite possible for the pain cause by spicy peppers to trigger a heart attack via a spike in blood pressure. A similar scenario might occur with respiratory diseases. And of course an anaphylactic sho... |
17,924 | <p>I have a question about cancer cure statistics. Many of the cancer literature or databases I have come across speak about 5 year or 10 year survival rates. In this case survival means that the patient with cancer is still alive 5 or 10 years after diagnosis. I am in need of references about the statistics which explain what is the percentage of people in these groups who are in progression-free survival group and disease-free survival group. That is for instance among the cancer patients which survive for some X years, who are completely cured of cancer (which means that the cancer is completely cured and has not reoccured with in this X years). </p>
<p>Update: USA data is preferred</p>
<p>Thanks</p>
| [
{
"answer_id": 17903,
"pm_score": 5,
"text": "<p>The more "dangerous" properties of spicy peppers are chiefly due to capsaicin.</p>\n<p>Sigma-Aldrich sells <a href=\"http://www.sigmaaldrich.com/catalog/product/sigma/m2028?lang=en&region=US\" rel=\"noreferrer\">purified capsaicin</a>, for w... | [
{
"answer_id": 17910,
"pm_score": -1,
"text": "<p>If you have cardiovascular problems, then it should be quite possible for the pain cause by spicy peppers to trigger a heart attack via a spike in blood pressure. A similar scenario might occur with respiratory diseases. And of course an anaphylactic sho... |
17,926 | <p>I received a gift that is a jug of Pure Mexican Vanilla. Having never dealt with large quantities of vanilla, it made me curious as to what would happen if a person had too much vanilla.</p>
<p>I understand that the alcohol has a higher toxicity rate and is probably more fatal than the actual vanilla itself, but I'm curious as to what ratio of mass of pure vanilla to mass of the human would be considered fatal.</p>
<p>Also, what is the physiological effect of a vanilla overdose as it pertains to inhibiting critical bodily functions? That is -- specifically what about a vanilla overdose would cause fatality?</p>
| [
{
"answer_id": 17928,
"pm_score": 5,
"text": "<p>Vanillin is the chemical that gives vanilla its flavour and smell <sup>[1]</sup>.</p>\n\n<blockquote>\n <p>Vanillin is pharmacologically active, causing depressed blood pressure, increased respiratory rate & death due to cardiovascular collapse <sup>... | [
{
"answer_id": 17927,
"pm_score": 2,
"text": "<p>Out of interest, I've had a look around a bit and it seems like the most dangerous part of that bottle might be the alcohol.</p>\n\n<p>According to the <a href=\"http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=169.3\" rel=\"nofoll... |
17,980 | <p>In a documentary on fitness I saw it was stated that women can't get big like men because of their low concentration of testosterone. If it is true that women have testosterone, where is it made? Why do some women, especially later in life, develop facial hair (though obviously not as much as men)? Do men also have "female" hormones in their body? </p>
| [
{
"answer_id": 17981,
"pm_score": 5,
"text": "<p>Yes, they do. The ovaries produce both testosterone and estrogen. Relatively small quantities of testosterone are released into your bloodstream by the ovaries and adrenal glands. Sex hormones are involved in the growth, maintenance, and repair of reprodu... | [
{
"answer_id": 19328,
"pm_score": 1,
"text": "<p>Healthy young males have estradiol levels in the area of 20-30 pg/ml.\nAlso, estrogen is a group of hormones, including estradiol and estrone for example. You shouldn't think of any hormones as women hormones or men hormones really, as both genders have t... |
18,987 | <p>Guanidium salts like (G-isothiocyanate) disrupt the hydrophobic interactions inside a protein or nucleic acid and denature it. What happens when hydrophobic interactions in DNA are broken? (I don't think it should get ssDNA because guanidium doesn't break hydrogen bonds within molecules)</p>
| [
{
"answer_id": 18989,
"pm_score": 3,
"text": "<p>Guanidium is a chaotrope i.e it increases the entropy in the solution. It doesn't <em>disrupt</em> hydrophobic interactions. Guanidium and urea act by forming hydrogen bonds. They can bond with both the dissolved macromolecule and water. The water molecul... | [
{
"answer_id": 18990,
"pm_score": 2,
"text": "<p>It is important to realize that the hydrophobic effect is largely due to the exclusion of water from non-polar surfaces, which increases entropy. This effect is a major contributor to the helical structure of DNA, which effectively brings the bases closer... |
19,002 | <p>Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.</p>
| [
{
"answer_id": 19003,
"pm_score": 3,
"text": "<p>The paper titled <a href=\"http://jcs.biologists.org/content/119/5/858.full\" rel=\"nofollow\">Identification of α-tubulin as a granzyme B substrate during CTL-mediated apoptosis</a> mentions it as 51KDa and the paper titled <a href=\"http://www.nature.co... | [
{
"answer_id": 19004,
"pm_score": 2,
"text": "<p>This is not so easy to answer, since alpha-tubulin has at 10 known genes in this family (data from <a href=\"http://www.ensembl.org/Homo_sapiens/Gene/Family/Genes?cdb=compara;db=core;family=ENSFM00250000000217;g=ENSG00000167552;r=12:49578579-49583107\" re... |
19,013 | <p>Why are some neurons tetraploid, and how does this result from it's ancestor cell ?</p>
| [
{
"answer_id": 19015,
"pm_score": 3,
"text": "<p>Neurons are tetraploid in pathological situations like Alzheimer disease:</p>\n<blockquote>\n<p>Neurons that duplicate their DNA are rarely observed to undergo mitosis, and they remain for long time as tetraploid cells, in accordance with the chronic cour... | [
{
"answer_id": 73131,
"pm_score": 0,
"text": "<p>It's not all pathological. From the same second article cited:</p>\n\n<blockquote>\n <p>Modern techniques such as flow cytometry, fluorescent in situ\n hybridization (FISH), slide-based cytometry (SBC) and quantitative PCR\n analysis of DNA from isolat... |
19,020 | <p>I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50.</p>
<p>Please can someone explain the naming convention for this? i.e. what does the 'E' stand for? Does the number refer to the amino acid that has changed?</p>
| [
{
"answer_id": 19015,
"pm_score": 3,
"text": "<p>Neurons are tetraploid in pathological situations like Alzheimer disease:</p>\n<blockquote>\n<p>Neurons that duplicate their DNA are rarely observed to undergo mitosis, and they remain for long time as tetraploid cells, in accordance with the chronic cour... | [
{
"answer_id": 73131,
"pm_score": 0,
"text": "<p>It's not all pathological. From the same second article cited:</p>\n\n<blockquote>\n <p>Modern techniques such as flow cytometry, fluorescent in situ\n hybridization (FISH), slide-based cytometry (SBC) and quantitative PCR\n analysis of DNA from isolat... |
19,051 | <p><a href="https://en.wikipedia.org/wiki/Botulinum_toxin" rel="nofollow noreferrer">Botulinum toxin</a> is the neurotoxin protein created when botulism spores grow. The requirements for growth and/or for keeping the toxin from denaturing would seem to be very difficult to create in bale of hay.</p>
<p>There are well documented <a href="http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_botulism.htm" rel="nofollow noreferrer">incidents of botulism in horses</a> who are eating hay, all the references I found were centered around hay in large plastic wrapped bales. </p>
<p>I have been <a href="https://pets.stackexchange.com/questions/4407">involved in an event</a> where the presumed DX is botulism secondary to ingestion from hay from last year. In this case the hay is second cutting timothy hay (making it 6 plus months old), in rectangular 50 pound (22 kg) bales that are not wrapped, have been barn kept, and when purchased from the vendor where stacked in rows 4 feet wide, by 6 feet (2 meters) high. The bale then spent more then a week on an shelf (chrome platted heavy wire) with good air circulation. </p>
<p>Three pet <a href="http://rabbit.org/" rel="nofollow noreferrer">house rabbits</a> appear to have been effected. with 2 dead and one recovering from a case of descending paralysis. Several tests are underway, but my understanding is that it may be difficult to conclusively show either the botulism in the rabbits, or significant presence of 'botulinum toxin' or 'clostridium botulinum' in the hay (samples from the mangers of effected animals are being tested).</p>
<p>Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria? </p>
<p><strong>Note</strong> </p>
<p>If there is an awareness of a plant based neurotoxin that would cause similar symptoms that may be growing in the hay field please offer that in an answer at <a href="https://gardening.stackexchange.com/questions/11007">Gardnening</a>. </p>
| [
{
"answer_id": 19130,
"pm_score": 4,
"text": "<p>As an addendum to Spinorial's answer, and after some research, the Center for Food Security and Public Health <em>specifically</em> lists hay / grass / <strong>decaying vegetable matter</strong> as a potential source for <em>C. botulinum</em> growth in th... | [
{
"answer_id": 19129,
"pm_score": 3,
"text": "<p>Clostridium botulinum toxin is present ubiquitously in soil. As such it is more than plausible that hay bails, which come into contact with soil can and I should expect almost probably will be infected with these bacteria. However it is not the mere prese... |
19,081 | <p>It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 <em>grams</em> of DNA. This is clearly absurd and not the case.</p>
<p>Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an <em>upper bound</em> - but even so, a very uninformative one), and in practice, yields will fall far short of it because:</p>
<ul>
<li>Every single duplex of DNA does not denature at each cycle</li>
<li>Primers do not bind to every single molecule of DNA at each cycle</li>
<li>Not every DNA strand gets bound by a polymerase at every cycle</li>
<li>Not every polymerase that binds manages to complete the entire product in time in every cycle</li>
<li>The reaction inhibits itself by depleting dNTPs</li>
<li>The heat denatures the reaction by degrading enzyme</li>
</ul>
<p>In fact, cursory examination of qPCR output often follows saturation kinetics:</p>
<p><img src="https://i.stack.imgur.com/JlTkp.png" alt="enter image description here"></p>
<p>Mathematical methods for modeling qPCR are obviously well developed.</p>
<p>My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?</p>
<p>For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).</p>
| [
{
"answer_id": 42267,
"pm_score": 4,
"text": "<p><strong>An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.</strong></p>\n\n<p>Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in... | [
{
"answer_id": 19094,
"pm_score": 1,
"text": "<p>The equation is correct, but there's an additional asymptotic limit to a maximum concentration of product depending on the starting concentration of NTPs, template and primer pairs in solution too. </p>\n"
}
] |
19,095 | <p>For example, what's a $dt^{sz}$ hamster? (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/" rel="nofollow">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/</a>). </p>
<p>What's a Rgs9-Cre/+;gtROSA/+ mouse? (<a href="http://www.sciencedirect.com/science/article/pii/S2212877813000719" rel="nofollow">http://www.sciencedirect.com/science/article/pii/S2212877813000719</a>)</p>
| [
{
"answer_id": 19097,
"pm_score": 4,
"text": "<p>Those describe the genotype of an animal (or plant, virus etc.).</p>\n\n<p>The nomenclature can be very varied and domain-specific, but for those two examples:</p>\n\n<p>$dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred... | [
{
"answer_id": 19096,
"pm_score": 3,
"text": "<p>These strings are specific genotypes of these animals. They often denominate mutations or transgenes. \nFor the hamster $dt^{sz}$ stands for dystopic, the sz comes from the first denomination of this symptoms as seizure. See <a href=\"http://books.google.... |
19,115 | <p>Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?</p>
| [
{
"answer_id": 19118,
"pm_score": 4,
"text": "<p>The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1].</p>\n<p>Basepairing also occurs in RNA, so it can form a double helix. In ... | [
{
"answer_id": 19119,
"pm_score": 3,
"text": "<p>RNA (single or double stranded) actually can and does form a helix in the absence of certain complex 3D structures. The RNA helix is typically A-form, as opposed to B-form for typical DNA. The A-form helix is right-handed like the B-form but is more compa... |
19,162 | <p>Once, as a child, I found a spider in my parents' garden. I remember catching it in a jar because I thought it looked unusual, but I never figured out what kind of spider it was and unfortunately didn't get any pictures. I've been looking for it in books and on the Internet since, based on memory, with no luck.</p>
<p>This was twenty years ago now, and I realize my memory of it may not be good enough to identify it now, but here's trying.</p>
<p>What I remember best was its abdomen, which was a dark metallic blue and sort of rectangular in shape. Its body was probably about 1.5 cm long, without the legs, and maybe 1 cm wide or a little less (I was a child, things look bigger when you're small.) It was found in a garden in the suburbs of Copenhagen, Denmark, sitting on a bed sheet drying in the sun. It left only a few strings of web, almost like a bridge, from the bottom of the jar to the lid where it had escaped during the night because the lid wasn't sealed. I never found it again or saw another spider like it.</p>
| [
{
"answer_id": 19698,
"pm_score": 3,
"text": "<p>This may be what you are searching for:</p>\n\n<p><img src=\"https://i.stack.imgur.com/dDlkk.jpg\" alt=\"enter image description here\"></p>\n\n<p>It's actually a <strong>male purseweb spider</strong> (Atypus affinis), the color fades to black, eventually... | [
{
"answer_id": 97043,
"pm_score": 0,
"text": "<p>Was it this? This is another purseweb spider species.</p>\n<p><a href=\"https://i.stack.imgur.com/r9Gtv.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/r9Gtv.jpg\" alt=\"enter image description here\" /></a></p>\n"
}
] |
19,204 | <p>Say you have a needle, and you poke a very specific area on your left thumb.
A signal gets sent from that nerve up your spine and into your brain.</p>
<p>How does the brain know exactly where this signal has come from to such accuracy?</p>
<ul>
<li>Does each nerve in every conceivable part of the body have a unique path that goes up the spine and into the brain, so that's how the brain knows where it came from?</li>
<li>Or does the nerve encode the signal as data which travels up a generic nerve, and the brain decodes the information, which contains the "address" of the particular spot that was stimulated? If this is the case, how are the data encoded? Binary?</li>
</ul>
| [
{
"answer_id": 19209,
"pm_score": 3,
"text": "<p>In addition to what Spinoral has said, and in response to your comment above, I will add a bit more about the mechanisms.</p>\n\n<p>Essentially, in some form or another it's receptive fields all the way up.</p>\n\n<p>A brief outline of the anatomy:\nThe c... | [
{
"answer_id": 19206,
"pm_score": 3,
"text": "<p>The accuracy of sensation is actually quite variable depending on the region of our body. Highly innervated areas such as our fingers have a higher degree of accuracy than sparsely innervated areas such as our legs.</p>\n\n<p>There is a simple experiment ... |
19,210 | <p><strong>Background:</strong> I'm currently performing research in mathematical biology,
specifically on the treatment dynamics of HIV and TB co-infection.</p>
<p><strong>Question:</strong> Can a person infected with TB disease, who are undergoing treatment for it, infect a person with no history of TB bacteria in their body? </p>
<p><strong>Reformulation:</strong> In other words, is there a similar analogue for TB as for HIV, wherein an HIV+ person undergoing treatment for HIV will have a lowered viral load and thus have negligible chances of infecting a person with no history of HIV?</p>
<p>Please note that my model does not incorporate latent TB because it would become too complicated to analyze. I am focusing only on TB disease because <strong>only it</strong> is infectious.</p>
<p>Thanks for any help.</p>
| [
{
"answer_id": 19211,
"pm_score": 4,
"text": "<p>First there is one major difference between HIV and TB: As long as the TB bacteria are still susceptible to treatment (which is developing into a major problem in some regions of the world) there is a effective treatment which can eradicate the infection.... | [
{
"answer_id": 19217,
"pm_score": 2,
"text": "<p>I think its a bit difficult to compare HIV and TB this way because TB is transmitted mainly through respiratory droplets whilst HIV is mainly through contamination of blood products/sex, etc but not via the respiratory route. As far as I know, there's sti... |
19,303 | <p>I bought a blood pressure monitor (A&D UA-851) which has the option to measure irregular heartbeat. I do understand what 'irregular' means, but why do irregular heartbeats happen and what are it's implications short and long term? </p>
| [
{
"answer_id": 19306,
"pm_score": 5,
"text": "<p>The normal cardiac cycle is comprised of two distinct phases: <strong>the systolic phase</strong> in which the heart contracts, ejecting the blood, followed by the <strong>the diastolic phase</strong> when the cardiac muscle relaxes, refilling the heart w... | [
{
"answer_id": 27472,
"pm_score": 3,
"text": "<p>Very simply putting, irregular heat beat means that the pulse is not regular. It can be diagnosed by checking your pulse clinically. </p>\n\n<p>Irregularities are further classified as: </p>\n\n<ol>\n<li><p>Regularly Irregular: this occurs in heart blocks... |
19,310 | <p>Not all carcinogens are mutagens. Alcohol and estrogen, for example, does not damage DNA.</p>
<p>It's one of the assumptions of the Ames test that mutagenicity implies carcinogenicity, but is this <em>always</em> the case? I assumed that it was, but then I <a href="https://biology.stackexchange.com/questions/14399/carcinogens-how-do-they-work?rq=1">saw one of the comments here</a>. I did some more research but the internet seems to be reluctant to be definitive on the subject. <a href="https://answers.yahoo.com/question/index?qid=20120324145935AAa36mO" rel="nofollow noreferrer">This guy</a> claims 'no', but I'd prefer sources or at least a response that handles counterexamples like HPV. <a href="http://carcin.oxfordjournals.org/content/25/3/299.abstract" rel="nofollow noreferrer">This paper</a> claims 'yes', but doesn't list any specific examples. Some mutagens might be more specific to genes involved in cell cycle regulation, so I could see how a weak mutagen is a powerful carcinogen.</p>
<p>My question is, can you go the other way? Are there mutagens that just do not cause cancer? If they do not exist or are not known to exist, are they even possible?</p>
| [
{
"answer_id": 19331,
"pm_score": 5,
"text": "<h3>Short answer</h3>\n<p>All mutagens are potential carcinogens unless the mutagen is highly specific to a site. As noted in the question, carcinogens need not be mutagenic.</p>\n<hr />\n<p>HPV causes oncogenic transformation of a cell because of certain pr... | [
{
"answer_id": 19311,
"pm_score": 1,
"text": "<p>I'm no expert on the matter, but just quoting from <a href=\"http://en.wikipedia.org/wiki/Mutagen\" rel=\"nofollow noreferrer\">Wikipedia</a>:</p>\n<blockquote>\n<p>Mutagens are not necessarily carcinogens, and vice versa. Sodium Azide for example may be ... |
19,312 | <p>I am not comparing a cat with leopard.</p>
<p>I am just saying that we humans are all one type of creature and we are diverse (I am not saying we are class of mammals and phylum of etc and kingdom etc, because my religion doesn't believe in it).</p>
<p>So consider the class of cats they are one type of species so why aren't they diverse in phenotype like us? </p>
<p>Why do other animals, plants, unicellular organisms not have diversity in their phenotype and how they can recognize each other, like a bird always brings food to his offspring and it can't make mistake by giving it to other offspring of its own species? </p>
<p>So can I say they aren't diverse because of in their meiosis division their chromosomes don't cross over and random assort (alignment)? </p>
| [
{
"answer_id": 19313,
"pm_score": 5,
"text": "<p>In your question, your assumption that animal species are less diverse phenotypically than humans is wrong. I am sure you will appreciate @terdon's answer to <a href=\"https://biology.stackexchange.com/questions/14414/do-humans-have-enough-biological-diff... | [
{
"answer_id": 19315,
"pm_score": 3,
"text": "<p>I'd like to add that the variations in individuals within a species are a fundamental observation upon which modern biology is standing. Darwin wrote at least <a href=\"http://www.markhannam.com/essays/essay5a.htm\" rel=\"nofollow noreferrer\">2 chapters... |
19,381 | <p>I visited a bird enclosure close to where I live in Australia. The enclosure had several different species. The birds that stood out most were these doves sitting right along the fence railing, making a deep "Wo-wo-wo-woo" sound. That and also I thought they looked and sounded similar to Spotted Doves.</p>
<p><img src="https://i.stack.imgur.com/X6Jxl.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/cgtAi.jpg" alt="enter image description here"></p>
<p>Does anyone know what the species of this birds may be?</p>
| [
{
"answer_id": 19382,
"pm_score": 3,
"text": "<p>I think this is a Barbary dove (or Ringneck dove). See this image (from the <a href=\"http://nzbirdsonline.org.nz/species/barbary-dove\" rel=\"nofollow noreferrer\">here</a>):</p>\n\n<p><img src=\"https://i.stack.imgur.com/dFbDY.jpg\" alt=\"enter image de... | [
{
"answer_id": 19383,
"pm_score": 1,
"text": "<p>it is symi bird and more over it is commonly called as collared dove its a resident of symi and would have brought to australia by other means\n<img src=\"https://i.stack.imgur.com/dX223.jpg\" alt=\"enter image description here\">\nyou can find a list off... |
19,411 | <p>I got this doubt when I was studying about <a href="http://en.wikipedia.org/wiki/Hematocrit" rel="nofollow">haematocrit</a> value. According to my NCERT textbook males have greater number of RBCs than females. But who will have more RBCs when comparing a normal male and a female who lives at a higher altitude?</p>
<p>*edit</p>
<p>the magnitude of altitude would be less than <a href="http://en.wikipedia.org/wiki/Kangchenjunga" rel="nofollow">8,586 m (28,169 ft</a>) as the woman I know is not exactly at the top summit of <a href="http://en.wikipedia.org/wiki/Kangchenjunga" rel="nofollow">Kanchenjunga</a> so what would be the answer then?</p>
| [
{
"answer_id": 19413,
"pm_score": 3,
"text": "<p>Currently impossible to give a definite answer... It depends what altitude you look at. </p>\n\n<p>Going from @Alan_boyd's answer the normal range is 40-50% for males and 36-44% for females. If the altitude at which a person is acclimatized to correlates ... | [
{
"answer_id": 19412,
"pm_score": 2,
"text": "<p>According to the <a href=\"http://www.nlm.nih.gov/medlineplus/ency/article/003646.htm\" rel=\"nofollow\">MedlinePlus site</a> these are the normal ranges for haematocrit:</p>\n\n<p>Male: 40.7 - 50.3%</p>\n\n<p>Female: 36.1 - 44.3%</p>\n\n<p>Unfortunately ... |
19,416 | <p>FRET only works for interactions between 1nm to 20nm.</p>
<p>How can you be sure that the interaction that you want to study isn't less than 1 nm/greater than 20nm apart?</p>
| [
{
"answer_id": 19413,
"pm_score": 3,
"text": "<p>Currently impossible to give a definite answer... It depends what altitude you look at. </p>\n\n<p>Going from @Alan_boyd's answer the normal range is 40-50% for males and 36-44% for females. If the altitude at which a person is acclimatized to correlates ... | [
{
"answer_id": 19412,
"pm_score": 2,
"text": "<p>According to the <a href=\"http://www.nlm.nih.gov/medlineplus/ency/article/003646.htm\" rel=\"nofollow\">MedlinePlus site</a> these are the normal ranges for haematocrit:</p>\n\n<p>Male: 40.7 - 50.3%</p>\n\n<p>Female: 36.1 - 44.3%</p>\n\n<p>Unfortunately ... |
19,442 | <p>I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of <a href="http://www.rcsb.org/pdb/101/motm.do?momID=168" rel="nofollow noreferrer">DNA Helicase</a> below. Does anyone know how they were made or how one might create something similar?</p>
<p><a href="https://i.stack.imgur.com/GDfyn.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/GDfyn.jpg" alt="DNA Helicase" /></a><br />
<sub>(source: <a href="http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/images/168-DNAHelicase_4esv.jpg" rel="nofollow noreferrer">rcsb.org</a>)</sub></p>
| [
{
"answer_id": 19447,
"pm_score": 4,
"text": "<p>Those (really cool) pictures are created by David Goodsell using custom-written software.</p>\n<p>From an <a href=\"http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/about.html\" rel=\"noreferrer\">interview to the artist</a>:... | [
{
"answer_id": 81545,
"pm_score": 2,
"text": "<p>I don’t actually consider these pictures either “gorgeous” or “cool” — they are not to my taste — and I’m not really sure that the question is about biology, but as it has resurfaced after almost 5 years I thought I’d give an answer which explained how on... |
19,455 | <p>I have a list of gene name in a file </p>
<pre><code>CHRNB2
EGR2
GCK
KRT14
LMNA
FGF3
TK2
ABCC8
</code></pre>
<p>How can I map them to uniprot ID ? <br>
<strong>P.S</strong> I tried Uniprot "ID mapping" (from-"GENEID" to-"UNIPROTKB AC"), but it couldn't map.<br>
Please suggest me what to do.</p>
| [
{
"answer_id": 19471,
"pm_score": 1,
"text": "<p>for biomart goto below link<br>\n<a href=\"http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2\" rel=\"nofollow\">http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2</a></p>\n\n<p>Also there is one more conver... | [
{
"answer_id": 48427,
"pm_score": 2,
"text": "<h1>ID mapping</h1>\n<p>This is called ID mapping. It used to be a headache as programmatic access was the only real way, but it is pretty trivial these days.</p>\n<p>As mentioned in the comments, by far the most popular and easy method is to use <strong>Uni... |
19,472 | <p>Last night I laid on my bed and tried to go to sleep with the light off.
I closed my eyes (but hadn't gone to sleep). My younger brother touched the wireless mouse (which had laser) for the laptop. He wiggled the mouse and it's laser contacted my closed eye . I knew some light was thrown on my face, and it's color was red. The laser on the mouse was actually red. So my question is, when my eyes are not functioning (not seeing, closed) how did I come to know that there was a light aimed at my eyes, and it was red? </p>
| [
{
"answer_id": 19474,
"pm_score": 5,
"text": "<p>There are two reasons for light to appear red through the eyelids.</p>\n\n<ol>\n<li><p>Eyelids get a rich supply of blood which contains iron (in hemoglobin). The iron in blood absorbs all colors of light but reflects red light. (<a href=\"http://www.chem... | [
{
"answer_id": 19473,
"pm_score": 5,
"text": "<p>Short answer, your eyelids does not block all light. Since they are only a thin layer of skin, the light is able to pass through although not completely obviously. Since the eyes are still completely functional when you close them, only covered by the eye... |
19,495 | <p>How does a woodpecker go about smacking it's head into a tree without killing itself?</p>
| [
{
"answer_id": 19496,
"pm_score": 5,
"text": "<p>Various features of brain,skull and beak anatomy help to achieve protection.</p>\n<p>A paper was published in PLoSOne in 2011 on this very topic:</p>\n<p><a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026490\" rel=\"noreferr... | [
{
"answer_id": 19497,
"pm_score": 3,
"text": "<p>Gibson (2006) identified three characteristics that help woodpeckers avoid brain injury:</p>\n<blockquote>\n<p>their small size, which reduces the stress on the brain for a given acceleration</p>\n<p>the short duration of the impact, which increases the t... |
19,508 | <p>I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? What is a possible reason for this? Is this phenomenon linked with our cell signaling pathways? If it is, then what would be the pathway that leads to the aggressive behavior?
<p>
To summarize the question: </p>
<p><strong>When a person is hungry and they get angry, is it due to a cell signaling pathway? If so, what pathway?</strong></p>
| [
{
"answer_id": 19511,
"pm_score": 4,
"text": "<p>Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].</p>\n<p>When it comes to humans, here is a study that claims low glucose leads to i... | [
{
"answer_id": 19615,
"pm_score": 2,
"text": "<p><em>This is a short review about the issue and not complete.\nThis and the earlier answer are not proofs of the link between the two proceses.</em></p>\n\n<p>To investigate this better, I think it would be much easier first to narrow the case to </p>\n\n<... |
19,514 | <p>It is said that the stonefish (Synanceia) is able to stay out of the water for up to 24 hours. I wonder how they get oxygen from the air. Could someone explain this?</p>
| [
{
"answer_id": 19511,
"pm_score": 4,
"text": "<p>Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].</p>\n<p>When it comes to humans, here is a study that claims low glucose leads to i... | [
{
"answer_id": 19615,
"pm_score": 2,
"text": "<p><em>This is a short review about the issue and not complete.\nThis and the earlier answer are not proofs of the link between the two proceses.</em></p>\n\n<p>To investigate this better, I think it would be much easier first to narrow the case to </p>\n\n<... |
19,515 | <p>A steroid, testosterone was injected in female body which led to development of secondary sexual characters but these characters were not developed over night (Response was very slow). What could be possible explanation of this phenomenon</p>
<ol>
<li>a Steroid hormones produce a slow response because they do not have secondary messenger </li>
<li>Slow response is due to lack of cell membrane receptors and amplification enzymes</li>
<li>Movement of this hormone is very slow in blood</li>
<li>None of the above</li>
</ol>
<p>I think option 3 is correct because steroid hormones are hydrophobic in nature and cant be transported in the blood without the help of any carrier protein so this may be the reason but I am not sure about this.. </p>
| [
{
"answer_id": 19511,
"pm_score": 4,
"text": "<p>Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].</p>\n<p>When it comes to humans, here is a study that claims low glucose leads to i... | [
{
"answer_id": 19615,
"pm_score": 2,
"text": "<p><em>This is a short review about the issue and not complete.\nThis and the earlier answer are not proofs of the link between the two proceses.</em></p>\n\n<p>To investigate this better, I think it would be much easier first to narrow the case to </p>\n\n<... |
19,540 | <p>does the order of genes within a chromosome matter? or is the main thing that the genes are there.</p>
<p>so for example, our DNA is very similar to that of apes not only by the genes themselves but also by the arrangement of those genes in the chromosomes.</p>
<p>is the order of this arrangement significant? Or if it were shuffled around, then the functional impact would be more or less the same?</p>
<p>Another example, an <a href="http://www.genome.gov/page.cfm?pageID=10005831" rel="nofollow noreferrer">international study</a> in the mouse genome has revealed that virtually all mouse genes have direct counterparts in humans, i.e. humans and mice contain virtually the same set of genes. is the difference between humans and mice due primarily to the different order of the genes or to the slight differences in the genes themselves?</p>
<p>This question was raised from a claim <a href="https://biology.stackexchange.com/a/5568/6202">here</a> which seems to imply it does not matter.</p>
<blockquote>
<p>The chances are infinitesimal that human chr 2 were to resemble those
of other primates at random. This is what you say in science when you
mean 'impossible'. One simply doesn't see a segment of DNA the size of
Chr 2A and 2B being so similar for such a length when we look at rats,
dogs, worms or any more distantly related living thing.</p>
</blockquote>
| [
{
"answer_id": 19555,
"pm_score": 4,
"text": "<blockquote>\n <p>is the difference between humans and mice due primarily to the\n different order of the genes or to the slight differences in the genes\n themselves?</p>\n</blockquote>\n\n<p>The latter.</p>\n\n<blockquote>\n <p>This question was raised... | [
{
"answer_id": 19541,
"pm_score": 2,
"text": "<p>Ye, the order matters. This can be seen in chromosomal translocations which can cause cancer.\nA example for that would be the translocation of IRF4 which happens in a subtype of multiple myeloma. The translocation is permanently activating the transcript... |
19,545 | <p>What features make one plant able to withstand dry spells better than another with relatively similar structure? For instance, one of my <a href="http://en.wikipedia.org/wiki/Rudbeckia" rel="nofollow">Rudbeckias</a> is wilting from drought at the moment, and an <a href="http://en.wikipedia.org/wiki/Oenothera" rel="nofollow">Oenothera</a> next to it is not yet showing signs of dryness.</p>
<p>Or like <a href="http://plants.usda.gov/core/profile?symbol=IMCA" rel="nofollow">jewelweed (Impatiens capensis)</a>, which wilts even while the soil is damp, in full sun, and <a href="http://en.wikipedia.org/wiki/Ambrosia_artemisiifolia" rel="nofollow">ragweed (Ambrosia artemisiifolia)</a>, which will grow in very dry locations without being phased.</p>
<p>Is it caused by a faster transpiration rate in some plants than in others?</p>
| [
{
"answer_id": 20092,
"pm_score": 3,
"text": "<p>The difference may be related to how the plants fix carbon. While all plants convert CO₂ and H₂O to glucose and oxygen, there are at least three pathways that are used to do it. The C3 pathway is older and less efficient than the CAM and C4 pathways. Many... | [
{
"answer_id": 19589,
"pm_score": -1,
"text": "<p>Plants in drier conditions usually have reduced surface area, thick waxy cuticle covering the epidermis, reduced number of stomata, and water storage tissues that presides in its roots and leaves.</p>\n\n<p>This means that even if the plants are similar,... |
19,548 | <p>It seems like being nearsighted for much of your life due to elongated eyes would make it easier in general to focus on near objects rather than far since the lens would not have to change much. Since in old age we lose the ability to focus close images due to a hardening of the lens over time, wouldn't having eyes shaped more for near images be helpful in maintaining the ability to see close up, and thus nearsighted, or myopic people, would be less likely to develop farsightedness, or hyperopia, with age? It seems then that nearsightedness is more of an adaptation that occurs at a young age, so that these people can work up close for longer periods of time both in the the short term(studying) and long term(age). I'd love to hear if any research has been done on this subject, and any other input you have.</p>
| [
{
"answer_id": 19551,
"pm_score": 3,
"text": "<p>It is generally understood that we tend to become hyperopic as we age (<a href=\"http://www.journalofvision.org/content/8/4/29.short\" rel=\"nofollow\">reference</a>). As to whether this aids in decreasing myopia is stated as marginal in papers. One paper... | [
{
"answer_id": 24026,
"pm_score": 1,
"text": "<p>Let me see whether I can explain this quickly. The eye size is tightly regulated genetically. Babies don't have big eyes, they have exactly the same sized eyes like adults, only their head is smaller. Myopic eyes are larger than normal and hyperopic eyes ... |
19,575 | <p>I'm studying a TCGA dataset trying to find correlations between gene expression and clinical data which might shed light on some pathways. One column of the clinical data provides a list of chemotherapy drugs the patient received and I'm pretty sure there's a wealth of possibility in this column but I don't know anything about how chemotherapy drugs work or what kinds of things it makes sense to classify about them. </p>
<p>I'm making a spread sheet that will have the following columns: </p>
<pre><code>Drug_Name
Number_of_Patients_Received
Mechanism
Associated_Drugs
</code></pre>
<p>But I don't know what else is important to know about these drugs. What would you think is important to know to help understand how these drugs might have played an interactive role with the pathways. Also, if you have any recommendations of online resources, I'll appreciate you mentioning them with a short explanation of what I might find there.
But my primary question is else should I look up about these drugs to help me understand their role/impact.</p>
| [
{
"answer_id": 19579,
"pm_score": 3,
"text": "<p>There's <a href=\"http://www.pharmgkb.org/\" rel=\"nofollow\">this database</a> of genetic/drug interactions, which I think is pretty much exactly what you're looking for. </p>\n\n<p>Probably your best approach is to classify your drugs into a couple diff... | [
{
"answer_id": 34644,
"pm_score": 1,
"text": "<p>Resonating provided a good general classification scheme that could be implemented for categorizing chemotherapeutic agents. Another resource that could be used is the following: <a href=\"http://www.genome.jp/kegg/drug/\" rel=\"nofollow\">http://www.geno... |
19,590 | <p>In <a href="http://www.simonsfoundation.org/quanta/20140710-hints-of-lifes-start-found-in-a-giant-virus/#comment-142465" rel="nofollow">this piece</a> about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states:</p>
<blockquote>
<p>In order to move from RNA to DNA, you need an enzyme called reverse transcriptase</p>
</blockquote>
<p>Is this true though? Don't many DNA polymerases work with both, ssDNA and ssRNA templates, i.e. they function as reverse transcriptases although they're not "true" reverse transcriptases. So, in order to move from RNA to DNA, a reverse transcriptase was not a necessity like ribonucleotide reductase was for RNA to Uracil-DNA and thymidylate synthase was for Uracil-DNA to DNA?</p>
| [
{
"answer_id": 19579,
"pm_score": 3,
"text": "<p>There's <a href=\"http://www.pharmgkb.org/\" rel=\"nofollow\">this database</a> of genetic/drug interactions, which I think is pretty much exactly what you're looking for. </p>\n\n<p>Probably your best approach is to classify your drugs into a couple diff... | [
{
"answer_id": 34644,
"pm_score": 1,
"text": "<p>Resonating provided a good general classification scheme that could be implemented for categorizing chemotherapeutic agents. Another resource that could be used is the following: <a href=\"http://www.genome.jp/kegg/drug/\" rel=\"nofollow\">http://www.geno... |
19,593 | <p>why plants can only synthesize D-glucose why not L-glucose along with D glucose. I know it very well that plants have only enzymes which can synthesize D-glucose but Why not they have enzymes which can also manufacture L-glucose. So that we could have mixture of L and D glucose molecules? What is the significance of synthesis of only D-glucose by the plants ?</p>
| [
{
"answer_id": 19579,
"pm_score": 3,
"text": "<p>There's <a href=\"http://www.pharmgkb.org/\" rel=\"nofollow\">this database</a> of genetic/drug interactions, which I think is pretty much exactly what you're looking for. </p>\n\n<p>Probably your best approach is to classify your drugs into a couple diff... | [
{
"answer_id": 34644,
"pm_score": 1,
"text": "<p>Resonating provided a good general classification scheme that could be implemented for categorizing chemotherapeutic agents. Another resource that could be used is the following: <a href=\"http://www.genome.jp/kegg/drug/\" rel=\"nofollow\">http://www.geno... |
19,612 | <p>This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?</p>
<p><img src="https://i.stack.imgur.com/2YcJL.png" alt="Full view">
<img src="https://i.stack.imgur.com/MrjTJ.jpg" alt="Flower">
<img src="https://i.stack.imgur.com/GPiDX.jpg" alt="Root"></p>
<p>Thanks, looks like it is something like this:</p>
<p><a href="http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034" rel="nofollow noreferrer">http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034</a></p>
<p>Related question:</p>
<p><a href="https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610">https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610</a></p>
| [
{
"answer_id": 19618,
"pm_score": 4,
"text": "<p>This looks like some species of <em>Phytolacca</em> to me.</p>\n\n<p>It's possibly <em>Phytolacca americana</em>, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but <a href=\"http://books.google.com/books?id=5vd_ZE7UDV8C... | [
{
"answer_id": 55311,
"pm_score": 1,
"text": "<p>It is <a href=\"https://fr.wikipedia.org/wiki/Phytolacca_acinosa\" rel=\"nofollow noreferrer\">Phytolacca acinosa</a> because the flowers grow upwards and the fruits are ribbed. <a href=\"https://en.wikipedia.org/wiki/Phytolacca_americana\" rel=\"nofollow... |
19,648 | <p>Is it possible for a device to measure how much air we breathe in and out over the entire day and at what rate? I think if we have access to this data we can compare it across people.</p>
| [
{
"answer_id": 19682,
"pm_score": 3,
"text": "<p>What you are looking for is a spirometer. There are different types of spirometers serving different purposes like the Incentive spirometer and the peak flow meter. I would suggest that you go through the <a href=\"http://en.wikipedia.org/wiki/Spirometer\... | [
{
"answer_id": 19684,
"pm_score": 1,
"text": "<p>Another possibility is <a href=\"http://www.serinth.gr/en/products/ergospirometers/portable-ergospirometers/cosmed-k4b2.html\" rel=\"nofollow\">K4 device</a> and <a href=\"http://www.cosmed.com/en/products/cardio-pulmonary-exercise-testing/k4-b2-mobile-cp... |
19,653 | <p>I recently watched the video <a href="https://www.youtube.com/watch?v=R3unPcJDbCc">This Is Not Yellow</a> explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?</p>
| [
{
"answer_id": 96315,
"pm_score": 1,
"text": "<p>Below is a summary of the information found <a href=\"https://commandcenter.blogspot.com/2020/09/color-blindness-is-inaccurate-term.html\" rel=\"nofollow noreferrer\">here</a> and from how <a href=\"https://enchroma.com/pages/how-enchroma-glasses-work\" r... | [
{
"answer_id": 19661,
"pm_score": 2,
"text": "<p>Normal people see color due to the bellow mentioned combination of red, green and blue:</p>\n\n<p><img src=\"https://i.stack.imgur.com/l99xj.jpg\" alt=\"enter image description here\"></p>\n\n<p>But due to genetic factors, The graph Distorts:</p>\n\n<p><i... |
19,656 | <p>I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept of phyla. With this in mind, I'm curious which of widely accepted biological phyla appeared most recently, and what evidence do we have of their relatively recent appearance? </p>
<p>I'm most interested in animals, but I'd also welcome any information about other organisms.</p>
| [
{
"answer_id": 19659,
"pm_score": 4,
"text": "<p>In my view, we simply don't have good enough data to answer this question. The fossil evidence is too sparse prior to the Cambrian and the evidence that we do have suggests that the phyla were already too separated. Meanwhile, the depth of time and the di... | [
{
"answer_id": 19657,
"pm_score": 2,
"text": "<p>As far as I know there is no phylum which appeared after the Cambrian. Every discussion beyond that is close to speculation, as the divergence estimates of different studies vary significantly. \nYou might want to look into one of the resources mentioned ... |
19,658 | <p>I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.</p>
<p>First, I downloaded a complete human genome from <a href="http://hgdownload.cse.ucsc.edu/downloads.html#human" rel="noreferrer">http://hgdownload.cse.ucsc.edu/downloads.html#human</a> There is a FASTA file for each chromosome.</p>
<p>Then, I wrote a java program which can convert FASTA DNA sequences into the appropriate amino acid chain.</p>
<p>Next, I made my program look for the "start" code (ATG) and "stop" codes (TAA, TAG, TGA).</p>
<p>So, now I have sequences of amino acids which might theoretically end up folding into proteins. But, before I start diving into protein folding, I wanted to try to verify that the steps I took so far were done correctly. I looked up some important human genes in an online database and found their amino acid sequences. I then searched through my program's data for those sequences and confirmed that they were there. However, the gene was in a different base-pair location than the database said that it should be in.</p>
<p>This led me to some questions, which, so far I have been unable to answer and hopefully people here will be able to help shed some light.</p>
<ol>
<li><p>I know there are a lot of different publicly available genomes. Maybe the UCSC one that I downloaded is different from the one used by the gene database. How much does each genome vary from each other genome and in what ways do they vary?</p></li>
<li><p>In attempting to answer that first question, I was going to download a bunch of genomes from the 1000genomes website and do some comparisons, but I wasn't sure which files to download. Each of the files begins with either ERR or SRR and I'm not sure what that means. This is the folder I'm currently looking in <a href="ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/" rel="noreferrer">ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/</a></p></li>
<li><p>Lets say I'm trying to model a white blood cell. How do I know which parts of the genome get turned into proteins for that type of cell?</p></li>
</ol>
<p>Sorry if anything I said doesn't make sense. As I said, my expertise lies in programming, not biology/genetics.</p>
| [
{
"answer_id": 19662,
"pm_score": 5,
"text": "<p>No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are:</p>\n<ul>\n<li><p>Genes (eukaryotic genes anyway) are <a href=\"https://en.wikipedia.org/wiki/RNA_splicing\" ... | [
{
"answer_id": 19664,
"pm_score": 2,
"text": "<p>Why bother predicting proteins badly from DNA sequence when you could have just as well downloaded the manually curated human proteome?</p>\n\n<p>As to your questions:</p>\n\n<ol>\n<li><p>Are you asking about human genomes or genomes in general? The vast ... |
19,668 | <p>Take for example the human and the chimpanzee, they are "closely related" species since they are "close" to each other in a phylogenetic tree. However, this terminology seems pretty informal, what would be the formal way to specify that two or more species are "closely related"?</p>
| [
{
"answer_id": 19673,
"pm_score": 3,
"text": "<p>Are you looking for something like \"<a href=\"http://en.wikipedia.org/wiki/Sister_group\" rel=\"nofollow\">sister lineage</a>\" (or \"sister taxon\" or \"sister group\")</p>\n\n<p>This term may be more specific than what you're looking for, and to use it... | [
{
"answer_id": 19672,
"pm_score": 2,
"text": "<p>As <a href=\"http://en.wikipedia.org/wiki/Genus\" rel=\"nofollow\">genus</a> comes above species I'd consider using this term for the species which are close genetically (\"these two species are from the same genus\"). Above genus comes family etc...</p>\... |
19,708 | <p>As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why are only specific cells responsive against steroid hormones?</p>
<p>For example, all of our body cells almost contains the genes for the development of secondary sexual characters but why do only specific cells show a response against these steroid hormones because the development of secondary sexual characters occur only in specific region of our body, that is, beard formation occur only in a specific region of the face, etc.</p>
<p>IN SUMMARY: When steroid hormones can pass through every cell of our body then why do they show only a localized response?</p>
| [
{
"answer_id": 20402,
"pm_score": 3,
"text": "<p>Unlike other types of hormones, steroid hormones do not have to bind to plasma membrane receptors. Instead, they can interact with intracellular receptors that are themselves transcription activators. Steroid hormones too hydrophobic to dissolve readily i... | [
{
"answer_id": 19709,
"pm_score": 3,
"text": "<p>The quick answer is that only certain cell types express the required <a href=\"http://en.wikipedia.org/wiki/Steroid_hormone_receptor\">steroid hormone receptors</a> that are necessary to induce signaling and gene regulation when bound to their target ste... |
19,725 | <p>In an animal cell, especially neuron and in particular its axon, while there is electrical resistance and capacitance mechanism in the cell, which play essential roles in the cable theory model of neuronal action potential transmission, is there a prominent self <a href="http://en.wikipedia.org/wiki/Self_inductance" rel="nofollow noreferrer">inductance</a> mechanism in the sense of electromagnetism?</p>
| [
{
"answer_id": 20252,
"pm_score": 4,
"text": "<p>What one thinks, no matter how intuitive it may appear is not particularly relevant in science. The inductance associated with a neural axon has been well documented since Cole (1966). Its role in the propagation of neural signals is developed extensive... | [
{
"answer_id": 78594,
"pm_score": 1,
"text": "<p>There surely is inductance in neurons. This inductance is introduced by two different mechanisms. \n1. The coil structure of myelin sheaths can introduce a real electrical inductance. The solid evidence for this is the opposite spiraling directions betwee... |
19,744 | <p><a href="https://cooking.stackexchange.com/a/45589/11251">An answer on another SE site</a> mentions that sugar "at a certain level acts as a preservative". I've always been taught that microorganisms eat sugar and expel acids, that is why sugary food are damaging to teeth. <strong>How is it that sugar acts as a preservative, then?</strong></p>
<p>Googling the question I've found <a href="http://sciencefocus.com/qa/how-does-sugar-act-preservative" rel="nofollow noreferrer">conflicting</a> <a href="https://answers.yahoo.com/question/index?qid=20080423133918AAt7NvX" rel="nofollow noreferrer">answers</a> though I don't credit the sources as being especially reputable. What is the real reason that sugar can act as a preservative?</p>
| [
{
"answer_id": 19748,
"pm_score": 4,
"text": "<p>Sugar in high concentrations acts osmotic. This means that the water available in the cells is drawn towards the high concentration of a solutant (sugar), like in the image below (this is demonstrated with a plant cell, but the principle is the same for b... | [
{
"answer_id": 43042,
"pm_score": 2,
"text": "<p>Sugar participate in food preservation only at high concentrations. When microbes are introduced to high sugar concentrated environment, water inside the microbial cell diffuses out to the high sugar concentrated solute due to the phenomenon called <stron... |
19,749 | <p>I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring function to take a look at the energy components - I don't want to re-dock the ligands into the protein binding sites.
From what I have found on the internet, I came up with this procedure, but I am not sure if this is the right approach, and also I get an error in the last step saying that "atoms are outside the grid".</p>
<p>It would be nice if someone could take a look at it and tell me whether this make sense and if this is the right procedure (and maybe a suggestion for the error source)</p>
<p><strong>1) Preparing the receptor</strong></p>
<ul>
<li><p>need to add hydrogens if not present</p></li>
<li><p>adds gasteiger charges to peptide</p></li>
</ul>
<p><strong>input</strong></p>
<ul>
<li>protein.pdb</li>
</ul>
<p><strong>output</strong></p>
<ul>
<li>protein.pdbqt</li>
</ul>
<p><strong>script:</strong> </p>
<ul>
<li>prepare_receptor4.py -r protein.pdb [options]</li>
</ul>
<hr>
<p><strong>2) Preparing the ligand</strong></p>
<ul>
<li>add hydrogens if not present </li>
</ul>
<p><strong>input:</strong> </p>
<ul>
<li>ligand.pdb or ligand.mol2</li>
</ul>
<p><strong>output:</strong> </p>
<ul>
<li>ligand.pdbqt</li>
</ul>
<p><strong>script</strong></p>
<ul>
<li>prepare_ligand4.py -l ligand.mol2 [options]</li>
</ul>
<hr>
<p><strong>3) Generate grid parameter file</strong></p>
<p><strong>inputs</strong></p>
<ul>
<li>ligand.pdbqt</li>
<li>protein.pdbqt</li>
</ul>
<p><strong>output</strong></p>
<ul>
<li>protein.gpf</li>
</ul>
<p><strong>script:</strong> </p>
<p>prepare_gpf4.py -l ligand.pdbqt -r protein.pdbqt [options]</p>
<hr>
<p><strong>4) AutoGrid: generate maps and grid data file</strong></p>
<p><strong>inputs:</strong> </p>
<ul>
<li>protein.pdbqt </li>
<li>protein.gpf</li>
</ul>
<p><strong>outputs:</strong></p>
<ul>
<li>protein.glg Grid Log File</li>
<li>protein.*.map affinity maps for different atoms</li>
<li>protein.maps.fld Grid data file</li>
<li>protein.d.map desolvation map</li>
<li>protein.e.map electrostatic map</li>
</ul>
<p><strong>command:</strong></p>
<p>autogrid -p protein gpf</p>
<hr>
<p><strong>5) Generate docking parameter file</strong></p>
<p><strong>inputs</strong></p>
<ul>
<li>ligand.pdbqt</li>
<li>protein.pdbqt</li>
</ul>
<p><strong>output</strong></p>
<ul>
<li>ligand_protein.dpf</li>
</ul>
<p><strong>script:</strong> </p>
<p>prepare_dpf4.py -l ligand.pdbqt -r protein.pdbqt [options]</p>
<hr>
<p>**
**</p>
<p><strong>6) Prepare .dpf file and run autodock for re-scoring</strong></p>
<p>**
**</p>
<p>Remove seach parameters and append the "epdb" keyword, so that an
examplary .dpf would look like this:</p>
<p>autodock_parameter_version 4.2 # used by autodock to validate
parameter set </p>
<p>outlev 1 # diagnostic output level </p>
<p>intelec # calculate internal
electrostatics </p>
<p>ligand_types C HD N NA OA # atoms types in ligand </p>
<p>fld rec.maps.fld # grid_data_file </p>
<p>map rec.C.map # atom-specific affinity map </p>
<p>map rec.HD.map # atom-specific affinity map </p>
<p>map rec.N.map # atom-specific affinity map </p>
<p>map rec.NA.map # atom-specific affinity map </p>
<p>map rec.OA.map # atom-specific affinity map </p>
<p>elecmap rec.e.map # electrostatics map </p>
<p>desolvmap rec.d.map # desolvation map </p>
<p>move lig.pdbqt # small molecule </p>
<p>about 17.6 22.2 32.6 # small molecule center </p>
<p>epdb # small molecule to be
evaluated </p>
<p>**
**</p>
<p><strong>inputs</strong></p>
<ul>
<li>ligand_receptor.dpf</li>
</ul>
<p><strong>command:</strong> </p>
<p>autodock -p ligand_protein.dpf</p>
<h1>Edit</h1>
<p>I managed to use AutoDock Vina for re-scoring now, however, the output is not as detailed as the one that would be produced by AutoDock 4.2.</p>
<p>For example, what I get is:</p>
<p>Affinity: -2.06943 (kcal/mol)
Intermolecular contributions to the terms, before weighting:<br>
gauss 1 : 51.97697<br>
gauss 2 : 1133.84012<br>
repulsion : 7.41516<br>
hydrophobic : 34.56441<br>
Hydrogen : 0.00000 </p>
<p>(what is also weird is that the <code>prepare_ligand4.py</code> script to generate the .pdbqt file from the mol2 file removed the hydrogens)</p>
<p>In AutoDock4.2, the output would be, for example,</p>
<p>epdb: USER Estimated Free Energy of Binding = -6.54 kcal/mol [=(1)+(2)+(3)-(4)]<br>
epdb: USER Estimated Inhibition Constant, Ki = 15.95 uM (micromolar) [Temperature = 298.15 K]<br>
epdb: USER<br>
epdb: USER (1) Final Intermolecular Energy = -7.14 kcal/mol<br>
epdb: USER vdW + Hbond + desolv Energy = -6.33 kcal/mol
epdb: USER Electrostatic Energy = -0.81 kcal/mol<br>
epdb: USER (2) Final Total Internal Energy = -0.20 kcal/mol<br>
epdb: USER (3) Torsional Free Energy = +0.60 kcal/mol<br>
epdb: USER (4) Unbound System's Energy [=(2)] = -0.20 kcal/mol </p>
<p>Anyone knows if this might be available through VINA somehow?</p>
| [
{
"answer_id": 20001,
"pm_score": 3,
"text": "<p>Okay, I finally figured it out. Basically there are those following 6 steps:</p>\n\n<ol>\n<li>Preparing a protein</li>\n<li>Preparing a ligand</li>\n<li>Generating a grid parameter file</li>\n<li>Generating maps and grid data files</li>\n<li>Generating a ... | [
{
"answer_id": 19751,
"pm_score": 2,
"text": "<p>You can use Autodock Vina. It provides an option to calculate local score only.</p>\n\n<blockquote>\n <p>displaying the individual contributions to the intermolecular score, before weighting (these are shown with \"--score_only\")</p>\n</blockquote>\n\n<... |
19,809 | <p>Cooperativity in gene expression is an important feature of many regulatory networks. Described using the <a href="http://en.wikipedia.org/wiki/Hill_equation_(biochemistry)" rel="nofollow">Hill function</a>, the most common example is a transcription factor (TF) that when bound to its target regulatory site, increases the rate of binding of other transcription factors (usually through TF-TF dimerization). </p>
<p>There are numerous example of TF dimerization-based cooperativity in the literature. However, I am trying to find examples of positive transcriptional cooperativity that involve mechanisms <em>other than</em> TF dimerization. In the dimer model, an unbound TF binds to its cognate promoter (containing multiple enhancers) with a certain affinity. With the first TF bound, another identical TF now has increased affinity for its target - binding to the enhancer and binding (dimerization) to the first TF. The expression profile is sigmoidal (near binary) and represents sharp on/off switching in activity. </p>
<p>Although peer-reviewed articles experimentally or theoretically characterizing alternative mechanisms are preferred, I'm also interested in user hypotheses and discussions that are more speculative. Specifically, I'm interested in positive cooperativity that occurs without feedback from the regulated genes.</p>
<p>One potential mechanism could involve a DNA-binding TF consisting of a transcriptional activator domain and a chromatin remodeling or DNA methylation domain. When the TF binds it not only activates transcription but remodels local chromatin. If the remodeling increases affinity for the next TF, they act cooperatively (and positively). Perhaps something similar to this has already been described. </p>
| [
{
"answer_id": 19825,
"pm_score": 3,
"text": "<p>Positive co-operativity without feedback from the downstream genes:</p>\n\n<p>I guess Polycomb/Trithorax complexes will fit this criterion nicely.</p>\n\n<p>Polycomb group (PcG) represses Hox and other differentiation related genes (such as neurogenin) wh... | [
{
"answer_id": 19815,
"pm_score": 2,
"text": "<p>Interesting question. I think I have two examples for you which might be interesting.\nThe first is the co-regulation of the microphthalmia-associated transcription factor (MITF) in pigmentation by SOX10 and PGC1a/b. See this paper:</p>\n\n<ul>\n<li><a hr... |
19,811 | <p>I have an ant queen in a jar. This is what she looks like:</p>
<p><img src="https://i.stack.imgur.com/jTC29.jpg" alt="black ant queen captured in jar"></p>
<p>Because I'm planning to start an artificial ant nest, I'd like to learn something about that specific species of ant. This particular queen is very common in the Czech Republic, central Europe. It's also very common in cities.</p>
<ol>
<li>Could you tell what kind of queen is that?</li>
<li>Is there any image reference that would help me find out? Ideally with some location search possibility.</li>
</ol>
| [
{
"answer_id": 71876,
"pm_score": 2,
"text": "<p>This cannot be a Lasius queen, it is a Formica queen. Although one of the main characteristic is the shape of the first segment of the funicula which cannot be seen on this picture, the general aspect of this queen (elongated, with red legs, does not have... | [
{
"answer_id": 19826,
"pm_score": 2,
"text": "<p>As @skymnige said it is definitely <strong>Black garden ant (<em>Lasius niger</em>)</strong></p>\n\n<p><img src=\"https://upload.wikimedia.org/wikipedia/commons/4/4c/Lasius_Niger_wingless_queen.jpg\" alt=\"\"></p>\n"
}
] |
19,827 | <p>Can epistaxis or nosebleeds be a cause of death?</p>
<p><img src="https://i.stack.imgur.com/o3wRX.png" alt=""></p>
| [
{
"answer_id": 19831,
"pm_score": 5,
"text": "<p>Yes, it can, but it is extremely rare.</p>\n\n<blockquote>\n <p>... nosebleeds are rarely fatal, accounting for only 4 of the 2.4 million deaths in the U.S. in 1999 [1].</p>\n</blockquote>\n\n<p>The main issue is that epistaxis can be a sign of potential... | [
{
"answer_id": 19830,
"pm_score": 3,
"text": "<p>Any injury, that results in external bleeding can lead to death, since it is a breach in the body's defenses and an entry point for pathogens.</p>\n\n<p>Explanation:</p>\n\n<p>When you have nose bleeding the blood must be coming from somewhere. Usually fr... |
19,836 | <p>I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms from the MOL2 file (the PDBQT file doesn't contain hydrogen atoms).</p>
<p>The command I used for OpenBabel is </p>
<pre><code>babel -i mol2 my.mol2 -o my.pdbqt
</code></pre>
<p>When I look at the documentation, they babel has a dedicated "-d" flag for removing hydrogens. So I assume that this shouldn't happen by default?</p>
<p>The same thing happens if I use MGLTools</p>
<pre><code>prepare_ligand4.py -l my.mol2
</code></pre>
<p>Any ideas of what might be going on here?</p>
<p>Thanks for your help!</p>
<p>will append the MOL2 file if someone wants to try it:</p>
<pre><code>@<TRIPOS>MOLECULE
mymol2
25 25 0 0 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 -1.0341 29.2934 -14.5590 C.ar 1 <0> -0.1745
2 C2 -0.1917 29.9513 -13.6630 C.ar 1 <0> -0.1483
3 C3 -2.3919 29.1585 -14.2689 C.ar 1 <0> -0.1608
4 C4 -0.7068 30.4744 -12.4770 C.ar 1 <0> -0.0956
5 C5 -2.9070 29.6816 -13.0828 C.ar 1 <0> -0.1543
6 C6 -2.0573 30.3323 -12.2033 C.ar 1 <0> -0.0209
7 C7 -5.0136 30.3602 -8.9792 C.2 1 <0> 0.9092
8 C8 -1.1556 29.8264 -9.1470 C.2 1 <0> 0.9071
9 C9 -2.6151 30.8987 -10.9189 C.3 1 <0> -0.0262
10 C10 -3.5221 30.2951 -8.6255 C.3 1 <0> -0.1568
11 C11 -2.5717 29.8912 -9.7583 C.3 1 <0> -0.1554
12 O1 -5.7013 31.2223 -8.3667 O.co2 1 <0> -0.8817
13 O2 -0.7003 30.9084 -8.6799 O.co2 1 <0> -0.8929
14 O3 -5.3714 29.5329 -9.8669 O.co2 1 <0> -0.8807
15 O4 -0.6188 28.6818 -9.1887 O.co2 1 <0> -0.8571
16 H1 -0.6331 28.8861 -15.4824 H 1 <0> 0.0899
17 H2 0.8655 30.0564 -13.8891 H 1 <0> 0.1079
18 H3 -3.0478 28.6460 -14.9665 H 1 <0> 0.0917
19 H4 -0.0427 30.9855 -11.7849 H 1 <0> 0.2049
20 H5 -3.9661 29.5717 -12.8653 H 1 <0> 0.1145
21 H6 -2.0757 31.8190 -10.6595 H 1 <0> 0.0142
22 H7 -3.6485 31.2140 -11.1119 H 1 <0> 0.0547
23 H8 -3.4370 29.5769 -7.7988 H 1 <0> -0.0109
24 H9 -3.2268 31.2722 -8.2199 H 1 <0> 0.0482
25 H10 -2.8394 28.8903 -10.1212 H 1 <0> 0.0739
@<TRIPOS>BOND
1 1 2 ar
2 1 3 ar
3 2 4 ar
4 3 5 ar
5 4 6 ar
6 5 6 ar
7 6 9 1
8 7 10 1
9 7 12 1
10 7 14 2
11 8 11 1
12 8 13 1
13 8 15 2
14 9 11 1
15 10 11 1
16 1 16 1
17 2 17 1
18 3 18 1
19 4 19 1
20 5 20 1
21 9 21 1
22 9 22 1
23 10 23 1
24 10 24 1
25 11 25 1
@<TRIPOS>SUBSTRUCTURE
</code></pre>
<h1>EDIT:</h1>
<p>The solution to the problem with <code>prepare_ligand4.py</code> would be</p>
<pre><code>prepare_ligand4.py -l my.mol2 -U \""" -C
</code></pre>
<p>to keep the partial charges and hydrogen atoms (oddly, <code>-U ""</code> didn't work for me: <code>prepare_ligand4.py: option -U requires argument</code>)</p>
| [
{
"answer_id": 19837,
"pm_score": 3,
"text": "<p>You saw my last <a href=\"https://biology.stackexchange.com/questions/19749/how-to-use-autodock-just-for-rescoring\">answer of your question</a>? you can do that easily, just use </p>\n\n<pre><code>prepare_ligand4.py -l my.mol2 -A \"hydrogens\"\n</code><... | [
{
"answer_id": 34897,
"pm_score": 0,
"text": "<p>In babel: </p>\n\n<pre><code>babel my.mol2 my.pdbqt -xh\n</code></pre>\n\n<p>-x states options for writing .pdbqt files\n-h says keep hydrogens</p>\n"
}
] |
19,891 | <p>There are approximately 20k protein-coding genes found in the human genome. This number is presumably very small when considering all the genomes found in the diverse microbes associated with the human body. </p>
<p>Is there an estimate for the total number of protein-coding genes found in human microbiome? </p>
| [
{
"answer_id": 19897,
"pm_score": 4,
"text": "<p>The Human Microbiome Project collected samples as shown in the image below from healthy volunteers:</p>\n\n<p><img src=\"https://i.stack.imgur.com/FMnKs.jpg\" alt=\"enter image description here\"></p>\n\n<p>They give an estimate of about 8 Million genes i... | [
{
"answer_id": 19894,
"pm_score": 2,
"text": "<h2>Human Microbiome Project</h2>\n\n<p>According to Published data on HMP website:</p>\n\n<ul>\n<li>The human microbiome consists of all the microorganisms that reside in or on the human body. </li>\n<li>They may cause illness but some are necessary for goo... |
19,942 | <p>The metabolic rate measures how much energy an organism <strong>expends</strong> over a unit of time. Its breakdown for the human body in terms of its functions is well documented : so much for the heart, for the brain, etc.</p>
<p>In West et al, 2002 I have found an estimate for the metabolic rate of a single cell. But how does this breakdown in terms of elementary functions in the cell?</p>
<p>E.g., how much of the energy made available from nutrients is used in the process of replicating genome, of expressing proteins, of trafficking...?</p>
<p>Following Jeremy Kemball's link suggestions, I find in <a href="http://www.ncbi.nlm.nih.gov/pubmed/7492307%2C7708012?dopt=Abstract" rel="nofollow">this paper</a> the fraction of ATP consumption for the following processes:</p>
<pre><code>Protein synthesis 0.34
Na+/K+ ATPase 0.16
Ca2+ ATPase 0.17
RNA/DNA synthesis 0.25
Unidentified 0.09
</code></pre>
<p>(which adds up to 1.01 rather than 1 for spurious reasons). Their measurement is indirect, based on $O_2$ consumption for an assumed steady-state regeneration of ATP. I wonder how GTP-based processes are accounted for? Or are they negligible compared to ATP ones?</p>
<p>This is for a specific cell type, rat thymocyte, is there a reason to expect that this will be hugely different for say a fibroblast? Also, they stimulate their thymocyte with concanavalin A. I understood they are not getting RNA/DNA consumption signal without Con-A, but didn't get why it would be so.</p>
<p>Finally, what would be in the remaining 9% ? One candidate for ATP consumption suggested by Jeremy Kemball is actin turnover, I guess it fits only in the "unidentified" line. Tubulin turnover is a GTP process, not sure about intermediate filaments (do they turnover?). All ATP-molecular motors (myosin, kinesin, dynein at least?) have to be there too. What else?</p>
<p>I am particularly interested in the total amount of ATP energy that goes to myosin.</p>
| [
{
"answer_id": 20031,
"pm_score": 4,
"text": "<p>I was musing on this and did some strange googling, and have some ballpark figures for a bunch of different organisms. It's far from a complete answer but it's at least a start, and all this won't fit in a comment.</p>\n\n<p>DNA replication, I assumed, w... | [
{
"answer_id": 20149,
"pm_score": 1,
"text": "<p>A significant amount of heat generated by the cell does not come from the hydrolysis of an NTP. ATP is generated by a H+ gradient in the mitochondria, and this gradient is created by mechanisms which rely only in part by ATP. Most of the energy stores in... |
19,967 | <p>Besides religious prohibition, there are several non-religious arguments against eating pork. A few of which are: </p>
<ol>
<li>Pigs and swine are so poisonous that you can hardly kill them with strychnine or other poisons. </li>
<li>Swine and pigs have over a dozen parasites within them, eg tapeworms, flukes, worms, and trichinae. There is no safe temperature at which pork can be cooked to ensure that they will be killed</li>
<li>The swine carries about 30 diseases which can be easily passed to humans</li>
</ol>
<p>I would like to hear some scholarly verification regarding these points. Simple Yes-No-Yes will be enough, elaboration is welcome, though.</p>
<p>Thank You</p>
| [
{
"answer_id": 19968,
"pm_score": 6,
"text": "<blockquote>\n<p>Pigs and swine are so poisonous that you can hardly kill them with strychnine or other poisons.</p>\n</blockquote>\n<p>This is a <em>non-sequitur</em>. An animal being poisonous does not imply that it resists to poison, nor the reverse is tr... | [
{
"answer_id": 19969,
"pm_score": 3,
"text": "<p>First: There is no biological reason to not eat pork. These bans (Jewish and Islamic) are based on religious rules, so this is more a cultural, not so much a biological answer.</p>\n\n<p>The reasoning that pork meat would deteriorate pretty fast in warm c... |
19,972 | <p>As a child I watched tiny fiddler crabs living in conical shells, and many years later I find that people study fossil turritellids. So now I wonder: how old are shells, typically, that you see on beaches? Do they wear out after a year of sand abrasion? 100 years, a million? Is it known? </p>
| [
{
"answer_id": 39960,
"pm_score": 4,
"text": "<p>Mollusk shells found on typical east coast (US) beaches can range from days old (the animal that made the shell died recently) to thousands of years old. Some shells in our state, North Carolina, have been dated as 40,000 years old. A high number of \"s... | [
{
"answer_id": 19981,
"pm_score": 2,
"text": "<p>Ages of shell as a piece can be checked or counted. </p>\n\n<p><img src=\"https://njsurfriderdrafts.files.wordpress.com/2012/03/seashells1.jpg\" alt=\"\"></p>\n\n<p>Procedure:</p>\n\n<p>1) Examine the shell's ridges with a magnifying glass.</p>\n\n<p>2) T... |
19,998 | <p>Which part of the brain is the first place (from top to bottom) where all 31 pairs of spinal nerves (on each side) meet? Or if they all start at one place - where is that?</p>
<p>Nominally, the beginning of the spinal cord is the medulla oblongata, but perhaps the spinal nerves or some sort of "root" of every nerve start at the Thalamus?</p>
| [
{
"answer_id": 21289,
"pm_score": 4,
"text": "<p>They don’t meet. </p>\n\n<p><strong>Some framework:</strong> </p>\n\n<ul>\n<li>Spinal nerves contain motor, sensory, and autonomic fibers. Each of these have different pathways. </li>\n<li>Spinal nerves don’t go to the brain. Rather, they synapse in the ... | [
{
"answer_id": 20296,
"pm_score": 0,
"text": "<p>I am not sure whether I grasped the gist of your question appropriately, but let me provide some clarifications. </p>\n\n<p>$\\text{Nerve}$ is simply a collection of axons. Therefore, all the spinal nerves are just bundles of assorted nerve axons. </p>\... |
20,002 | <p>Let's say I drink some Kefir Milk, what happens to the lactic acid in the Kefir Milk that has entered my digestive system?</p>
| [
{
"answer_id": 20012,
"pm_score": 4,
"text": "<p>First, there are two different isomers of the lactic acid, the L(+)- and the D(-)-form. Both differ in the position of the OH-group in the molecule:</p>\n\n<p><img src=\"https://i.stack.imgur.com/FdfH2.png\" alt=\"enter image description here\"></p>\n\n<p... | [
{
"answer_id": 20003,
"pm_score": 3,
"text": "<p>Lactic acid has been found to act as a fuel for the muscles. Refer to: <a href=\"http://www.nytimes.com/2006/05/16/health/nutrition/16run.html?_r=0\">http://www.nytimes.com/2006/05/16/health/nutrition/16run.html?_r=0</a></p>\n\n<blockquote>\n <p>Most at... |
20,006 | <p>I sometimes use <a href="http://www.ruralking.com/agristar-2-4-d-amine-1-gallon.html?utm_medium=cse&utm_source=google&CAWELAID=1624250989&CAGPSPN=pla&catargetid=520009190000031013&cadevice=c&gclid=CjwKEAjwxtKeBRDMzoeQmYn5uHcSJACGCF3Dhs22FITlehPhZgOacOeZU5_PbIz8W8iI4BOsuTyoPBoCeW7w_wcB" rel="noreferrer">2,4-Dichlorophenoxyacetic acid</a> to control broadleaved weeds in lawns. It is selective, and quickly kills the dicot weeds, while other plants are unharmed.</p>
<p><img src="https://i.stack.imgur.com/tGMsm.png" alt="enter image description here"></p>
<p>2,4-D is a synthetic auxin, a class of plant hormones. It is gets taken in through the stomata on the leaves, and is transported to the meristems of the plant. This causes uncontrolled, unsustainable growth, and the plant wilts, and dies.</p>
<p>Why doesn't this affect most monocotyledons?</p>
| [
{
"answer_id": 20138,
"pm_score": 4,
"text": "<p>According to <a href=\"http://www.purdue.edu/newsroom/research/2011/111122MurphyTransporter.html\" rel=\"noreferrer\">this link</a> from Purdue, the seed of the answer is this:</p>\n\n<blockquote>\n <p>The herbicide is used to kill broadleaf weeds, which... | [
{
"answer_id": 88996,
"pm_score": -1,
"text": "<p>The specificity of 2,4 D may be due to either limited translocation or rapid degradation ,altered vascular anatomy or altered perception of auxin in monocot</p>\n"
}
] |
20,019 | <p><a href="https://i.stack.imgur.com/lZrzJ.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/lZrzJ.jpg" alt="enter image description here"></a></p>
<p>In the picture above (Source: <a href="http://ecx.images-amazon.com/images/I/71zKixilmEL._SL1500_.jpg" rel="nofollow noreferrer">Amazon.com</a>, United Scientific MCT001 Hand Microtome) we can see a microtome. How is it operated?</p>
| [
{
"answer_id": 20022,
"pm_score": 3,
"text": "<p>The imnstrument is shown here upside down. If it is turned around, it looks like this:</p>\n\n<p><img src=\"https://i.stack.imgur.com/cwWXG.jpg\" alt=\"enter image description here\"></p>\n\n<p>The glass disc are placed around the middle tube. The operati... | [
{
"answer_id": 58826,
"pm_score": 1,
"text": "<blockquote>\n <p>Also, are these still used in everyday biological research? Teached\n for students?</p>\n</blockquote>\n\n<p>It's a hand microtome allright. As Chris explained, these are used to section thin slices of plant tissue, to be examined using a... |
20,034 | <p><strong>Dry Humping</strong>, is:</p>
<blockquote>
<p>dry humping is the process of two people repeatedly moving up and down and back and forth on top of each other fully clothed( or missing various pieces, but the penis must not come in contact with the vagina with out some sort of fabric separating them ex: boxers,panties, or even sheets!!)</p>
</blockquote>
<p>We all know that the basic rule for impregnation is that the sperm must come in contact with the egg, and even be able to fertilize it. While sperm can get through clothes, semen (but this is yet been proven or disproved) gets stuck, thus the sperm dies.</p>
<p>What is your opinion about this? If two people are on top of each other, fully clothed, and the male comes to ejaculation, is there any chance that pregnancy can happen, in the <strong>realistic</strong> and biological look at it (and not some probability or statistical way)? What advice should be given to teens on the matter?</p>
<p>I am a computer scientist with no biology knowledge, and am very interested in getting the opinion of biologists.</p>
<p>But since I know that the stackexchange community likes to see work done before asking questions, I did my own research (I am used to googling code and algorithms):
Very few research has been done on the subject. There is one shining research that concluded, as I recall, that:</p>
<blockquote>
<p>If the underwear is <strong>completely saturated</strong> with semen, and is in <strong>direct</strong> contact with the woman's vagina, pregnancy is <strong>possible</strong> statistically, but <strong>highly unlikely</strong>.</p>
</blockquote>
| [
{
"answer_id": 20036,
"pm_score": 5,
"text": "<p>If there has been an ejaculation by the male, and semen is present, there is a chance of getting pregnant. Period. Teens really need to know that.</p>\n<p>I think you may have your terms confused - semen is the overall fluid released during an ejaculation... | [
{
"answer_id": 43572,
"pm_score": -1,
"text": "<p>It is effectively impossible to get pregnant by <a href=\"http://beforeplay.org/2014/01/can-sperm-go-through-clothes-and-get-a-woman-pregnant/\" rel=\"nofollow\">dry-humping</a> because the conditions that would have to be met for sperm to pass through m... |
20,086 | <p>Can you please give me some advice for a book in (evolutionary) <a href="http://en.wikipedia.org/wiki/Conservation_genetics" rel="nofollow">conservation genetics</a> that offers an in-depth review of the mathematical formulations used in this field.</p>
<p>I read the book <a href="http://www.amazon.fr/Evolutionary-Conservation-Biology-R%C3%A9gis-Ferri%C3%A8re/dp/0521116082/ref=sr_1_3?ie=UTF8&qid=1406725200&sr=8-3&keywords=evolutionary%20conservation%20biology" rel="nofollow">Evolutionary Conservation Biology (Ferrière and Dieckmann, 2009)</a> and I really liked it. I'm seeking for another book of the same kind that goes further on the part A (Theory of Extinction) and especially on the concern of the importance of population structure and the genetic load. I am also interested in <a href="http://en.wiktionary.org/wiki/landscape_genetics" rel="nofollow">landscape genetics</a>.</p>
| [
{
"answer_id": 20101,
"pm_score": 3,
"text": "<p>This book \"<a href=\"http://www.cambridge.org/se/academic/subjects/life-sciences/ecology-and-conservation/primer-conservation-genetics\" rel=\"nofollow\">A primer of conservation genetics</a>\" would suit quite well I think. In particular chapter five de... | [
{
"answer_id": 20115,
"pm_score": 2,
"text": "<p>If you're interested in learning about the mathematics of population genetics, <a href=\"http://onlinelibrary.wiley.com/book/10.1002/0470047356\" rel=\"nofollow\">Population Genetics and Microevolutionary Theory</a> by Alan Templeton is an absolutely amaz... |
20,129 | <p><strong>Very simple:</strong> Why (and how) is regenerated skin different from original ?</p>
<p>As we know we lose skin cells that becomes the dust in out homes and it always grows back to full thickness right ? So when I have a cut, I imagined it to heal provisionally with whatever possible and then after some time to replace itself with the normal skin that is coded in my chromosomes. So why doesn't it do that ? Scars remain and the color is always different from the neighbor parts.</p>
<h2>Update:</h2>
<ul>
<li>Why we get scars?</li>
<li>What about skin transplants ? </li>
<li>Why doesn't skin actually grow/replace itself? </li>
</ul>
<h2>Update 2:</h2>
<ul>
<li>(I've been thinking) Skin has lots of different layers, right ? So when an area is damaged does it regenerate all layers or just one for being simple and efficient (in "hope" the subject will take precautions not to damage this part of body again, so that regenerating everything back to 100% would be overkill) ?</li>
<li>I'm not a scientist, I have only the basics from school, so I'll probably not understand most of the technical terms</li>
<li>also I'm more interested about an explanation that goes towards the "survival of the fittest" rule, and not so much about the biochemical reactions in our bodies (because it was just some random mutation that turned out to be the better choice for us → why?)</li>
</ul>
| [
{
"answer_id": 20210,
"pm_score": 4,
"text": "<p>Human skin is made up of three layers [1]:</p>\n\n<ol>\n<li>Epidermis; it contains no blood vessels; it has 5 cellular layers (starting from surface):\n\n<ul>\n<li><strong>stratum corneum</strong></li>\n<li>stratum lucidum</li>\n<li>stratum granulosum</li... | [
{
"answer_id": 20147,
"pm_score": 2,
"text": "<p>You're confusing an emergent system with a determined system. Your cells have programming which emerges as the form you see. You are using determinism to decide what your form should be. Determinism gives one reaction for every action. Biology is emergent... |
20,176 | <p>There are many plants and animals named for the naturalist Charles Darwin, such as Darwin's Frog <em>(Rhinoderma darwinii)</em>, but which were named by him? I'm finding it difficult to find such a list.</p>
| [
{
"answer_id": 20200,
"pm_score": 4,
"text": "<p>I've discovered that searching for <a href=\"http://eol.org/search?q=darwin&type%5B%5D=taxon_concept\" rel=\"nofollow\">Darwin on the Encyclopedia of Life</a> (EOL) appears to prioritise in its search results those species named by Darwin rather than ... | [
{
"answer_id": 20186,
"pm_score": 3,
"text": "<p>I don't know if these are his earliest descriptions but Darwin did describe several species of Planaria, such as <em>Planaria vaginuloides</em>, <em>P. oceania</em>, plus a new genus, <em>Diplanaria</em> in 1844.</p>\n\n<p><a href=\"http://darwin-online.o... |
20,215 | <p>I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact. </p>
<p>I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20. </p>
<p>My primary question is: <strong>how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?</strong></p>
<p>I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.</p>
| [
{
"answer_id": 20216,
"pm_score": 4,
"text": "<p>I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have <a href=\"https://en.wikipedia.org/wiki/Zygosity#Homozygous\">homozygotes</a> an... | [
{
"answer_id": 20236,
"pm_score": 0,
"text": "<p>Also I don't know what kind of genetic input your given but if there is variation in origin ie some saliva some cheek skin then there could be a tissue based difference in the genome. </p>\n"
}
] |
20,217 | <p>I saw this pic while crawling online and it was a bit different for me to predict which worm is this. </p>
<p><img src="https://i.stack.imgur.com/grEvP.jpg" alt="enter image description here"></p>
<p><strong>Source:</strong> <a href="http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/" rel="nofollow noreferrer">http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/</a></p>
<p>It appears somewhat different form other annelids as parapodia or setae are somewhat transparent and very attractive too.</p>
<p>What worm is this?</p>
| [
{
"answer_id": 20219,
"pm_score": 2,
"text": "<p>As Cornelius correctly pointed out, it's not a living worm :)</p>\n\n<p>As to the question, what kind of worm they tried to imitate, I'd say, they had a <a href=\"https://www.google.com/search?channel=fs&q=nereidae&tbm=isch\" rel=\"nofollow\">nere... | [
{
"answer_id": 20218,
"pm_score": 2,
"text": "<p>If you would have read the text from the source of that image (which by the way you didn't mention, I did a Google Image search and edited your question to include it), you would have known that what is seen in the picture is not a living thing, it is a l... |
20,225 | <p>Haven't looked into this to very long, but an initial search didn't return anything. </p>
<p>HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed proteins that mimic cell receptors, either locking the virus out of vulnerable cells, or even causing the virus to release its genetic material (pre-mature ejc. for viruses... :|), so it can't accidentally get away and infect a cell anyway? It seems like an obvious idea, so the fact that it may not already be happening must mean there are a host of challenges to it? Basically we design a protein that acts like a strait jacket, with tags that allow our body to recognize it as a 'friendly' body. T-cells use the same receptor though, so are there ways to identify a T-cell compared to a HIV virion?</p>
<p>Obviously this wouldn't prevent some viruses managing to infect actual cells, but over time, if we can attack enough, say 2/3 of the virions, for each generation, we could seriously harm the population, and maybe keep it in check?</p>
| [
{
"answer_id": 20231,
"pm_score": 4,
"text": "<p>Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against <a href=\"http://en.wikipedia.org/wiki/Rabies#Treatment\">rabies</a>. There you get a dose of immunoglobulins directed against the rabies vi... | [
{
"answer_id": 64317,
"pm_score": 1,
"text": "<p>This approach actually works on almost anything, given enough proteins and nanoscale \"griefing\".</p>\n\n<p>There was an experiment a few years back where scientists wrapped normal cell membranes around polyurethane beads. The surface looks like a normal... |
20,264 | <p>According to my textbook, Davson-Danielli's model of a phospholipid bilayer sandwiched between two layers of globular protein was incorrect. The nonpolar protein portions would separate the polar portions of the phospholipids from water, causing the bilayer to dissolve. Meaning, the Davson-Danielli model is not only incorrect, but it is also impossible.</p>
<p>I understand why the model is incorrect, but not why it is impossible. In my view, the nonpolar proteins would remain together in a micelle shape due to hydrophobic exclusion. Because of this, the phospholipid bilayer sandwiched on the inside would remain isolated from the water.</p>
<p>Why would a bilayer dissolve if the proteins were in contact with water and the phospholipids were isolated from the water? </p>
<p>I think that my confusion stems from many misunderstandings about the chemistry and structure of the cell membrane. In depth illustration of the error that my book mentioned would be most helpful.</p>
| [
{
"answer_id": 20265,
"pm_score": 4,
"text": "<p>The original figure that Danielli and Davson proposed looks like this (from the <a href=\"http://onlinelibrary.wiley.com/doi/10.1002/jcp.1030050409/abstract\" rel=\"nofollow noreferrer\">original publication</a>):</p>\n\n<p><img src=\"https://i.stack.imgu... | [
{
"answer_id": 24051,
"pm_score": 0,
"text": "<p><strong>Problems with the davson danielli model :</strong></p>\n\n<ol>\n<li><em>freeze-etched micrographs</em>:</li>\n</ol>\n\n<p>This is a technique of rapidly freezing the cell and then fracturing them. The fracture occurs along lines of weakness and in... |
20,266 | <p>I understand that in PCR we're able to amplify only selected portions of the DNA... however despite reading it from multiple sources, I cannot figure out how this selection actually takes place.</p>
<p>I know that by using proper primers, one each for coding and template strands, we can direct the DNA polymerases to specific sites to start with. I also understand that these primers make the replication proceed in opposite directions, towards each other. Like follows:</p>
<p><img src="https://i.stack.imgur.com/9N6Ug.png" alt="My understanding of so far"></p>
<p>However, I wonder what makes the replication terminate when the polymerase reaches the primer at the other end? Because as far as I understand, replication should continue indefinitely until the physical end of the sample strand is reached... such that we may decide the starting points but never the ending points.</p>
| [
{
"answer_id": 20267,
"pm_score": 4,
"text": "<p>Note: In your PCR program you always set extension time.</p>\n\n<p>Case:</p>\n\n<ul>\n<li>Product length = 500bp</li>\n<li>PCR extension time = 50sec</li>\n<li>Assuming that polymerase adds 1000 nt/min</li>\n</ul>\n\n<p>Cycle 1:</p>\n\n<ul>\n<li>Strand th... | [
{
"answer_id": 20268,
"pm_score": 2,
"text": "<p>I'm not completely clear when you say \"what makes the replication terminate when the polymerase reaches the primer at the other end\" since when you perform a PCR you go through three phases. The denaturation, whereby the two DNA strands become single st... |
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