qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
35,262 | <p>I am working in the field of neuroscience with a background in computer science. I try to find new ways of analyzing brain imaging data (mostly MRI, EEG, MEG, fMRI) with modern machine learning methods.</p>
<p>I would like to take a step up by adding genetics to the data arsenal. My work this far has found connections between some X and Y but not really shed insight to <em>why</em> things should be like that. I hope I could get a partial answer from biology.</p>
<p>To get started, I would need some good material to read. It does not matter if the content would be difficult in mathematical/statistical/technical aspects, but it should be approachable with limited knowledge in biology and/or chemistry and physics.</p>
<p>Suggestions?</p>
| [
{
"answer_id": 35244,
"pm_score": 4,
"text": "<p>In biology ligand is a very broad term. Everything is called a ligand that has a receptor for it, regardless whether it is free or membrane-bound. There is very much sense in membrane bound ligands, because many cells in our body are capable of actively m... | [
{
"answer_id": 35246,
"pm_score": 3,
"text": "<p>A perfectly reasonable definition of a ligand from <a href=\"https://en.wikipedia.org/wiki/Ligand_(biochemistry)\" rel=\"nofollow noreferrer\">Wikipedia</a>:</p>\n<blockquote>\n<p>In biochemistry and pharmacology, a ligand is a substance that forms a comp... |
35,404 | <p>I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). </p>
<p>I am curious about the "regular expression (regex)" (pattern/motif) in bioinformatics. Can anyone help point out some repository where I can see some "regex" instances (used by people in real cases)? </p>
<p>So that I can get a sense how complex they are and the possibility to apply our techniques. </p>
<p>Thank you!</p>
| [
{
"answer_id": 35411,
"pm_score": 2,
"text": "<p>Prosite (<a href=\"http://prosite.expasy.org/\" rel=\"nofollow\">http://prosite.expasy.org/</a>) uses regular expressions to search for protein domains, in contrast with Pfam. If you look at an entry, such as <a href=\"http://prosite.expasy.org/cgi-bin/pr... | [
{
"answer_id": 35406,
"pm_score": 2,
"text": "<p>Regular expressions are not commonly used for DNA or Protein analysis, but many people use Hidden-Markov-Models (HMMs).</p>\n\n<p>If you are looking at protein domains, you can find many HMMs here:\n<a href=\"http://pfam.xfam.org/\" rel=\"nofollow\">http:... |
35,415 | <p>Chromosome number differs across species.</p>
<p>Is the amount of DNA comparable between organisms, just being split into smaller chunks in those species with more chromosomes, or do species have different genome sizes? If so, does the genome size correlate roughly with the complexity of the species?</p>
| [
{
"answer_id": 35422,
"pm_score": 6,
"text": "<p>Chart of C-values (the mass of DNA in a single haploid cell); there is no logical order to the groups:</p>\n\n<p><img src=\"https://i.stack.imgur.com/nxOdG.jpg\" alt=\"enter image description here\"></p>\n\n<p>[<a href=\"https://www.genomesize.com/statist... | [
{
"answer_id": 35418,
"pm_score": 2,
"text": "<p>I can show the facts here. </p>\n\n<p><strong>Human:</strong></p>\n\n<p>total length: about 3,000,000,000</p>\n\n<p>coding genes: about 50,000 (included predicted ones)</p>\n\n<p>3,000,000,000/50,000=60,000</p>\n\n<p>Chromosome number: 23</p>\n\n<p><stron... |
35,442 | <p>The figures below are from Felsenstein's paper "Phylogenies and the Comparative Method". I was wondering if there was a specific name for this effect where there is an apparant correlation that is actually the result of the data being structured into two separate groups, where there is no correlation within groups but an apparent correlation between groups. "Phylogenetic non-independence" doesn't seem specific enough.</p>
<p><img src="https://i.stack.imgur.com/DuDSs.png" alt="enter image description here"></p>
| [
{
"answer_id": 35455,
"pm_score": 4,
"text": "<p>I've seen this termed \"phylogenetic pseudoreplication\", but I can't remember offhand where. I'll see if I can find it. Without a tree, the boxes and Xs essentially represent 2 data points. As Remi.b suggests, this is really just high phylogenetic signal... | [
{
"answer_id": 35445,
"pm_score": 2,
"text": "<p>The fact that species are not independent observations because of their specific phylogenetic relationship is sometimes called <strong>phylogenetic dependence</strong> (see its use in <a href=\"http://www.sciencedirect.com/science/article/pii/S10557903070... |
35,509 | <p>Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the protein eventually stop? Would it keep coding into the poly-A chain and insert a bunch of phenylalanine?</p>
| [
{
"answer_id": 35510,
"pm_score": 4,
"text": "<p>No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premat... | [
{
"answer_id": 35524,
"pm_score": 2,
"text": "<p>Yes you are correct. These mRNAs, that lack stop codon will cause translation to continue into the poly-A tail (it will result in addition of lysines not phenylalanine). Since no stop codon is present, the ribosome remains attached to the mRNA. Under thes... |
35,514 | <p>Metaphorically thinking, if one endured the pain of constant burning for decades, would the pain slowly lose its strength?</p>
| [
{
"answer_id": 35510,
"pm_score": 4,
"text": "<p>No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premat... | [
{
"answer_id": 35524,
"pm_score": 2,
"text": "<p>Yes you are correct. These mRNAs, that lack stop codon will cause translation to continue into the poly-A tail (it will result in addition of lysines not phenylalanine). Since no stop codon is present, the ribosome remains attached to the mRNA. Under thes... |
35,544 | <p>Coming out of the pool the other day, I felt very cold because I was wet and the wind picked up. My idea is that a "cold" feeling should be associated with low temperatures, but it's indeed wrong. </p>
<p>Why do we perceive wind at a farely normal temperature as cold?</p>
| [
{
"answer_id": 35555,
"pm_score": 5,
"text": "<p>One important point that you might not be considering is the heat of vaporization.</p>\n\n<p>You may be aware that while it normally takes 4.18 J (1 calorie) of heat to raise 1 gram of water 1 °C, it takes around 2250 J of heat to raise 1 g of water from ... | [
{
"answer_id": 35548,
"pm_score": 3,
"text": "<p>This phenomena has nothing to do with any different kinds of receptors.\nWhen we are wet, we have lots of water on our surface. The evaporation of water causes cooling.</p>\n\n<p>Blowing wind tends to make evaporation faster. So, even if wind blows at nor... |
35,569 | <p>I know what the effects are of a dangerous situation on the brain, <em>i.e.</em>, an activation of the <a href="https://en.wikipedia.org/wiki/Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis" rel="nofollow noreferrer">hypothalamic-pituitary-adrenal (HPA) axis</a> which eventually results in an increased heart rate and elevated blood pressure. However, I do not understand why enhanced blood circulation would result in a paling of the skin? Do red blood cells actively change direction? </p>
| [
{
"answer_id": 35574,
"pm_score": 6,
"text": "<p>Red blood cells are not equipped with a motor system to propel them through the blood stream. Instead, they are passively transported through the vasculature by the the pumping action of the heart. The effects of dangerous situations on the skin have to d... | [
{
"answer_id": 35570,
"pm_score": 2,
"text": "<p>It has nothing to do with blood cells <em>per se</em>. Blood vessels constrict in areas not necessary for flight-and-fight response (sympathetic nervous system response).</p>\n\n<p>By constricting blood vessels around face, blood is redirected to organs m... |
35,713 | <p>Almost everyone nowadays wants that nice summer tan, but what exactly is going on beneath the skin? I've heard a few different theories about tanning - such as a tan is nothing but the pigmentation in your cells burning, but is this true?</p>
<p><strong>My questions:</strong></p>
<ul>
<li>What exactly is happening to our skin as we tan?</li>
<li>Are pigments being burned (like I was told in school), or is pigment being produced by the cells. ?</li>
</ul>
<hr>
<p><strong>Bonus related question:</strong>
<a href="https://biology.stackexchange.com/questions/35718/why-do-some-people-burn-and-others-tan">Why do some people burn and others tan?</a> </p>
<p><strong>Bonus related question:</strong> <a href="https://biology.stackexchange.com/questions/35719/how-does-our-tan-disappear">https://biology.stackexchange.com/questions/35719/how-does-our-tan-disappear</a></p>
| [
{
"answer_id": 35716,
"pm_score": 5,
"text": "<p>When our skin is exposed to the sun, this can cause some damage in the upper layers of skin. This activates DNA damage repair and also induces signalling towards the melanocytes (which produce the pigment). Signalling means the excretion of signalling mol... | [
{
"answer_id": 35715,
"pm_score": 2,
"text": "<p>First, one should mention types of skin: skin type defines how the person will tan - </p>\n\n<p><img src=\"https://i.stack.imgur.com/xrKTh.jpg\" alt=\"enter image description here\"></p>\n\n<p><img src=\"https://i.stack.imgur.com/oMfmg.gif\" alt=\"enter i... |
35,773 | <p><strong>Question</strong></p>
<p>Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals have the exact same fitness.</p>
<p><em>What is the fraction of sites that we'd expect to be polymorphic in the population (SNPs)?</em></p>
<p><strong>Motivation behind this question</strong></p>
<p>I am asking this question to verify the results of simulations I run. For example, I run a simulation with $x$ ($x$ will be varying below) neutral sites, with a per-site mutation rate $\mu = 10^{-9}$ and a population size of $N=100$. I run the simulations for 10,000 generations. There is no recombination. When the number of sites:</p>
<ul>
<li>$x=10^3$ I get 0 SNP</li>
<li>$x=10^4$ I get 1 SNP</li>
<li>$x=10^5$ I get 3 SNPs</li>
<li>$x=10^6$ I get 25 SNPs</li>
<li>$x=10^7$ I get 238 SNPs</li>
</ul>
<p><em>Is there a bug in my model or is it what we'd expect given the parameters?</em></p>
<p>In the human genome, 1 out of 300 sites are polymorphic (SNPs) (<a href="http://ghr.nlm.nih.gov/handbook/genomicresearch/snp" rel="nofollow">ref.</a>). This is a frequency of SNPs that is 100 times greater than what I observe in my simulations. Note however, that the assumption of neutrality and out demographic assumptions would not perfectly hold and this result could pretty far off neutral expectation. My goal is not to reproduce something that look like the human genome but only to reproduce the neutral expectations for the moment.</p>
| [
{
"answer_id": 35914,
"pm_score": 3,
"text": "<p>Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model.</p>\n\n<p>The general form of the estimation for a diploid population is $E[S]=4N\\mu\\... | [
{
"answer_id": 35777,
"pm_score": 2,
"text": "<p>The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [<a hre... |
35,806 | <p>Many instances of this worm-like creature were found in a water system for a mountain cabin in the Sierra Nevada mountains of the US, in late June / early July. The water system collects water from an enclosed spring. Can you help identify this creature? </p>
<p>Clues:</p>
<ol>
<li>The worms have two "points" on their heads. </li>
<li>They can stretch out and be long and thin, or when poked (or are resting) they contract into a small blob. </li>
<li>Here is a picture of a single worm with markings shown.
<img src="https://i.stack.imgur.com/hIiWZ.jpg" alt="enter image description here"></li>
<li>Here is a picture of a few worms, somewhat contracted.
<img src="https://i.stack.imgur.com/Ux4HJ.jpg" alt="enter image description here"> </li>
<li><a href="https://www.youtube.com/watch?v=xCBjzdkL7lA&authuser=0">Here</a> is a movie of them moving, in natural light. </li>
<li><a href="http://www.youtube.com/watch?v=XgaZMEjlLK0&authuser=0">Here</a> is a movie of them moving, with backlight.</li>
<li>Here are pictures of their undersides and their internal structures.
<img src="https://i.stack.imgur.com/KDGUr.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/ZRxBe.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/nh1ne.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/TIYig.jpg" alt="enter image description here"></li>
<li>Whenever I pull some out of the water and put them into a tupperware with the same water, they only survive for around 24 hours, after which they seem to disintegrate. Here is a picture of about 20 of the worms after about 24 hours, the bulk of them have halfway-decomposed and form a heap in the upper right. After another day it'll just look like debris in the water, you wouldn't even recognize that there were worms in it. There is a piece of bacon in there because some suggested putting it there to test if they were leeches, but this disintegration happens repeatably and regardless of the bacon; please ignore the bacon.<br>
<img src="https://i.stack.imgur.com/V5xvH.jpg" alt="enter image description here"></li>
<li>Someone suggested that they are trematodes, but there are no snails, frogs, or other creatures in the storage and collection sections of the water system; we have looked very closely. There may be something within a 30-foot section of pipe, but we doubt it. </li>
</ol>
<p>Can you help us identify this creature? Even just possible families of creatures or general categories would be helpful for us. </p>
| [
{
"answer_id": 35809,
"pm_score": 5,
"text": "<p>I am not too sure but this looks like <em>Polycelis sierrensis</em>.</p>\n\n<p>Though it is apparent that the worm in your pictures is a tricladid planarian, I was not too sure about the species and the geographical distribution. </p>\n\n<p>However, from ... | [
{
"answer_id": 35807,
"pm_score": 3,
"text": "<p>Their capacity to elongate / contract and their two head lobes make me think they are <a href=\"https://en.wikipedia.org/wiki/Planarian\" rel=\"noreferrer\">Planarians</a>.</p>\n\n<p>The two points on their heads must be their eyes: <a href=\"https://en.... |
36,079 | <p>Often the names of herbal ingredients in certain cosmetics products are given by their scientific names like <em>Anthemis nobilis</em> instead of chamomile or <em>Lavandula angustifolia</em> instead of lavender. </p>
<p>Is there any reason why this practice is followed? Wouldn't those who have allergies to certain plant materials be better off reading "coriander leaf extract" instead of scratching their heads over what "<em>Coriandrum sativum</em> leaf extract" is? Why put something more complex when something simpler would be more beneficial to the consumer?</p>
| [
{
"answer_id": 36082,
"pm_score": 6,
"text": "<p>The use of a <em>genus-species</em> notation gives <strong>more exact information</strong>. For example there are <a href=\"http://www.encyclopedia.com/topic/chamomile.aspx\">multiple species of chamomile</a>: There is Roman chamomile (<em>Chamaemelum nob... | [
{
"answer_id": 36089,
"pm_score": 3,
"text": "<p>The Latin names are known in all countries. The \"popular\" names are only popular in one or maybe two languages/countries. So, learning the Latin names, enables you to communicate international more easily.</p>\n"
},
{
"answer_id": 36094,
"pm... |
36,150 | <p>I have a time-dependent system of varying number of particles (~100k particles). In fact, each particle represents an interaction in a 3D space with a particular strength. Thus, each particle has (X,Y,Z;w) which is the coordinate plus a weight factor between 0 and 1, showing the strength of interaction in that coordinate. Here <a href="http://pho.to/9Ztti" rel="nofollow">http://pho.to/9Ztti</a> I have uploaded 10 real-time snapshots of the system, with particles are represented as reddish small dots; the redder the dot, the stronger the interaction is.</p>
<p>The question is: how one can produce a 3D (spatial) density map of these particles, preferably in Matlab or Origin Pro 9 or ImageJ? Is there a way to, say, take the average of these images based on the red-color intensity in ImageJ?</p>
<p>Since I have the numerical data for particles (X,Y,Z;w) I can analyze those data in other software as well. So, you are welcome to suggest any other analytical approach/software</p>
<p>Any ideas/comments are welcome!</p>
| [
{
"answer_id": 36163,
"pm_score": 2,
"text": "<p>R packages <a href=\"https://cran.r-project.org/web/packages/misc3d/misc3d.pdf\" rel=\"nofollow noreferrer\"><code>misc3d</code></a> and <a href=\"https://cran.r-project.org/web/packages/rgl/rgl.pdf\" rel=\"nofollow noreferrer\"><code>rgl</code></a>. The ... | [
{
"answer_id": 36151,
"pm_score": 0,
"text": "<p>Trying to analyze that much data in ImageJ seems likely to end in frustration. Matlab is probably a more productive angle. Personally, I would use Python. Specifically, the numpy module. Try looking into the <a href=\"http://docs.scipy.org/doc/numpy/refer... |
36,189 | <p>Why can't plasma proteins shift from capillaries to connective tissue but WBCs can be very rich in connective tissue even though obviously the WBCs had to go through capillaries. Another example: in alveolar sacs neutrophils are there in the lumen despite the presence of epithelia of alveolar sacs, and it can only reach there via capillaries. So, how can they get into lumen despite the epithelia lining? Histology textbooks say that no plasma proteins can enter or leave capillaries, but WBCs (which are much larger than proteins) can move to connective tissue via capillaries?</p>
| [
{
"answer_id": 36193,
"pm_score": 4,
"text": "<p>Cells of the endothelium are joined by tight cell junctions which are impermeable or selectively permeable. Generally, proteins can only migrate through the endothelium via active transcytosis.</p>\n<p>Leukocytes (specifically neutrophils, lymphocytes and... | [
{
"answer_id": 36191,
"pm_score": 1,
"text": "<p>Generally, for plasma proteins to enter the tissue space, they must be able to passively diffuse out of the vessel into the tissue. This requires sufficiently large gaps between the endothelial cells of the vessel wall (and if passing into the lumen, spac... |
36,222 | <p>I have heard from a (usually very knowledgeable) friend before, that a human can only tap his fingers 7 times per second.</p>
<p>I generalized this to "our muscles are limited to 7 hertz"</p>
<p>When my wife heard this she was like "no way, I'm faster" and we recorded a video of her blinking as fast as she could (her eyes hurt afterwards) and over 5 seconds she averaged <strong>exactly</strong> 7 blinks per second.</p>
<p>I can't find any articles on the subject, but I did find this <a href="http://www.telegraph.co.uk/news/newsvideo/weirdnewsvideo/10187844/Worlds-fastest-drummer-sets-record-with-over-20-beats-per-second.html" rel="noreferrer">video</a> of a drummer doing 1208 beats in 60 sec, setting him up at 20.13hz, meaning 10hz each hand. However if you look at his hand, his muscles are not even really tapping, they are just in a vibration (like a spasm), while holding the drumsticks, which than do all the tapping...</p>
<p>Ussain Bolt sprinted 100m in 9.6 seconds, with 41 steps, that's a little over 4 steps per second.</p>
<p>Both these are very impressive. The drummer sticks out for coordinating his 10 taps per second on each hand, alternating with the other hand, while the motion is certainly faster then our eyes can see.</p>
<p>So what's up with the 7 Hz speed limit? Is it a thing, or did the drummer disprove it? Could the 100m world record be beaten by another 25% when we can find a tall guy capable of doing 7 or even 10 steps per second?</p>
| [
{
"answer_id": 36687,
"pm_score": 3,
"text": "<p>Our muscles are not limited to 7 hertz. </p>\n\n<p>You provide two examples yourself. I can provide a third: world's fastest clapper: 804 claps in 1 minute (<a href=\"https://www.youtube.com/watch?v=ORp2nzwHXN0\" rel=\"nofollow\">video here</a>), which is... | [
{
"answer_id": 36685,
"pm_score": 2,
"text": "<p>According to the book, <a href=\"https://play.google.com/store/books/details?id=cWwiAQAAQBAJ&source=productsearch&utm_source=HA_Desktop_US&utm_medium=SEM&utm_campaign=PLA&pcampaignid=MKTAD0930BO1&gl=US&gclid=CNmY4eWcl8cCFQfqfgo... |
36,223 | <p>I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest.</p>
<p>In order to validate the type of cells I have collected using this marker, I want to perform qPCR on their extracted RNA, using certain known cell-type marker primers.</p>
<p>My problem is that in each sorting session, I am only able to collect anywhere from 5,000 - 10,000 cells. Do you know if it is possible to perform RT-qPCR on such a small sample size?</p>
<p>I have collected the cells in 1mL of Trizol.</p>
<p>Would I maybe have to amplify the cDNA after reverse transcription in a general manner ( using random primers)?</p>
<p>Thanks for your help. </p>
| [
{
"answer_id": 36687,
"pm_score": 3,
"text": "<p>Our muscles are not limited to 7 hertz. </p>\n\n<p>You provide two examples yourself. I can provide a third: world's fastest clapper: 804 claps in 1 minute (<a href=\"https://www.youtube.com/watch?v=ORp2nzwHXN0\" rel=\"nofollow\">video here</a>), which is... | [
{
"answer_id": 36685,
"pm_score": 2,
"text": "<p>According to the book, <a href=\"https://play.google.com/store/books/details?id=cWwiAQAAQBAJ&source=productsearch&utm_source=HA_Desktop_US&utm_medium=SEM&utm_campaign=PLA&pcampaignid=MKTAD0930BO1&gl=US&gclid=CNmY4eWcl8cCFQfqfgo... |
36,344 | <p>I'm curious about what happens when you insert organelles from a cell into another. In particular, mitochondria.</p>
<p>Take two cells from your own body. Somehow extract a mitochondria from one cell and somehow insert it in the other cell.</p>
<p>Will the cell with the foreign mitochondria make use of it (respiration), or will it dispose it?</p>
<p>What if the foreign mitochondria comes from someone else's body?</p>
<p>What if the foreign mitochondria comes from another species' cell?</p>
| [
{
"answer_id": 36364,
"pm_score": 5,
"text": "<p>There is evidence that cells can exchange mitochondria. There are some donor cells that transfer mitochondria to recipient cells via cytoplasmic nanotubes (within the same species). This happens endogenously and triggering factors may include stress.</p>\... | [
{
"answer_id": 36346,
"pm_score": 2,
"text": "<p>I'm not entirely sure about cross species organelle transfer (lets focus on mitochondria), but some people have already made three parent babies, therefore mitochondria are at least transferable between individuals of the same species. </p>\n\n<p>The reas... |
36,496 | <p>Most amphibians - at least, all the ones I know of - start their lives in the water (at least, after they hatch). They then spend time maturing before venturing onto land, where they can breed. The cycle than begins again.</p>
<p>Are there any cases where the reverse is true, i.e. a young amphibian starts life on land before venturing into the water as an adult?</p>
<p><a href="https://en.wikipedia.org/wiki/Amphibian" rel="nofollow">Wikipedia</a> hints that this may be the case, but fails to provide examples:</p>
<blockquote>
<p>Amphibians typically start out as larvae living in water, but some
species have developed behavioural adaptations to bypass this.</p>
</blockquote>
| [
{
"answer_id": 36498,
"pm_score": 4,
"text": "<p>From <a href=\"https://en.wikipedia.org/wiki/Amphibian\" rel=\"nofollow\">wiki</a>:</p>\n\n<blockquote>\n <p>Most amphibians lay their eggs in water and have aquatic larvae that undergo metamorphosis to become terrestrial adults</p>\n</blockquote>\n\n<p>... | [
{
"answer_id": 36534,
"pm_score": 1,
"text": "<p>Arguably, since <a href=\"http://io9.com/5621249/ultra-tiny-frogs-discovered-living-like-faeries-inside-pitcher-plants/\" rel=\"nofollow noreferrer\">this frog</a> spends the entire larval stage inside a pitcher plant on land, it has started its life cycl... |
36,501 | <p>I am reading <a href="http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=3317&fileId=S0016672397002954" rel="nofollow noreferrer">Charlesworth et al. 1997</a>. They talk about diversity within and between allelic classes.</p>
<blockquote>
<p>Nucleotide diversities (<span class="math-container">$π$</span>) at each neutral site were estimated from the mean of <span class="math-container">$2 \sum z_t (1-z_t)$</span>, over replicated introductions at the site of single variants, where zt is the frequency of the neutral variant at time t, and summation is over all times until either fixation or loss occurs.</p>
<p>The total genetic diversity at the neutral sites (<span class="math-container">$π_T$</span>) was also decomposed into that within and between allelic classes at the polymorphic locus. Diversity within allelic classes, which will be written here as <span class="math-container">$π_A$</span>, was estimated from the mean of <span class="math-container">$2 \sum \left( x_t(1-x_t)+y_t)(1-y_t) \right)$</span> where <span class="math-container">$x_t$</span> and <span class="math-container">$y_t$</span> are the frequencies of the neutral variant within the first and second allelic classes, respectively. Diversity between allelic classes with respect to the polymorphic locus was calculated as the difference between the total diversity values and <span class="math-container">$π_A$</span></p>
</blockquote>
<p><em>Note that the parentheses don't match up but this this is what is written in the paper!</em></p>
<p><strong>Why am I confused about this text?</strong></p>
<p>I am confused about the term allelic class. I first think there is anything fancy in here and I think we can simply replace the term "allelic class" by "allele". but then when I saw the equation for <span class="math-container">$\pi_A$</span> I realize that the frequency of the two allelic classes does not necessarily adds to 1 (even though we consider only two allelic classes).</p>
<p>I also got also a little confused about the difference between <span class="math-container">$\pi$</span> and <span class="math-container">$\pi_T$</span> but I think that they just used two notations for the same think (<span class="math-container">$\pi = \pi_T$</span>)</p>
<p>In population genetics's jargon, diversity just mean expected heterozygosity. <span class="math-container">$\pi_T$</span> makes sense to me. It is just the average heterozygosity <span class="math-container">$\left(2 z(1-z)\right)$</span> calculated over all time steps. Maybe a more intuitive to put it would to integrate rather than summing over time rather than time steps.</p>
<p><strong>Question</strong></p>
<p>I can read the equation for <span class="math-container">$\pi_A$</span> but I fail to get any intuition behind what it means. For example, I have no idea why it should be called within-allelic class diversity. Where does <span class="math-container">$2(x(1-x)+y)(1-y)$</span> come from? My whole issue might boil down to the definition of <em>allelic class</em>.</p>
<p><strong>EDIT</strong></p>
<p>The term <code>allelic class</code> is defined in <a href="http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=3317&fileId=S0016672397002954" rel="nofollow noreferrer">Innan and Tajima (1997)</a></p>
<blockquote>
<p>Suppose that there are two nucleotides, say A and T, in a particular site. Then, we can divide DNA sequences into two classes: one class includes sequences with A and the other includes sequences with T in this site. We call such a class an allelic class</p>
</blockquote>
<p>(<a href="http://www.ncbi.nlm.nih.gov/pubmed/8722806" rel="nofollow noreferrer">Slatkin 1996</a> might help as well).</p>
<p>I am still not quite sure what the <code>within allelic class variance</code>. Maybe it is: Take the most common sequence in the considered allelic class. For each, sequence, calculate the number of pairwise differences to the most common sequence and square this value. Sum over all sequence and divide by the number of sequences. In math form it would be: <span class="math-container">$\frac{1}{2N}\sum_i^{2N} (D_i)^2$</span>, where <span class="math-container">$N$</span> is the population size and <span class="math-container">$D_i$</span> is the number of pairwise difference between the sequence <span class="math-container">$i$</span> and the most common sequence in the considered allelic class. Does it sound right to you?</p>
| [
{
"answer_id": 36498,
"pm_score": 4,
"text": "<p>From <a href=\"https://en.wikipedia.org/wiki/Amphibian\" rel=\"nofollow\">wiki</a>:</p>\n\n<blockquote>\n <p>Most amphibians lay their eggs in water and have aquatic larvae that undergo metamorphosis to become terrestrial adults</p>\n</blockquote>\n\n<p>... | [
{
"answer_id": 36534,
"pm_score": 1,
"text": "<p>Arguably, since <a href=\"http://io9.com/5621249/ultra-tiny-frogs-discovered-living-like-faeries-inside-pitcher-plants/\" rel=\"nofollow noreferrer\">this frog</a> spends the entire larval stage inside a pitcher plant on land, it has started its life cycl... |
36,595 | <p>It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. </p>
<p>So here's to putting all those questions to rest.</p>
<p>Is the reference genome a positive or a negative strand? And why so.</p>
| [
{
"answer_id": 36596,
"pm_score": 4,
"text": "<p>First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying ... | [
{
"answer_id": 77241,
"pm_score": 2,
"text": "<p><strong>Answer</strong></p>\n<p>There is <em>no such thing</em> as a positive or negative strand for a <strong>genome</strong> (reference or otherwise), for the simple reason that the genomes of almost all organisms contain genes in both orientations, and... |
36,710 | <p>This is a basic question but I couldn't find an answer through a web search; hopefully this is the right place to ask. Is the number of base pairs in a
particular chromosome the same in all individuals? For example if I take an
X-chromosome from two random humans would I count <strong>exactly</strong> 155,270,560
base pairs in both cases? or are there mutations that would make one longer than the other? If they're not exactly the same, what's the range in length variation?</p>
| [
{
"answer_id": 36714,
"pm_score": 5,
"text": "<p>Welcome to Biology.SE.</p>\n\n<blockquote>\n <p>if I take an X-chromosome from two random humans would I count exactly 155,270,560 base pairs in both cases</p>\n</blockquote>\n\n<p>No, you would probably not find the exact same number of base pairs becau... | [
{
"answer_id": 36728,
"pm_score": 1,
"text": "<p><strong>Are there mutations that would make one longer than the other? If they're not exactly the same, what's the range in length variation?</strong></p>\n\n<p>As pointed out in the other answers, there can be mutations that change the length of the DNA ... |
36,867 | <p>If a cancerous tumor has a lot of mutations in them why can't the immune system detect them? If a person has cancer could this somehow alter the person's immune system so it doesn't function effectively to detect greatly mutated cells? Does the fact that a tumor is 'made' of 'mutated' non-foreign human cells help it to be undetectable?</p>
| [
{
"answer_id": 36877,
"pm_score": 3,
"text": "<p>This is a good question and it gets to the most basic foundations of immunology. Your immune system is made to be flexible - able to adapt to almost any challenge. However, with so much flexibility comes the potential to generate immune cells that react a... | [
{
"answer_id": 36878,
"pm_score": 2,
"text": "<p>Great question and in part, you are correct. However, you must also remember that this greatly depends on what genes have undergone mutation. </p>\n\n<p>In the case of cancer, it's usually either a gene that regulates cell proliferation rates, induces pro... |
36,940 | <p>According to a guy in a Facebook group I belong to, this fish was caught in the Missouri River near Omaha, NE, US. I have never seen one like it in my life, not in person or photo or anywhere. What on earth is this fish?! Is it even real? I've not seen it in person, only the photo below, but he says its real.</p>
<p><a href="https://i.stack.imgur.com/0ebmD.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/0ebmD.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 36945,
"pm_score": 5,
"text": "<p><strong>Original Answer</strong></p>\n\n<hr>\n\n<p>It looks to me like a species of sculpin, for example, the \"short-horned sculpin\" <em>Myoxocephalus scorpius</em>.</p>\n\n<p><a href=\"https://i.stack.imgur.com/iV96q.jpg\" rel=\"noreferrer\"><img src=\... | [
{
"answer_id": 36969,
"pm_score": 2,
"text": "<p>I looked your strange fish and I think that it is a short horned sculpin because of its spikes.So, don't imagine that it is a sea robin because sea robins live in very deep waters (500 meters depth aproximately).In fact, I think that this sculpin was trap... |
36,985 | <p><a href="https://i.stack.imgur.com/G24JI.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/G24JI.jpg" alt=""></a></p>
<p>3 pairs of legs, a pair of antenna, wings absent, compound eye, 4-6 centimeter approx. in size.
I found this beetle at my door, in Pune, India.</p>
| [
{
"answer_id": 37159,
"pm_score": 4,
"text": "<p>It is a longhorn beetle (Cerambycidae), most certainly from the subfamily Lamiinae (flat-faced longhorns). The overall apparence with a downward-pointing face, partially divided eyes, robust build and spined pronotum fits well with Lamiinae.</p>\n<p>The b... | [
{
"answer_id": 36986,
"pm_score": 2,
"text": "<p>I think it is from Cerambycidae family, </p>\n\n<p>Batocera parryi - </p>\n\n<p><a href=\"https://i.stack.imgur.com/wqt7M.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/wqt7M.jpg\" alt=\"enter image description here\"></a></p>\n"
... |
37,167 | <p>I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in <a href="http://hyper.ahajournals.org/content/55/2/494.full.pdf+html?sid=64cdc47e-92e4-46bf-a021-9365d4919132">this</a> article, they test 9 - 12 rats in a control group and compare it to an experimental group. They use p values to claim that their results are statistically significant. This type of use of p values seems to be very common in the literature. </p>
<p>So here are my concerns : </p>
<ol>
<li><p>Why is it so often assumed that biological measurements follow a normal distribution? To my knowledge, this isn't known <em>a priori</em>.</p></li>
<li><p>From my physical intuition, it seems quite challenging to claim "statistically significance" when using such low sample sizes.</p></li>
</ol>
| [
{
"answer_id": 37199,
"pm_score": 5,
"text": "<p>kmm's answer is correct; I just want to add some of my points on what kind of data should follow Gaussian distribution.</p>\n\n<hr>\n\n<blockquote>\n <p>Unless you know from observation that a process doesn't follow a\n Gaussian distribution (e.g., Pois... | [
{
"answer_id": 37168,
"pm_score": 3,
"text": "<p>You raise two issues, both of which might be better suited for stats.SE, but I think the questions are suitably biological to warrant an answer here.</p>\n\n<h2>Do most biological processes follow a Gaussian distribution?</h2>\n\n<p>Unless you know from o... |
37,207 | <p>What evolutionary process has provided humans with the ability of feeling electric current? Besides lightning and electric eel, what natural hazards include electricity that poses a threat to humans? </p>
| [
{
"answer_id": 37209,
"pm_score": 5,
"text": "<p>Electrical currents stimulate neurons <em>aspecifically</em>. For example, the <a href=\"http://www.wicab.com/en_us/\" rel=\"nofollow noreferrer\">BrainPort</a> artificial vision device conveys visual information through electrical stimulation of mechanor... | [
{
"answer_id": 37230,
"pm_score": -1,
"text": "<p>Electricity directly stimulate neurons. You have to understand that neurons basically work via electric currents , which occur due to a difference in membrane charge. So when you give electricity to a neuron, you basically give electrons to the extracell... |
37,220 | <p>I confused myself during studying, and wanted to confirm something. Since transcription via RNA polymerases only takes place in the 5'to 3' direction, that would mean that that 5' to 3' strand is the only one that contains the information to be translated later into a protein or mRNA or w/e.</p>
<p>So then the 3' to 5' strand would NOT contain any genes, but just the base pair complement to them? Or am I thinking of the concept of a gene wrong?</p>
| [
{
"answer_id": 37209,
"pm_score": 5,
"text": "<p>Electrical currents stimulate neurons <em>aspecifically</em>. For example, the <a href=\"http://www.wicab.com/en_us/\" rel=\"nofollow noreferrer\">BrainPort</a> artificial vision device conveys visual information through electrical stimulation of mechanor... | [
{
"answer_id": 37230,
"pm_score": -1,
"text": "<p>Electricity directly stimulate neurons. You have to understand that neurons basically work via electric currents , which occur due to a difference in membrane charge. So when you give electricity to a neuron, you basically give electrons to the extracell... |
37,343 | <p><strong>In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, aneuploidy, and polyploidy?</strong></p>
<p>For example would have normal whole genome sequencing techniques detected that humans have 46 rather than 48 chromosomes?</p>
<p>Maybe a better way to put this question would be as follows:</p>
<p>Given the whole genome sequence for humans and a belief that chimpanzee had 46 chromosomes would whole genome sequencing of the chimpanzee most likely say </p>
<p>1) Here are the sequences for those 46 and by the way there was material left over.</p>
<p>2) Here is the best representation of all the chimpanzee's DNA mapped onto 46 chromosomes.</p>
<p>3) Here are the sequences for those 46 and chimpanzee's appear to have 48 chromosomes.</p>
| [
{
"answer_id": 37351,
"pm_score": 2,
"text": "<p>What Biomed_guy says is basically the answer, I just wanted to clarify a bit. When you sequence DNA, you do something during the preparation of your DNA library to turn it into small fragments if it isn't already, like shearing the DNA. This gives you ver... | [
{
"answer_id": 37345,
"pm_score": 2,
"text": "<p>I'm pretty sure that it relies on a reference genome. As in, since the original human genome sequencing, most of the techniques used today rely on that original construction (with modifications).</p>\n\n<p>That's how people use it to detect copy number va... |
37,348 | <p><strong>Do whole genome sequencing techniques detect B chromosomes if such chromosomes are present?</strong></p>
<p>My understanding is as follows:</p>
<p>How the DNA material in a B Chromosome is mapped depends on the reference map and not on how the material is packaged into chromosomes for the sample being sequenced.</p>
<p>Is this correct?</p>
| [
{
"answer_id": 37391,
"pm_score": 2,
"text": "<p>You can use differences in coverage (number of reads mapping to certain regions in reference) to infer if there is a B chromosome.</p>\n"
}
] | [
{
"answer_id": 39570,
"pm_score": 1,
"text": "<p>The analysis of NGS reads coverage rate can give information on B chromosome genomic content. Have a look at the article mentioned below: </p>\n\n<p><hr>\n<sub> Valente GT et al. (2014). <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/24770715\" rel=\"nofoll... |
37,376 | <p>First, I am not a biologist, so this question might be naive:</p>
<p>Computer information processing and storage is based on 2-digit system of bits with values 0 and 1. Now, DNA stores the information in a 4-digit system: A, C, G, T. Three base pairs form a codon and can encode 4<sup>3</sup> amino acids.</p>
<p>Is there a good reason why a 4-level system (which can store 2 bits per encoding entity) evolved rather than a 2-level or a system with a larger number of symbols in the alphabet?</p>
<p>Put differently: Why was a binary system not preferred for storage and processing of data? In computing, binary is much easier, and the very few tests of exotic higher-level data processing have not really been successful.</p>
| [
{
"answer_id": 37454,
"pm_score": 5,
"text": "<p>The current hypothesis is that RNA came first, DNA and proteins came later. So the reason that four bases are used might be related to the initial RNA world, and then DNA just reused the already existing RNA bases in a slightly modified form. In the RNA w... | [
{
"answer_id": 81723,
"pm_score": 3,
"text": "<blockquote>\n <p>Why does nature use a 4-level system (DNA) to encode information?</p>\n</blockquote>\n\n<p>Short answer: Ease of manufacture, simplicity of matching, sufficiency for requirements. Fewer simple bases take less effort to create, provide fewe... |
37,396 | <p>I started raising chickens this year. They have amazing appetites, and I often wonder what eating is like for them. They have no teeth, so they don't chew their food as they eat it. They do seem to have some sense of taste, because they often bite off a bit of something and then spit it right back out. But the only equivalent of chewing for them occurs in their gizzard. Because the gizzard is pretty far down the digestive tract, I would assume that it's an involuntary muscle. But all chewing being unconscious for them also sounds kind of crazy.</p>
<p>I'm trying to discover the answer to this question on the internet and I'm surprised that the answer hasn't been easier to find. Does anyone here know? Do birds masticate unconsciously?</p>
| [
{
"answer_id": 37454,
"pm_score": 5,
"text": "<p>The current hypothesis is that RNA came first, DNA and proteins came later. So the reason that four bases are used might be related to the initial RNA world, and then DNA just reused the already existing RNA bases in a slightly modified form. In the RNA w... | [
{
"answer_id": 81723,
"pm_score": 3,
"text": "<blockquote>\n <p>Why does nature use a 4-level system (DNA) to encode information?</p>\n</blockquote>\n\n<p>Short answer: Ease of manufacture, simplicity of matching, sufficiency for requirements. Fewer simple bases take less effort to create, provide fewe... |
38,708 | <p>After reading about how recombinant insulin is produced, the following question occured to me. Does the current level of technology allow <em>any</em> enzyme to be produced in a similar way? </p>
<p>As I see, producing amino acid sequences is not an issue. A possible difficulty I can think of is modifying the amino acid chains. In the case of insulin the problem has been solved. Are there some generally applicable solutions available to this problem, or do they have to be researched on a case-by-case basis?</p>
<p>Are there any other limitations to producing enzymes?</p>
<p>EDIT: As pointed out by P. Jay, the question might seem to suggests that insulin is an enzyme which it is not.</p>
| [
{
"answer_id": 38722,
"pm_score": 5,
"text": "<p>No, not all enzymes (or other proteins for that matter) can be obtained in functional form by recombinant expression with today's methods. As you suspect, problems arise when complex post-translational modifications are necessary to obtain the correct fun... | [
{
"answer_id": 38711,
"pm_score": -1,
"text": "<p>Yes enzymes can be produced and even be optimized like restriction enzymes which are now mostly recombinant thou to low efficiency or biosafety level of source bacteria leaving that behind ,the greatest problem here is the size of protein and it's gene a... |
38,757 | <p>As <a href="https://en.wikipedia.org/wiki/Grafting" rel="nofollow noreferrer">Wikipedia</a> says:</p>
<blockquote>
<p>Grafting is a horticultural technique whereby tissues from one plant are inserted into those of another so that the two sets of vascular tissues may join together.</p>
<p>In most cases, one plant is selected for its roots and this is called the stock or rootstock. The other plant is selected for its stems, leaves, flowers, or fruits and is called the scion or cion. <strong>The scion contains the desired genes to be duplicated in future production by the stock/scion plant.</strong></p>
</blockquote>
<p>So why I <em>don't</em> get the apple-tree of the <em>scion</em> kind if I plant the seeds from an apple which has grown on such a tree? I would expect that the genes in the apple seeds must be the same. However if I plant the seeds, I have to graft the new seedling again.</p>
| [
{
"answer_id": 38788,
"pm_score": 3,
"text": "<p>The reason most apples are produced from grafted trees is that apples don't breed true.</p>\n\n<p>In a large number of crops, you have \"lines\" of crops. Basically, if you breed two plants of the same cultivar together, their offspring are similar enough... | [
{
"answer_id": 38786,
"pm_score": 2,
"text": "<p>According to such sources as North Dakota State University Ag Department (<a href=\"https://www.ag.ndsu.edu/hort/info/fruit/graft.htm\" rel=\"nofollow\">https://www.ag.ndsu.edu/hort/info/fruit/graft.htm</a>) one primary reason for continued grafting is un... |
38,807 | <p>The knee-jerk reflex (<a href="https://en.wikipedia.org/wiki/Patellar_reflex" rel="noreferrer">patellar reflex</a>) is an example of a stretch reflex (<a href="https://en.wikipedia.org/wiki/Stretch_reflex" rel="noreferrer">myotatic reflex</a>). Stretch reflexes are monosynaptic reflexes happening in the spinal cord without involvement of the brain.</p>
<p>Does it mean that this reflex will continue to function in an unconscious person, e.g. under general anaesthesia? Does it depend on the "deepness" of anaesthesia? Does it depend on a specific drug? I would also be interested to know if spinal reflexes keep working in unconscious states such as e.g. alcohol poisoning or a knockout.</p>
| [
{
"answer_id": 38879,
"pm_score": 4,
"text": "<p><strong>The issue is complicated. In general it depends on the specific spinal reflex and on the specific anaesthetic. But it seems that the modern general anaesthetics usually do NOT block monosynaptic spinal reflexes (such as knee-jerk).</strong></p>\n<... | [
{
"answer_id": 38817,
"pm_score": 2,
"text": "<p>I am not a surgeon. \nHowever, I might have some insight:</p>\n\n<ul>\n<li><p>General anesthesia often (most of the time ?) include curare derivated drugs (such as pancuronium) that will effectively block any muscular response (by interfering in the neuro... |
38,905 | <p>I found a <a href="http://in.mathworks.com/help/bioinfo/ref/palindromes.html" rel="nofollow">function</a> called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of finding palindrome in DNA sequences?</p>
| [
{
"answer_id": 38906,
"pm_score": 3,
"text": "<p>My knowledge of biology is extremely limited, but this is what I know of palindromic sequences:</p>\n\n<p>Palindromic sequences are their own reverse complements. I have seen many restriction sites be palindromic. Also, some Transcription Factor Binding s... | [
{
"answer_id": 39401,
"pm_score": 2,
"text": "<p>Palindrome sequences are important in bioinformatics understanding, it helps us to extract patterns in the genomic sequences. I'll give an example in HIV (very important application).</p>\n\n<p>HIV has a nasty requirement that the virus must keep the cell... |
38,920 | <p>As I understand it, both cortisol and glucagon cause an increase in blood sugar concentrations. However, I don't understand how they work differently or why they work separately. I would be very grateful if someone could explain the separate roles and functions of these two hormones and also the different effects that they have (I believe cortisol also has something to do with promoting lypogenesis in adipose tissue at the trunk of the body and lypolysis at the extremities).</p>
| [
{
"answer_id": 40971,
"pm_score": 4,
"text": "<p>Glucagon and cortisol are <strong>VERY</strong> different types of hormones, though each of them can affect glucose metabolism and effectively can increase glucose concentrations in the blood (albeit through different mechanisms).</p>\n\n<p><a href=\"http... | [
{
"answer_id": 38927,
"pm_score": 1,
"text": "<p>Glucagon increase the blood sugar level in normal physiological pathway. It just mediate the blood sugar level when the level is too low.</p>\n\n<p>On the other hand, cortisol is used when body under stress. It is used for \"fight or flight\" response in ... |
39,027 | <p>I watched (IMHO canibalistic) movie <a href="https://en.wikipedia.org/wiki/Seven_Pounds" rel="nofollow">"Seven Pounds"</a> where protagonist donated many of his organs to other people and I noticed, that most recipients were black also as protagonist was.</p>
<p>Is race really taken into account when organ transplanting?</p>
<p><strong>UPDATE</strong></p>
<p>The question is not just about if interracial transplantation really good or bad. I can imagine, that transplantation is done same-race just in case, in favor of "do not harm" principle.</p>
| [
{
"answer_id": 39028,
"pm_score": 4,
"text": "<p>No, race is not a factor taken into account. However, due to higher genetic similarities between people of the same race, it is usually easier to find a match within a race.</p>\n\n<p><a href=\"http://mi.gov/sos/0,1607,7-127-29843-152055--F,00.html\">Sour... | [
{
"answer_id": 39033,
"pm_score": 3,
"text": "<p>Here is a really interesting <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954674/\" rel=\"noreferrer\">article</a> discussing this topic and finding no statistically significant difference in survival rates between donations across race and thos... |
39,038 | <p>What is the function of the bacterium, <em>E. coli</em>, in the human gut?</p>
<p>I have tried to find the answer by searching the Internet (e.g. <a href="http://www.uni-kiel.de/pressemeldungen/?pmid=2014-395-bakterielle-adhaesion&lang=en" rel="nofollow noreferrer">here</a>), but have been unsuccesful.</p>
| [
{
"answer_id": 39039,
"pm_score": 4,
"text": "<p>Nonpathogenic <em>E. coli</em> strains are a component of the gut microbiome of humans and many other organisms.</p>\n<p>They are commensals, meaning that when they remain in the areas they have evolved to live in, and when they do not acquire virulence f... | [
{
"answer_id": 39040,
"pm_score": 2,
"text": "<p><em>E. coli</em> do not serve a human function but live inside our digestive system because our bodies can't prevent bacteria like them from living there. They live there because they can prosper and reproduce there. Most strains of <em>E. coli</em> do ... |
39,202 | <p>in my molecular bio class we were asked a trick question: </p>
<p>If the bacteria has a plasmid with that grants it ampicillin ressistance, can the bacteria survive if placed in penicillin?</p>
<p>I gave it a thought and said that it cant, since amp differs from pen by an extra amino acid that could harm the bacteria, the answer corresponds with the class material but amp is known as the broad spectrum antibiotic.... so should i go with the class flow lured by the experimental assumption and assume it dies or persist on whether it will survive? i'm really confused at this point, any input is appreciated</p>
| [
{
"answer_id": 39252,
"pm_score": 2,
"text": "<p>Neither of the two answers provided give the full answer, both touch on it, from different perspectives, but neither address it completely.</p>\n\n<p>Given your description, it sounds as though the question is being asked in the context of a lab strain. <... | [
{
"answer_id": 39204,
"pm_score": 1,
"text": "<p>Short answer: Your assumption is wrong and bacteria, which are resistant to penicillin are are also resistant to ampicillin.</p>\n\n<p>Long answer: There are different classes of antibiotics, which have different mechanisms of action. Penicillin (and also... |
39,257 | <p>I am learning about frameshift mutations. Frameshifts can occur due to a nucleotide deletion. Suppose that due to a frameshift, because of a deletion somewhere upstream from the original start codon, two additional start codons are generated, just before the stop codon in the new reading frame. What would happen in terms of translation?</p>
<p>AUG-GCC-AUA-AUG--------UAA
Start Start then stop</p>
| [
{
"answer_id": 39273,
"pm_score": 4,
"text": "<p>There is a basic misconception in the question you have asked, which @biogirl has explained. <strong>There is only one start Codon in any mRNA</strong> and it defines the <strong>open reading frame.</strong> </p>\n\n<p>All other AUGs in the open reading f... | [
{
"answer_id": 39259,
"pm_score": 2,
"text": "<p>The start codon is not sufficient to start translation. A ribosomal binding site is also required. It's likely that translation would initiate at its normal location and then simply proceed through any additional start codons in the new ORF until it reach... |
39,298 | <h1>An Overview of the Experiment.</h1>
<p><a href="http://rspb.royalsocietypublishing.org/content/260/1359/245" rel="noreferrer">In 1995 there was an experiment that involves young people smelling T-shirts</a> worn by another gender and rating their preference. The researchers found that people preferred shirts belonging to people with a dissimilar Major Histocompatibility Complex (MHC). Another interesting finding was that this preference reversed for the women 'sniffers' that were using oral contraceptives.</p>
<p><a href="https://en.wikipedia.org/wiki/Claus_Wedekind" rel="noreferrer">Here is a link to the wikipedia entry.</a></p>
<p><a href="http://www.sciencedirect.com/science/article/pii/S0018506X04002491" rel="noreferrer">These findings were reiterated by a study in 2005</a>.</p>
<h1>My Question.</h1>
<p>I'm very ignorant in the subject of pheromones, particularly in humans. For those of us not 'in the know' a result like this seems like magic! I want to get a better grasp on how set in stone pheromone preferences like this are.</p>
<p>Unfortunately I do not have access to these articles at the moment. The actual statistical difference in populations isn't mentioned in the abstracts (the cynical sceptic alarm bells are ringing!) other than the 2005 one stating that the total sample size was 58, which sounds low given that the total population is split into two.</p>
<p>Generally I'm looking for any supporting or opposing critiques of the study, specifically I want to know more about the statistics of the studies.</p>
<p>My question is:</p>
<ul>
<li><strong>What statistical validations and scores appear in these studies?</strong></li>
</ul>
<p>I also am willing to accept answers discussing validation in similar studies. I'm after a number or quantification for how consistent pheromone preferences are.</p>
| [
{
"answer_id": 39337,
"pm_score": 5,
"text": "<p>First, let's consider the original Wedekind et al (1995) study.</p>\n\n<p>Sample sizes seem reasonable, if the effect is not very noisy:</p>\n\n<blockquote>\n <p>[...] 49 female students (average age: 25.2 years, s.d. = 4.0) and 44 male students (averag... | [
{
"answer_id": 52432,
"pm_score": -1,
"text": "<p>I have seen many studies on that matter, but I am far from convinced that MHC really effects mate choice. Reasons for this are the following:\n - iayork mentioned it already, the premise for the studies about mice mate choice has been disproved. \n - In ... |
39,386 | <p><a href="https://i.stack.imgur.com/94J4T.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/94J4T.jpg" alt="flower."></a></p>
<p>This is from Bangladesh though I am not sure it's native here</p>
| [
{
"answer_id": 39387,
"pm_score": 4,
"text": "<p><a href=\"https://www.google.co.in/imghp\">Google</a> image search gave me answer as \"<a href=\"https://en.wikipedia.org/wiki/Plumeria\">Plumeria</a>\"</p>\n"
}
] | [
{
"answer_id": 39393,
"pm_score": 1,
"text": "<p>Also known as FrangiPani in Africa. Has lovely sweet scent, I have a white and pink tree in my garden, they are about 8 ft tall. Doesn't like frost</p>\n"
},
{
"answer_id": 73714,
"pm_score": 1,
"text": "<p><a href=\"https://www.google.ca/... |
39,479 | <p>My question is simple. Why is a virus considered a microbe? Considering a microbe is considered to be a "living" unit of life, which viruses are not. </p>
| [
{
"answer_id": 39480,
"pm_score": 5,
"text": "<p><strong>What is a microbe?</strong></p>\n\n<p>A <a href=\"https://en.wikipedia.org/wiki/Microorganism\" rel=\"nofollow noreferrer\">microbe</a> (or microorganism) is a microscopic organism. Anything that is considered alive and that is small enough is cal... | [
{
"answer_id": 39495,
"pm_score": -1,
"text": "<p>Viruses are small bits of genetic code in a protective covering. Viruses are not \"alive,\" that is, they cannot replicate, unless they are inside another organism. A virus is definitely too small to be seen without a microscope. Since viruses are so sma... |
39,539 | <p>Why is it that the reaction we get from absurdity is laughter? Everyone does it, even babies. Is there a reason why it is our instinct to laugh when we see or hear something absurd/humorous</p>
| [
{
"answer_id": 39540,
"pm_score": 5,
"text": "<h1>Like so much of biology, we just don't know!</h1>\n<p>I'll preface this answer by disappointing you; this answer doesn't entirely answer your question. That's because this is a pretty big mystery in research and a fascinating topic. I'll start with a cou... | [
{
"answer_id": 39580,
"pm_score": 2,
"text": "<p>It is not known for sure. But I find Hurley and Dennett's theory very convincing. </p>\n\n<blockquote>\n <p>Our brains are engaged full time in real-time (risky) heuristic search, generating presumtpions about what will be experienced next in every domai... |
39,733 | <p>How is the primer present in the daughter, leading strand replaced? I've circled the primer in question. </p>
<p><a href="https://i.stack.imgur.com/NuAjr.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/NuAjr.png" alt="enter image description here"></a></p>
<p>I don't see how this primer can be replaced by DNA polymerase; there is no free 3' end for DNA pol to act on.</p>
<p>My book, however, says there is no telomere problem with the leading strand. </p>
<p>Other sources say there is a telomere problem. </p>
<p>So what is it? </p>
| [
{
"answer_id": 39737,
"pm_score": 3,
"text": "<p>Replication doesn't start at the very end of a chromosome, so there is no problem with leading strand synthesis. It's probably easiest to see if the other half of the image was there:</p>\n\n<p><a href=\"https://i.stack.imgur.com/4RqgM.jpg\" rel=\"nofollo... | [
{
"answer_id": 39736,
"pm_score": 1,
"text": "<p>I think the confusion is coming from the way this picture is drawn. The leading strand does not begin at the end of a chromosome, there is in fact more DNA to the right of your picture that is not shown. This picture is showing the left half of a replicat... |
39,835 | <p>I only know splice variants are produced by different combinations of introns and exons. I wish to know why there is a need of such function. Perhaps using the same amount of DNA sequence to produce multiple proteins saves genetic material. Also, I want to know what contribute to the need for splice variants feature (e.g. evolutionary pressure, the need to increase the complexity)</p>
<p>I find that in human, protein CD81 is predicted by Ensembl to have a lot of splice variants (<a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000110651;r=11:2398547-2418649;t=ENST00000475945" rel="nofollow">http://grch37.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000110651;r=11:2398547-2418649;t=ENST00000475945</a>). However, only 1 of them is characterized. Thus, splice variants seem redundant. Any examples of splice variants actually carry different function?</p>
| [
{
"answer_id": 39839,
"pm_score": 3,
"text": "<p>The reason is very simply to provide enough variation in a limited sized genome to produce the repertoire of proteins produced by the cells of multicellular organisms. It is also a matter of efficiency and reduced energy consumption.</p>\n\n<p>Consider th... | [
{
"answer_id": 39884,
"pm_score": 0,
"text": "<p>Insofar organismal complexity is defined as the number of known cell types, there is a strong relationship between splicing, the repertoire of isoforms and organismal complexity.</p>\n\n<p><a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032128/\" r... |
39,861 | <p>What product of cellular respiration creates an acid when in solution with water?</p>
<p>Topic question really, haven't been able to find a direct answer.</p>
| [
{
"answer_id": 39892,
"pm_score": 4,
"text": "<p>Cellular respiration itself, defined as the activity of the respiratory chain complexes I -- V (including ATP synthase), is <em>not</em> acidifying. On the contrary, free protons are captured during ATP synthesis, so cellular respiration acts to raise pH.... | [
{
"answer_id": 39871,
"pm_score": 1,
"text": "<p>In tissue and cell culture I recall that after the vascular smooth muscle cell line i was working with had used up the compounds in the buffer the supernatant started to turn acidic due to presence of lactic acic. </p>\n\n<p>The cells aerobicaly produce l... |
39,894 | <p>I have read that general soap can kill bacteria by opening holes in the bacterial membrane.</p>
<p><a href="http://questions.sci-toys.com/node/90" rel="noreferrer">http://questions.sci-toys.com/node/90</a></p>
<p>However, I found some articles as well saying that it cannot.</p>
<p><a href="http://goaskalice.columbia.edu/answered-questions/does-soap-kill-germs" rel="noreferrer">http://goaskalice.columbia.edu/answered-questions/does-soap-kill-germs</a></p>
<p>There seems split answers among experts,
so I would like to know which one is correct.</p>
<p>Could anyone advise me?</p>
<p>Thanks.</p>
| [
{
"answer_id": 39902,
"pm_score": 4,
"text": "<p>Soap kills nearly all the bacteria it comes into contact with by dissolving the bacterial membrane. Some viruses with protein coats can resist soap, but many viruses have similar membranous coats (like HIV) and are usually disrupted by soap. I'm sure it... | [
{
"answer_id": 39900,
"pm_score": 2,
"text": "<p>Generally, the goal for using non-antimicrobial soap is simply to pick up and remove organisms and dirt from our skin. This is achieved first by the soap chemically bonding to certain molecules (i.e. oil or lipids). Second, friction from rubbing mechanica... |
39,976 | <p>Can anyone actually tell me how acupuncture works? </p>
<p>There are numerous websites with little actual explanation, but assert that it works. For example the below article:</p>
<p><a href="http://www.health.harvard.edu/blog/acupuncture-is-worth-a-try-for-chronic-pain-201304016042">http://www.health.harvard.edu/blog/acupuncture-is-worth-a-try-for-chronic-pain-201304016042</a></p>
<p>However I have failed to find any article about how acupuncture works, or the mechanism at play. Can anyone tell me how it works?</p>
| [
{
"answer_id": 39981,
"pm_score": 2,
"text": "<p><strong>What is acupuncture</strong></p>\n\n<p>Acupuncture is a form of alternative medicine by which needles are pierced through the skin and helps to treat diseases.</p>\n\n<p><strong>Science behind acupuncture</strong></p>\n\n<p>So far, the research on... | [
{
"answer_id": 39983,
"pm_score": 2,
"text": "<p>It works via the placebo effect which according to recent research, is <a href=\"http://www.dailymotion.com/video/x1moo91_horizon-2013-2014-8-the-power-of-the-placebo_lifestyle\" rel=\"nofollow noreferrer\">not the sort of trivial effect as it was thought... |
40,003 | <p>I've got a project where we collect leaves, classify them, etc. There are some required classifications. One of the requirements is to get a doubly-compound leaf. What are some trees that are doubly-compound? Please help! I have Hickory, but that's just compound I think.</p>
<p>Edit: I did try googling, but it's hard for me to know what's available in my region.</p>
<p><strong>From Comments:</strong> <em>I live in Tennessee, U.S.</em></p>
| [
{
"answer_id": 42531,
"pm_score": 3,
"text": "<p><strong><em>Albizia julibrissin</em> (Persian silk tree)</strong> is doubly compound (AKA <strong><em>bipinnate</em></strong>) and has a conspicuous pink/white fluffy flower. This tree is an Asian native, but it's a commonly cultivated (and equally common... | [
{
"answer_id": 40028,
"pm_score": 1,
"text": "<p>Many ferns have multiply-compound leaves</p>\n\n<p>Take the one in this image, for instance:</p>\n\n<p><a href=\"https://i.stack.imgur.com/MSB9Q.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/MSB9Q.jpg\" alt=\"enter image descripti... |
40,175 | <p>I have some understanding of how PCR testing works. What I have always been wondering: how can we be sure that a primer reacts with the targeted gene(s) regardless of where¹ the genes are inside a sample?</p>
<p>¹: Specifically with "where" I mean what cells or other barriers they are inside. In other terms my question is: how can we be sure primers reach every possible target?</p>
<p>In more detail: when targeting a gene that is part of the host organism's own genome things might be quite clear, we can have strong assumptions of "where" the gene is. But when targeting genes that are part of organisms that have a parasitic relationship with the host, a very complex system of interactions (mostly called "immune system") should govern the (co)existence of host and parasite. These complex interactions might lead to situations in which the parasitic organism is present in a very special, isolated manner / place in the host. To give one example: micro organisms in the cell walls of macrophages that are about to undergo lysis. Can we be sure that common PCR would detect genes of such micro organisms? Why?</p>
<p>EDIT: as pointed out in the comments the perhaps most correct phrasing is, how do the DNA isolation techniques employed guarantee that primers reach every possible target?</p>
| [
{
"answer_id": 40180,
"pm_score": 4,
"text": "<p>There are many methods of DNA isolation, so it is difficult to make broad statements about all situations. Typically, though, during the DNA isolation protocol, essentially all proteins are denatured and removed, as is RNA, cell membrane components, extra... | [
{
"answer_id": 40178,
"pm_score": 1,
"text": "<p>The polymerase chain reaction is done on free DNA that has been released from the cell by a variety of chemical or physical methods.</p>\n\n<p>There are no cells involved in PCR as the components you don't want are separated by high-speed centrifugation.<... |
40,269 | <p>I found a short video on the Internet of a toad and I wonder if anybody could identify it? </p>
<p>It was posted on a social-media/blogging website called 'Tumblr', </p>
<ul>
<li>so I don't know much about it (e.g., where the video took place). </li>
</ul>
<p><strong>EDIT:</strong> The original link is no longer active. Here's an <a href="https://youtu.be/YBDejUj2w3A" rel="nofollow noreferrer">alternate link</a>.</p>
<ul>
<li>Useful for hearing the specimen's "squeak"/scream. </li>
</ul>
<p><strong>EDIT 2:</strong> Here's a gif of some frames from the video for permanence on this site:</p>
<p><a href="https://i.stack.imgur.com/s1GGR.gif" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/s1GGR.gif" alt="enter image description here"></a></p>
<p>P.s. I <strong>think</strong> it's a <em>toad</em>. Please, don't hesitate to correct me/edit my question, if i'm mistaken.</p>
| [
{
"answer_id": 57757,
"pm_score": 3,
"text": "<p>This indeed looks like a species of \"Pacman Frog.\"</p>\n\n<p>Specifically, this specimen most resembles the terrestrial <a href=\"https://en.wikipedia.org/wiki/Cranwell%27s_horned_frog\" rel=\"nofollow noreferrer\"><strong><em>Ceratophrys cranwelli</em>... | [
{
"answer_id": 44146,
"pm_score": 1,
"text": "<p>It is almost certainly a toad, not a frog as the name of the video suggests. It probably belongs to the familie <em>Pseudepidalea</em>, aka the green toads. The live in Europe, Asia and North-America. <a href=\"https://en.m.wikipedia.org/wiki/Pseudepidale... |
40,436 | <p>I read the wikipedia page about <a href="https://en.wikipedia.org/wiki/Sequence_alignment" rel="noreferrer">sequence alignment</a> and <a href="https://en.wikipedia.org/wiki/Sequence_assembly" rel="noreferrer">sequence assembly</a> but I have not been able to find any difference between the two. What is the difference between sequence alignment and sequence assembly? If there is no different why are the terminologies different? </p>
| [
{
"answer_id": 40438,
"pm_score": 4,
"text": "<p><strong>Sequence alignment</strong></p>\n<p>It is done for checking sequence similarity between two or more <strong>different sequences</strong>. This will give information about how two sequences are different, what is their evolutionary relationship, wh... | [
{
"answer_id": 40439,
"pm_score": 0,
"text": "<p>Not necessarily. A good analogy for differentiating the two sequencing strategies (not to be confused with sequencing technologies i.e. illumina, smrt, oxford nanopore etc...) would be a puzzle. In the case of sequence alignment, you would have a bunch of... |
40,456 | <p>The food they eat seem extremely low on protein. Do they need less protein per mass unit than carnivores? Most of them grow quite a lot in the first year, is most of that from the mothers milk?</p>
| [
{
"answer_id": 40463,
"pm_score": 5,
"text": "<p>It boils down to the anatomy.</p>\n\n<p>Herbivores are very good at digesting plant matter, which us monogastrics are not particularly good at. Many herbivores (such as ruminants) have large, highly developed gastrointestinal tracts containing symbiotic b... | [
{
"answer_id": 71023,
"pm_score": 2,
"text": "<p>The protein RDA of another mammal, the human, is 70g every day, that's about 700g of hay if he can get 100% of the protein from it, that's 4 kilos of grass. So a 700 kilo cow would need about 40 kilos every day, and actually 700kg cows consume about 70kg ... |
40,634 | <p>How far back along the evolutionary tree do we have to go to find divergence to a completely different species to Hom. sapiens? I don't count Neanderthals because it seems that part of our genome contains fragments of Neanderthal DNA, and therefore, according to the species definition, Humans and Neanderthals could not have been an entirely different species. What about Denisovans? Is enough known about their DNA to consider them a completely different species? In fact, is it even possible to distinguish 'a species' from the DNA alone?</p>
| [
{
"answer_id": 54625,
"pm_score": 3,
"text": "<p>Do you also consider tiger and lions as different species? (Limited) Gene flow between the two groups has occurred. (Due to female hybrids being fertile.)</p>\n\n<p>There is evidence that gene flow between humans and neanderthals was also restricted. Nean... | [
{
"answer_id": 53761,
"pm_score": 2,
"text": "<p>The <em>erectus</em> line that gives rise to <em>antecessor</em> is your best bet, at about 1.2 MYA. <a href=\"http://www.nature.com/nature/journal/v485/n7396/full/485033a.html\" rel=\"nofollow noreferrer\">http://www.nature.com/nature/journal/v485/n7396/... |
40,703 | <p>So with my basic understanding of biology, DNA can change over time. </p>
<p>Does this mean that if one (or both) parents have something major missing (like a limb), the kid will come out without a limb? Does it matter if the parents had limbs amputated or were born like that? If someone got melanoma from laying in the sun <strong>a lot</strong>, would their kid have a higher risk of getting it?</p>
| [
{
"answer_id": 40716,
"pm_score": 3,
"text": "<blockquote>\n <p>Does this mean that if one (or both) parents have something major missing (like a limb), the kid will come out without a limb?</p>\n</blockquote>\n\n<p>Unless there is a genetic basis to the missing limb, no. Even for people born with miss... | [
{
"answer_id": 40709,
"pm_score": 0,
"text": "<blockquote>\n <p>Does this mean that if one (or both) parents have something major missing (like a limb), the kid will come out without a limb?</p>\n</blockquote>\n\n<p>If the parents are born without a limb, it could have a genetic reason or from external... |
40,773 | <p>Since Cancer cells have unlimited growth potential, can they be induced towards totipotency and pluripotency?
If so, can cancer cells be used in stem cell culture because of similar properties of unlimited replication?
Can they be used in cell lines to culture viruses even? </p>
| [
{
"answer_id": 40774,
"pm_score": 4,
"text": "<p>Cancer cells can be and are used in cell culture. HeLa cells were the first human cell line to be grown in culture and they were derived from a cervical tumor.</p>\n\n<p>That being said, Cancer cell lines would not <em>necessarily</em> be used for stem ce... | [
{
"answer_id": 40777,
"pm_score": 3,
"text": "<p>Adding onto AMR's answer, cancer cell lines are used extensively for research. They are typically fast to grow. <a href=\"http://bigpictureeducation.com/quick-guide-hela-cells\" rel=\"nofollow\">HeLa Long</a> grow to capacity of a 10cm dish within about 4... |
40,902 | <p>If I find the exact starting position (say 1152471) of the coding sequence of a given gene in the genome of a bacterium, is the genome of the bacterium in general stable enough so that I can expect to find the same position in a different member of the same species? </p>
| [
{
"answer_id": 55573,
"pm_score": 3,
"text": "<p>Genetic variation within bacterial species can be much higher than one might expect. </p>\n\n<p>First, this can be a difficult question to answer quantitatively because even just testing whether two strains are part of the same bacterial species is diffic... | [
{
"answer_id": 41131,
"pm_score": -1,
"text": "<p>The locations of a gene on a bacterial chromosome is determined arbitrarily, so you would not expect coding sequences to necessarily have the same numerical values. Remember that the bacteria's transcription machinery will use <a href=\"https://en.wikipe... |
40,963 | <p>On the website <a href="http://www.whatisepigenetics.com/fundamentals/2/" rel="nofollow">http://www.whatisepigenetics.com/fundamentals/2/</a> it states that </p>
<blockquote>
<p>the imprint disorders Prader-Willi syndrome and Angelman syndrome, display an abnormal phenotype as a result of the absence of the paternal or maternal copy of a gene, respectively. In these imprint disorders, there is a genetic deletion in chromosome 15 in a majority of patients. The same gene on the corresponding chromosome cannot compensate for the deletion because it has been turned off by methylation, an epigenetic modification. Genetic deletions inherited from the father result in Prader-Willi syndrome, and those inherited from the mother, Angelman syndrome.</p>
</blockquote>
<p>To me it seems like this is suggesting the same problem in both Prader-Willi and Angelman sydrome- lack of expression of a particular gene. However in Prader-Willi syndrome it is the paternal chromosome that is missing and the maternal copy of this gene is silenced by methylation and the reverse applies for Angelman syndrome. Therefore it seems that in boh cases the problem is the lack of expression of this gene. Why, then, if both are caused by lack of expression of this gene, do these two illnesses have such different symptoms (constant hunger in Prader-Willi syndrome and mental disability and jerky movements in Angelman syndrome)? </p>
| [
{
"answer_id": 40976,
"pm_score": 3,
"text": "<p>In a wild-type human, you will inherit one paternal chromosome and one maternal chromosome, in this case, chromosome 15.</p>\n\n<p>The paternal chromosome which is packaged into the sperm will be methylated in such a way that the <a href=\"http://omim.org... | [
{
"answer_id": 40968,
"pm_score": 2,
"text": "<p>Within that region, there are multiple genes.</p>\n\n<blockquote>\n <p>Although the same gene may control imprinting for both disorders, the\n gene(s) causing their phenotypes differ. AS results from\n underexpression of a single gene, UBE3A, which cod... |
41,036 | <p>i want to know what if i made a sequence of cDNA of a specific gene in different plants - what is the important from the sequence and can if found difference between plants , and can i use this sequence to determine cis regulating element</p>
| [
{
"answer_id": 41037,
"pm_score": 3,
"text": "<p>No, cDNAs are copies of spliced mRNAs, and typically contain a 5'-UTR (untranslated region), an open reading frame, or ORF, and a 3'-UTR.\nThe <em>cis</em>-regulatory information might be revealed by sequencing the genomic DNA upstream of the gene(s). Th... | [
{
"answer_id": 41060,
"pm_score": 0,
"text": "<p><strong>The importance of sequencing</strong></p>\n\n<p>Sequence comparison is important because biologists tend to use prior knowledge to make inferences about the function of unknown entities. </p>\n\n<p><strong>Determing flanking sequences</strong></p>... |
41,390 | <p>If we observe that a miRNA, say hsa-mir-233, targets a mRNA, say XXX, in a given tissue in disease condition, can we say that always hsa-mir-233 targets mRNA XXX regardless of type of tissue and disease condition?</p>
| [
{
"answer_id": 41399,
"pm_score": 4,
"text": "<p>First you have to define what you really mean by miRNA-X targets mRNA-Y. If you mean direct targeting then there are assays to verify it.</p>\n\n<p>To verify if the miRNA can potentially target the mRNA independently, what is routinely done is a reporter ... | [
{
"answer_id": 41425,
"pm_score": 1,
"text": "<p>mRNA targeting mechanism is highly specific and depends on various factors. the target mRNA and miRNA complex is highly conserved even from an evolutionary point of view.There are many in-vitro studies which shows the importance of miRNA concentration.Now... |
41,503 | <p>Are there species that occupy several roles in the food hierarchy?</p>
<p>By role, I am referring to producer, primary consumer, secondary consumer, tertiary consumer, quaternary consumer and so on.</p>
<p><strong>Examples of more specific questions</strong></p>
<ul>
<li><p>Are there species that are both primary and secondary consumer?</p></li>
<li><p>Are there species that are primary consumer, secondary consumer and a tertiary consumer?</p></li>
<li><p>Are there species that are both producer and primary consumer?</p></li>
</ul>
| [
{
"answer_id": 41504,
"pm_score": 5,
"text": "<p><strong>Food hierarchy and food web</strong></p>\n\n<p>Ecological trophic interactions are better represented by food webs rather than simple hierarchical relationships. As a consequence, the concepts of primary/secondary/tertiary/... consumers sometimes ... | [
{
"answer_id": 41509,
"pm_score": 2,
"text": "<p>To follow up with Remi.b's answer, there <em>is</em> an example of an organism that is a combination of <strong>producer + primary consumer + secondary consumer</strong>: </p>\n\n<p><strong>Bladderwort (Utricularia spp.)</strong> is a carnivorous plant ... |
41,520 | <p>The reflex arc is composed of 5 parts:</p>
<p>sensory receptors, afferent neuron(s), synapses within the central integrating station, efferent neuron(s) and the effector (includes transmission across the neuro-muscular junction and contractile mechanism - Assuming this is a myotatic reflex).</p>
<p>Which part takes the longest time & why?</p>
| [
{
"answer_id": 41504,
"pm_score": 5,
"text": "<p><strong>Food hierarchy and food web</strong></p>\n\n<p>Ecological trophic interactions are better represented by food webs rather than simple hierarchical relationships. As a consequence, the concepts of primary/secondary/tertiary/... consumers sometimes ... | [
{
"answer_id": 41509,
"pm_score": 2,
"text": "<p>To follow up with Remi.b's answer, there <em>is</em> an example of an organism that is a combination of <strong>producer + primary consumer + secondary consumer</strong>: </p>\n\n<p><strong>Bladderwort (Utricularia spp.)</strong> is a carnivorous plant ... |
41,665 | <p>Isn't phosphorous a macro nutrient? So it should be present in the soil in sufficient quantities... but still we add phosphate. Why?</p>
| [
{
"answer_id": 41668,
"pm_score": 3,
"text": "<p><strong><a href=\"http://www.lenntech.com/phosphorus-cycle.htm\" rel=\"nofollow\">Phosphorus</a></strong> (P) is a macronutrient and, after nitrogen (N), typically <em>the</em> limiting factor for plant growth. Potassium (K) is also often added in fertili... | [
{
"answer_id": 41718,
"pm_score": 0,
"text": "<p>I'll try to give a wide answer, not only to why we have to add chemical fertilizers, but also to why this is not our best choice.</p>\n\n<p>One thing is the isolated chemical compounds we add to the soil (like N, P and K), other is its natural fertility (... |
41,844 | <p>Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information? </p>
<p>Is there a freely accessible database online with these statistics? Or, one that contains something for each protein from which this could be derived? (and if so how?)</p>
| [
{
"answer_id": 41846,
"pm_score": 5,
"text": "<p>There's a fantastic database available from the United States Department of Agriculture that includes almost <strong>9,000</strong> common foods, including their nutritional information. This database is searchable and available from the USDA Agricultural... | [
{
"answer_id": 41845,
"pm_score": 2,
"text": "<p>you need to know the protein sequence to be able to do this.</p>\n\n<p>Paste the protein sequence into this tool and press 'Compute Parameters'. This will give the percentage amino acid composition of the protein.</p>\n\n<p><a href=\"http://web.expasy.org... |
42,342 | <p>It has always been my understanding that humans have two eyes so that we can have 3D vision: the left eye sees more of the left side of an object than the right eye and vice versa. This helps us to estimate depth among other things.</p>
<p>Now when I close one eye, I still am able to perceive depth. I assume this is because my brain fills in the blanks For how long does this work? Do people eventually lose the depth perception (or at least it diminishes significantly) when they lose a single eye?</p>
<p>If so, how low does it take? If not, clearly we are capable of perceiving everything with one eye. Why do we then have two (besides redundancy and a larger field of view)? What is considering the evolution of man better in having two eyes as opposed to one or three, or four,..?</p>
| [
{
"answer_id": 42629,
"pm_score": 4,
"text": "<p>It seems like you suffer from a misconception. "The left eye sees more of the left side of an object..." is not how distance perception works. Otherwise we wouldn't be able to estimate the distance from flat objects, such as traffic signs and sh... | [
{
"answer_id": 97335,
"pm_score": -1,
"text": "<pre><code>Edit01 (here and scattered throughout) \n</code></pre>\n<p>[Not meaning to be antagonistic… but admittedly somewhat defensive.]<br />\nInsofar as the following is a citation of an existing work, it is the below Martin and Foley item, pp165-185 (... |
42,600 | <p>I'm confused over the two terms <strong>vascular cambium</strong> and <strong>intrafascicular cambium</strong>.</p>
<p>Is vascular cambium the same as intrafascicular cambium?</p>
| [
{
"answer_id": 42604,
"pm_score": 4,
"text": "<p>I know nothing about plant physiology but I googled your question and here is what I found</p>\n<p><strong>Vascular cambium</strong></p>\n<p>From <a href=\"https://en.wikipedia.org/wiki/Vascular_cambium\" rel=\"noreferrer\">wiki</a></p>\n<blockquote>\n<p>... | [
{
"answer_id": 72221,
"pm_score": 0,
"text": "<p>The Vascular cambium is responsible for secondary growth, which is growth in thickness. Whereas, primary is growth in length. Once, the length-wise growth of the xylem and phloem are accomplished, growth in thickness or growth inwards through the vascular... |
42,619 | <p>I am an ex smoker who now vapes (uses e-cigs). Various authorities are equating vaping with smoking by calling it a 'tobacco product' - which is in a sense true given that the majority of nicotine sold is extracted from the leaves of tobacco. I am interested in the practicality (or otherwise) of extracting nicotine from other botanical sources.</p>
<p>Of course, it is not just tobacco that contains nicotine, it is common in other plants of the nightshade family, as suggested by <a href="http://www.nejm.org/doi/full/10.1056/NEJM199308053290619" rel="nofollow noreferrer">The Nicotine Content of Common Vegetables</a> & <a href="https://en.wikipedia.org/wiki/Nicotine#Occurrence_and_biosynthesis" rel="nofollow noreferrer">Nicotine: Occurrence and biosynthesis</a>. The second source notes:</p>
<blockquote>
<p>Nicotine is a natural product of tobacco, occurring in the leaves in a range of 0.5 to 7.5% depending on variety.[84] Nicotine also naturally occurs in smaller amounts in plants from the family Solanaceae (such as potatoes, tomatoes, and eggplant).[85] </p>
</blockquote>
<p>Reference 85 points back to the first link, which shows this table.</p>
<p><a href="https://i.stack.imgur.com/VoHfY.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/VoHfY.png" alt="Table of nicotine levels in common food plants"></a></p>
<p>But looking at the numbers, it seems unlikely. At even .5%, the 'low nicotine' tobacco leaf comes in at 5 mg/g, which is 5,000,000 ng/g - around 50,000 times more concentrated than eggplant. In fact, here is a graph of the log<sub>10</sub> value (2 is <strong><em>ten times larger</em></strong> than 1) of each.</p>
<p><a href="https://i.stack.imgur.com/QvhsP.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/QvhsP.png" alt="enter image description here"></a></p>
<p>On the other hand, the ability of a plant to produce nicotine is retained and handed down to ancestors because <em>nicotine is a pesticide</em> that ..discourages insects from eating the plant, and larger herbivores will also get sick if they eat too much of it. Logically, levels of nicotine would be higher in the leaves and stems of a plant than in the fruits/food that we & animals are more interested in eating. That again makes sense, since most fruits are 'designed' to be put through the stomach of a larger animal as part of the process of regeneration.</p>
<p>That logic seems to be borne out by the levels of nicotine in tomatoes, that start around 40 ng/g in green tomatoes, but end up at just over 4 ng/g in ripe tomatoes (not sure what's going on with that 'pureed tomato' level of over 50 ng!). The drop suggests to me that's the plant's way of preventing consumption while the fruits are still developing, but making them safe(r) to eat once ripe.</p>
<p>But what about the nicotine content in the leaves of those plants? Logically they might have a higher nicotine content. Does anyone know of studies of the levels of nicotine in the <em>other parts</em> of plants of the nightshade family?</p>
| [
{
"answer_id": 42734,
"pm_score": 2,
"text": "<blockquote>\n <p>.. I'm not aware of large nicotine levels in other parts of plants. I assume tobacco will still have the highest nicotine levels, because <em>that's what people have been <strong>selecting for</strong> for centuries.</em> .. - <strong>user... | [
{
"answer_id": 95195,
"pm_score": 2,
"text": "<p>Tomato leaves have something like 184 ng/g of nicotine, in the same ballpark as tomatoes (the fruit) and not close to tobacco. I think this is not peer-reviewed, but it cites other papers that are: <a href=\"https://content.sciendo.com/view/journals/cttr... |
42,633 | <p><strong>Do animals demonstrate any sort of accuracy-motivated play?</strong> (please provide examples!)</p>
<p>Consider most human sports and related hobbies. Most share the common goal of hitting a target or being accurate, and in the case of organized sports, points are typically awarded for being accurate. Archery, firearm past times, football, soccer, basketball, hockey, baseball, tennis, billiards, bowling, darts, beer pong, horseshoes, and countless other examples all are based on competitive accuracy.</p>
<p>Humans seem to be <em>obsessed</em> with accuracy in our competitive past-times. Examination of more ancient sport interests demonstrate less preoccupation with accuracy (though of course there is variation between cultures -- see <a href="https://en.wikipedia.org/wiki/Category:Ancient_sports" rel="noreferrer">here</a> or <a href="http://www.perseus.tufts.edu/Olympics/sports.html" rel="noreferrer">here</a>, ), and perhaps just more with demonstrations of strength and dominance. However, competitive accuracy was alive and well in ancient times: boxing, sword fighting, lacrosse, hoop rolling, golf (and Chinese equivalent Chuiwan), and others already listed are just a few examples of accuracy games with more ancient origins. It seems, then, that the human species has had a fascination with accuracy for a long time.</p>
<p>However, do animals have the same (or really <em>any</em>) preoccupation with accuracy? I've seen countless examples of animals 'playing' or competing (e.g., pets & captive animals playing with toys & enrichment objects, young males of various taxa sparring or wrestling, <a href="https://www.youtube.com/watch?v=O0qMT2YBIcg" rel="noreferrer">whales playing with their food</a>, <a href="http://www.nfl.com/videos/nfl-game-highlights/0ap2000000119231/Monkeys-riding-dogs" rel="noreferrer">monkeys sheep herding on dogs</a>, etc.), but <strong>is there any evidence or example of wild animals playing 'games' based on accuracy</strong>?</p>
| [
{
"answer_id": 42734,
"pm_score": 2,
"text": "<blockquote>\n <p>.. I'm not aware of large nicotine levels in other parts of plants. I assume tobacco will still have the highest nicotine levels, because <em>that's what people have been <strong>selecting for</strong> for centuries.</em> .. - <strong>user... | [
{
"answer_id": 95195,
"pm_score": 2,
"text": "<p>Tomato leaves have something like 184 ng/g of nicotine, in the same ballpark as tomatoes (the fruit) and not close to tobacco. I think this is not peer-reviewed, but it cites other papers that are: <a href=\"https://content.sciendo.com/view/journals/cttr... |
42,710 | <p>Where can I find values, or estimates, of the density of cells in human tissues? Maybe an overall estimate, or distinct values for distinct tissues? Or maybe not human, but mammal tissues (which should be similar)?</p>
| [
{
"answer_id": 42717,
"pm_score": 4,
"text": "<p>Well, Sender, Fuchs, and Milo wrote a paper to discuss the total number of cells in the body and compare it to the number of bacteria in the body (<a href=\"http://dx.doi.org/10.1101/036103\" rel=\"noreferrer\">http://dx.doi.org/10.1101/036103</a>). Their... | [
{
"answer_id": 42790,
"pm_score": 2,
"text": "<p>The 'cleanest' data I am aware of is on studies using density gradient centrifugation. In density gradient centrifugation, a preparation of cells is layered on top of a density gradient media which has higher density than water (water=1g/ml). Centrifuga... |
42,784 | <p>I was reading some questions in the test bank. Then in Chapter 27, I wonder why the answer is A. (undergo death by plasmolysis). Is the high concentration of sugar that kills them or the effects of sugar on bacteria?
<a href="https://i.stack.imgur.com/WW12C.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/WW12C.jpg" alt="enter image description here"></a></p>
<blockquote>
<p>Reece et al. <em>Campbell Biology Test Bank</em>. 9th ed. Boston: Benjamin Cummings / Pearson, 2011: 563.</p>
</blockquote>
| [
{
"answer_id": 42810,
"pm_score": 4,
"text": "<p>In (very) short: enzymes are necessary for life. Cytoplasm is necessary for enzymes to function. Water is necessary for cytoplasm to exist. Cells have osmotic membranes.</p>\n\n<p>Given a cell in a solution (even a goopy one, like jam) with a very high co... | [
{
"answer_id": 42797,
"pm_score": 0,
"text": "<p>Actually, it doesn't kill them. As far as I am aware people with weak immune responses shouldn't eat honey or jams because of risk of fungal or bacterial infections. </p>\n\n<p>Resource:\n<a href=\"http://www.mayoclinic.org/drugs-supplements/honey/evidenc... |
42,803 | <p>In the BLAST+ packages, you can align two sequences instead of searching a database:</p>
<p><code>tblastn -query seq1.fa -subject seq1.fa</code></p>
<p>The web BLAST documentation states that e-values are calculated from the nr database:</p>
<blockquote>
<p>Because BLAST 2 Sequences uses the <strong>size of the current nucleotide or protein nr database to calculate Expect values</strong>, you may need to significantly increase the Expect threshold in order to see shorter alignments. </p>
</blockquote>
<p>However, the command-line documentation explicitly states that you cannot provide both a database and a <code>subject</code> sequence:</p>
<pre><code>-db <String>
BLAST database name
* Incompatible with: subject, subject_loc
-subject <File_In>
Subject sequence(s) to search
* Incompatible with: db, gilist, seqidlist, negative_gilist,
db_soft_mask, db_hard_mask
</code></pre>
<p>How is the e-value calculated when using BLAST-2-Sequences on the command line? (I am fairly certain I do not have the nr database downloaded.)</p>
<p>Thanks!</p>
| [
{
"answer_id": 42810,
"pm_score": 4,
"text": "<p>In (very) short: enzymes are necessary for life. Cytoplasm is necessary for enzymes to function. Water is necessary for cytoplasm to exist. Cells have osmotic membranes.</p>\n\n<p>Given a cell in a solution (even a goopy one, like jam) with a very high co... | [
{
"answer_id": 42797,
"pm_score": 0,
"text": "<p>Actually, it doesn't kill them. As far as I am aware people with weak immune responses shouldn't eat honey or jams because of risk of fungal or bacterial infections. </p>\n\n<p>Resource:\n<a href=\"http://www.mayoclinic.org/drugs-supplements/honey/evidenc... |
42,819 | <p>According to Campbell Biology,</p>
<blockquote>
<p>A <strong>growth factor</strong> is a protein released by certain cells that stimulates other cells to divide.</p>
</blockquote>
<p>and according to Wikipedia,</p>
<blockquote>
<p>A <strong>mitogen</strong> is a chemical substance that encourages a cell to commence cell division, triggering mitosis.</p>
</blockquote>
<p>What’s the difference between them? I suppose a mitogen specifically refers to mitosis, but if something is stimulating mitosis, isn’t it stimulating growth? Are mitogens all growth factors? Are all growth factors mitogens?</p>
| [
{
"answer_id": 42810,
"pm_score": 4,
"text": "<p>In (very) short: enzymes are necessary for life. Cytoplasm is necessary for enzymes to function. Water is necessary for cytoplasm to exist. Cells have osmotic membranes.</p>\n\n<p>Given a cell in a solution (even a goopy one, like jam) with a very high co... | [
{
"answer_id": 42797,
"pm_score": 0,
"text": "<p>Actually, it doesn't kill them. As far as I am aware people with weak immune responses shouldn't eat honey or jams because of risk of fungal or bacterial infections. </p>\n\n<p>Resource:\n<a href=\"http://www.mayoclinic.org/drugs-supplements/honey/evidenc... |
42,891 | <p>The Zika virus <a href="https://en.wikipedia.org/wiki/Zika_virus_outbreak_timeline" rel="noreferrer">was already present and known to the world</a> (mostly in Southeast Asia) before the current outbreak. </p>
<p>Why has the virus caused such an extreme outbreak? </p>
<p>Has it mutated from its ancestral form such as that found in Southeast Asia?</p>
| [
{
"answer_id": 42894,
"pm_score": 6,
"text": "<p>There is one main answer to this question: The Zika virus spreads so fast because it never emerged in this part of the world. Hence there is no natural immunity available in the population and a lot of infections occur. Once this \"first wave\" of infecti... | [
{
"answer_id": 42897,
"pm_score": 4,
"text": "<p>A mutation isn't <em>necessary</em> to explain the outbreak in the Americas, given the low immunity of the population, but there is tentative evidence that this strain of the Asian lineage of the virus may have developed some novel characteristics, which ... |
43,064 | <p>If a person without diabetes or any diabetes-related issues receives an injection of insulin, what happens? Would the blood glucose level drop or does the body naturally compensate for the added insulin? What biological process occurs? </p>
| [
{
"answer_id": 43065,
"pm_score": 4,
"text": "<ol>\n<li>Blood sugar drops (Hypoglycaemia)</li>\n<li>There are several other uses of insulin (other than diabetic treatment) </li>\n</ol>\n\n<p><strong>Some of those could be:</strong> </p>\n\n<ul>\n<li>Diagnostics</li>\n<li>Psychology (Narcoanalysis)</li>\... | [
{
"answer_id": 43069,
"pm_score": 1,
"text": "<p>It is possible to overdose and die of an insulin injection. Obviously, if enough is injected fast enough, the body can't recompense appropriately and and the person would die of hypoglycaemia. Below around 20mg/dL of blood sugar levels in the blood you ar... |
43,116 | <p>I used to see these insects frequently in Chennai and Bangalore (South India). I just would like to know if this is a kind of <a href="https://en.wikipedia.org/wiki/Lovebug" rel="nofollow noreferrer">lovebug</a>. The lovebug as mentioned in the Wikipedia page is, however, different in appearance, although they too are walking as pairs.</p>
<p>Why are they always walking as attached pairs? It also seems to me that the bigger one drives the motion and decides the direction. Is that true?</p>
<p><a href="https://i.stack.imgur.com/FnPzX.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/FnPzX.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 43121,
"pm_score": 4,
"text": "<p>I believe this is a member of the <a href=\"https://en.wikipedia.org/wiki/Pyrrhocoridae\" rel=\"nofollow\">family of Phyrrocoridae</a> also called firebugs. A more detailed identification would require a more high resolution image of the head and also an ... | [
{
"answer_id": 43131,
"pm_score": 2,
"text": "<p>I agree with Phillip C's comment – this pretty much seems to look like a <em>melamphaus</em></p>\n<blockquote>\n<p><em>Melamphaus Stål, 1868</em></p>\n<p><strong>kingdom</strong> Animalia</p>\n<p><strong>phylum</strong> Arthropoda</p>\n<p><strong>class</s... |
43,368 | <p>Nando's chain of restaurants (UK) refers to chili peppers as just "chilies". My friend and I had a discussion with regard to whether chilies can be called "peppers" or if they do not belong to the pepper family at all. In fact, my friend added that there are 2 types of this specimen - "chilies" and "chili peppers."<br>
To what extent is this all true, and what exactly are chilies?</p>
| [
{
"answer_id": 43370,
"pm_score": 4,
"text": "<p>Chili is a common reference to chili peppers in an abundance of countries, but they fall within the same designation as other so-called \"peppers\" such as bell pepper, cayenne, jalapeno, etc. because they are all of the same genus <em>Capsicum</em>. They... | [
{
"answer_id": 43667,
"pm_score": -1,
"text": "<p>Chilis are from the New World, and as CMosychuk <a href=\"https://biology.stackexchange.com/a/43370/10456\">has answered</a>, belong in the <em>Capsicum</em> genus. Their name <a href=\"http://www.etymonline.com/index.php?allowed_in_frame=0&search=ch... |
43,673 | <p>A couple of years ago I saw a BBC Horizon television documentary about sugar and fat. One section mentioned three experiments in which rats were given their ordinary rat food plus and unlimited supply of:</p>
<p>Experiment A. Unlimited sugar</p>
<p>Experiment B. Unlimited fat</p>
<p>Experiment C. Unlimited sugar&fat mixed together (50:50)</p>
<p>The stated results were that in experiment A the rats did not put on any weight, in experiment B the rats put on weight but not much and in experiment C they put on loads of weight and would eat the 50:50 mixture to the exclusion of their ordinary food. I also remember the documentary said the 50:50 ratio was critical and if the ratio was shifted too far in either direction then the weight gain effect reduced sharply.</p>
<p>I have two questions. 1. What was the original research paper. and 2. Have there been any related new results with other mixtures like sugar/salt fat/salt?</p>
<p><strong>EDIT:</strong> I have just found <a href="http://www.ncbi.nlm.nih.gov/pubmed/2326345" rel="nofollow noreferrer">this related paper</a>. I don't know if its the exact one relied upon by the documentary, but it's certainly close... perhaps the documentary employed the results from multiple papers.</p>
<p><strong>EDIT:</strong> You can see the whole documentary here: <a href="https://www.dailymotion.com/video/x1arpze" rel="nofollow noreferrer">https://www.dailymotion.com/video/x1arpze</a> - the rat experiment discussion begins around 46 minutes in.</p>
<p><strong>EDIT:</strong> years later... I found <a href="https://www.sciencedirect.com/science/article/pii/S1550413118303255" rel="nofollow noreferrer">this</a> and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431128/" rel="nofollow noreferrer">this</a>.</p>
| [
{
"answer_id": 72343,
"pm_score": 4,
"text": "<p><strong>1. What was the original research paper?</strong></p>\n\n<p>This one appears close: <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/2326345\" rel=\"nofollow noreferrer\">Hyperphagia in rats produced by a mixture of fat and sugar (PubMed, 1990)</a></... | [
{
"answer_id": 43824,
"pm_score": 1,
"text": "<p>It is easier for the body to use carbohydrates as energy source rather than lipids.\nWhen the food is full of fat, the mouse will use fat as a source of energy and only a little part of it is stored.\nFurthermore, when the food is full of sugar, the mouse... |
43,701 | <p>Lets take the case of a person doing heavy exercise. Aerobic respiration is taking place, but oxygen is about to be finished up. Glycolysis occurs, Krebs cycle finishes. Now NADH and FADH<sub>2 </sub> enter electron transport system (ETS) to form ATP, but at the last step, cytochrome c oxidase cannot get oxygen as it just finished up. Now, what happens to the ongoing ETS? Does it go in reverse order and then arnon cycle to get back Acetyl co-A and respire anaerobically, or does this process get paused and respiration switches over to anaerobic mode till oxygen supply is replenished?</p>
| [
{
"answer_id": 43775,
"pm_score": 3,
"text": "<p>I think both @David and @SatwikPasani have given nice answers, but none of them seems complete and involving all details. So I am posting another answer which involves much of the required details for benefit of readers as well as myself.</p>\n\n<p>The si... | [
{
"answer_id": 43717,
"pm_score": 4,
"text": "<p>The simple answer to your question is that in the absence of oxygen the electron transport chain stops. (It can't go backwards, that would generate oxygen.) However your assumption that it stops at the last step is incorrect, all the cytochromes are conve... |
43,710 | <p>I recently fell ill with a cold, and began to take a vitamin C capsule each day to help my immune system. When I noticed no change in my condition, I began to incorporate an abundance of citrus into my diet instead of taking the capsules. When I ate the citrus my condition began to improve markedly. </p>
<p>The ingredients listed by the vitamin manufacturer are:</p>
<ul>
<li>Ascorbic Cellulose Gel</li>
<li>Hydroxypropyl Cellulose</li>
<li>Croscarmellose Sodium</li>
<li>Stearic Acid</li>
<li>Magnesium Stearate</li>
<li>Silicon Dioxide</li>
</ul>
<p>Not excluding the possibility of coincidence, I was was intrigued. Has evidence been published to suggest that nutrients in whole foods like vitamin C in citrus fruits are more readily utilized in the body than nutrients in vitamin capsules? </p>
| [
{
"answer_id": 89161,
"pm_score": 3,
"text": "<h2>Vitamin C bioavailability</h2>\n\n<p>According to the review <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847730/\" rel=\"nofollow noreferrer\">Synthetic or Food-Derived Vitamin C—Are They Equally Bioavailable? (Nutrients, 2013)</a>, the bioav... | [
{
"answer_id": 44494,
"pm_score": 0,
"text": "<p>This is not a coincidence. Food-sourced vitamins are prized because of being in bio-available form, soluble and absorbable. The only way to make a vitamin more absorbable is to deliver it elementally, with no digestion required at all. </p>\n\n<p>The b... |
43,914 | <p>In electrocardiography, electrodes have the typical names of:</p>
<ul>
<li>RA (Right Arm)</li>
<li>LA (Left Arm)</li>
<li>RL (Right Leg)</li>
<li>LL (Left Leg)</li>
<li>V1, V2, V3, V4, V5 and V6</li>
</ul>
<p>What does the <em>V</em> stand for? Is it perhaps from <em>vector</em>, <em>ventricular</em>, or maybe from something else entirely?</p>
| [
{
"answer_id": 43919,
"pm_score": 4,
"text": "<p><strong>Short answer</strong><br>\nV stands for <em>voltage</em>.</p>\n\n<p><strong>Background</strong><br>\nThe various leads in an ECG montage are shown below:</p>\n\n<p><a href=\"https://i.stack.imgur.com/LiO64.jpg\" rel=\"nofollow noreferrer\"><img sr... | [
{
"answer_id": 69198,
"pm_score": 0,
"text": "<p>Very likely it means Unipolar. Please note only unipolar leads aVL, aVR, aVF, and all precordial leads have the letter V. They are all unipolar. Long time ago, the \"U\" may have been misspeled as \"V\".</p>\n"
},
{
"answer_id": 70924,
"pm_sco... |
43,968 | <p>Both are examples of genetic drift in which there is a change in the allele frequency when the population size becomes small.
What is the difference between the two?</p>
| [
{
"answer_id": 43974,
"pm_score": 3,
"text": "<p><strong>Genetic drift is an EVOLUTIONARY PROCESS</strong></p>\n\n<p>Source: <a href=\"https://en.wikipedia.org/wiki/Genetic_drift\" rel=\"nofollow\">Wikipedia > Genetic Drift</a></p>\n\n<blockquote>\n <p>Genetic drift (also known as allelic drift or the ... | [
{
"answer_id": 43971,
"pm_score": 0,
"text": "<p>The Founder and Bottleneck effect are both examples of Genetic drift as you mention. The end result is pretty much the same, i.e., a reduction in the genetic diversity of the population. The main difference is the <em>cause</em> underlying the drift.</p>\... |
44,156 | <p>From school, I remember that for something to be considered life, it must be able to reproduce. With the creation of seedless fruits (such as watermelon), would this be considered life as they don't have seeds so they can't reproduce?</p>
| [
{
"answer_id": 44158,
"pm_score": 4,
"text": "<p><strong>Definition of life</strong></p>\n\n<p>The definition of what is alive and what is not is not a matter of biology but a matter of philosophy. Most definitions are based on:</p>\n\n<ul>\n<li>Physiology\n\n<ul>\n<li>Existence of a metabolism</li>\n</... | [
{
"answer_id": 44157,
"pm_score": 2,
"text": "<p>According to Wiki:</p>\n\n<p>Life is a characteristic distinguishing physical entities having biological processes (such as signaling and self-sustaining processes) from those that do not, either because such functions have ceased (death), or because they... |
44,623 | <p>I always knew about the <em>sympathetic and para-sympathetic nervous systems</em>, and today I was told about the <strong>meta-sympathetic nervous system</strong>, but I didn't understand well the man who told me about it and I didn't find enough or reliable information about this system, and if it's accepted in the scientific world or it's arguable. </p>
| [
{
"answer_id": 44637,
"pm_score": 3,
"text": "<p>The concept of a metasympathetic part of the autonomic nervous system (distinct from the sympathetic and parasympathetic parts) seems to be an idea discussed almost exclusively in the Russian scientific literature.(<a href=\"https://scholar.google.com/sch... | [
{
"answer_id": 44631,
"pm_score": 2,
"text": "<p>As @mgkrebbs says, metasympathetic nervous system is still a matter of debate and is not fully accepted in the scientific world due to lack of research and evidence.</p>\n\n<p>Metasympathetic nervous system, just like sympathetic and parasympathetic nervo... |
44,736 | <p>If DNA is more or less the same in all cells, and DNA is used to produce proteins from aminoacids, then do all cells produce the same proteins or are they specialised/controlled by something?</p>
| [
{
"answer_id": 44749,
"pm_score": 4,
"text": "<p>Each cell <a href=\"https://biology.stackexchange.com/questions/43063/is-the-dna-different-in-each-type-of-cell-what-dna-is-passed-to-offspring\">will indeed have the same DNA sequences</a> and ability to produce any given protein. However, there are cert... | [
{
"answer_id": 44804,
"pm_score": 0,
"text": "<p>Protein expression in cells is majorly governed by a concept called <a href=\"https://en.wikipedia.org/wiki/RNA_splicing\" rel=\"nofollow\">RNA splicing.</a> This also forms the basis of different types of cells which has different proteins expressed at d... |
44,769 | <p>I have read quite some articles but I can't figure out the main reason for gc content deviation in prokaryotes. In eukaryotes I can understand it, because the genome isn't composed at random, like TATA boxes and CpG island, because they are important for functioning in the production of proteins. </p>
<p>However in prokaryotes there is such a variety, GC% is ranging from 20% up to 70%. Most of the time it depends on the environment, high temperature needs a stable genome (= high gc content). </p>
<p>I also read the answer to this question <a href="https://biology.stackexchange.com/questions/16447/how-does-gc-content-evolve">How does GC-content evolve?</a> however it's still not clear to me. I hope someone can explain the deviation a little bit more. </p>
<p><strong>Question</strong></p>
<p>Prokaryotes have an AT drift, but what mechanism causes some of these bacteria to higher their GC% instead of lowering it. </p>
| [
{
"answer_id": 44749,
"pm_score": 4,
"text": "<p>Each cell <a href=\"https://biology.stackexchange.com/questions/43063/is-the-dna-different-in-each-type-of-cell-what-dna-is-passed-to-offspring\">will indeed have the same DNA sequences</a> and ability to produce any given protein. However, there are cert... | [
{
"answer_id": 44804,
"pm_score": 0,
"text": "<p>Protein expression in cells is majorly governed by a concept called <a href=\"https://en.wikipedia.org/wiki/RNA_splicing\" rel=\"nofollow\">RNA splicing.</a> This also forms the basis of different types of cells which has different proteins expressed at d... |
44,955 | <p>I am trying to understand <em>why</em> Fast Fourier Transform (<strong>FFT</strong>) is used in the analysis of raw EEG channel data.</p>
<p>My understanding (at the 30,000 ft view) is that FFT decomposes linear differential equations with non-sinusoidal source terms (which are fairly difficult to solve) and breaks them down into component equations (<em>with</em> sinusoidal source terms) that are easy to solve. It then combines each of these component/partial solutions to solve the original equation. In laymen's terms, it's like taking a smoothie, and breaking it down into its recipe of ingredients. Doing so would allow us to study and analyze each ingredient as it relates to the final product (the smoothie).</p>
<p><strong>But how does this relate to raw (non-FFT-decomposed) EEG data?</strong> My understanding of a single channel of EEG data is that it is essentially a measurement of voltage over time. What is to be gained by using FFT to break this voltage/time signal down into its constituent frequencies (alpha/beta/gamma/delta/mu waves), etc.? What additional information can each frequency tell us about the raw data?</p>
<hr>
<h3>Update:</h3>
<p>Here is my updated understanding of how FFT relates to raw EEG data per @Mark's description below:</p>
<p><a href="https://i.stack.imgur.com/mcsPm.png" rel="noreferrer"><img src="https://i.stack.imgur.com/mcsPm.png" alt="enter image description here"></a></p>
| [
{
"answer_id": 44960,
"pm_score": 5,
"text": "<p><a href=\"http://www.dspguide.com/ch12/2.htm\" rel=\"noreferrer\">Fast-Fourier Transform</a> (FFT) transforms a signal from the time domain into the frequency domain. Basically, any time-dependent signal can be broken down in a collection of sinusoids. In... | [
{
"answer_id": 44957,
"pm_score": 3,
"text": "<p>Any periodic waveform can be produced by adding up a series of sin waves of the appropriate frequency and amplitude. The FFT looks at a complex waveform and calculates those frequencies and amplitudes. The result is a new curve which plots amplitude vs ... |
44,956 | <p>Within the catalytic core of <em>mitochondrial ATP-synthase</em> there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so clearly it is in these where ATP is synthesised. </p>
<p>However, I can't find <strong>what the function of the $\alpha$ subunit is</strong>. A source would be appreciated. </p>
| [
{
"answer_id": 45244,
"pm_score": 2,
"text": "<p><a href=\"https://en.wikipedia.org/wiki/ATP_synthase_alpha/beta_subunits\" rel=\"nofollow noreferrer\">Wikipedia</a> tends to answer your question by this (emphasis mine):</p>\n\n<blockquote>\n <p>In F-ATPases, there are three copies each of the alpha an... | [
{
"answer_id": 45224,
"pm_score": 0,
"text": "<blockquote>\n <p>The α- and β-subunits have a similar fold, as would be expected from\n their sequence similarity. All of the α- subunits are bound to the ATP\n analogue AMP–PNP, and the three subunits adopt very similar\n conformations. The three β-sub... |
44,958 | <p>In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as.</p>
<p>It seems that it could be defined as the difference in pre-mRNA between the transcription and translation, is that right?</p>
<p>If so, does the transcription begin immediately after the end of the promoter sequence? Immediately after the promoter region on the DNA ends, does the next nucleotide become part of the 5'UTR?</p>
| [
{
"answer_id": 45168,
"pm_score": 3,
"text": "<p><strong>Concise Answer</strong></p>\n\n<p>The 5′-UTR region of a eukaryotic mRNA is derived from the RNA transcript of the region of a gene between the transcription start site and the DNA corresponding to the translational initiation codon. It differs fr... | [
{
"answer_id": 44959,
"pm_score": 1,
"text": "<p>The UTR is the region of the transcript upstream of the starting methionine. The promotor is not itself transcribed.</p>\n"
},
{
"answer_id": 44972,
"pm_score": 2,
"text": "<p><strong>Short answer</strong></p>\n<p>The 5' UTR on the mRNA i... |
44,962 | <p>Actinomycetes are known for their ability to produce rich variety of natural products, and particularly, polyketides. Many of the genes that encode the biosynthetic pathways are pretty big, as they could reach 20kb. These bacteria most probably have some kind of mechanism that would ensure efficient transcription and translation of these long ORFs. This could be done in two ways: either by stablizing the mRNA:RNA polymerase complex, or by stabilizing the mRNA:ribosome complex. Have any of you heard of such mechanisms in bacteria?</p>
| [
{
"answer_id": 45168,
"pm_score": 3,
"text": "<p><strong>Concise Answer</strong></p>\n\n<p>The 5′-UTR region of a eukaryotic mRNA is derived from the RNA transcript of the region of a gene between the transcription start site and the DNA corresponding to the translational initiation codon. It differs fr... | [
{
"answer_id": 44959,
"pm_score": 1,
"text": "<p>The UTR is the region of the transcript upstream of the starting methionine. The promotor is not itself transcribed.</p>\n"
},
{
"answer_id": 44972,
"pm_score": 2,
"text": "<p><strong>Short answer</strong></p>\n<p>The 5' UTR on the mRNA i... |
45,037 | <p>It is known that viruses contain DNA or RNA- either one and not both.</p>
<p>I came across a question: Which virus contains both DNA and RNA?</p>
| [
{
"answer_id": 45039,
"pm_score": 3,
"text": "<p>Here is the results summary of the study that describes the discovery of DNA:RNA hybrid virus:</p>\n\n<blockquote>\n <p>Results\n Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively singl... | [
{
"answer_id": 53675,
"pm_score": 2,
"text": "<p>Most virions have either RNA or DNA - never both. The exception to this rule is human cytomegalovirus (HCMV). In 2000, researchers reported that although HCMV contains mainly DNA, it also carries four pieces of RNA that are used to synthesize viral protei... |
45,207 | <p>I realized I only have a vague understanding based on what remember from high school and I don't know if they ever really broke it down for us but:</p>
<p>In general how do both prokaryotic and eukaryotic cells organize their chemical reactions? In prokaryotic cells I thought there were no organelles so does that mean that every reaction depends on the diffusion of the reactants throughout the cell and that any reaction could happen anywhere in the cell? And in eukaryotic cells, are organelles always used to compartmentalize stages in chemical synthesis?</p>
<p>What I'm getting at is that if everything is just floating around freely within a cell, wouldn't a lot of reactions interfere with each other? I'm wondering how these two types of cells approach this problem.</p>
| [
{
"answer_id": 45208,
"pm_score": 3,
"text": "<p>Okay, this is my first post on this site so please bear with me when it comes to the format of my response!</p>\n\n<p>To begin with I'm going to try and answer your question by clarifying some things.</p>\n\n<blockquote>\n <p>In prokaryotic cells I thoug... | [
{
"answer_id": 45210,
"pm_score": 1,
"text": "<p>Organization of reactions occurs in both prokaryotic and eukaryotic cells. A very basic example of this would be that of multiprotein complexes such as <a href=\"https://en.wikipedia.org/wiki/Fatty_acid_synthase\" rel=\"nofollow\">fatty acid synthases</a>... |
45,213 | <p>Some researches had found that Human DNA has a bit of Neanderthal DNA. So they suggested there would have been crossing between <em>Homo sapiens</em> and Neanderthals. </p>
<p>Now the Neanderthal looked a bit different from <em>Homo sapiens</em>, so is there something in human that has some neanderthal looks? </p>
<p>And is it only found in European people or also in Asian or African people. Could it be be possible that a larger hairiness of European man is due to Neanderthal DNA?</p>
| [
{
"answer_id": 45208,
"pm_score": 3,
"text": "<p>Okay, this is my first post on this site so please bear with me when it comes to the format of my response!</p>\n\n<p>To begin with I'm going to try and answer your question by clarifying some things.</p>\n\n<blockquote>\n <p>In prokaryotic cells I thoug... | [
{
"answer_id": 45210,
"pm_score": 1,
"text": "<p>Organization of reactions occurs in both prokaryotic and eukaryotic cells. A very basic example of this would be that of multiprotein complexes such as <a href=\"https://en.wikipedia.org/wiki/Fatty_acid_synthase\" rel=\"nofollow\">fatty acid synthases</a>... |
45,303 | <p>I know all my family up to my grandparents, with the exception of the grandfather on my mother's side. At the time my mother was conceived, my grandmother was having an affair so no one in my family knows for sure who the grandfather was.</p>
<p>In high school we learnt that blue eyes are a recessive trait and brown eyes are a dominant trait, as such I should be able to figure out who my grandfather is, but I only studied up to that level and I want to check with someone more knowledgeable than myself if it is correct.</p>
<p><em>So here's my reasoning:</em>
I have blue eyes, meaning I have two blue eyed genes and got one from my father and one from my mother.
My mother has brown eyes, meaning that she has one brown eyed gene and one blue eyed gene to pass it on to me.
My grandmother has blue eyes, so she passed one on to my mother.
One of my potential grandfathers had blue eyes, so if it had been him my mother would have received two blue eyes genes and have blue eyes. But she has brown eyes so it must be the other potential grandfather (who's eyes I don't know the colour of).
Can someone tell me if this is correct, and if not, why not?</p>
| [
{
"answer_id": 45326,
"pm_score": 3,
"text": "<p>You are trying to work out who your mother's father was. You know that your mother's mother had blue eyes, but your mother had brown eyes. You also have blue eyes. <strong>You make an assumption that eye colour is a <a href=\"https://en.wikipedia.org/wiki... | [
{
"answer_id": 45319,
"pm_score": -1,
"text": "<p>On a high-school level you are right. Still, the answer to your question is no.</p>\n\n<p>As you may have already noticed, nothing in reality is as simple as schools tell us. Eye colour is generally determined by one gene, but there are other genes which... |
45,347 | <p>I was reading this article : <a href="https://en.wikipedia.org/wiki/Perspiration" rel="nofollow">Perspiration</a><br>
The first question which came to my mind after reading the composition of <a href="https://simple.wikipedia.org/wiki/Sweat" rel="nofollow">sweat</a> was whether it contains any information about the DNA or not?</p>
<p>I haven't had much interaction with biology since 12th grade (2010), so kindly answer in layman's terms and detail as well.</p>
| [
{
"answer_id": 45355,
"pm_score": 4,
"text": "<p>The Wikipedia page you linked says that sweat is composed of a liquid similar to blood plasma. As all DNA in humans is stored in the nucleus of a cell, it seems unlikely that the sweat itself would contain any DNA.</p>\n\n<p>However, when someone sweats s... | [
{
"answer_id": 45378,
"pm_score": 1,
"text": "<p>I believe the answer is no.</p>\n\n<p>Sweat is the liquid secretion of body cells, not including the cells themselves. If the cells are secreted when sweating, then you may find some DNA in your sweat. You are right on that. Serum contains many different ... |
45,373 | <p>Can photosynthesis take place in a plant even if the plant is kept in ice cold water? I have googled this question, but so far have not found a satisfactory answer. </p>
| [
{
"answer_id": 45355,
"pm_score": 4,
"text": "<p>The Wikipedia page you linked says that sweat is composed of a liquid similar to blood plasma. As all DNA in humans is stored in the nucleus of a cell, it seems unlikely that the sweat itself would contain any DNA.</p>\n\n<p>However, when someone sweats s... | [
{
"answer_id": 45378,
"pm_score": 1,
"text": "<p>I believe the answer is no.</p>\n\n<p>Sweat is the liquid secretion of body cells, not including the cells themselves. If the cells are secreted when sweating, then you may find some DNA in your sweat. You are right on that. Serum contains many different ... |
45,376 | <p>I have properly googled this and got various answers. However, those answers do not provide an answer to the "Why" part of my question. Why is it that the upper surface of leaves is more green than the lower one? Some sites suggest that it is because of the thick cuticle. Yet, that sounds weird and doesn't fully convince me. What other reasons to why the upper surface of leaves is more green and shiny than the lower one, could there be?</p>
| [
{
"answer_id": 45686,
"pm_score": -1,
"text": "<p>Photosynthesis is the process of trapping sunlight and converting the energy into chemical energy which is then provided as a food source. </p>\n\n<p>So the sunlight is trapped through chlorophylls. This is a pigment in the organelle called the chloropla... | [
{
"answer_id": 45689,
"pm_score": 2,
"text": "<p>You can find two chlorophylls in most plant leaves, chlorophyll a and b. We'll use as a reference <a href=\"http://treephys.oxfordjournals.org/content/21/10/701.full.pdf\" rel=\"nofollow\"><em>Leaf characteristics and chlorophyll concentration of Schyzolo... |
45,623 | <p>I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or downstream of these exons that remain in the nascent RNA.</p>
<p>Does this reflect the biology or is it just a consequence of the spliced read mapping? In other words: Do transcribed regions upstream of the first exon and downstream of the last exon exist in nascent RNA?</p>
<p>These regions, if they exist, cannot be called introns when those are defines as 'spliced sequences between exons'. How would one call them?</p>
| [
{
"answer_id": 45636,
"pm_score": 4,
"text": "<p>Most (almost all, AFAIK) mRNAs and lncRNAs start with exons for the reasons already mentioned by David. In a typical splicing event, the nucleotide that is 5' to the splice donor site (lets call it pre-donor) and the one that is 3' to the acceptor site (l... | [
{
"answer_id": 45624,
"pm_score": 2,
"text": "<p>As far as I am aware, transcripts always start and end with exons. The reasons I wouldn’t expect otherwise (apart from my observations when examining Drosophila transcripts) are given below.</p>\n\n<p>As you will be aware, the spliceosome (at least for mR... |
45,694 | <p>I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to keep them in place'. </p>
<p>But how does the hydrophobicity of both the protein and the cell membrane prevent the protein from moving?</p>
| [
{
"answer_id": 45695,
"pm_score": 6,
"text": "<h1>Proteins can move around the membrane.</h1>\n<p>Most proteins do move within the membrane. The membrane is a liquid crystal and has <a href=\"https://en.wikipedia.org/wiki/Membrane_fluidity\" rel=\"noreferrer\">fluid behaviour</a>. Specifically, this is ... | [
{
"answer_id": 56322,
"pm_score": 3,
"text": "<p>There are two types of proteins that are present in a membrane, because you have not been specific about which type of protein you are talking about I will consider that you are talking about <em>Integral membrane proteins.</em>\nFor more clarity I will b... |
45,825 | <p>The question struck me the other day when I drank a glass of water. I understand that there are at least two conditions under which the brain signals thirst: extracellular thirst, when there's not enough fluid in the blood, and intracellular thirst, when the cells need more water to lower the concentration of osmolites.</p>
<p>However, it takes time for water to enter the bloodstream after it has been ingested, and it spends at least a little while in the stomach. </p>
<p>Why does the sensation of thirst disappear despite the water having not yet made it into my bloodstream?</p>
| [
{
"answer_id": 45850,
"pm_score": 4,
"text": "<p>There are two different aspects to or drivers of thirst, osmolality and hypovolemia, with plasma osmolality elevation being the more potent stimulus of thirst. \nAs stated by @arboviral (and supported by his link), not a lot is known about the mechanisms ... | [
{
"answer_id": 45834,
"pm_score": 2,
"text": "<p>Satiety is divided into pre-absorption and post-absorption - the mechanism you're asking about is preabsorption satiety, which as you point out occurs long before the water can be absorbed into the bloodstream and appears to be remarkably accurate. The re... |
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