qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
5,360 | <p>We're trying to do emulsion PCR using HA-coated polystyrene beads and we're noticing that the beads are seeing drastic issues with thermal degradation above 90C. As PCR has an unfortunate requirement of requiring a high temperature, I was curious about what options are out there to reduce the temperature during PCR denaturation or to stabilize the beads.</p>
| [
{
"answer_id": 5375,
"pm_score": 2,
"text": "<p>Perhaps isothermal amplification is possible (<a href=\"http://en.wikipedia.org/wiki/NASBA_%28molecular_biology%29\" rel=\"nofollow\">NASBA</a>)? </p>\n\n<p>Amplification of DNA also seems possible (<a href=\"http://www.biomerieux-diagnostics.com/servlet/s... | [
{
"answer_id": 5382,
"pm_score": 1,
"text": "<p><a href=\"http://nar.oxfordjournals.org/content/29/11/2377.full\" rel=\"nofollow\">Look at chemical hydrogen bond breakers.</a> Guanadine hydrochloride is included in the buffer conventionally to compete with the the hydrogen bonds that form the double he... |
5,383 | <p>In the University labs, we have used Beta-galactosidase as a reporter gene to quantify the expression initiated by the stress-response promoter in yeast. This was done by exposing one of the two groups to osmotic stress (high salt concentration) whilst the other was unstressed. Then the levels of beta-galactosidase were compared.
A question given to us afterwards asked to give advantages & disadvantages of using Beta-galactosidase compared to Luciferase as a reporter gene in this experiment. And which one would be, overall, more suitable?</p>
| [
{
"answer_id": 5386,
"pm_score": 4,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Beta-galactosidase\" rel=\"nofollow\">Beta-galactosidase</a> (B-gal for short) is an enzyme that will process the substrate lactose. In applications using B-gal as a reporter (lacZ gene), two lactose analogues are com... | [
{
"answer_id": 5387,
"pm_score": 2,
"text": "<p>I think that @leonardo has this backwards. β-galactosidase can be assayed accurately and cheaply using <a href=\"http://en.wikipedia.org/wiki/Ortho-Nitrophenyl-%CE%B2-galactoside\" rel=\"nofollow\">ONPG</a> as a colorimetric substrate with no solubili... |
5,395 | <p>Microorganisms constitute the bulk of all the biomass on Earth. I weighed myself yesterday, and wondered how much less I would weigh if I were completely free of bacteria and microbes, inside and out. </p>
<p><strong>Approximately how much weight and volume do microbes occupy within the average human body? How were these values obtained?</strong></p>
| [
{
"answer_id": 5415,
"pm_score": 4,
"text": "<p>@AlanBoyd's calculations are reasonable, I think the estimate is off though. The human microbome includes other bacteria which are not necessarily E.coli equivalent. </p>\n\n<p><a href=\"http://www.nih.gov/news/health/jun2012/nhgri-13.htm\" rel=\"nofollo... | [
{
"answer_id": 5399,
"pm_score": 3,
"text": "<p><strong>The bacterial flora weighs approximately 90 g and, assuming bacterial cell density is approximately 1 g ml<sup>-1</sup>, occupies a volume of 90 ml.</strong></p>\n\n<p><a href=\"http://en.wikipedia.org/wiki/Orders_of_magnitude_%28numbers%29#1012\">... |
5,405 | <p>If it were possible to live forever, would our brains grow infinitely with the number of memories that we store? Or would we remove old memories as we create new ones?</p>
| [
{
"answer_id": 5408,
"pm_score": 5,
"text": "<p>You would need to live a long, long, long, long time for this to become remotely problematic.</p>\n\n<p>Your question seems to suppose that a memory is \"stored\" by a neuron, and since neurons have mass, then the more memories we have the more our brains ... | [
{
"answer_id": 5406,
"pm_score": 1,
"text": "<p>We already remove old ones and create new ones. I doubt you remember most of Geometry, for instance.</p>\n<p>As for capacity, <a href=\"http://www.scientificamerican.com/article.cfm?id=what-is-the-memory-capacity\" rel=\"nofollow noreferrer\">this article ... |
5,421 | <p>The title does, <em>prima facie</em>, appear absurd.</p>
<p>Performing a swallowing action whilst pinching the nostrils shut gives the impression of listening through a bucket filled with water around the head; audible sound levels are perceptibly reduced. Some humans may encounter a similar sensation blowing their nose - hard.</p>
<p>This makes sense give the ears connect to the mouth/nose through the eustachian tubes. Can an odour make its way to the olfactory sensors through the ears?</p>
| [
{
"answer_id": 5424,
"pm_score": 5,
"text": "<p>A quick diagram to point out to people who may not know what Eustachian tubes are (#2).</p>\n\n<p><img src=\"https://i.stack.imgur.com/uRzEC.gif\" alt=\"Anatomy of the Ear\"></p>\n\n<p>In order for the aromatic molecule to reach the olfactory bulb, it woul... | [
{
"answer_id": 5422,
"pm_score": -1,
"text": "<p>Modified 6 Dec 2012: One approach to this question is to perform a sequence similarity search for genes encoding genes with a functioning in sensing external stimuli, be they\nolfactory receptor, taste receptor or other such genes that are expressed in cD... |
5,471 | <p>Most plants require carbon dioxide for their photosynthesis, which Mars has in overabundance. </p>
<p>Would atmosphere composition (let's ignore temperatures for the purpose of this question) of Mars allow vegetation to grow?</p>
| [
{
"answer_id": 5472,
"pm_score": 4,
"text": "<p>This is not my field by a long shot, so take what I say with a grain of salt. However, this question is very hard to answer because whether or not a plant will grow depends on a great variety of factors. Even if we ignore the temperature as you say, there ... | [
{
"answer_id": 5473,
"pm_score": 4,
"text": "<p><strong>I'll stick to considering the atmospheric composition, as referred to in the original question:</strong> Although there may be some rare exceptions that I can't recall, under normal circumstances all green plants use aerobic respiration with O<sub>... |
5,488 | <p>Apparently all living humans are matrilineal descendants of a single woman who lived 200.000 years ago. She is called Mitochondrial Eve.</p>
<p>But at the time she lived there was a different matrilineal ancestor that all living humans shared. And between then and now I imagine many other women have been Mitochondrial Eves of the human population that lived at a particular time.</p>
<p>What I'm wondering is what kinds of events would cause a different, more recent matrilineal ancestor to become the Mitochondrial Eve of all living humans?</p>
<p>One scenario I can image is that the human population is on the brink of extinction and literally only a few people survive. Because there are so few people alive, I imagine that the chance that they share a more recent matrilineal ancestor is high.</p>
<p>Are there other scenarios possible? Does the chance of a new Mitochondrial Eve emerging decrease if the human population is large (billions) instead of small (hundreds or thousands)? Suppose that the human population will not decrease, is it likely future human populations will ever have a different Mitochondrial Eve than the current population? Does it depend on the amount of people that migrate?</p>
<p>The same questions could be posed for Y-Chromosomal Adam and the most recent common ancestor of all humans, I guess...</p>
| [
{
"answer_id": 5494,
"pm_score": 2,
"text": "<p>The new mitochondrial eve is alive right now.</p>\n\n<p>When humans reproduce, mothers pass their mitochondria to their offspring without a contribution from the father. As a result, each human can trace back their mitochondrial lineage as an unbroken cha... | [
{
"answer_id": 5492,
"pm_score": 3,
"text": "<p>One possible scenario would be that a particular woman develops a mutation rendering her much more 'fit' (in the evolutionary sense) than her peers. For the sake of argument, lets take the very simplistic case of an X-linked recessive mutation causing the ... |
5,562 | <p>Warm blooded animals like us keep their temperature constant irrespective of their surroundings. But how do they do that? Energy should be supplied from the inside. I assume that reactions like making ATP from glucose are exothermic. That means in winter our body reacts more. Water is absorbed by those reaction.We should need more water in winter. Which is contradictory with our real life experience.</p>
<p>On the other hand what prevents cold blooded animals from making heat? Don't they need ATP? Do they use different types of reactions to make energy? Do they have different evolutionary path? They don't seems very different from us.</p>
| [
{
"answer_id": 5658,
"pm_score": 4,
"text": "<p>Since there seems to be several distinct sub-topics in your question, I will answer them one-by-one:</p>\n\n<p>1). There are a variety of mechanisms that allow endothermic animals to maintain thermal homeostasis in a cold environment. The main ones are:</p... | [
{
"answer_id": 5563,
"pm_score": 2,
"text": "<p>Here answers a part of your question. Warm blood animal burns more food in the winter, so they can keep their body warm. They are not consuming much more ATP in the winter, just a bit more. Usually they have mechanism to reduce the heat loss, like growing ... |
5,571 | <p>It is a common observation that food is tasteless when we have a cold. Why is that so?<br>
<strong>What is the cause of inability to taste when we have a cold? Are the nose and ability to taste connected?</strong></p>
| [
{
"answer_id": 5574,
"pm_score": 4,
"text": "<p>This <a href=\"http://www.ncbi.nlm.nih.gov/pubmed?term=disturbances%20of%20taste%20and%20smell%20flu\">German review</a> supports common wisdom that the sense of taste is predominantly informed by the sense of smell. For instance, common advice to children... | [
{
"answer_id": 5573,
"pm_score": 2,
"text": "<p>There are many factors that contribute to the flavor of food - the five \"traditional\" tastes (sweet, sour, bitter, salty, umami), smell, texture, spiciness, \"coolness\" (like peppermint), temperature, etc. Smell and taste are detected in similar ways, b... |
5,587 | <p>I wonder if there people who were cured of HIV only by means of highly active anti retro-viral therapy (HAART) or other drugs rather than by bone marrow transplant?</p>
<p>I know that HAART can suppress HIV below detectable level but are there people who stopped HAART and did not experience the HIV levels rising?</p>
| [
{
"answer_id": 10123,
"pm_score": 4,
"text": "<p>This very recent (and freely available) review pretty much sums the problem up in the introduction:</p>\n\n<p><a href=\"http://dx.doi.org/10.1038/clpt.2012.202\">http://dx.doi.org/10.1038/clpt.2012.202</a> (Barton et al., 2013: Prospects for Treatment of ... | [
{
"answer_id": 5655,
"pm_score": 2,
"text": "<p>While it's difficult to prove a negative, I know of no cases where a patient has been treated with HAART to the extent that their viral load never rises again. Keep in mind that, if nothing else, such a study would be extremely hard to do, as proving you'v... |
5,597 | <p>In the majority of human beings, the apex of the heart (left ventricle) points towards the left side of the body. Sometimes however (approx. 1/12000 births), a person is born with a condition known as "Dextrocardia", in which the apex of the heart points to the right side of the body instead.</p>
<p>Is there an evolutionary reason as to why the human heart usually points to the left side as opposed to the right side of the body?</p>
<p>(Note: Please don't answer with, "because there is a notch in the left lung", because I will simply reply with, "is there an evolutionary reason for the apex of the heart AND the cardiac notch being on the left as opposed to the right side of the body").</p>
| [
{
"answer_id": 9011,
"pm_score": 4,
"text": "<p>From a quick look at the paper @ChinmayKanchi links to (<a href=\"https://www.sciencemag.org/content/306/5697/828.full\" rel=\"noreferrer\" title=\"Palmer. 2004. Symmetry Breaking and the Evolution of Development. Science 306\">Palmer, 2004</a>) it seems t... | [
{
"answer_id": 9010,
"pm_score": -1,
"text": "<p>I think it is because of the reason that the left ventricle pumps blood throughout body, thus is bigger than the right ventricle. So, actually, the human heart is along the center septum, but seems just a bit to the right. 1.5 cm to be precise.</p>\n"
}... |
5,632 | <p>I'm a computer programmer deeply interested in Biology.</p>
<p>I wish to write a computer simulation for cell differentiation. I understand there will be seemingly impossible challenges in doing this. But first I am looking for answers to some basic questions. </p>
<ol>
<li>I've learned that a zygote turns into 'embryonic stem cells' which results in the organism. How does the zygote turn into embryonic cells ?</li>
<li>What are the factors that determine the specialization of embryonic stem cells into more specialized types of cells and how does this transformation take place physically ?</li>
<li>Where is the data stored which acts as the "guide" for all these processes ? Is it stored in the DNA ? If it's stored in the DNA , is it known how the cells interpret the information in the DNA?</li>
<li>What are some textbooks I should be referring for this project ?</li>
</ol>
<p>PS : Pardon my ignorance if these questions sound stupid, but I'm willing to commit time for learning anything needed to do this. Also , I understand all these questions cannot be answered in a few lines. Please provide references/pointers . Thanks !</p>
| [
{
"answer_id": 5633,
"pm_score": 2,
"text": "<p>Trying to answer this question in a few lines is a tedious task. Mostly I'm not sure that as of today we know all there is to know about it.</p>\n\n<p>I'll try to give you some hints though.</p>\n\n<ol>\n<li><p>The process is called <a href=\"http://en.wik... | [
{
"answer_id": 5634,
"pm_score": 1,
"text": "<p>I would start with <a href=\"http://rads.stackoverflow.com/amzn/click/0878933840\" rel=\"nofollow\">Developmental Biology, 9th Ed.</a> It's not up to the absolute cutting edge, as it was published in 2010, but it has a lot of good stuff in it. Wikipedia is... |
5,665 | <p>We cultivate a number of terrestrial organisms in greenhouses and stables where they live in completely artificial environments. This seems to extend far less to marine organisms, such as fish. Aquariums (especially the salt water variety) seem to be quite unstable and require a lot of maintenance, and commercial scale installations, like salmon farms, are set up in the ocean, rather than in a separate tank.</p>
<p>Are there inherent difficulties in cultivating marine organisms, or is it just that mankind has not tried as hard as with land species?</p>
| [
{
"answer_id": 7637,
"pm_score": 3,
"text": "<p>It probably depends on the type of marine organism you're referring to, some will be much more hardy than others and some will not be able to adapt to change at all. Due to the vast scale of the environment that marine fish come from it's likely that in th... | [
{
"answer_id": 8064,
"pm_score": 2,
"text": "<p>Large numbers of marine animals are actually cultivated in large aquaria. They're just generally not as conspicuous as farms and farm animals and are often located in difficult to access areas around estuaries or close to ports. There are also a number of ... |
5,670 | <p>I overheard a rather heated argument about whether or not animal cells have vacuoles.</p>
<p>One person said that they do, but they're much smaller than vacuoles in plant cells.</p>
<p>The other person said they don't. While there is <em>something</em> there that acts similar to a vacuole, it's slightly different. The person also noted that the only websites that say that <em>something</em> as a vacuole aren't credible sites (ie. not University sites, etc...)</p>
<p>I'm really curious as to which it is: Do animal cells have vacuoles or not?</p>
| [
{
"answer_id": 5671,
"pm_score": 5,
"text": "<p>They are both right.</p>\n\n<p>Animal cells do have vacuoles, but they are smaller, larger in number (plant cells usually have just one or a few large vacuoles) AND serve a somewhat different purpose than those of plants.</p>\n\n<p>A vacuole is basically a... | [
{
"answer_id": 10977,
"pm_score": 2,
"text": "<p>Yes! As a matter of fact Animal Cells do have vacuoles. Even though they are much smaller than the Large Central Vacuole of Plant Cells, they still do exist in Animal Cells. Unlike the Large Central Vacuole of the Plant Cells, they do not take up 90% of... |
5,720 | <p>The ABO blood type divides each blood type according to whether they have the "A" and "B" antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.</p>
<p>Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)</p>
| [
{
"answer_id": 5724,
"pm_score": 5,
"text": "<p>According to <a href=\"http://en.wikipedia.org/wiki/ABO_blood_group_system#cite_note-13\">the Wikipedia entry for the ABO blood group system</a>:</p>\n\n<blockquote>\n <p>Anti-A antibodies are hypothesized to originate from immune response towards influen... | [
{
"answer_id": 7444,
"pm_score": 3,
"text": "<p>We each inherit either A, B, AB or no antigens from our parents.</p>\n\n<p>The current thought is that when you're between 0-6 months old you are exposed to bacteria/viruses that contain very similar antigens (A or B). These antigens are similar enough to ... |
5,728 | <p>If I would show someone a yellow object and ask them, "is this object yellow?"
That person would say "yes".</p>
<p>But I could never know if my perception of the color yellow is the same as that other person's.<br>
Because he or she could actually be seeing, what I know to be the color green.<br>
But then tells me that its the color yellow because that has been taught to him or her from young age.</p>
<p>So how can you test if people are really seeing the same color?<br>
(originally posted this question on physics.stackexchange but was advised to try it here)
<a href="https://physics.stackexchange.com/questions/48731/how-can-you-test-what-color-different-people-perceive">https://physics.stackexchange.com/questions/48731/how-can-you-test-what-color-different-people-perceive</a></p>
| [
{
"answer_id": 5731,
"pm_score": 4,
"text": "<p>One way we can get evidence <a href=\"http://en.wikipedia.org/wiki/Qualia\">qualia</a> are the same or very similar for different people is by reactions to it, beyond just the word. </p>\n\n<p>For example, beyond the word \"pain\", we have other strong rea... | [
{
"answer_id": 5735,
"pm_score": 2,
"text": "<p>I have often wondered this myself and have never found a way this could be asserted.</p>\n\n<p>In fact we know that not all people perceive color the same way: up to 5% of humans are colorblind and about 2-3% of the women are tetrachromates, they have an e... |
5,751 | <p>Okay, I was learning about mitosis and meiosis in school and had a question. I know in Mitosis you first start off with a <code>Diploid (2N)</code> cell and then end up with two daughter cells that are also <code>Diploid</code>. However, in Meiosis, I know you end up with four <code>Haploid Cells (N)</code>, but what exactly do you start off with? Is it like a single egg makes four more eggs or something? Or does it start off with a <code>Diploid Cell</code> and then end up with the <code>Haploids</code>? If so, what exactly is the starting cell called?</p>
| [
{
"answer_id": 5781,
"pm_score": 4,
"text": "<p>Meiosis starts with a diploid cell and produces four haploid cells. In animals, the starting diploid cell is usually called a <a href=\"http://en.wikipedia.org/wiki/Germ_cell\"><em>germ cell</em></a> and the surviving haploid cells become <a href=\"http:/... | [
{
"answer_id": 5753,
"pm_score": 1,
"text": "<p>During mitosis a diploid cell (2n = two copies of each chromosome, one from each parent) replicates its DNA so that it now has four copies of each chromosome. Then it divides, each daughter cell receives two copies of each chromosome and is again 2n. </p>\... |
5,752 | <p>The inbreeding coefficient of a sibling mating for a diploid organism is 0.25 (each allele has a 25% of being identical by descent in the offspring).</p>
<p>In haplodiploid organisms, males result from unfertilized eggs, so they don't have fathers (they get half of mom's diploid genome, and that's it). Females have both a mom and a dad, and are diploid in the standard way (dads give their daughters their entire genome).</p>
<p>What is the inbreeding coefficient for the daughter of a sib mating?</p>
| [
{
"answer_id": 6840,
"pm_score": 1,
"text": "<p>I think the answer is 0.25.</p>\n\n<p>Here's how I arrived at it:</p>\n\n<p>The only way a daughter of a sib-mating can have an IBD (identical-by-decent) genotype is by being homozygous for one of the two alleles belonging to her grandmother (her mother an... | [
{
"answer_id": 5765,
"pm_score": 0,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Inbreeding\" rel=\"nofollow\">http://en.wikipedia.org/wiki/Inbreeding</a></p>\n\n<p>I'm thinking that the answer is not defined as there is probably an explicit or implicit assumption about both parents having the sam... |
6,846 | <p>There is a potential difference, but ions can not go through wires, right? Though there is a electric field, but there is no electron source, I am thinking the answer is no, or will there be some chemical reaction?</p>
| [
{
"answer_id": 6848,
"pm_score": 3,
"text": "<p>Let's start with the basics. The inside of the cell contains predominantly positive potassium ions, and negative phosphate ions, and other negative ions (e.g. from amino acids). The outside of the cell contains predominantly positive sodium ions, and neg... | [
{
"answer_id": 6852,
"pm_score": 2,
"text": "<p>Just to clarify your ion/electron question - a neutral atom or molecule becomes <em>ionized</em> when it either loses one or more electrons, becoming positively charged, or gains electron(s), becoming negatively charged. Since the negatively charged phosph... |
6,858 | <p><strong>(1)</strong>. Why does having cold hands create a painful sensation?</p>
<p>Is it a physical effect, maybe a protection mechanism from evolution?</p>
<p><strong>(2)</strong>. Why, if one's hands are cold, does it feel as if they are more <em>susceptible</em> to pain?</p>
<p>Note: I have (2) as a separate question because the painful sensation in (1) refers to that from the coldness, whereas in (2), I mean that certain 'ordinary tasks' would feel painful, for example, holding a shopping bag.</p>
| [
{
"answer_id": 6898,
"pm_score": 5,
"text": "<p>For question 1 it's just a biochemical response from thermoreceptor nerves in the skin, temperatures that are likely to cause lasting damage from prolonged exposure cause a neurological response - in this case it's pain.</p>\n\n<p>In address to question 2 ... | [
{
"answer_id": 6904,
"pm_score": 2,
"text": "<p>It doesn't matter if its hand or any other human body organ, cold would hurt, the reason being that we humans being warm blooded animal require an optimal temperature-pressure balance to be maintained for our nervous system to work in its natural order.</p... |
6,884 | <p>I have heard that the <a href="http://en.wikipedia.org/wiki/Hydra_%28genus%29"><em>Hydra</em></a> organism is <a href="http://en.wikipedia.org/wiki/Biological_immortality">biologically immortal</a> (later I found that there are more immortal organisms). Now I know that its immortality is related to its telomerase. The thing is that we all have telomerase, but we age and <em>Hydra</em> don't. What are the proteins (especially telomerase) related to aging in humans and <em>Hydra</em> and how do they work differently?</p>
| [
{
"answer_id": 6887,
"pm_score": 5,
"text": "<p><img src=\"https://i.stack.imgur.com/atid9.jpg\" alt=\"a somewhat smaller picture of a Hydrae\"></p>\n\n<p>Hydra are just one of the many organisms which are immortal. That is to say all their cells divide forever - there is no senescence (planned cell de... | [
{
"answer_id": 7009,
"pm_score": 2,
"text": "<p>Actually, most adult cells do not express telomerase or express it only at a very low levels. <a href=\"http://en.wikipedia.org/wiki/Telomerase\" rel=\"nofollow\">Telmoerase</a> is highly expressed only in cells that need to divide (e.g. stem cells), thus ... |
6,939 | <p>I'm a math undergrad looking for some papers on modelling the process of natural selection. The only paper I've been able to find is by the pre-eminent mathematician Herbert Wilf from 2010,</p>
<p><a href="http://arxiv.org/abs/1010.5178">There's Plenty of Time for Evolution</a></p>
<p>Unfortunately, Wilf's model is extremely simplistic - he calculates the number of 'generations' required to spell out a 'word', if we allow each letter to 'mutate' with certain probability every generation, and we stop mutating a letter once it is correct (this is the 'selective' feature of the model). So to spell the word 'Evolution' by randomly placing scrabble tiles would require 5.4 trillion generations, but if we keep the correctly placed letters each generation and only allow incorrect letters to 'mutate', Wilf calculates we'd only need about 57 generations on average.</p>
<p>Wilf's model is a good first step towards modelling natural selection, but it's clearly only a first step. In particular, the fact that nature seems to know in advance exactly what letters it needs to keep in particular places and what it needs to throw out to construct a complex genetic 'word' is dubious at best.</p>
<p>As a young maths student the idea of the incredible complexity and diversity of life developing by a directed stochastic process gets me shamelessly excited :) I have been very surprised at just how little mathematical literature there seems to be on this topic, as I say, Wilf's one super-simplistic model is all I've been able to find. Can someone direct me to any other theoretical analyses of the power of natural selection?</p>
<p>Thanks</p>
| [
{
"answer_id": 7929,
"pm_score": 5,
"text": "<p>Mathematical and computational modeling of evolution is a huge field. To start you off with some broad strokes, there are two main approaches to evolutionary modeling with their own communities: frequency-independent and frequency-dependent models. Of cour... | [
{
"answer_id": 6941,
"pm_score": 4,
"text": "<p>Modeling evolutionary processes has a long history in evolutionary biology. Initially, these models were only theoretical or back-of-the-envelope quantitative (e.g., Simpson's <a href=\"http://en.wikipedia.org/wiki/Tempo_and_Mode_in_Evolution\">Tempo and M... |
7,010 | <p>I asked a question about <a href="https://biology.stackexchange.com/questions/6884/why-is-the-hydra-biologically-immortal">immortality of hydra</a> and learned good things about senescence. Now I would like to know about immortality in plants, if there is some kind of immortality in plants and how this occurs - how does it protect itself from senescence? </p>
| [
{
"answer_id": 8849,
"pm_score": 4,
"text": "<p>I can find no examples of immortal plants, but then again <strong>immortality is rather hard to prove</strong>, it's rather like trying to prove that space will never turn in to a pony - as long as time exists it could still occur, only if you go beyond th... | [
{
"answer_id": 8845,
"pm_score": 1,
"text": "<p>Since meristems (the parts of plants from which growth happens) are constantly creating new stem cells, plants have a theoretical capacity for immortality. Of course, in practice, the vast majority of plants still senesce and die. But there are some notabl... |
7,046 | <p>I've read that the eye color at birth for most humans and for cats may not always be the the true genetic color at first. This is due to the lack of melanin in the iris. This makes sense as there is no light in the womb to stimulate the production of melanin.</p>
<p>My question(s) though is:</p>
<ul>
<li>Why does the lack of said melanin produce a blue/bluish colored iris?</li>
<li>Why is it not say green, red, clear, etc?</li>
</ul>
| [
{
"answer_id": 7049,
"pm_score": 6,
"text": "<p>The blue colour is an example of <a href=\"http://en.wikipedia.org/wiki/Structural_color\"><strong>structural colour</strong></a>, caused by light interacting physically with something. Some examples of structural colour are the iridescence of insect wings... | [
{
"answer_id": 7048,
"pm_score": 4,
"text": "<p>The generation of iris color is quite complex and the exact color of the eyes depends upon many different factors, not just melanin. In fact, blue coloration does not depend on a specific chemical, but on the structure of the eye itself.</p>\n\n<p>This ver... |
7,071 | <p>Are there some living things where the distinction between plant and animal is blurry or unclear? I wouldn't know where to put something like yeast. I also thought of photosynthesis, but then I heard that some salamanders have photosynthetic cells. So, what's the difference between a plant and an animal, formally? </p>
| [
{
"answer_id": 7073,
"pm_score": 5,
"text": "<p>Yeast are neither plants nor animals; they are fungi. The old classification where things were lumped into only two buckets - plants or animals - has long since broken down. In fact, even things you might think of as plants, like algae or most seaweed are ... | [
{
"answer_id": 7078,
"pm_score": 1,
"text": "<p>Classification is not only based on one or a few features, but you have to consider lots of features in classification of livings. for example plant cells globally have chloroplast, cell wall, and vacuole and have not centrioles. Animals are different in a... |
7,076 | <p>In explaining energy and work to an 8 year-old I said that all conversion of energy generates heat as a by-product. For example, cars generate heat in their engines and running generates heat in our bodies. Then the 8 year-old said, except for cold-blooded animals.</p>
<p>So my question is, do cold-blooded animals generate any heat in their conversion of stored energy (food, fat, etc) into motion? If they generate heat, why are they cold-blooded?</p>
| [
{
"answer_id": 7080,
"pm_score": 5,
"text": "<p>They do generate heat. They just do not SPEND energy specifically on heating their bodies by raising their metabolisms. This is a form of energy conservation. The metabolic rate they need to live is not nearly enough to heat their bodies.</p>\n\n<p>An exam... | [
{
"answer_id": 7077,
"pm_score": 1,
"text": "<p>I'm fairly certain that you were right in your initial hunch that heat is almost always a byproduct of metabolism (which is never 100% efficient). The difference between endothermic ('warm-blooded') and ectothermic ('cold-blooded') organisms is just where ... |
7,190 | <p>I have to do a task for a university task and I need to understand some things
before figuring out how to do it.</p>
<p>The task is the following:</p>
<blockquote>
<p>Find matches of known proteins (DNA-PolyI,II,III) to the specific E.Coli DNA, sequence.</p>
</blockquote>
<p>I downloaded in <a href="http://en.wikipedia.org/wiki/FASTA_format" rel="nofollow">FASTA</a> format the protein sequence of <s>DNA-Poly3</s> DNA-Poly1 of E.coli (strain K-12) and the entire DNA sequence
of the E.Coli.</p>
<p>I've studied a bit on-line and using the <a href="http://bioruby.org/" rel="nofollow">BioRuby</a> gem and the Ruby programming language I wrote a program that translates DNA to protein sequence.
Then I tried to match the known DNA-Poly3 sequence but it did not match. After searching a bit on-line again, I learned about <a href="http://en.wikipedia.org/wiki/Open_reading_frame" rel="nofollow">ORF</a> and
and the 6 possible reading ways of each frame. The longer, in terms of codons, ORF conformation is chosen but there's no way of telling for sure that the protein was made using
this frame.</p>
<p>Then I've read about TATA boxes, but I can't use those since they can be found only in Eukaryotic and Archaea.</p>
<p>So how should I proceed in order to solve this problem: How can I <em>prove</em> that the DNA-Poly3 gets produced by a specific area (gene) in the DNA sequence?</p>
<p>Thanks for your time,</p>
<p>ps. Insights and hints are very much welcomed as this is just the tip of the iceberg for me and I'm very willing to study bioinformatics :-)</p>
<p><strong>EDIT</strong>: This is an update for info requested in relevant answer</p>
<p>The files I have used are the following:</p>
<pre><code>➜ Bioinfo ruby dogma.rb
----------------
DNA Length: 4639675
gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome
----------------
DNA Poly-1 sample: 928
gi|16131704|ref|NP_418300.1| fused DNA polymerase I 5'->3' polymerase/3'->5' exonuclease/5'->3' exonuclease [Escherichia coli str. K-12 substr. MG1655]
</code></pre>
<p>You can download them here: <a href="https://dl.dropbox.com/u/1184138/bio/e-coli-K12.fasta" rel="nofollow">E.Coli DNA</a> and <a href="https://dl.dropbox.com/u/1184138/bio/dna-polyI.e-coli.fasta" rel="nofollow">E.Coli DNA-Poly1</a>.</p>
<p><strong>NOTE</strong>: My sample protein is <strong>DNA Polymerase I</strong> (and not 3). </p>
| [
{
"answer_id": 7192,
"pm_score": 5,
"text": "<p><strong>IMPORTANT EDIT :</strong> In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend ... | [
{
"answer_id": 7197,
"pm_score": 3,
"text": "<p>For what its worth - I have replicated what you are trying to do using a Python script. This is not elegant, but I just wanted to check for you that it is possible, and that there really is a match.</p>\n\n<p>pseudocode is</p>\n\n<blockquote>\n <p>take th... |
7,206 | <p>Our body does not produce two polyunsaturated fatty acids (PUFA): linoleic acid and alfa-linolenic acid.</p>
<p>I am thinking reasons for it.</p>
<p>Saturated fatty acids have more energy than unsaturated.
Saturated fatty acids do not need NADPH and some many other enzymes as unsaturated in beta oxidation.
This means that less storage places in the body needed to have energy in the form of saturated fatty acids such as for muscles and heart.</p>
<p>There are four main reasons why our body does not use PUFAs as the primary source of the energy but saturated:</p>
<ul>
<li>PUFAs lower metabolism and interfere with thyroid function</li>
<li>PUFAs spontaneously oxidize, speed up the process of glycation, since too much glucose</li>
<li>PUFAs decrease mitochondrial respiration - more oxygen and CO2, less lactate</li>
</ul>
<p><strong>where one reason is missing.</strong> </p>
<p>One complication of PUFA is</p>
<ul>
<li>PUFAs promote diabetes, cancer, inflammation and biological stress</li>
</ul>
<p>which cannot be thought as a reason why our body does not use PUFAs as the primary source of the energy.</p>
<p>There are positive sides of the PUFAs when they are used in other way.
- PUFAs replace trans fats and saturated fats in certain types of foods.
- PUFAs can help your body to eliminate high cholesterol levels
- PUFAs decrease the risk of heart disease</p>
<p>There are also some types of essential fats that your body cannot produce on its own - omega-6 and omega-3 fatty acids.
PUFAs are used to create these.
You can get PUFAs from vegetable oil, fish and nuts for instance.
Balanced diet is essential.</p>
<p>Normal lipid metabolism depends directly on food lipids.
Both the essential fatty acids and right amounts of PUFAs can be obtained from food.
Body converts the essential fatty acids to long PUFAs, which serve as the precursors of prostaglandins and leucotrienes for instance.</p>
<p>There are so many reasons why our body does not produce polyunsaturated fatty acids.</p>
<p><strong>Why our body does not produce polyunsaturated fatty acids?</strong></p>
| [
{
"answer_id": 7192,
"pm_score": 5,
"text": "<p><strong>IMPORTANT EDIT :</strong> In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend ... | [
{
"answer_id": 7197,
"pm_score": 3,
"text": "<p>For what its worth - I have replicated what you are trying to do using a Python script. This is not elegant, but I just wanted to check for you that it is possible, and that there really is a match.</p>\n\n<p>pseudocode is</p>\n\n<blockquote>\n <p>take th... |
7,242 | <p>I was walking through a park this afternoon and observed a few birds having fun flying around and it got me thinking why would natural selection favour birds with flesh at all if it hinders their flight.</p>
<p>We started first with single-cell and micro-organisms flourishing the ponds and then they evolved into massive dinosaurs. It therefore seems, there are some unique reasons for growing to such a large size.</p>
<p>However, I thought it's counter intuitive because the large body slows down locomotion, requires lots of food and energy upkeep, is a big flesh target for predators, makes hiding ineffective.</p>
<p>Although it is obvious that the flesh protects the internal organs, but it seems like a chicken and egg problem because without a massive body, perhaps then there is no need for the internal organs.</p>
<p>On a different perspective, perhaps those animals that evolved without flesh are called plants.</p>
<p>That sums up my naive train of thoughts.</p>
<p>So, any expert can shed some light?</p>
| [
{
"answer_id": 7244,
"pm_score": 4,
"text": "<p>Well first of all I don't know if natural selection favors larger animals - most of the living things in the world are single celled. </p>\n\n<p>Still there are advantages to being larger. I don't know if I can list them all! In no particular order: </p... | [
{
"answer_id": 7262,
"pm_score": 2,
"text": "<p>Another reason could be that bigger animals can better fight for resources like food or sex. Ususally it's the stronger (and often bigger) male that gets a chance to mate or defend their prey.</p>\n\n<p>Bigger animals are also harder to kill and therefore ... |
7,267 | <blockquote>
<p>"Males do not show meiotic recombination, facilitating genetic studies."</p>
</blockquote>
<p>For a while I have known that this phenomenon occurs, this quote comes from the <a href="http://en.wikipedia.org/wiki/Drosophila_melanogaster" rel="noreferrer">Wikipedia page on <em>Drosophila melanogaster</em></a>, and I frequently use this feature of <em>Drosophila</em> in constructing hemiclones for my own research in quantitative genetics. </p>
<p>But, until now, I have never asked <strong><em>why</em></strong> doesn't recombination happen? Why would this feature evolve? </p>
<p>Further, why is the absence of recombination sex-limited to males, why do females have recombination?</p>
| [
{
"answer_id": 7278,
"pm_score": 5,
"text": "<p>This is a venerable fact. <a href=\"http://www.pnas.org/content/68/2/268.full.pdf\" rel=\"nofollow noreferrer\">Exceptions in <em>D. melanogaster</em> strain Y-007 have been observed</a> and <em>D. ananassae</em> has consistent male cross-overs, but this ... | [
{
"answer_id": 7276,
"pm_score": 2,
"text": "<p>To the best of my knowledge there is no strong evidence as to the reason why. The most reasonable explanation seems to be that it evolved as a crude mechanism for preventing recombination of the male sex-chromosome.</p>\n\n<p>You might then ask why a mecha... |
7,290 | <p>I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what the modern "commercial grade" genotyping really does. <strong>What are the limitations of commercial-grade "genotyping"?</strong> From what I've been reading, they test DNA against ~100 different markers, but do not really sequence it.</p>
<p>If I understand correctly, if DNA is sequenced, genetic markers and genes can be identified in it, including the newly discovered ones. However, (if I understand correctly) if DNA is genotyped, the genotyping is a one shot operation which states if some genetics markers are present in the DNA. To test against newly discovered markers, it would have to be genotyped again, right?</p>
<p>Thank you for any clarifications!</p>
| [
{
"answer_id": 7295,
"pm_score": 3,
"text": "<p>23andme briefly describes the technology they use <a href=\"https://www.23andme.com/more/genotyping/\" rel=\"nofollow\">here</a>. They are testing the genotype of your DNA at roughly 1 million locations. The technology they use to do this is known as a <a ... | [
{
"answer_id": 7297,
"pm_score": 2,
"text": "<p>I want to give the OP a slight variation on Steve's answer.</p>\n\n<p>It is important to note that most of the genome is the same between different people. That isn't surprising, since we belong to the same species.</p>\n\n<p>For example, it is estimated t... |
7,310 | <p>This is what a friend of mine said:</p>
<blockquote>
<p>When there's human offspring, it will look a rough 'medium' between
the two parents, with it sharing features from the two. well if the
offspring of one set of parents has sex with the offspring of another
set, the outcome becomes a 'medium' of those two. So the range from
what we shall call 'completely average looks' (a hypothetical state of
the average of everyone in the world, which is acceptable as we're
looking at a process of millions of years) becomes less and less the
further into the future we go. Eventually, there is almost no range
between people and 'completely average looks'.</p>
</blockquote>
<p><strong>In summary: take the hypothetical average of everyone in the world, and because the offspring of two people is a slight mixture of those two people, they are a tiny bit closer to the hypothetical average of everyone in the world, which means that eventually people will be getting closer and closer to this average, so will one day look the same.
So he's suggesting that slowly people will become more and more similar.</strong></p>
<p>My argument is that, although this baby may be that tiny bit closer to the overall average, they're new look has effectively altered the average, meaning that they aren't actually getting closer to the average. </p>
<p>I'd like an opinion and flaw from some experts, such as yourselves, so please...</p>
| [
{
"answer_id": 7314,
"pm_score": 4,
"text": "<p><strong>Quantitative genetics</strong> is one reason why this doesn't happen. For example height is affected by many genetic loci, not just 1 gene, and we can for the sake of the following illustration call them Locus A through Locus J - 10 Loci. </p>\n\n<... | [
{
"answer_id": 7332,
"pm_score": 2,
"text": "<p>The basic point your friend is missing is that offspring appearance is not <em>simply</em> a mixture of their parents'. Each child also has individual characteristics which were not present in the parents. This is due to a variety of processes, the most im... |
7,350 | <p>Sure it's <em>convenient</em> to decide when to urinate but not <em>essential</em> for survival or reproduction, as I understand. But just convenience is not a drive for evolution.</p>
<p>Does the bladder serve any essential purpose? If not why did bladders evolve?</p>
| [
{
"answer_id": 7353,
"pm_score": 5,
"text": "<p>Here are just a few points that might apply:</p>\n\n<ul>\n<li>Urine is used for scent marking by some species, so the ability to store urine could be useful. </li>\n<li>At the opposite side, controlling the release of a strong scent would help in stealth ... | [
{
"answer_id": 9757,
"pm_score": 3,
"text": "<p>A few observations to add to Paul's:</p>\n\n<p>Urinating on yourself in winter could be a fatal thermoregulatory mistake.</p>\n\n<p>Urinating on your substrate could hinder locomotion.</p>\n\n<p>Having a continual slick of high osmolarity fluid on your ski... |
7,457 | <p>I can't think of any reason why plants wouldn't be able to get cancer, but I've never heard of a plant growing a tumor. I've also never seen a plant with a noticeable abnormal growth. Can plants get cancer?</p>
| [
{
"answer_id": 7463,
"pm_score": 5,
"text": "<p>Yes, plants of all sizes can have cancerous growths.</p>\n\n<p><em>Agrobacterium tumifaciens</em>, the causative agent of crown gall disease, produces what is called a tumor. See this <a href=\"http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens\">link<... | [
{
"answer_id": 17621,
"pm_score": 2,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Burl\" rel=\"nofollow\">Burls/Burrs</a> are often defined as tree tumours, and as analogous to cancer in animals. There seems to be numerous reasons why burls are formed (more research is needed on the topic), which ... |
7,465 | <p>I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.
I've found a huge amount of extremely interesting papers about how biological network data is accumulated and how it can be studied.</p>
<p>However, what I haven't found is any examples where the network data was used to make a novel prediction which was later experimentally shown to actually exist. What are some of the cases where this has happened?</p>
| [
{
"answer_id": 7463,
"pm_score": 5,
"text": "<p>Yes, plants of all sizes can have cancerous growths.</p>\n\n<p><em>Agrobacterium tumifaciens</em>, the causative agent of crown gall disease, produces what is called a tumor. See this <a href=\"http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens\">link<... | [
{
"answer_id": 17621,
"pm_score": 2,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Burl\" rel=\"nofollow\">Burls/Burrs</a> are often defined as tree tumours, and as analogous to cancer in animals. There seems to be numerous reasons why burls are formed (more research is needed on the topic), which ... |
7,494 | <p>As I know three nucleotide pairs (triplus) code one gene. But I have found next information in the "Molecular biology of the cell" by Bruce Alberts:</p>
<blockquote>
<p>Mycoplasma genitalium: it has only about 480 genes in its genome of 580 070 nucleotide pairs.</p>
</blockquote>
<p>But 480 genes * 3 ~ 1500 nucleotide pairs.</p>
<p>Where I have made mistake ?</p>
| [
{
"answer_id": 7495,
"pm_score": 4,
"text": "<p>You seem to have some confusion, so let's clear things up.</p>\n\n<p>A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.\nEach gene consists of nucleotides bound together, which are int... | [
{
"answer_id": 68370,
"pm_score": -1,
"text": "<p>Why are you multiplying 480 * 3? Do you think every gene is only 3 bases long?</p>\n\n<p>If the average protein length as 500 amino acids, every gene would have on average 1500 nucleotides. 480 genes 1500 bases long = 720,000. So the proteins of m.gen... |
7,496 | <p>When a biologist is talking about a genetically engineered mouse strain which is a "tool strain", what does that mean? What is the exact definition of a tool strain? What is the difference between a tool strain and any other mouse strain? </p>
<p>Also, how are tool strains connected to recombinase techniques? Does using a recombinase automatically create a tool strain? Or are the properties "tool strain" and "recombinase containing strain" independent from each other? </p>
<p>If it is important, the context is mouse (and possibly other animal) strains used in cancer research. </p>
<p>It would help if you could keep the explanation high-level. I only have high-school biology knowledge and I am trying to make sense of the requirements for a software application for use by biologists. </p>
| [
{
"answer_id": 7495,
"pm_score": 4,
"text": "<p>You seem to have some confusion, so let's clear things up.</p>\n\n<p>A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.\nEach gene consists of nucleotides bound together, which are int... | [
{
"answer_id": 68370,
"pm_score": -1,
"text": "<p>Why are you multiplying 480 * 3? Do you think every gene is only 3 bases long?</p>\n\n<p>If the average protein length as 500 amino acids, every gene would have on average 1500 nucleotides. 480 genes 1500 bases long = 720,000. So the proteins of m.gen... |
7,504 | <p>Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.</p>
<p>EDIT: both @rg255 and @shigeta have provided solutions to the underlying issue, but I am curious to know if something exists for miRNAs that is similar to a site like <a href="http://idconverter.bioinfo.cnio.es/" rel="nofollow">this</a>.</p>
<p>EDIT 2: miRNA names are of the form 'hsa-let-7a' and Accession IDs are of the form 'MI0000060'</p>
| [
{
"answer_id": 7495,
"pm_score": 4,
"text": "<p>You seem to have some confusion, so let's clear things up.</p>\n\n<p>A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.\nEach gene consists of nucleotides bound together, which are int... | [
{
"answer_id": 68370,
"pm_score": -1,
"text": "<p>Why are you multiplying 480 * 3? Do you think every gene is only 3 bases long?</p>\n\n<p>If the average protein length as 500 amino acids, every gene would have on average 1500 nucleotides. 480 genes 1500 bases long = 720,000. So the proteins of m.gen... |
7,553 | <p>Some human tissue can survive without oxygen a couple of minutes, even hours. </p>
<p>Why are the neurons are so "weak" and depends so much on oxygen and other nutrients and cannot live without them for more than a few seconds or 1 or 2 minutes?</p>
<p>Are they missing some parts of their cells which can store nutrients for worse times in favor of their function or what is the case?</p>
| [
{
"answer_id": 7831,
"pm_score": 4,
"text": "<p>Neurons use lot of energy to maintain their polarized state, this is not required to other cells [1,2].</p>\n\n<p>When O2 or blood flow (which is carrying the nutrients) is reduced, the neuronal ATP levels breaks down very fast, with 90% ATP depleted in le... | [
{
"answer_id": 7794,
"pm_score": 2,
"text": "<p>There are many factors contributing to neurons dying much faster than other cell types.</p>\n\n<p>This website does not provide original references (for this question, it does for the rest of the article) but sounds trustworthy: <a href=\"http://neuropatho... |
7,556 | <p>I hope this is the right StackExchange forum for such a question.</p>
<p>I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂ concentration in the atmosphere and in the oceans, data about the insect population, plants, algae, and so on.</p>
<p>Is there any research institute or NGO collecting such data and making it available to the public?</p>
| [
{
"answer_id": 42340,
"pm_score": 5,
"text": "<p>Adding some additional database sources:</p>\n\n<p>-- <strong>Climate</strong> -- </p>\n\n<p><a href=\"http://www.prism.oregonstate.edu/\" rel=\"nofollow noreferrer\"><strong>Prism</strong></a></p>\n\n<p>The PRISM Climate Group gathers climate observatio... | [
{
"answer_id": 7719,
"pm_score": 3,
"text": "<p>For climate related data you can start from <a href=\"http://www.realclimate.org/\">Realclimate</a> pages on data repository. For ecological data I always found less global data, but a good starting point may be the <a href=\"http://data.esa.org/esa/style/... |
7,789 | <p>Since <a href="https://skeptics.stackexchange.com/questions/6375/do-bacteria-become-immune-to-antibiotics-if-you-dont-complete-your-course-of-th">bacteria becomes resistant to antibiotics</a> after an unfinished course, is it possible to do anything to be able to get treatment with the same antibiotic again, and reverse the resistance in the bacteria?</p>
<p>Or, the bacteria with the resistance will stay resistant forever (until death)?</p>
<p>Edit:</p>
<p>There are some websites that are claiming that some natural remedies might be effective, like taking "Honey", which doesn't seem to be medical facts.</p>
| [
{
"answer_id": 7793,
"pm_score": 4,
"text": "<p>Perhaps it is useful to first consider how resistance is gained:</p>\n\n<p>If you treat a population of bacteria with an antibiotic, some may die and some may live.</p>\n\n<p>If none die, they are obviously resistant.</p>\n\n<p>If all of them die, then all... | [
{
"answer_id": 7795,
"pm_score": 2,
"text": "<p>Bitwise has explained how antibiotic resistance develops in bacteria. To address how it might go away: as long as the antibiotic is around, there is selective pressure on the bacteria to preserve the parts of their genome that confer antibiotic resistance... |
8,024 | <p>My apologies if my question is too basic, and please point me to a more appropriate forum. I am reading the textbook "Essential Cell Biology" by Alberts et al, and am consulting other sources as well. I am reading Chapter 10 about DNA technology and have read how DNA is separated into strands of different lengths by restriction enzymes. The different size strands can then by separated by Gel Electrophoresis. I believe I understand these basics. My question is:</p>
<p><strong>Do all strands of the same length have the same sequence of base pairs? I wouldn't think so, and this would be a problem in the next step, determining the sequence of one size fragment by using special base pairs that are lacking a hydroxyl group. Isn't it possible I could have two strands that are 50 base pairs long (for example) that have the same beginning and same end and are thus cut by the restriction enzymes to a length of 50, but are most assuredly not the same within their sequence</strong></p>
<p>The text says that once the different size strands are separated by electrophoresis, you can just cut out one of the bands and work with that. That makes sense if you are guaranteed to only have 1 strand at that level of the gel agar or if the multiple strands are all the same exact sequence.</p>
<p>If you read this far, thank you. I think more generally I need to know how many of these segments are produced when you use restriction enzymes and how long the average one is. And is there any guarantee for one chromosone (or all 46 chrmosones) having all the segments be unique sizes (I wouldn't think so)?</p>
<p>And even more generally :), I need additional sources that explain DNA sequencing in simple to understand terms.</p>
<p>Thanks,</p>
<p>Dave</p>
| [
{
"answer_id": 8025,
"pm_score": 3,
"text": "<p>You are correct: strands of the same length do <em>not</em> necessarily have the same sequence. The separation of DNA in gel electrophoresis is purely based on the hydrodynamic size. </p>\n\n<p>The number of fragments produced by restriction enzyme digesti... | [
{
"answer_id": 8031,
"pm_score": 2,
"text": "<p>The answer to the part of your question concerned with average lengths of restriction fragments is: if the DNA molecule being digested is of random sequence, and is 50% GC/ 50% AT, then the probability of finding any given short sequence at any position is... |
8,048 | <p>Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)? </p>
<p>After that is done, it the complete genome can be stored and once the new genes (and their purposes are confirmed) are discovered, the scientist can simply go back to a previously sequenced data and to find it this particular person has this new gene or not.</p>
| [
{
"answer_id": 8050,
"pm_score": 4,
"text": "<p>A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident)... | [
{
"answer_id": 23744,
"pm_score": 1,
"text": "<blockquote>\n <p>Is that correct that a complete DNA sequencing (the whole genome) need\n only to be done once (per person)?</p>\n</blockquote>\n\n<p>Likely, yes. But I think you vastly overestimate how often this is done. If someone gets their DNA \"se... |
8,055 | <p>I'm looking at melanopsin, <a href="http://en.wikipedia.org/wiki/Melanopsin#Mechanism" rel="nofollow">a photo pigment in the human eye.</a> One of its actions is to trigger suprachiasmatic nuclei SCN to suppress <a href="http://en.wikipedia.org/wiki/Melanopsin#Mechanism" rel="nofollow">melatonin release</a>. <strong>I'm interested in learning what is the exact mechanism that actually suppresses melatonin release.</strong> Is it another hormone or some way of modulating the pineal gland function?</p>
| [
{
"answer_id": 8050,
"pm_score": 4,
"text": "<p>A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident)... | [
{
"answer_id": 23744,
"pm_score": 1,
"text": "<blockquote>\n <p>Is that correct that a complete DNA sequencing (the whole genome) need\n only to be done once (per person)?</p>\n</blockquote>\n\n<p>Likely, yes. But I think you vastly overestimate how often this is done. If someone gets their DNA \"se... |
8,066 | <p>As far as I know and could understand from reading about HIV, T helper cell is one of the main reasons to develop AIDS in patients infected with HIV virus, that because the absence of helper T cell suppresses the immune system because no T cell cytokines released to allow other white blood cells to attack or release antigens. </p>
<p><strong>Q1</strong>. Did I understand it correctly?</p>
<p><strong>Q2</strong>. Now if my understanding is correct, why don't scientists find a way to produce T cell cytokines in the lab? and then inject it to patients with HIV? wouldn't that in theory revive the immune system and perhaps heal them or at least make them live longer? </p>
<p>P.S. My knowledge is close to nothing in this topic, so excuse me if the question itself is wrong :)</p>
| [
{
"answer_id": 8070,
"pm_score": 3,
"text": "<p>Q1: Partially. T cells are important for the immune response through pathways other than cytokine release. Being activated by contact with another immune cell presenting their corresponding antigen, T cells proliferate and themselves activate their compati... | [
{
"answer_id": 8068,
"pm_score": 0,
"text": "<ol>\n<li>yes</li>\n<li><em>[Purely my guess]</em> : </li>\n</ol>\n\n<p>I think it will be difficult when simultaneously several infections pop up. There is no antigen presentation (as there is no receiver); it will be difficult to manually deliver different ... |
8,139 | <p>They all seem to describe molecules of similar function and many people seem to use them interchangeably.</p>
<p>Also please include any other similar molecules if I've forgotten any in the list above.</p>
| [
{
"answer_id": 8144,
"pm_score": 4,
"text": "<p>Cytokines is the general class of molecules to which chemokines, interferons, interleukins and others belong. Biologists dispute whether something is a hormone or a cytokine, but generally the consensus goes with if it's to do with immunology it's a cytoki... | [
{
"answer_id": 8737,
"pm_score": 0,
"text": "<p>In short, this is my understanding following my immunology course (which is mostly identical to AndroidPenguin's answer):</p>\n\n<ul>\n<li><p>Chemokines: Produce cell movement, i.e. act as chemoattractants. Typically these are used to recruit more immune c... |
8,142 | <p>Peach, pear, apple, cherry, and many other fruit trees seem to have flowers comprised of five petals. Assuming there is no evolutionary advantage to confusing students of trees, is there a plausible reason (evolutionary or otherwise) the morphology is so regimented? Are the trees related? Do they like the same pollinators? </p>
<p>Thanks for any insight. </p>
| [
{
"answer_id": 8150,
"pm_score": 5,
"text": "<p>Peach, apricot, plum, pear, apple, cherry trees are plants of the same family, <a href=\"https://en.wikipedia.org/wiki/Rosaceae\">Rosaceae</a>, so they are closely related. They share many more aspects than the five petals. In fact, other plants in this fa... | [
{
"answer_id": 9200,
"pm_score": 2,
"text": "<p>It is hard finding answers to this question, which also interests me a lot. The most satisfying answer I have found is detailed in this paper <a href=\"http://www.ijpam.eu/contents/2012-78-3/6/6.pdf\" rel=\"nofollow\">http://www.ijpam.eu/contents/2012-78-3... |
8,282 | <p>How does spacing apart sodium and potassium channels allow the action potential to travel faster down the axon? This is the reason always cited for saltatory conduction and myelination, but my mental model of conduction tells me that the density of ion gates along the axon should not affect the speed of the AP. </p>
<p>To illustrate, consider a myelinated axon. A wave of Na$^+$ from action potential site 1, a node of Ranvier, rushes into and quickly diffuses down the axon. (It travels in both directions, but backwards is still in the refractory period.) It diffuses through the myelinated region, its concentration always diminishing. Before it attenuates too much, however, it happens upon node of Ranvier 2, where it triggers another action potential. A new wave of Na$^+$ rushes in and the cycle repeats. This should be plain so far.</p>
<p>Now imagine that there is actually a node of Ranvier halfway between node 1 and 2, called node 1.5. The wave of Na$^+$, on its way to node 2, happens to trigger an action potential at node 1.5, from which a wave of Na$^+$ pours in and either boosts the original wave or replaces it by taking its momentum. Now the reinforced wave proceeds to node 2 and triggers it just as soon as, perhaps even sooner than, if node 1.5 had not existed. Repeatedly insert nodes at higher densities until the situation is simply lack of myelination, and we conclude that unmyelinated axons can transmit an action-potential-triggering wave of Na+ as fast as or faster than a myelinated one.</p>
<p>In short, my point of confusion is this: <strong>I cannot see how a higher density of gated channels can possibly slow down the wavefront of Na+ that triggers action potentials.</strong> If anything, the additional influxes of Na+ should speed up the all-important wavefront, assuming that new waves really "either boost the original wave or replace it by taking its momentum", and also assuming that the wavefront of Na$^+$ is really all-important for signal transmission, and also assuming that the mere presence of (voltage?) gated ion channels in the membrane does not significantly retard the wavefront.</p>
<p>But the usual explanation for why saltatory conduction is faster than continuous conduction (a fact I hope is empirically and <em>unambiguously</em> established) relies on <strong>the putative slowing effect of ion channels on the signal fore. Please explain this effect in more detail, if it is not a misconception.</strong></p>
| [
{
"answer_id": 57622,
"pm_score": 6,
"text": "<h1> Short Answer </h1>\n<p>Myelination acts as an electrical insulator and allows saltatory propagation.</p>\n<ul>\n<li>By reducing membrane capacitance and increasing membrane resistance, myelination increases the velocity of signal (i.e., Action Potential... | [
{
"answer_id": 8804,
"pm_score": 4,
"text": "<p>There are two factors that need to be taken into account here:</p>\n\n<p><strong>1. Myelination decreases membrance capacitance.</strong></p>\n\n<p>The rate at which sodium influx through a node can depolarize the axon at the next node is related to both t... |
8,317 | <p>If a person contracts a virus, viral conjunctivitis for example, is it possible for the individual to become "reinfected" with the exact same strain of the virus once the person has it treated and the symptoms have gone away? I am a nursing student and am fascinated with virology, but my basic microbiology class did not go very in-depth on the subject. </p>
| [
{
"answer_id": 8320,
"pm_score": 4,
"text": "<p>The nature of infectious agents is that they transmit between organisms. This means that they have reservoirs outside a single host, and hence of course encountering the exact same strain twice is possible if this strain leaves the body and at a later stag... | [
{
"answer_id": 78462,
"pm_score": -1,
"text": "<p>Viruses that mutate quickly (particularly notorious are respiratory viruses such as the flu and common cold) quickly produce new \"strains\" within the same virus family. While most people should be familiar with the terms \"influenza A\" and \"influenza... |
8,331 | <p>In a lecture during my undergraduate degree we were introduced to <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1084159/" rel="nofollow">the race to complete the human genome</a>. Celera were competing with Sanger and collaborators to sequence the human genome. Celera wanted to patent some sequences, whilst Sanger <em>et al.</em> wanted to keep their findings in the public domain. Celera knew they couldn't compete with Sanger <em>et al.</em> with conventional cloning techniques which required a lot of man-power, <em>"so instead opted for <a href="https://en.wikipedia.org/wiki/Shotgun_sequencing" rel="nofollow">shotgun sequencing</a>"</em>. </p>
<p>To me it seems like both clone based sequencing and shotgun sequencing could have been used together, however the lecturers semantics were a bit vague (<em>...okay, I wasn't paying close enough attention!</em>) and I didn't ask for clarification at the time.</p>
<p>Whilst I appreciate this is a large topic, what are the main differences between Celera's shotgun sequencing and Sanger's clone based sequencing during the late 1990s? Are "shotgun cloning" and "clone based sequencing" actually mutually exclusive terms?</p>
| [
{
"answer_id": 8340,
"pm_score": 4,
"text": "<p>The v short answer is that in shotgun sequencing, the sequencer is fed a set of random sequences from the target. This can be done for instance by mechanically shearing DNA and then building a set of shotgun sequencing jobs which are then compiled back to... | [
{
"answer_id": 8523,
"pm_score": 2,
"text": "<p>In short: the basis of the process is the same in both, the difference relies that in the clone based sequencing you make DNA library of the pieces of DNA clones you got from the sequence you used in first place. Like that, data management and the mounting... |
8,379 | <p>I don't work at the wet lab and don't know all the details about the knockdown techniques.<br>
My question is:<br>
How lncRNA knockdown is done?<br>
For example - you have lncRNA that is <strong>functional in the nucleus</strong>. How is it possible to do knockdown using iRNA if <strong>interference happens only in the cytoplasm</strong>?<br>
Sorry if there is biology related misconception in my question.</p>
| [
{
"answer_id": 8381,
"pm_score": 3,
"text": "<p>Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the <a href=\"http://www.pnas.org/content/69/11/3360.full.pdf\" rel=\"nofollow\">RNase H</a> enzyme, which d... | [
{
"answer_id": 8380,
"pm_score": 1,
"text": "<p>Nuclear RNAi happens.. check these articles:</p>\n\n<p><a href=\"http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html\" rel=\"nofollow\">http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html</a></p>\n\n<p><a href=\"http://nar.oxfordjourn... |
8,382 | <p>I am very interested in zoology,and I want to study zoology in my spare time.
Any undergraduate level zoology text book recommendation?</p>
| [
{
"answer_id": 8381,
"pm_score": 3,
"text": "<p>Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the <a href=\"http://www.pnas.org/content/69/11/3360.full.pdf\" rel=\"nofollow\">RNase H</a> enzyme, which d... | [
{
"answer_id": 8380,
"pm_score": 1,
"text": "<p>Nuclear RNAi happens.. check these articles:</p>\n\n<p><a href=\"http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html\" rel=\"nofollow\">http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html</a></p>\n\n<p><a href=\"http://nar.oxfordjourn... |
8,386 | <p>When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical Brownian diffusion signalling with receptor surface proteins is relatively slow and is often exploited by venoms and susceptible to toxins (on the plus side it's the reason a lot of medical drugs work). It seems flawed for evolution to have selected for this rather than some alternative quicker and more direct electrical interface.</p>
<p><strong>Question.</strong> Why are chemical synaptic interfaces used in higher organisms at the synaptic junction?</p>
| [
{
"answer_id": 8381,
"pm_score": 3,
"text": "<p>Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the <a href=\"http://www.pnas.org/content/69/11/3360.full.pdf\" rel=\"nofollow\">RNase H</a> enzyme, which d... | [
{
"answer_id": 8380,
"pm_score": 1,
"text": "<p>Nuclear RNAi happens.. check these articles:</p>\n\n<p><a href=\"http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html\" rel=\"nofollow\">http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html</a></p>\n\n<p><a href=\"http://nar.oxfordjourn... |
8,407 | <p><img src="https://i.stack.imgur.com/eMgX9.jpg" alt="enter image description here"></p>
<p>Can anyone identify this strange creature? I live in a very urban part of Montreal, Canada. It wasn't moving (seemed dead) and although the image is huge, it wasn't as big as it seems (a couple of centimeters).</p>
| [
{
"answer_id": 8409,
"pm_score": 4,
"text": "<p>It's a type of centipede.</p>\n\n<p>Based on the long legs, I would bet on something like that:\n<a href=\"http://en.wikipedia.org/wiki/Scutigera_coleoptrata\" rel=\"noreferrer\">http://en.wikipedia.org/wiki/Scutigera_coleoptrata</a></p>\n\n<p>Or at least ... | [
{
"answer_id": 8445,
"pm_score": 2,
"text": "<p>I live in Japan and here they are called \"gejigeji\". As mentioned, they are a member of the centipede family and are as creepy as hell. I live in a newly-built house, so thankfully there are no cockroaches, but every now and again one of these little bli... |
8,426 | <p>I got this question and don't really understand the difference between the answers.</p>
<p>Diffusion is (in cell membrane):</p>
<p>a) passive by nature, no metabolic energy is needed</p>
<p>b) driven process by pressure or voltage</p>
| [
{
"answer_id": 8427,
"pm_score": 2,
"text": "<p>Diffusion is always a passive process that doesn't require energy. Therefore it would seem that A is correct, B doesn't really make a whole lot of sense. In the case of the cell membrane diffusion will often be in the form of 'facilitated diffusion' thro... | [
{
"answer_id": 8429,
"pm_score": 0,
"text": "<p>Diffusion relies on the fact particles move randomly in whatever they're in. If they are concentrated (I.e. there are lots of them in one place) they will fill out the whole place. With respect to cell membranes, anything that can diffuse freely will be th... |
8,556 | <p>What happens to blood pressure when we exercise? Does it increase, decrease, or remain the same? If it does increase, why are patients with high blood pressure recommended to exercise?</p>
| [
{
"answer_id": 8776,
"pm_score": 4,
"text": "<p>As pointed out in the answers above, your blood pressure increases transiently as you exercise because more oxygen and nutrients are consumed by your muscles. However, regular exercise increases your \"cardiovascular reserve\"-this means your body will be ... | [
{
"answer_id": 8557,
"pm_score": 1,
"text": "<p>Increases during exercise, but as we get fitter it decreases. Vessels become more optimal, they grow to supply muscles better, the heart beats less as it becomes more efficient. However this goes beyond that, hypertensive patients are at risk of stroke and... |
8,630 | <p>I've done some research and it appears that dogs are the most diverse looking single species of mammals. The questions that interest me is - are dogs special in respect to genes/gene activation mechanisms related to appearance? Or does this dramatic difference in appearance have something to do with dog anatomy and how they give birth?</p>
<p>If dogs are not special, this makes me interested <strong>if other species of mammals can also be bred selectively (or genetically engineered) to produce such dramatic variation?</strong> </p>
| [
{
"answer_id": 8637,
"pm_score": 5,
"text": "<p>Dogs have a <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000451\" rel=\"nofollow noreferrer\">genomic structure that allows breeding with high variation</a> in size, shape, coat quality, color and <a href=\"http://dogcare.dai... | [
{
"answer_id": 8639,
"pm_score": 3,
"text": "<p>Rabbits have been bred domestically since at least ancient egypt. </p>\n\n<p>Rabbits vary in size from > 15 kg (35lb) for <a href=\"http://www.rabbitwelfare.co.uk/pdfs/GiantRabbitCareGuidelines.pdf\" rel=\"noreferrer\">a Continental Giant</a> to .5kg(1lb)... |
8,719 | <p>Once clonal selection is done, B cells would start dividing and producing antibodies. So, after an antigen is eliminated, what stops the division of B cells and antibody production?</p>
| [
{
"answer_id": 8726,
"pm_score": 3,
"text": "<p>Upon activation plasma B cells upregulate death receptors as part of being activated. Presence of the antigen overcomes the death signal, thus the cell survives. When antigen is lost, the death signals overcome the survival signals as there is no antigen, ... | [
{
"answer_id": 8722,
"pm_score": 1,
"text": "<p>My understanding of this question is: Antibodies are produced by plasma cells which are terminally-differentiated B cells. Maturation of B cells to plasma cells is stimulated by the presence of antigen (T cells, cytokines, etc. etc). </p>\n\n<p>In the abs... |
8,745 | <p>To me, the phenomenon of polymorphism in cnidarians is particularly troubling. I gather that it essentially refers to existence of various different <strong><em>forms</em></strong> or <strong><em>kinds</em></strong> of individuals, i.e. zooids and polyps in one species. But when we refer to the cnidarian <em>Physalia</em>, as an animal, aren't we actually referring to a colony of individuals? <em>Physalia</em> consists of several "entities" including <em>gastrozooids</em>, <em>dactylozooids</em>, and the <em>float</em>, and since each of these is a distinct "organism", therefore is what we refer to by saying <em>Physalia</em> is actually a colony of phenotypically distinct forms of the same species?</p>
<p>Therefore, can "animals" like <em>Physalia</em> or <em>Gorgonia</em> or <em>Pennatula</em> be thought of actually as "colony-beings" which always contain several individuals in group?</p>
| [
{
"answer_id": 9148,
"pm_score": 4,
"text": "<p>It seems like your question might contain two separate and linked issues, both of which are perhaps equally confusing and equally interesting. They're both really discussion questions in a sense, but they've also both been dealt with in the literature in t... | [
{
"answer_id": 9139,
"pm_score": -1,
"text": "<p>While refering to an animal say <em>Physalia</em>, we refer to its massive type colony, containing many zooids. Among the zooids, a large cup shaped float is seen, which is bright blue in color and remains above sea water normally. On the undersurface of ... |
8,748 | <p><img src="https://i.stack.imgur.com/goTGI.jpg" alt="Unknown insect in Russia">
<img src="https://i.stack.imgur.com/pI1x0.jpg" alt="Unknown insect in Russia"></p>
<p>Found in Russia. Approx. 7 cm.</p>
| [
{
"answer_id": 8749,
"pm_score": 4,
"text": "<p>This is <a href=\"http://en.wikipedia.org/wiki/Crane_fly\">Crane fly</a>, of the Tipulidae family. They don't bite humans, adults feed on nectar. Larvae prefer moist environments such as wet soil or decomposing vegetable matter and can consume roots and ve... | [
{
"answer_id": 8754,
"pm_score": 2,
"text": "<p>As a complement to Mattia Rovetta's answer, notice that this insect has only 2 wings, while insects typically have four.</p>\n\n<p>Like flies and mosquitoes, these are Diptera: the hind wings have evolved into a stucture called \"<a href=\"http://en.wikipe... |
8,750 | <p>[This is one more post in my <a href="https://stats.stackexchange.com/q/61303/4769">growing</a> "X for dummies/idiots/morons/etc." series.]</p>
<p>I've been enjoying Provine's <em>The origins of theoretical population genetics</em> for the last couple of days, but I must confess that I find his description (on pp 127-8) of the <em>logic</em> behind Sewall Wright's (and W. Castle's) selection experiments with "hooded rats" about as clear as if it had been chiseled in Linear A...</p>
<p>Which is really bumming me out, because I'd love to understand these experiments.</p>
<p>Does anyone know where I can find a description of these experiments aimed at those with only a very limited grasp of classical genetics? (I took a graduate-level genetics class a billion years ago, and I did not find it easy.)</p>
| [
{
"answer_id": 8749,
"pm_score": 4,
"text": "<p>This is <a href=\"http://en.wikipedia.org/wiki/Crane_fly\">Crane fly</a>, of the Tipulidae family. They don't bite humans, adults feed on nectar. Larvae prefer moist environments such as wet soil or decomposing vegetable matter and can consume roots and ve... | [
{
"answer_id": 8754,
"pm_score": 2,
"text": "<p>As a complement to Mattia Rovetta's answer, notice that this insect has only 2 wings, while insects typically have four.</p>\n\n<p>Like flies and mosquitoes, these are Diptera: the hind wings have evolved into a stucture called \"<a href=\"http://en.wikipe... |
9,018 | <p>I know that DNA molecules or proteins can be separated in electrophoresis because the electrical charge is used to pull the DNA through the gel. So instead of using electrical, can I using physical impact like pumping ?</p>
| [
{
"answer_id": 9023,
"pm_score": 3,
"text": "<p>If you tried to set up a system in which movement of DNA molecules through a gel matrix was driven by pumping buffer, the gel would become compressed. I am old enough to remember running vertical agarose gel electrophoresis overnight, and these gels would ... | [
{
"answer_id": 9019,
"pm_score": 0,
"text": "<p>No, you can't use mechanical pumping for gel electrophoresis. The nature of electrophoresis is the create a uniform electric field through the gel, and this electric field stimulates motion from the charged DNA/protein.</p>\n"
},
{
"answer_id": 904... |
9,032 | <p>I've always thought that the majority of the "work" in a cell is protein production, until I read the following.</p>
<p>The Wikipedia article on the <a href="http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology" rel="nofollow">central dogma of molecular biology</a> states this:</p>
<blockquote>
<p>80% of the human genome is transcribed even though only 1% codes for
proteins.</p>
</blockquote>
<p>and this:</p>
<blockquote>
<p>Current research focuses on investigating the function of non-coding
RNA, that is, RNA that does not follow the dogma trend and does not
code for polypeptides.</p>
</blockquote>
<p>If 99% of what's transcribed isn't used for creating proteins, what is it used for? If it's not known - are there any hypotheses? </p>
| [
{
"answer_id": 9043,
"pm_score": 3,
"text": "<p>As indicated in the comments there are several non-coding (untranslated) RNAs, that the cell produces. Most of these perform gene regulatory functions.\nHowever, widespread transcription is known to take place throughout the genome (<a href=\"http://www.pl... | [
{
"answer_id": 9052,
"pm_score": 2,
"text": "<p>Untranslated RNA is incredibly important. As mentioned it regulates gene control, siRNA or miRNA for example can cut up mRNA preventing it being translated. Others can cause an increase in expression like enhancer RNA. Then RNA can act as tRNA or ribosomal... |
9,075 | <p>Sometimes while tasting a very sour thing (like tamarind, lemon etc.) our eyes squint immediately and involuntarily for a second, but a little later becomes normal again. </p>
<p>Why, and how, does this reflexive movement occur?</p>
| [
{
"answer_id": 11342,
"pm_score": 1,
"text": "<p>Maybe it serves to show others that we may be consuming something poisonous. We cry when we are sad to alert others of our distress. There may be better ways to show something is poisonous, but a child doesn't have any real way to alert who ever is feedin... | [
{
"answer_id": 9079,
"pm_score": -1,
"text": "<p>Squinting is the organism's way to warn us that we are eating something that could eventually be dangerous, acidic or toxic. It's a reflex, developed many many years ago when the ancient people did not know much about the safety of plants, roots and other... |
9,176 | <p>I found a a few of these guys on my composter, so they could have easily been eating bugs or decaying organics (or both):</p>
<p><img src="https://i.stack.imgur.com/Xp9Ke.jpg" alt="Image 1">
<img src="https://i.stack.imgur.com/08hBR.jpg" alt="Image 2"></p>
<p>To me it looks like a stink bug with oversized legs, not like the ones I'm used to seeing. His body measures just under 3cm, and I haven't pulled on his legs to get a measurement (I haven't pulled on it at all). The legs seem to be at least 1.5 times the body length as do the antenna. The body is grayish brown and the antenna and parts of the leg seem reddish brown.</p>
<p>I'm a microbiologist, so things big enough to see in a jar are not really my specialty. That said, here's info that I've been trying to use ID it:</p>
<p>Wingless Normal compound forelimbs (don't seem to have any kind of prey modification) </p>
<p>Segments filiform antenna (I think) </p>
<p>2 Tarsomeres (I think) </p>
<p>In the middle of South East US </p>
<p>Have had (unusually) heavy rains </p>
<p>Underside of the limbs and antenna seem red, but to seems gray</p>
<p>I've never seen it before! (and I usually notice such things).</p>
<p>Update: Despite my 4 year old putting other bugs and some leaves in with it, the bug died. I took the opportunity to get some much better photos, and low and behold when I started manipulating it I was able to pull out a substantial rostrum that I missed! These guys are good at hiding those. So going back to assassin bugs, can anyone id which assassin bug it is?</p>
<p>More photos: [I would add more but I think this should be plenty]
<img src="https://i.stack.imgur.com/CopKO.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/lzt3b.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/ESqjy.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/uZ0zC.jpg" alt="enter image description here"></p>
<p>I at least think it's quite a pretty specimen (to betray my mammalian aversion to bugs).</p>
| [
{
"answer_id": 9178,
"pm_score": 4,
"text": "<p><strong>species ID</strong></p>\n\n<p>I feel reasonably confident this is a late-instar <em>Acanthocephala declivis</em> nymph (that is, almost-but-not-quite-adult).</p>\n\n<p>Compare your pictures with those on bugguide of a <a href=\"http://bugguide.net/... | [
{
"answer_id": 10759,
"pm_score": 0,
"text": "<p>It looks very much like a squash bug, which look close too assassin bugs but don't eat insects, probably explaining what it was doing in your mulch. I have the same thing.</p>\n"
},
{
"answer_id": 21503,
"pm_score": 0,
"text": "<p>Maybe th... |
9,244 | <p>Neural receptive fields map the spatial or temporal distribution of the data to individual neuron excitation, if I understand correctly, but I do not understand if receptive fields (especially in the higher cognitive areas such as the various layers of the visual cortex, etc.) are:</p>
<ol>
<li><p>Actual <em>structural</em> distributions of neurons that help map specific spatial or temporal properties of stimuli (such as concentric arrangement for contrast detection, rectangular arrangement for orientation detection, or movement detection, etc.), or,</p></li>
<li><p>Merely a <em>mapping</em> of the structure of the <em>stimuli</em> that can excite specific neurons.</p></li>
</ol>
<p>If it's the latter, isn't it basically as simple as a pattern/feature/vector that individual neurons are sensitive to?</p>
| [
{
"answer_id": 9255,
"pm_score": 3,
"text": "<p>No, it is not 1. the structural distribution of the neurons themselves. If by mapping you mean a kind of function that maps real space to cognitive space (or such) then it is not that either (at least, not explicitly/directly).</p>\n\n<p>The <strong>recep... | [
{
"answer_id": 9278,
"pm_score": 2,
"text": "<p>I think is closer to 2. It is the <strong>subset</strong> of <strong>sensory space</strong> that elicits a <strong>reaction</strong> in a given <strong>neural population</strong>.</p>\n\n<p>So you should:</p>\n\n<ul>\n<li><p>Pick your <strong>neural popula... |
9,276 | <p>I would like to understand which mechanism triggers the first cell differentiation after <em>n</em> divisions.</p>
<p>I read <a href="https://biology.stackexchange.com/questions/3720/how-are-different-types-of-cells-created-from-zygote/8309#8309">previous</a> <a href="https://biology.stackexchange.com/questions/3741/how-do-cells-know-what-type-to-differentiate-into">articles</a> on SE and Wikipedia articles on <a href="http://en.wikipedia.org/wiki/Cellular_differentiation" rel="nofollow noreferrer">cellular differentiation</a> and <a href="http://en.wikipedia.org/wiki/Embryogenesis" rel="nofollow noreferrer">embryogenesis</a> but still fail to understand what exactly makes it so that starting from a given division cells suddenly start to be different.</p>
<p>Wikipedia claims that</p>
<blockquote>
<p>In the first hours after fertilization, this cell divides into
identical cells. In humans, approximately four days after
fertilization and after several cycles of cell division, these cells
begin to specialize, forming a hollow sphere of cells, called a
blastocyst</p>
</blockquote>
<p>but do not explain <strong><em>why</em></strong> they begin to specialize.</p>
<p>I could imagine </p>
<ul>
<li>that a cell has a "counter" on the number of divisions which triggers differentiation after a given amount of divisions </li>
<li>or a chemical substance (either cell-borne or external) forces a change in the division</li>
</ul>
<p>but why some cells would become "cell A" and some others "cell B"?</p>
<p>I am fairly sure that the biochemical mechanisms which regulate the life of a grown up mechanism can explain cellular differentiation (through hormones for instance) -- I am however interested by this specific moment, this <em>n-th</em> division where identical cells become differentiated.</p>
| [
{
"answer_id": 24022,
"pm_score": 4,
"text": "<p>The first differentiation in human embryogenesis is from early blastomeres into trophoblast, which forms the outer layer of the blastocyst, and inner cell mass (ICM). It may be unsurprising then that cells on the inside of the 8-16 cell stage morula \ndif... | [
{
"answer_id": 23173,
"pm_score": 1,
"text": "<p>Why cells differentiate or specialize is an ephemeral question. I'll make an attempt to answer--the more specialized cells an organism has, the better equipped that organism is to function.</p>\n\n<p>In a given organism, differentiation after n divisions ... |
9,315 | <p>I was reading <a href="http://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00245/abstract" rel="nofollow">this(1)</a> and it led me back to ask a very basic question (I'm not a neuroscientist). All the way back to undergrad anthropology and neuroscience courses I remember being taught the general rule of relative intelligence was that one looked at the ratio of the brain mass over the total mass of the animal (or the estimations therein from let's say fossils).</p>
<p>I know a lot of the interesting neuroscience research going on these days does looks into bird brains, particularly within <em>Corvidae</em>. It would seem that birds are often much more efficient in the abilities they seem to show with considerably less brain mass. I do realize that birds often weigh very little as well, so perhaps the ratio is preserved? </p>
<p>I also realize that within birds, they see better ratios in more intelligent birds. But what about the comparison from mammals to birds?</p>
<p>Dinosaurs are often predicted to <strong>not</strong> be intelligent because of the enormous body size and small cavities for a brain. Now I realize that some dinosaurs were actually quite tiny, but this is just an example. </p>
<p>Given birds' close genetic link to dinosaurs, could it simply be that they were just doing more with less? The mammalian brain is a huge caloric burden, so perhaps this would show an efficiency that could be selected for?</p>
<p>Thus as the title suggests, my main question:</p>
<p>Is the ratio of brain mass to body mass still considered to be a valid indication of intelligence of a species in modern (current) neuroscience? Certainly there are exceptions, but is it still considered the rule of thumb?</p>
<p>EDIT: I also wanted to point out the <a href="http://www.karger.com/Article/FullText/102973" rel="nofollow">first article(2)</a> I started to read after formulating the question. It made me question the usefulness of encephalization in addressing this issue at all, but I don't/didn't feel adequately trained to evaluate the conclusions of the meta study. </p>
<p>Again, this still leaves us comparing within primates, which still leaves me feeling that <em>Corvidae</em> have some really impressive efficiency going on with their overall brain mass. Which then leads to hope that some dinosaurs could be at least equally intelligent, if not more so (noted that this is complete conjecture).</p>
<hr>
<p>(1) Front Hum Neurosci. 2013 Jun 6;7:245. doi:<a href="http://dx.doi.org/10.3389/fnhum.2013.00245" rel="nofollow">10.3389/fnhum.2013.00245</a>. Print 2013.</p>
<p>(2) Brain Behav Evol. 2007;70(2):115-24. Epub 2007 May 18.</p>
| [
{
"answer_id": 9317,
"pm_score": 4,
"text": "<p>I don't know about brain mass to body size, but ratio of neocortex to brain volume is correlated with primate evolution (Figure 3, <a href=\"http://www.nature.com/nature/journal/v411/n6834/full/411189a0.html\" rel=\"noreferrer\">here</a>). If you subscribe... | [
{
"answer_id": 57779,
"pm_score": -1,
"text": "<p>Considering that as humans had larger brains in prehistoric times, then no, brain size doesn't mean more intelligent.\nI aren't well versed into this subject, so I don't particularly know if they could learn better than us, but there are speculations of ... |
9,320 | <p>I recently finished reading Contact by Carl Sagan. In the book they talk about a pattern in the transcendental number like pi or e, and comment that it is found in base 10 or however many fingers the race has to count with.</p>
<p>When in the end they find a pattern in pi it is in base 11, which I found a strange choice since I can't think of an animal that has an uneven total number of fingers, and I would think that most evolution would result in a somewhat symmetrical design.</p>
<p>Do any animal exist that has an uneven total number of fingers or equal lim, excluding polydactyly and oligodactyly?</p>
| [
{
"answer_id": 9321,
"pm_score": 6,
"text": "<p>Your conclusion relies on the supposition that all beings must count using their finger tips (or the most paralogous, \"finger-like\" limb). In fact, even within humans this is not necessarily true: the Yuki native people of California count in base 8 by <... | [
{
"answer_id": 9322,
"pm_score": 5,
"text": "<p><em><a href=\"http://en.wikipedia.org/wiki/Coscinasterias_calamaria\" rel=\"noreferrer\">Coscinasterias calamaria</a></em>, the Eleven-Armed Sea Star! (Although I doubt it has much to do with pi)</p>\n\n<p><img src=\"https://i.stack.imgur.com/mp1KF.jpg\" a... |
9,324 | <p>I've been thinking about this lately. Would it be possible for a type of spider to gain the ability to fly freely by weaving its web between it's legs and creating wings much like those of a bat?</p>
<p>Is there anything like that in nature currently?
Is it plausible at all?</p>
| [
{
"answer_id": 9325,
"pm_score": 3,
"text": "<p>It takes more than wings to fly, just look at the poor penguins. The first problem is that simply weaving webs between a spider's legs would probably not generate enough lift to keep her airborne. Flying creatures have a specific body plan that allows them... | [
{
"answer_id": 9329,
"pm_score": 0,
"text": "<p>Very unlikely as spiders don't have direct muscle/exoskeleton connections like insects, it would be a more complicated mechanism for powered flight...</p>\n\n<p>imagine replacing a radial engine in an airplane with and engine that powers a hydraulic pump t... |
9,389 | <p>Verging on the realm of science fiction, my question is that is there any theoretically possible way, biologically/chemically, with which the entire human race can be killed without affecting the rest of the biosphere at all? I am only curious about theoretically possible no matter how unlikely. If we encounter a sufficiently advanced alien civilization bent on our destruction, would it be possible for them to make sure all humans die without harming any other living organism on our planet?</p>
<p>Is there anything biological/chemical which makes us unique or different than other lifeforms on Earth? Something which can be used against us? Or are we just so similar with a bunch of other species that we cannot be wiped out without other lifeforms getting harmed or our destruction cannot be ensured? Is it possible to artificially make humans extinct?</p>
<p>Thanks you.</p>
| [
{
"answer_id": 9395,
"pm_score": 3,
"text": "<p>Infectious diseases is probably the only way I can think of. Viruses for example may have tropisms based on receptors to which they attach. These receptors may be and often are unique to a species, and thus an infection could target humans very specificall... | [
{
"answer_id": 9403,
"pm_score": 2,
"text": "<p>Trick question. By driving humans to extinction, you almost certainly will be driving all human-specific parasites and pathogens to extinction as well.</p>\n"
},
{
"answer_id": 9555,
"pm_score": 2,
"text": "<p>This answer is building on the... |
9,427 | <p>I'm working on a piece of <a href="http://www.ebi.ac.uk/compneur-srv/melting/">software</a> that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base. At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U. Is there a standard letter for 5-methylcytosine? The only example I've found is this <a href="http://www.ncbi.nlm.nih.gov/pubmed/1945840">paper</a>, which uses an italic <em>C</em> for 5mc, but I want a distinct letter. The three candidates I've thought of are: </p>
<ul>
<li><strong>5</strong> - for '5-methylcytosine'</li>
<li><strong>M</strong> - for 'methyl'</li>
<li><strong>B</strong> - Since methylation of <strong>U</strong> gives you <strong>T</strong>, which is one place earlier in the alphabet, so methylation of <strong>C</strong> gives <strong>B</strong>. </li>
</ul>
| [
{
"answer_id": 9428,
"pm_score": 5,
"text": "<p>Well, don't use <strong>M</strong> or <strong>B</strong>, those are already taken (<strong>C</strong> or <strong>A</strong>, and <strong>not A</strong>, respectively). You can see the full list here: <a href=\"http://www.dna.affrc.go.jp/misc/MPsrch/InfoIU... | [
{
"answer_id": 9448,
"pm_score": 2,
"text": "<p>As Amory suggests the IUPAC \"Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc.\" (<a href=\"http://www.chem.qmul.ac.uk/iupac/\" rel=\"nofollow\">http://www.chem.qmul.ac.uk/iupac/</a>) are probably the best place to ... |
9,437 | <p>It's bothered me for a while now. I understand why a parasitoid would do this, as it only temporarily requires the host, and that not all parasites kill their hosts.</p>
<p>There seems to be no evolutionary advantage in killing a host, because the parasite relies on the host for resources. Yet some organisms, usually microscopic pathogens, seem to fatally damage the host with no immediate benefit to themselves. Why is this? </p>
<p>I know this is asking for a broad soft answer, but I don't want the question to get bogged down by a specific species, although bonus points for using examples.</p>
| [
{
"answer_id": 9443,
"pm_score": 6,
"text": "<p>I can think of several (non-exclusive and probably non-exhaustive) hypotheses:</p>\n\n<ol>\n<li><p><strong>Maladaptive</strong>. It is maladaptive. Maybe because it is a virus coming from another species (e.g. SIV and HIV) or because it is not adapted to o... | [
{
"answer_id": 9441,
"pm_score": 3,
"text": "<p>Some parasites aren't natural hosts of humans, instead we are an accidental host in which they cannot replicate. Zoonoses such as this can be quite fatal as the parasite is not adapted to us. Although viruses are often separated, they are parasites and you... |
9,506 | <p>I have heard that "The animals who have their 'EARS' outside their body give birth to their young ones and the animals who have their 'EARS' inside their body lay eggs." Is this true? Are there counterexamples?</p>
| [
{
"answer_id": 9565,
"pm_score": 5,
"text": "<p>Just to expand on @rg255's very good answer, you could make the same sort of claim using just about any characteristic that is more commonly found in mammals. </p>\n\n<p>Giving birth to live young is a characteristic of most (see the platypus below), if no... | [
{
"answer_id": 9508,
"pm_score": 4,
"text": "<p>You are quoting from Imam Ali, </p>\n\n<blockquote>\n <p>\"The animals who have their 'EARS' outside their body give birth to\n their young ones and the animals who have their 'EARS' inside their\n body lay eggs.\"</p>\n</blockquote>\n\n<p>And in short ... |
9,517 | <p>Reading <a href="https://biology.stackexchange.com/questions/9017/how-potent-is-the-venom-from-the-australian-platypus">this question</a>, I wondered why is it that we associate vertebrate venoms so often with snakes and fish, and more rarely with lizards, amphibians, mammals, and birds (apparently never, in birds?).</p>
<p>Are venoms more advantageous for snakes and fish, or more expensive or dangerous to produce for the other taxa? Or is it connected to evolutionary history – is venom somehow more 'evolvable' for snake and fish lineages?</p>
<p>Or, perhaps, is it just chance?</p>
| [
{
"answer_id": 9522,
"pm_score": 5,
"text": "<p><a href=\"http://phenomena.nationalgeographic.com/2013/01/09/on-the-origin-of-venom/\" rel=\"nofollow noreferrer\">This write up by Carl Zimmer</a> basically covers anything I could have said. He links to a number of resources, in particular <a href=\"htt... | [
{
"answer_id": 9529,
"pm_score": 3,
"text": "<p>Old answer:</p>\n<p>Venom production is a "hard" adaptation to achieve**. So it is conceivable that simpler organisms had enough evolutionary time to get the adequate mutations for this to happen, which would explain why venom is almost absent (I... |
9,668 | <p>Is it possible that a human or any other creature can die from pain?</p>
<p>I googled and found different answers. Some articles say Yes while others say No.</p>
| [
{
"answer_id": 9673,
"pm_score": 4,
"text": "<p>I very much doubt it. You may however die from whatever's <em>causing</em> the pain. The reason you feel pain is so you stop doing whatever is causing the pain. Hence someone knows not to touch a hot fire because it is painful. But the pain itself is not a... | [
{
"answer_id": 45867,
"pm_score": -1,
"text": "<p>I refer the honorable gentlemen to James Harriet. He reports discovering by accident by ending the pain he was in some cases able to reverse the pathology by ending the pain with anesthetic drugs, thus allowing the body's natural healing abilities to tak... |
9,758 | <p>I was looking at diabetes the other day, and I noticed something strange. Lower amounts of lipase are a symptom of diabetes, as is overweightness. However, since lipase is the enzyme that breaks down fats, shouldn't a lack of it mean that less of it enters your blood stream and is simply excreted instead? In that case, how come diabetic people are often overweight?</p>
<p>This question has been bugging me for ages, does anyone know why?</p>
| [
{
"answer_id": 9770,
"pm_score": 4,
"text": "<p>How are diabetes and obesity connected in light of low lipase activity?<br>\nShort answer: There's more than one type of diabetes. (And to complicate things, there's also more than one type of lipase. It's unclear from the question which type were mentio... | [
{
"answer_id": 9763,
"pm_score": 2,
"text": "<p>Source : Tortora and Derrickson Principles of anatomy and physiology</p>\n\n<p>I read in the section on diabetes that \" The breakdown of stored triglycerides causes weight loss\".\n I assume that diabetic people are often overweight not simply because the... |
9,774 | <p><strong>Actual question</strong></p>
<p>I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated together, a process during which at least the EcoRI site was lost: the plasmid had a BamHI site very near the XmaI site, and a BamHI/EcoRI digest produced only one band compared to three bands in the undigested control (three conformations of circular plasmid).</p>
<p>How could ends as incompatible as EcoRI and XmaI be ligated?</p>
<p><strong>Detailed Background or: Why I believe incompatible sites were ligated</strong></p>
<p>This is chronologically further to: <a href="https://biology.stackexchange.com/questions/9726/what-are-common-causes-of-unexpected-ligation-products">What are common causes of unexpected ligation products?</a>. Briefly: I digested two plasmids, one with EcoRI and XmaI (p1), the other with EcoRI and AgeI (p2) [XmaI and AgeI produce compatible sticky ends], then carried out a ligation between a 1.4kb insert isolated from p2 (structure EcoRI-1.4kb-AgeI) into the 3.4kb backbone isolated from p1 (structure XmaI-20bp-BamHI-3.4kb-EcoRI). After transformation, I tested the ligation product by digest with EcoRI and BamHI, which should produce again 3.4kb + 1.4kb. The gel was poor quality but allowed the conclusion that there were different ligation products.</p>
<p>Repeating the EcoRI/BamHI digest and gel more carefully showed there were only two variants: Variant A (8 colonies) produced the two expected bands 3.4kb and 1.4kb. Variant B (4 colonies) only produced a clear 3.4kb band, nothing else visible in the lane: in other words, it only carried either an EcoRI or a BamHI site and was in total smaller than variant A (confirmed by undigested controls). Thus, I conclude that B was simply the same 3.4kb backbone, re-ligated without the 1.4kb insert. Since the BamHI site was untouched in the backbone during the preparatory EcoRI/XmaI digestion, I assume that the EcoRI site was not recovered during the ligation of variant B.</p>
<p>(The ligation was carried out overnight at 16 deg C, using Promega T4 DNA ligase and buffer and a molar ratio of 3:1 insert:vector at a total volume of 20uL. The E.coli for transformation were Invitrogen OneShot Stbl3 and have been routinely and successfully used in the lab for a long time. The analytical digestion used Promega EcoRI and BamHI in Buffer Multi-Core, which Promega claims offers 75-100% efficiency for both enzymes. Incubation was 1.5h at 37°C.)</p>
| [
{
"answer_id": 13589,
"pm_score": 2,
"text": "<p>The answer from @Armatus got me looking at star activities again. EcoRI is prone to exhibit star activity in non-optimal buffers. In the case of this enzyme this tends to be a relaxation of site specificity, so HAATTC and GAATTD would be possible cut site... | [
{
"answer_id": 9925,
"pm_score": 0,
"text": "<p>My best guess to explain this phenomenon has been spontaneous degradation of the sticky ends, followed by blunt-ended ligation.</p>\n\n<p>Alternatively, single-stranded exonuclease activity either from a contaminating enzyme or from EcoRI/XmaI/AgeI could b... |
9,833 | <p>I saw a documentary where they inserted the gene of a mouse that basically is the starting "build an eye" command into a fruit fly, and a fruit fly eye grew. My question is, if eyes of different types of animal had different evolutionary beginnings (I don't know much about arthropod eye evolution, but for a different example, as I understand it, cephalopod eyes evolved from skin cells while vertebrate eyes evolved from brain cells), then <strong>how is it that the same gene controls the growth of two such evolutionary different eyes</strong>?</p>
| [
{
"answer_id": 9845,
"pm_score": 5,
"text": "<p>Both fruit flies (<em>Drosophila</em>) and mice (<em>Mus</em>) are classified under <em>Bilateria</em>.<br>\nThe presence of such a <a href=\"https://en.wikipedia.org/wiki/Conserved_sequence\">highly conserved sequence</a> in both species suggests that th... | [
{
"answer_id": 9838,
"pm_score": 3,
"text": "<p>The documentary was probably talking about Halder's paper in Science (<a href=\"http://courses.washington.edu/devbio/Halder1995.pdf\" rel=\"noreferrer\">Science, Halder et al., v.267</a>). If you'll read the abstract (especially the bottom part) You'll not... |
9,913 | <p>Type II Restriction enzymes usually cut only at palindromic sequences. Is there any specific reason for that? Is there any advantage for bacteria if they cleave phage DNA at this type of sequence?</p>
| [
{
"answer_id": 9915,
"pm_score": 3,
"text": "<p>First, not all restriction enzymes cut at palindromic sequences.\nA lot of them do though, simply because it is more effective. Recognising a palindromic sequence enables them to cut both strands of DNA at the \"same\" site, because the strand will have th... | [
{
"answer_id": 13498,
"pm_score": 2,
"text": "<p>These REs, that recognize palindromes, are mostly homodimers and hence the same sequences (for each monomer)for recognition, only they are reversed. This explains the palindromes.</p>\n"
},
{
"answer_id": 81713,
"pm_score": 3,
"text": "<p>... |
9,941 | <p>I want to know what makes the balance of the Prolactin abnormal. Is that related to the presence of a nodule near the pituitary? </p>
| [
{
"answer_id": 10576,
"pm_score": 3,
"text": "<p>The main abnormality in prolactin levels is hyperprolactinemia, meaning blood levels of prolactin above the normal range, not during pregnancy or lactation.</p>\n\n<p>The major cause of these abnormal prolactin levels are tumors consisting of pituitary la... | [
{
"answer_id": 10491,
"pm_score": 0,
"text": "<p>I am not sure whether I understand your question right, but prolactin levels can be abnormal under several conditions like cancer, drug abuse, stress, breast surgery etc.</p>\n\n<p>Its secretion is mainly controlled (inhibited) by Dopamine. Other hypothal... |
9,955 | <p>Is it true that wasps don't sting if struck by hand while flying? I know of one person who claims to have done this at least 20 times and has never been stung. And out of curiosity (not that I'd want to kill them), what about bees?</p>
| [
{
"answer_id": 9965,
"pm_score": 2,
"text": "<p>I think what your friend advised is incorrect, or they are very lucky. According to <a href=\"http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7449.html\" rel=\"nofollow\">\"Bee and Wasp Stings\"</a> from the University of California Davis, they specifically st... | [
{
"answer_id": 9967,
"pm_score": 3,
"text": "<p>I can confirm that I have often enough slapped a wasp or bee in flight without being stung. The reason is probably pure chance. </p>\n\n<p>It is kind of like asking if a human can bite when slapped. If I come up to you and slap you, fast and hard, you will... |
9,993 | <p>We all know CO₂ as a waste product of metabolism . Does CO₂ have any helpful role , apart from having a role in pH of blood ?</p>
| [
{
"answer_id": 10001,
"pm_score": 6,
"text": "<p>Before I restrict the answer to human metabolism, I recon it is important to mention that \nCO<sub>2</sub> is the source of the carbon atoms of glucose in photosynthesis (in the <a href=\"http://en.wikipedia.org/wiki/Light-independent_reactions\">Calvin c... | [
{
"answer_id": 10879,
"pm_score": 4,
"text": "<p>Some additional points about role of bicarbonate (which is directly formed from carbon dioxide as described by TomD):</p>\n\n<ol>\n<li>Helps is neutralizing the acidic chyme when it enters intestine.</li>\n<li>Formation of shells in invertebrates and eggs... |
10,009 | <p>The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is coded by 6 codons, tryptophan is coded only by one codon. </p>
<p>[I am aware that the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last base that does not affect the amino-acid that is encoded.] </p>
<p>I therefore do not think that the genetic code can be entirely be explained by “it happened to occur that way the first time” (at the origin of life or in the last universal common ancestor) “and it never changed”. </p>
<p>So, my questions are: </p>
<ul>
<li><p>Why are some amino acids coded by a several codons while others are coded only by one or two?</p></li>
<li><p>Specifically, why is methionine coded by only one codon — AUG — which has also to serve as a start signal?</p></li>
<li><p>In general, how (by what mechanisms, selective pressures) has the genetic code evolved to give this pattern of redundancies?</p></li>
</ul>
| [
{
"answer_id": 10014,
"pm_score": 5,
"text": "<p><a href=\"https://biology.stackexchange.com/questions/653/why-20-amino-acids-instead-of-64\">This question</a> is closely related, and the <a href=\"http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code\" rel=\"nofollow noreferrer\... | [
{
"answer_id": 16511,
"pm_score": 2,
"text": "<p>Some elements of response to your question.</p>\n\n<p>First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor ... |
10,022 | <p>I'm naturally thinking this is a bee, but I cannot find it anywhere in any insect identifiers. I caught this picture on top of my doorway, it's about 1 1/2 inches in length, and its torso seems to be coated in a layer of hair, and the rest of its body is narrow. The thick layer of hair may or may not be accurate, I didn't want to get too close to it, but that's how it appeared at least.</p>
<p><img src="https://i.stack.imgur.com/bwviH.jpg" alt="Unidentified Insect">
<img src="https://i.stack.imgur.com/qc8ng.jpg" alt="enter image description here">
<img src="https://i.stack.imgur.com/8Belf.jpg" alt="enter image description here"></p>
<p>What is this?</p>
<p>PS - Found in Kentucky, and I'm not sure why one pic shows wings and the other one doesn't...</p>
| [
{
"answer_id": 10025,
"pm_score": 5,
"text": "<p>From the general body plan, it looks like it's probably a <a href=\"http://en.wikipedia.org/wiki/Asilidae\">robber fly</a>. Here's a <a href=\"http://www.uky.edu/Ag/CritterFiles/casefile/insects/flies/robber/robber.htm\">page of specifically Kentucky robb... | [
{
"answer_id": 10754,
"pm_score": 2,
"text": "<p>Yes, I would say that is a bearded robber fly. Robber flies are similar to dragonflies in that they catch prey by catching it in midair. They will attack mostly bees, wasps, and hornets, and I have seen many catching bumblebees in the wild. I have even se... |
10,046 | <p><a href="http://en.wikipedia.org/wiki/Chargaff%27s_rules" rel="nofollow">Chargaff's rules</a> say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T.</p>
<p>But what about the ratio $\frac{nA+nT}{nC+nG}$?</p>
<p>Is there variation along species of this ratio that is higher than expected by random processes? If yes, what causes this variation?</p>
| [
{
"answer_id": 10052,
"pm_score": 4,
"text": "<p>That ratio is essentially, as WYSIWYG pointed out, called <strong>GC-content</strong>. In actuality, GC-content is reported as $(G+C)/(A+C+G+T)$, converted to percent; i.e., what percent of the genome is G or C.</p>\n\n<p>There is vast variation in GC-co... | [
{
"answer_id": 10049,
"pm_score": 2,
"text": "<p>Yes that ratio varies and is generally referred to as <strong>GC-content</strong> which is expressed as percentage. Earlier, people used GC-content as one of the identifiers for a group of organisms. </p>\n\n<p>Though there have been quite a few studies o... |
10,179 | <p>I have seen species of birds, insects and fishes with splendid colours. But when it comes to mammals (including us humans), they almost always appear in shades of brown, grey, orange, or in black and white. I don't recall seeing any pink, green and purple. Why is that so?</p>
<p><img src="https://i.stack.imgur.com/bBZdV.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 10685,
"pm_score": 4,
"text": "<p>I don't think, there is a precise answer about the evolutionary mechanisms, but \"mechanically\":</p>\n\n<ul>\n<li>mammals have principally just two types of pigments: eumelanin and pheomelanin, both of which have their color variants, but within a known ... | [
{
"answer_id": 10182,
"pm_score": -1,
"text": "<p>The Answer is simple..EVOLUTION..\nThe colour of an living organisms depends on 2 things 1) attracting other sex. 2) escape from the predators.</p>\n\n<p>In birds and insects: They doesn't much depend on other sex for living(except for the process of rep... |
10,237 | <p>In eukaryotes the nuclear envelope is continuous with the ER, so what helps it out of that?</p>
| [
{
"answer_id": 11387,
"pm_score": 2,
"text": "<p>I'd make a comment if I could, but I don't think mRNA ever enters the ER. When a ribosome is building a protein destined for export or for being inserted into the membrane, it travels to the ER membrane and binds to a protein in that membrane called Sec61... | [
{
"answer_id": 10240,
"pm_score": 0,
"text": "<p>Translation can occur either in the cytoplasm or in the ER. At one point it was believed that all mRNA begin being translated in the cytoplasm. However, if the protein the mRNA codes for happened to be a secretory protein or a membrane protein, it would h... |
10,256 | <p>Acetyl-CoA has a number of biochemical roles in the body and I'm curious as to whether anybody knows where I can find at least a semi-comprehensive list (i.e. comprising all the <strong>major</strong> roles in the human body it serves) of the biochemical reactions in which acetyl-CoA partakes in the human body. </p>
| [
{
"answer_id": 10258,
"pm_score": 2,
"text": "<p>I may be missing some fantastic resource, but my first thought is to send you to <a href=\"http://www.genome.jp\" rel=\"nofollow noreferrer\">KEGG</a>. Is that crazy? Maybe, but a simple search for Acetyl-CoA in humans can give you tons of useful inform... | [
{
"answer_id": 10270,
"pm_score": 0,
"text": "<p><a href=\"http://metacyc.org/\" rel=\"nofollow\">Metacyc</a> is an excelent methabolic pathways database that includes all kind of organisms. Of course you can search for methabolic compound.</p>\n"
},
{
"answer_id": 16438,
"pm_score": 0,
... |
10,264 | <p>I harvested some lentivirus from 293T cells and want to titre the result. I infected 293T cells on a well plate with 400,000 cells per well which I infected with virus stock, and 1 in 10, 100 and 1000 dilutions (as well as a few uninfected wells). After 72h incubation I trypsinised the cells and used FACS to titre first, but 293T do not express the promoter under which GFP is located in some samples and hence these do not appear on FACS. As an alternative, I extracted the genomic DNA from all samples using a QIAGEN DNeasy kit (also the samples which I was able to titre by FACS already) and then performed qPCR on them.</p>
<p>I used the ABI PRISM 7000 SDS: <a href="http://www.cgenetool.com/products/abi_prism_7000.shtml" rel="nofollow">http://www.cgenetool.com/products/abi_prism_7000.shtml</a></p>
<p>Included on the PCR plate were:</p>
<ul>
<li>Number standards: 1000, 10k, 100k, 1m copies</li>
<li>Samples in triplicate</li>
<li>No-template controls as well as untransduced controls</li>
</ul>
<p>Each of those was doubled, once with primers and probe for WPRE (an element specific for the lentivirus) and once with primers and probe for beta-actin (a housekeeping gene present in all cells).</p>
<p>The results returned by the machine include for each well the cycle at which the threshold fluorescence was crossed - along with the automatically calculated quantity of copies (which the software calculates from the standards I assume).</p>
<p>Since I named the triplicate samples identically, it also automatically calculated the mean quantitiy among each triplicate (practical, eh?). I checked if there were any outliers which should have been excluded from the means but everything was fine.</p>
<p>So now for example I have a result of 700k for the quantity of WPRE in sample A. The quantity of beta-actin in sample A was 6.82 x 10<sup>6</sup>. The transfection was 400,000 cells per well, sample A was transfected with 10uL of viral stock diluted 1:100.</p>
<p><strong>How do I calculate the virus titre per mL from this?</strong></p>
<p>I have been given the formula: WPRE Qty / (b-act Qty*0.5) * cells in well (400k) * dilution factor (100), but am struggling to figure out a) why b-act Qty is divided by 2, b) whether the result would be virus titre per uL or per 10uL (transfection volume) and c) how beta-actin can have almost 10<sup>7</sup> copy numbers consistently across all samples when there were only supposed to be about 10<sup>5</sup> cells...</p>
| [
{
"answer_id": 17133,
"pm_score": 1,
"text": "<p>Having gained a lot more experience with how research works, I can actually answer myself now:</p>\n\n<p>a) beta-actin quantity is divided by 2 because it is a human gene and hence present twice in mammalian cells, dividing it by 2 gives an estimate of th... | [
{
"answer_id": 10283,
"pm_score": 1,
"text": "<p>I have 2 doubts here. </p>\n\n<ol>\n<li>You obtain your viruses from the media whereas Actb measurements can be performed only in the cell lysates. </li>\n<li>Actb is just a reference to normalize for the cell count: higher the cell count higher will be t... |
10,294 | <p><img src="https://i.stack.imgur.com/Ukppe.jpg" alt="enter image description here"></p>
<p>I have two questions pertaining to this pedigree
I believe it to be an autosomal recessive trait.</p>
<ol>
<li><p><strong>The probability that individuals IV-1 and IV-2 would give rise to an affected individual would be:</strong>
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24</p></li>
<li><p><strong>Suppose individual IV-2 was unaffected. The probability of his marriage giving rise to an affected child would be:</strong>
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24</p></li>
</ol>
<p>I worked on this problem for the last hour or so and figured up question 1 to be 1/2 and question two to be 1/4. I don't feel this is correct. I feel like I am missing something. If you don't mind showing the calculations for how you came about an answer that would be greatly appreciated.</p>
| [
{
"answer_id": 10298,
"pm_score": 3,
"text": "<h1>Question 1</h1>\n\n<p>Okay, so I'll go through my own process for you here step by step, moving down the tree. Here's an annotated version of your diagram with my own thoughts (it's been a while since I've done this but should hopefully be accurate):</p... | [
{
"answer_id": 17432,
"pm_score": -1,
"text": "<p>From my own point of view, I think the answer to no. 1 is a 50% chance i.e. 2 out of 4. My reason is because, IV-1 could be a carrier of the trait and since the IV-2 is affected that means 2 will be affected.\nNo 2. For the second question, the answer is... |
10,313 | <p>FADH<sub>2</sub> is produced in the conversion of Succinate to Fumarate in the tricarboxylic acid cycle. Why is this so? Why not NADH?</p>
| [
{
"answer_id": 10315,
"pm_score": 4,
"text": "<p>In general, $\\ce{NADH}$ and $\\ce{FADH2}$ are coenzymes. The structure of the main part of an enzyme determines which coenzyme or which prosthetic group will work with the concerned enzyme. Unlike most other TCA cycle enzymes, Succinic Dehydrogenase invo... | [
{
"answer_id": 55840,
"pm_score": 0,
"text": "<p>I think that flavoproteins are more flexible than NAD. NAD carries exactly 2 electrons, while FAD can carry either 1 or 2 electrons. This is important, as succinate dehydrogenase is at the crossroad between the Krebs cycle and the electron transport chain... |
10,351 | <p>Consciousness is an electrical and chemical interaction in the brain, caused by neurons firing and chemical interactions. How does a mechanical "force" cause this to stop working?</p>
<p>i.e. How does a mechanical action (such as a punch to the head) cause this electrical/chemical system to stop working (leading to unconsciousness)?</p>
| [
{
"answer_id": 10393,
"pm_score": 4,
"text": "<p>Mechanical force can compress neurons and cause action potentials as you probably experienced in the form of hitting the funny bone. Strong enough acceleration of the brain tissue may be causing massive excitation of neurons as indicated by <a href=\"http... | [
{
"answer_id": 10388,
"pm_score": 0,
"text": "<p>A hit can break blood vessels, produce inflammation and exert pressure in the brain tissue. Pressure in fact can alter the composition and distribution of the cerebrospinal fluid. Since the nervous cells are very sensible to oxygen deficit and the composi... |
10,404 | <p>Mature mammalian erythrocytes have all the characteristics of a eukaryotic cell except that they don't have a nucleus, they don't have any cell organelles. Does this mean that erythrocytes are classified as prokaryotic? </p>
| [
{
"answer_id": 10406,
"pm_score": 5,
"text": "<p>No. Nobody considers red blood cells to be prokaryotic, perhaps most importantly because they are <em>part</em> of a eukaryotic organism. Red blood cells begin life with the full complement of organelles, including a nucleus and mitochondria, but our RB... | [
{
"answer_id": 71915,
"pm_score": 2,
"text": "<p>Note that the reason mature erythrocytes are eukaryotic is the same reason snakes and dolphins are tetrapods. \"Eukaryote\" and \"Tetrapod\" are clades, i.e. groups defined by common descent, which leads to pervasive similarities within the group and diff... |
10,551 | <p>In graphs of survivorship curves, I'm seeing that the Type II curves are straight lines, and the supplementary text says that the mortality rate is constant (i.e. the slope of the line is constant). However, it's also clearly stated that the y-axis is a logarithmic scale, which means that the original Type II curve is exponential:
$$\ln y=-rx+b$$
$$y=Ae^{-rx}$$</p>
<p>This implies that the real mortality rate is not constant, but changes as $$y'=-Ar(e^{-rx})$$
How are we defining the word <em>rate</em>, anyway?</p>
| [
{
"answer_id": 10555,
"pm_score": 4,
"text": "<p>$r$ is the individual mortality rate per time step. Survivorship curves (plotted on a log scale) show the proportion of individuals surviving with time, and with a Type II curve a constant proportion is dying at each time step (constant mortality with age... | [
{
"answer_id": 10589,
"pm_score": 0,
"text": "<p>This is a statistical property of the curve - in time to event analysis (which is what a survivorship curve is), a constant hazard (the instantaneous probability of an event occurring in time t given it has not occurred already) will yield an exponentiall... |
10,570 | <p>I am doing an experiment in which I am growing <em>S. mutans</em> in agar dishes, and I am not sure how I would measure the growth of the <em>S. mutans</em>. I am also not sure if I would do this by measuring cell mass or by cell count. Any ideas?</p>
| [
{
"answer_id": 10555,
"pm_score": 4,
"text": "<p>$r$ is the individual mortality rate per time step. Survivorship curves (plotted on a log scale) show the proportion of individuals surviving with time, and with a Type II curve a constant proportion is dying at each time step (constant mortality with age... | [
{
"answer_id": 10589,
"pm_score": 0,
"text": "<p>This is a statistical property of the curve - in time to event analysis (which is what a survivorship curve is), a constant hazard (the instantaneous probability of an event occurring in time t given it has not occurred already) will yield an exponentiall... |
10,572 | <p>I fell over on my bicycle trying to avoid running over a rattlesnake, and ended up badly skinning my knee. It immediately began to bleed, but soon clotted.</p>
<p>It has been <strong>2 days</strong> now and it has formed a thin scab and is healing well as far as I can tell. I was chilly from the air conditioning, and I noticed the wounded knee was much warmer than the healthy knee. It was very warm, while the other was rather cold to the touch.</p>
<p>I read <a href="https://biology.stackexchange.com/a/8741/1827">here</a> about skin healing, and thought, maybe it is because the blood rushed there to clot the wound. But, the wound is already clotted and sealed and the worst is over. So my question is:</p>
<ul>
<li>Why is my wound and the area around it so much warmer <em>days</em> after the injury?</li>
</ul>
| [
{
"answer_id": 10577,
"pm_score": 4,
"text": "<p>This is a normal part of the inflammatory process. Inflammation is your body's localised defensive response to tissue injury of any kind, and it is characterised by four cardinal signs- redness, swelling, heat and pain (severe inflammation involves a fift... | [
{
"answer_id": 10574,
"pm_score": 2,
"text": "<p>The increase in temperature is due to dilatation of the capillaries in an area of inflammation, here brought about by trauma and is one of the five cardinal signs of inflammation'. This is a natural process which helps to bring in more blood supply for re... |
10,662 | <p>What determines if a metal is suitable for transplantation such as in the hip? What I am most interested in however is why might some metals be toxic to animals once in the body?</p>
| [
{
"answer_id": 10668,
"pm_score": 3,
"text": "<p>There are a number of reasons why a given metal may be toxic to an animal:</p>\n\n<ul>\n<li>Radioactive metals are the easy ones.</li>\n<li>Some metals can affect the normal biosynthetic pathways within the body. Lead is a good example of this, as it can... | [
{
"answer_id": 10671,
"pm_score": 1,
"text": "<p>I think @Amory answer is a good one but I would like to add a new point for the last part of your question. </p>\n\n<p>Our normal body cells can recruit the immune system when there is infection but the transplants can not. Some findings suggest that bac... |
10,683 | <p>Imagine that I built a concrete-walled pool the size of a football field and filled it with fresh water - obtained from another lake but free of bacteria, plantlife, eggs, etc.</p>
<p>Would it ever, over time, become a life-filled "lake" - with fish, amphibians, algae, plants and other water-dwellers?</p>
<p>If yes, how?</p>
<p>What would the chain of events look like? I'm assume plant-life would get there first but how would it develop an established eco-system?</p>
<p>Please re-tag as appropriate as I am new to this SE site.</p>
| [
{
"answer_id": 10686,
"pm_score": 4,
"text": "<p>if the pool were just sitting out in open air, on earth and all that good stuff, it certainly would, given enough time. </p>\n\n<p>This thought experiment is in the same vein that inspired Darwin when he reflected on his experiences on his visit to the Ga... | [
{
"answer_id": 10691,
"pm_score": 2,
"text": "<p>I recently dug a pond in a forest, and the first things to happen was not actually plant life. First I found small aquatic animals that lived in the mud, then I found salamander axolotyls and water striders, and crawdads. Salamanders (especially newts), w... |
10,694 | <p>I just learned that in video cameras, every frame of the video has its own shutter speed.</p>
<p><a href="http://www.mediacollege.com/video/camera/shutter/shutter-vs-fps.html" rel="noreferrer"><img src="https://i.stack.imgur.com/UZPfP.png" alt="shutter speed vs framerate">
</a></p>
<p>And I know how frame-rate in human eye works out, well, not completely, hence the question.</p>
<p><a href="http://en.wikipedia.org/wiki/Frame_rate" rel="noreferrer">http://en.wikipedia.org/wiki/Frame_rate</a></p>
<blockquote>
<p>The human eye and its brain interface, the human visual system, can process 10 to 12 separate images per second, perceiving them individually.</p>
</blockquote>
<p>How much (or what is the equivalent of) shutter-speed in those individual images?</p>
| [
{
"answer_id": 21529,
"pm_score": 3,
"text": "<p>The light receptor of the eye is a protein called <a href=\"https://en.wikipedia.org/wiki/Rhodopsin\" rel=\"nofollow noreferrer\">Rhodopsin</a>. To me the equivalent of shutter speed for the eye is the (de)<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/127... | [
{
"answer_id": 10734,
"pm_score": 1,
"text": "<p>Not all of your rods/cones fire at any given moment. Exception is when a bright flash of light is viewed. Recovery time from the resulting flash blindness is pretty slow -- seconds. But there's some photobleaching there, so maybe that's not fair.</p>\n... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.