qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
9 | <p>I shipped 10 µL of my vector miniprep to a collaborator in a 1.5 mL eppendorf parafilmed shut and stuffed into a 50 mL conical with some paper-towel padding. However, something happened on the way and there was nothing (no liquid) in the tube when it arrived. They didn't make any comments about the microcentrifuge... | [
{
"answer_id": 36,
"pm_score": 5,
"text": "<p><strong>Summary</strong></p>\n\n<ul>\n<li>the 10 uL of plasmid miniprep may have been splattered in the cap of the tube (AnnaF)</li>\n<li>the eppendorf tube may have depressurized during air shipment and allowed the 10 uL to escape and evaporate</li>\n<li><s... | [
{
"answer_id": 17,
"pm_score": 4,
"text": "<p>Did they try to centrifuge the tube when it got there to push all the liquid to the bottom? I know that especially when working with such little amounts that even shaking it up a little can disperse the contents all over the tube.\nWe have received plasmids ... |
38 | <p>I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found:</p>
<ol>
<li><a href="http://openwetware.org/wiki/One_step_%27miniprep%27_method_for_the_isolation_of_plasmid_DNA" rel="nofollow">Using phenol/chloroform</a>
<ul>
<li>extract with phenol:chloroform:isoamylalcohol,</li>
<... | [
{
"answer_id": 55,
"pm_score": 3,
"text": "<p>In my experience, the P:C:I method will get you higher yields, and is a bit more simple (in steps and chems involved), but as @Mad Scientist has said, phenol use might be an issue. It depends on the age of your students.</p>\n"
}
] | [
{
"answer_id": 47,
"pm_score": 3,
"text": "<p>The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation <a href=\"http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1667\">similar to this one</a>. Nothing terribly toxic or requiring a fume hood (at le... |
58 | <p>We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic distance is probably less than 200 base pairs.</p>
<p>The two genes are expressed in opposite directions towards ea... | [
{
"answer_id": 55,
"pm_score": 3,
"text": "<p>In my experience, the P:C:I method will get you higher yields, and is a bit more simple (in steps and chems involved), but as @Mad Scientist has said, phenol use might be an issue. It depends on the age of your students.</p>\n"
}
] | [
{
"answer_id": 47,
"pm_score": 3,
"text": "<p>The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation <a href=\"http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1667\">similar to this one</a>. Nothing terribly toxic or requiring a fume hood (at le... |
90 | <p>I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional double-helix DNA as we know it? Have any serious alternatives been theorized?</p>
| [
{
"answer_id": 106,
"pm_score": 6,
"text": "<p>To follow up what mbq said, there have been a number of \"origin of life\" studies which suggest that RNA was a precursor to DNA, the so-called \"RNA world\" (1). Since RNA can carry out both roles which DNA and proteins perform today. Further speculations... | [
{
"answer_id": 95,
"pm_score": 5,
"text": "<p>There has been a recent report on Science, which had much return in the general press, in which a bacteria was identified that could live in an environment where arsenic was subsituted to phosphorus (one of the components of DNA, forming the backbone of the ... |
257 | <p>I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge is weak. </p>
<p>I'm finding it impossible to know where to look in a big book like Alberts, or to read Lodish with... | [
{
"answer_id": 266,
"pm_score": 4,
"text": "<p>MIT's OCW is weak when it comes to biology videos. </p>\n\n<p>UC Berkeley has some good video content for molecular and cell biology.</p>\n\n<ul>\n<li><p>See, for example, this playlist:\n<a href=\"http://www.youtube.com/playlist?list=59C08AE05E752758\">ht... | [
{
"answer_id": 258,
"pm_score": 3,
"text": "<p>This one is not precisely molecular and cell biology, but rather systems biology. It might help you as some kind of introduction, though:</p>\n\n<p><a href=\"http://www.youtube.com/watch?v=Z__BHVFP0Lk\">Systems biology lecture 1</a></p>\n\n<p>Also, if you a... |
328 | <p>In what ways has DNA been studied to see if there a "programmable" aspect to it? </p>
<p>Has nature produced anything resembling a Turing machine within the cell, perhaps using the "junk DNA" as its code? I expect nature's way would probably be very round-about and not compact.</p>
<p>NOTE: I am not asking about b... | [
{
"answer_id": 427,
"pm_score": 5,
"text": "<p>Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function. </p>\n\n<p>In the human genome, out of ~5 billion bases <a href=\"http://www.ornl.gov/sci/techresources/Human_Genome/faq/genenumber.shtml\">there are ... | [
{
"answer_id": 418,
"pm_score": 3,
"text": "<p>By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus. The answer is \"no\" for both. Well, sort of.</p>\n\n<p>Does noncoding DNA contain information? By definition, no. There are probab... |
344 | <p>There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of <a href="https://biology.stackexchange.com/questions/186/is-telomere-length-a-reliable-measure-of-health-lifespan">telomere length</a> during ce... | [
{
"answer_id": 362,
"pm_score": 6,
"text": "<p>The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.</p>\n\n<p>To set up the argument, we need two things:\nFirst, each individual has got a 'reproductive poten... | [
{
"answer_id": 404,
"pm_score": 3,
"text": "<p>Once could argue that we die because it is advantageous to get rid of mature individuals once they have reproduced. Because mature individuals have no more offspring to convey beneficial genes, those offspring which will benefit from knocking off their anc... |
378 | <p>I am very interested in the evolution of the evolution process itself. There are of course a lot of things that influence how evolution will work, but for this question, I am interested in things that are only related to the evolution process. Examples could be increase chance of mutations in newborns, change in rep... | [
{
"answer_id": 382,
"pm_score": 6,
"text": "<p>Bacteria such as E. coli are known to increase their mutation rate (by switching to a more error prone polymerase among other things) when under stress. This can mean being placed in a medium where it's not adapted to grow (<a href=\"http://www.ncbi.nlm.nih... | [
{
"answer_id": 379,
"pm_score": 4,
"text": "<p>I think this falls into your criteria but correct me if i'm wrong :).</p>\n\n<p>The <a href=\"http://en.wikipedia.org/wiki/HIV\">HIV</a> reverse transcriptase protein has evolved to have relatively low fidelity (leading to a high mutation rate in replicated... |
450 | <p>I know plants are green due to chlorophyll.</p>
<p>Surely it would be more beneficial for plants to be red than green as by being green they reflect green light and do not absorb it even though green light has more energy than red light.</p>
<p>Is there no alternative to chlorophyll? Or is it something else?</p>
| [
{
"answer_id": 462,
"pm_score": 8,
"text": "<p>Surely it would be even more beneficial for plants to be black instead of red or green, from an energy absorption point of view. And <a href=\"http://en.wikipedia.org/wiki/Solar_cell\" rel=\"noreferrer\">Solar cells</a> are indeed pretty dark.</p>\n\n<p>But... | [
{
"answer_id": 451,
"pm_score": 5,
"text": "<p>I believe it is because of a trade off between absorbing a wide range of photons and not absorbing too much heat. Certainly this is a reason why leaves are not black - the enzymes in photosynthesis as it stands would be denatured by the excess heat that wo... |
452 | <p>My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. Now in my AP Biology class we finally learned the specifics of how oxygen is used in the <a href="http://www.science... | [
{
"answer_id": 456,
"pm_score": 6,
"text": "<p>Oxygen is actually highly toxic to cells and organisms – <a href=\"http://en.wikipedia.org/wiki/Reactive_oxygen_species\" rel=\"noreferrer\">reactive oxygen species</a> cause <a href=\"http://en.wikipedia.org/wiki/Oxidative_stress\" rel=\"noreferrer\">oxida... | [
{
"answer_id": 455,
"pm_score": 5,
"text": "<p><a href=\"http://en.wikipedia.org/wiki/Superoxide\" rel=\"noreferrer\">Superoxide</a>, O<sub>2</sub><sup>−</sup> is created by the immune system in <a href=\"http://en.wikipedia.org/wiki/Phagocyte\" rel=\"noreferrer\">phagocytes</a> (including neutrophils, ... |
551 | <p>I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I g... | [
{
"answer_id": 556,
"pm_score": 4,
"text": "<p>It doesn't have very many reviews, but <a href=\"http://rads.stackoverflow.com/amzn/click/073820577X\">The Epic History of Biology</a> sounds like it's perfect.</p>\n\n<p>Flipping through the first chapter in the preview, it doesn't seem overly technical in... | [
{
"answer_id": 552,
"pm_score": 2,
"text": "<p>I don't know very many books that might be referred to as the Grand History of Biology or anything like that. That's...a big topic. Really big. How about some suggestions for good Biology/Medical History books accessible to lay people:</p>\n\n<ul>\n<li>And ... |
594 | <p>Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?</p>
| [
{
"answer_id": 615,
"pm_score": 6,
"text": "<p>I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very importan... | [
{
"answer_id": 597,
"pm_score": 4,
"text": "<p>As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A <a href=\"http://www.nature.com/news/frontier-experiments-tough-science-1.9723\">recent article</a> speculates that the <a href=\"http://en.wikipedia.org/wiki/We... |
623 | <p>From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to "accelerate" as we age.</p>
<p>Digging a little, most explanations I found basically reduced this to two reasons:</p>
<ul>
<li>As we age physically, a time frame of constant length becomes ever sm... | [
{
"answer_id": 1240,
"pm_score": 6,
"text": "<p>This is not really a biological answer, but a psychological one:</p>\n\n<p>One important fact to consider is that the perception of time is essentially a recollection of past experience, rather than perception of the present.</p>\n\n<p>Researchers who stud... | [
{
"answer_id": 713,
"pm_score": 3,
"text": "<p>There may be some clues in neurobiology.</p>\n\n<p>A possibility may be that a person's general emotional state may affect their perception of the passage of time, as argued in this <a href=\"http://www.robinson.cam.ac.uk/academic/robinson_rationality_luchi... |
757 | <p>As far as I understand, various abilities like flying, sight, hearing etc. were caused by slow evolution, where those with a greater ability to to these things had better chance of survival. (If this assumption is wrong, then I am happy to delete this question). </p>
<p>Are there, however, any documented examples o... | [
{
"answer_id": 7921,
"pm_score": 4,
"text": "<p>@kmm and @shigeta provided you with a nice observational account of sudden leaps in large organisms. However, if you want to look at where this is the norm and try to build a mathematical theory then you need to look at something much smaller; the prime ca... | [
{
"answer_id": 759,
"pm_score": 4,
"text": "<p><a href=\"http://rsbl.royalsocietypublishing.org/content/2/4/521.full?sid=36ce9d7f-9cc9-4c07-92f4-4808ec90f451\">Zuk et al. (2006)</a> document the rapid evolution of song-less crickets in a population of crickets that previously used song for courtship.</p... |
762 | <p>Humans have, in a relatively short amount of time, evolved from apes on the African plains to upright brainiacs with nukes, computers, and space travel. </p>
<p>Meanwhile, a lion is still a lion and a beetle is still a beetle.</p>
<p>Is there a specific reason for this? Do we have a particular part of brain that... | [
{
"answer_id": 766,
"pm_score": 6,
"text": "<p>We have the <a href=\"http://en.wikipedia.org/wiki/Human_accelerated_regions\">Human Accelerated Regions</a> (HARs) which are some of the most rapidly evolving RNA genes elements. While heavily conserved in vertebrates, they go haywire in humans and are lin... | [
{
"answer_id": 767,
"pm_score": 3,
"text": "<p>The ability to walk on two legs was hugely significant in human evolutionary development. This led to the hands being freed up to develop into precision tools rather than having to be durable for walking on rough terrain. Increased dexterity in the hands l... |
832 | <p>A student asked me this the other day and I thought that I would ask it again here. If one organism is said to be "more evolved" than another, what exactly does this mean?</p>
| [
{
"answer_id": 833,
"pm_score": 6,
"text": "<p>\"More evolved\" is actually meaningless in all contexts. See terdon's answer for a good explanation.</p>\n\n<p>In the strictest sense, an organism can be said to be more divergent than another when comparing both to an outgroup, such that there is an infer... | [
{
"answer_id": 834,
"pm_score": 4,
"text": "<p>I cannot improve on Thomas Ingalls' description of when \"more evolved\" is appropriately used, but the inappropriate/lazy use of the phrase is so prevalent that it deserves further comment. In my experience, the most common use of the phrase \"more evolved... |
884 | <p>This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.</p>
<p>Regarding Evolution, nothing, absolutely nothing, that a person does to herself in life can ... | [
{
"answer_id": 886,
"pm_score": 5,
"text": "<p>The assertion \"You cannot change in life what will be genetically inherited in any possible way\" is true, as you cannot (healthily) change the DNA in your germ cells.</p>\n\n<p>However, the assertion \"You cannot change in life what will be inherited in a... | [
{
"answer_id": 887,
"pm_score": 4,
"text": "<p>In general, Darwin's theory has been supported over and over again by experiments - our modern understanding of evolution is fundamentally what Darwin suggested. However, apart from appreciating many more details than Darwin ever could have, we also now kno... |
1,228 | <p>I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (<a href="http://www.sciencedirect.com/science/article/pii/S0092867400804031">Skowrya et al., 1997</a>). I have heard of phosphorylation sites, but I can't find out wh... | [
{
"answer_id": 1231,
"pm_score": 5,
"text": "<p>Phosphorylation can occur on specific amino acids only, what you have called phosporylation sites. These amino acids are Ser, Tyr, Asp, Thr and His. In theory any of these amino acids may be phosphorylated, but in reality it may not actually occur for a nu... | [
{
"answer_id": 1230,
"pm_score": 3,
"text": "<p>Phosphorylation requires exposed serine, threonine, tyrosine, or histidine residues (in eukaryotes). This is because the transfer of phosphate groups to proteins is mediated by a class of proteins called kinases. Kinases can have broad or specific activi... |
1,446 | <p>I don't know if this question applies to only humans but why can cones see much greater detail than rods? Is it possible to have a rod that can detect light intensity and color?</p>
| [
{
"answer_id": 1461,
"pm_score": 6,
"text": "<p>The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).\n<img src=\"https://i.stack.imgur.com/fF2eT.png\" alt=\"Spectral sen... | [
{
"answer_id": 1454,
"pm_score": 4,
"text": "<p>Cone cells are each connected to their own neurone. This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon. However in order to improve low light vision, multiple r... |
1,448 | <p><a href="http://www.uniprot.org/uniprot/P36659">CbpA</a> is DNA binding protein found in E. coli and binds non-specifically to curved DNA (<a href="http://dx.doi.org/10.1111/j.1365-2958.2010.07292.x">Cosgriff et al., 2010</a>), when the bacterium is in a static phase of growth. </p>
<p>The use of "curved DNA" confu... | [
{
"answer_id": 1461,
"pm_score": 6,
"text": "<p>The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).\n<img src=\"https://i.stack.imgur.com/fF2eT.png\" alt=\"Spectral sen... | [
{
"answer_id": 1454,
"pm_score": 4,
"text": "<p>Cone cells are each connected to their own neurone. This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon. However in order to improve low light vision, multiple r... |
1,495 | <p>I know death and cancer doesn't hurt humans' reproductive success. It's not helping either.</p>
<p>Why do we die? Why dying humans (all of us) are common? What's the point of dying?</p>
| [
{
"answer_id": 1496,
"pm_score": 6,
"text": "<p>Death is not only for humans. All 'complicated enough' organisms die (with a notable exception of <a href=\"http://en.wikipedia.org/wiki/Hydra_(genus)\" rel=\"nofollow noreferrer\">Hydra</a>, though you may argue when it comes to the complexity). It is is ... | [
{
"answer_id": 1497,
"pm_score": 3,
"text": "<p>Who is to say that having living Humans isn't hurting our reproductive success? Older non-reproducing humans cost the human network valuable resources and take up a sizeable portion of our living niche. Metabolically unstreamlined aged organisms are certai... |
1,515 | <p>This is my first post here, so please be gentle. I recently learned that I have Rh- blood (I'm A-), and was idly looking into blood types on Wikipedia. I was surprised to find that relatively few (~15% of all) humans have it, and most of those seem to be European. Looking just a little further, I found a bunch of cr... | [
{
"answer_id": 1539,
"pm_score": 4,
"text": "<p>Your question has many questions in it. </p>\n\n<p>As for the evolution of Rh factor, <a href=\"http://jhered.oxfordjournals.org/content/91/3/205.abstract\">Blancher and Apoil (2000)</a> attribute the high level of sequence similarity (92%) of the two <em>... | [
{
"answer_id": 9033,
"pm_score": -1,
"text": "<p>It's my opinion the rh antigen developed from toxoplasmosis infection. I only recently learned that this protozoan can actually insert its genes into a host's genome. Once it's in the genes, it can be passed in the germline. Toxoplasmosis can infect all p... |
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