qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
1,559 | <p>I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session files so they're email-able (a.k.a. not 200 MB) and ease the burden on my POS computer.</p>
<p>I currently have a Python script that can <code>fft</code> (CCP4) to create the map and <code>mapmask</code> to fix unit cell tiling issues. What I want to add now is something that can take a PDB file and strip out most of it except, for example, residues within 10 Å of #123.</p>
<p>I've been looking at <a href="http://www.csb.pitt.edu/ProDy/index.html">ProDy</a>, but not quite sure where to start. I would also be open to using something in the CCP4 toolkit.</p>
| [
{
"answer_id": 1598,
"pm_score": 4,
"text": "<p><a href=\"http://www.csb.pitt.edu/ProDy/index.html\">ProDy</a> works quite well, especially from within an existing Python script. </p>\n\n<p>The following code takes an existing PDB file, performs some <a href=\"http://www.csb.pitt.edu/prody/reference/at... | [
{
"answer_id": 1566,
"pm_score": 3,
"text": "<p>With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).</p>\n"
}
] |
1,568 | <p>In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating. </p>
<p>I've usually substituted LB medium for this step for easy retransformations, but I gather that the SOC medium is supposed to make some difference in efficiency, or else the simpler LB medium would be recommended in the protocols.</p>
<p>Why is SOC medium used for transformations? What difference does substituting with LB medium cause for the transformation efficiency? </p>
| [
{
"answer_id": 1570,
"pm_score": 5,
"text": "<p>To summarize from <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/6345791\" rel=\"nofollow noreferrer\">Hanahan's paper</a> (see below for reference), he carried out a systematic review of conditions necessary to improve transfection efficiency. Among the con... | [
{
"answer_id": 1569,
"pm_score": 3,
"text": "<p>(<a href=\"http://en.wikipedia.org/wiki/Super_Optimal_Broth\" rel=\"nofollow noreferrer\"><strong>Super Optimal</strong> broth with <strong>Catabolite</strong> Repression</a>) SOC media contains glucose whereas <a href=\"http://en.wikipedia.org/wiki/Lysoge... |
1,579 | <p>I was watching the video at this link:
<a href="http://www.bbc.co.uk/news/science-environment-17436365" rel="noreferrer">http://www.bbc.co.uk/news/science-environment-17436365</a></p>
<p>The speaker says that a cell is taken and its original DNA content is stripped out and replaced with synthetic DNA.</p>
<p>Does this mean scientists are not able to create a synthetic cell yet? Is this why they use existing cells, stripping them out and replacing the DNA?</p>
| [
{
"answer_id": 1583,
"pm_score": 4,
"text": "<p>The J. Craig Venter Institute recently has indeed created a synthetic, self-replicating cell (see the <a href=\"http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-ins... | [
{
"answer_id": 2504,
"pm_score": 2,
"text": "<p>There is this guy, Martin Hanczyc, working on protocells to better understand how the beginning of life occurred. He makes synthetic protocells. They don't have any DNA in them but they are pretty cool and maybe the beginnings to making synthetic cells. Pe... |
1,580 | <p>I have a biology assignment and we have to explain various methods and strategies for conservation, two of which are:</p>
<blockquote>
<p>Biological control<br>
Introduced Species</p>
</blockquote>
<p>What is the difference between these? I was under the impression that they are essentially the same thing – <a href="http://en.wikipedia.org/wiki/Biological_control" rel="nofollow">biological control</a> being the introduction of species to predate pests (eg. the abysmal failure of the cane toad).</p>
<p>Any clarification would be great.</p>
| [
{
"answer_id": 1600,
"pm_score": 3,
"text": "<p>After talking to my teacher, he said that biological control is the introduction of species to control another species, however species may be introduced for other reasons (the \"Introduced Species\" method), such as to \"assist an ecosystem cope, flourish... | [
{
"answer_id": 7662,
"pm_score": 2,
"text": "<p>Biological control does not have to be with an introduced species. It can also be accomplished by either artificially inflating the number of existing predators.</p>\n\n<p>E.g. Spruce bud worm has a natural predator in the form of a tiny wasp. But budwo... |
1,585 | <p>Every bloody protocol suggests adding in DTT when doing <em>in vitro</em> RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein we care about is the T7 polymerase, why is this necessary.</p>
| [
{
"answer_id": 1586,
"pm_score": 4,
"text": "<p>A quick search on T7 cysteines gave some clues:</p>\n\n<blockquote>\n <p>Bacteriophage T7-induced DNA polymerase is composed of a 1: 1\n complex of phage-induced gene 5 protein and Escherichia coli\n thioredoxin. Preparation of active subunits in the ... | [
{
"answer_id": 96155,
"pm_score": 1,
"text": "<p>I always assumed it was because DTT is useful in inactivating ribonucleases (by reducing their disulfides) which are notoriously stable and pervasive. It would be pretty unfortunate to get your RNA synthesized only to have it immediately be destroyed by a... |
1,588 | <p>I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible.
But I also learned from biochemistry that they <em>are</em> digestible. What is the reason for this, or is it true at all?</p>
| [
{
"answer_id": 1592,
"pm_score": 4,
"text": "<p>Trans fatty acids are digestible, but they cause an increase in LDL and a decrease in HDL, which is the leading mechanism for atherosclerosis. So, they increase the risk of a cardiac infarct. </p>\n\n<p>LDL means Low Density Lipoprotein, it's one of the 5 ... | [
{
"answer_id": 10611,
"pm_score": 0,
"text": "<p>Studies have been done in which saturated fats and cis-unsaturated fats in the diet were replaced with trans-fatty acids. In all cases there were increases in LDL cholesterol, blood triglycerides and Lp(a) lipoprotien, and decreases in HDL cholesterol and... |
1,589 | <p>Many DNA isolation and protein expression protocols contain instructions to use a starter culture of E. coli that is then used to inoculate the main culture. </p>
<p>What are the advantages of using starter cultures compared to just let the bacteria grow in the same medium for a longer time? When should one use starter cultures and when can one safely skip that first culture?</p>
| [
{
"answer_id": 1590,
"pm_score": 5,
"text": "<p>Growth can be quite slow for some species under certain conditions when the concentration of cells is too low. Log-phase growth is powerful, and so one would like to keep cells in this state for the experiment at hand. Different genes are expressed then co... | [
{
"answer_id": 1599,
"pm_score": 3,
"text": "<p>I agree that a starter culture would out-comete a contaminant (especially if there is no antibiotic in the media).</p>\n\n<p>Another advantage of inoculating with starter culture is that your results concerning plasmid preps or preparing competent cells wi... |
1,601 | <p>Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be performed.</p>
<p>I've seen anything from precipitating at room-temperature and centrifugating immediately without any delay to precipitating at -20 °C over night in various protocols.</p>
<p>Is there any published data about the influence of duration and temperature on the yield of the nucleic acid precipitation?</p>
| [
{
"answer_id": 1607,
"pm_score": 4,
"text": "<p>I always did mine at -80 C, but I never compared the results to other protocols (<em>I don't fix what's not broken</em>). But, I was curious about the same thing, so I looked around. I found one paper discussing this: <a href=\"http://www.ncbi.nlm.nih.gov/... | [
{
"answer_id": 1603,
"pm_score": 2,
"text": "<p>As a first year molecular biology student, I did a class project on this very question: trying to see if buffer temperature had an effect on yield during DNA precipitation. This is a far cry from peer reviewed research, but my finding was that there was n... |
1,635 | <p>I recently came across <a href="http://www.nature.com/news/cyborg-snails-power-up-1.10210" rel="nofollow">this article</a> from Nature. In it, it states that the snails have "tiny biofuel cells that extract electrical power from the glucose and oxygen in the snail’s blood", and that the power obtained is dependent on "how quickly sugar and oxygen can be taken from the creatures' blood". They go on to say that the power obtained decreases over time, and that these implants could power future pacemakers in humans. </p>
<p>Would this application in humans require that a patient eats more and "breathes more" than average? Why does the power output decrease over time, and couldn't that potentially lead to the malfunctioning of a pacemaker?</p>
<hr>
<h2>References</h2>
<ul>
<li><strong>Van Noorden, Richard.</strong> <em>“Cyborg Snails Power Up.”</em> Nature (March 12, 2012). <a href="http://www.nature.com/doifinder/10.1038/nature.2012.10210" rel="nofollow">http://www.nature.com/doifinder/10.1038/nature.2012.10210</a>.</li>
</ul>
| [
{
"answer_id": 1639,
"pm_score": 4,
"text": "<p>You'd think if such devices were used in humans, they wouldn't require a change of lifestyle.</p>\n\n<p>They don't say the power <em>always</em> decreases over time:</p>\n\n<blockquote>\n <p>Katz’s snails, for example, produced up to 7.45 microwatts, but ... | [
{
"answer_id": 1645,
"pm_score": 2,
"text": "<blockquote>\n <p>Would this application in humans require that a patient eats more and \"breathes more\" than average? </p>\n</blockquote>\n\n<p>From the cellular standview, each glucose and O<sub>2</sub> molecule that you substract to the cell for use in a... |
1,638 | <p>Please forgive the obviously silly appearance of this question, and/or of the tenor which may come across as flippant or dismissive of real world suffering. My intention is none of the above.</p>
<p>As a layperson, I have always understood that the expression of our various colds/flus etc, while frequently mis-understood as being caused by the virus, are actually just manifestations of our own immunity fighting same. In other words, all the snot, and fever and inflammation are not caused *by the virus, they are a reaction *to the virus, as we fight it off. </p>
<p>My question then is why do people with AIDS (or similar immunity destroying affliction) appear sick? If they have weak or non-existent immune systems, following the above logic, would one expect to see them passing away while looking entirely healthy? </p>
| [
{
"answer_id": 42224,
"pm_score": 5,
"text": "<p>Many of the symptoms of disease are indeed related to inflammation, but inflammation depends heavily (though not solely) on the innate immune response. Patients with AIDS and some of the other immunodeficiencies lose their adaptive immune response, not t... | [
{
"answer_id": 1643,
"pm_score": 4,
"text": "<p>They appear sick because they <em>are</em> sick, but with other, opportunistic infections. The \"immune deficiency\" part of AIDS means that the immune system is not functioning normally and, thus, is unable to protect them. Typical illnesses that are more... |
1,686 | <p>In practice, when you have vasoconstriction of the glomerular capillaries and subsequently an increase in blood pressure, glomerular filtration rate increases. However, this seems counterintuitive to Bernoulli's principle. </p>
<p>During vasoconstriction, because the radii of the capillaries are getting smaller, we should expect an increase in flow rate and blood velocity. According to Bernoulli's principle, the outward hydrostatic pressure should drop. </p>
<p>How does this lead to an increase in filtration rate?</p>
| [
{
"answer_id": 3042,
"pm_score": 4,
"text": "<p>The previous answer isn't quite correct, because, well, blood flow is complicated and the body has autoregulatory mechanisms. As Alex mentioned, <a href=\"http://en.wikipedia.org/wiki/Vasoconstriction\" rel=\"nofollow noreferrer\">vasoconstriction</a> does... | [
{
"answer_id": 1769,
"pm_score": 1,
"text": "<p>To my knowledge, capillaries in general and the renal capillaries in glomeruli in particular do not have muscle cells to constrict. The latters have only a basal layer with podocytes lying directly on it (<a href=\"http://www.worldscibooks.com/etextbook/p1... |
1,730 | <p><a href="http://en.wikipedia.org/wiki/Trichloroacetic_acid" rel="nofollow">Trichloroacetic Acid</a> (TCA) is commonly used for protein precipitation but the wash waste needs to be neutralized prior to disposal. What exactly is required to effectively neutralize TCA waste? Do I just add caustic?</p>
| [
{
"answer_id": 1743,
"pm_score": -1,
"text": "<p>I've been fortunate to find a protocol hidden away in my lab archives.</p>\n\n<ul>\n<li>The acid waste can be accumulated for 10 days before it needs to be neutralized. The waste should be kept in a carboy in a <strong>fume hood</strong>.</li>\n<li>50 mL ... | [
{
"answer_id": 1732,
"pm_score": 2,
"text": "<p>A neutralization reaction occurs between Brönsted acids and bases to form a salt.</p>\n\n<p>In this case, you have to add a Brönsted base to neutralize your acid. If the final pH is important, you should work out the exact quantity of base to add. Otherwis... |
1,731 | <p>Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:<br>
<a href="http://dx.doi.org/10.1101/gr.130583.111" rel="nofollow"> <strong>Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV</strong>. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.</a></p>
<p>I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.</p>
| [
{
"answer_id": 1864,
"pm_score": 3,
"text": "<p>The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them. </p>\n\n<p>I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting the... | [
{
"answer_id": 7136,
"pm_score": 1,
"text": "<p>The answer is yes, not only meiotic, but any DNA double-strand breaks will be detected as long as they are processed by homologous recombination. This method (SSDS) is based on the detection of resected ssDNA ends at DSBs. The only difference for the mitot... |
1,762 | <p>Why do almost all plants in shade have a smaller stem structure and larger leaf than that same species grown in a well lit, sunny area? </p>
| [
{
"answer_id": 1763,
"pm_score": 4,
"text": "<p>I have no idea of the biological mechanisms behind what I'm about to propose. Consider this a hypothesis.</p>\n\n<p>If the purpose of the leave is to collect sunlight for photosynthesis, then the behavior you mention is predictable. I order of <em>trying</... | [
{
"answer_id": 9562,
"pm_score": 2,
"text": "<p>The main factors that affect leaf shape are water and light needs. The plant needs a certain area of leaf to provide enough energy to live, so smaller leaves means more leaves(grasses), as opposed to one enormous leaf like a lilypad. </p>\n\n<p>Generally, ... |
1,771 | <p>I'm still not sure about the mechanics that lead to rabies being incurable. I know that it can be treated before any symptoms show up, but why is it that once symptoms show the person is a dead man walking?</p>
| [
{
"answer_id": 1772,
"pm_score": 6,
"text": "<p>This is because <a href=\"http://en.wikipedia.org/wiki/Rabies\">rabies</a> is a viral infection of nervous tissue that propagates through peripheral nerves into the brain and causes brain tissue inflammation (encephalitis).</p>\n\n<p>As long as the virus i... | [
{
"answer_id": 3253,
"pm_score": 3,
"text": "<p>It may actually be curable, as shown by success stories involving the <a href=\"http://en.wikipedia.org/wiki/Milwaukee_protocol\">Milwaukee protocol</a> in which the brain is effectively shut down to allow for the immune system to eradicate the virus. In ... |
1,803 | <p>I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I don't have a stringent requirement to have a high resolution structure, I'm fine with a 6-10 angstrom resolution prediction to help me visualize the protein.</p>
<p>I'm imagining I-TASSER to get an initial idea of the topology. SWISS-MODEL doesn't find any homologs to template against. I'm trying to avoid using Robetta since it will probably take a month. What other low-resolution webservers should I test?</p>
<p>Alternatively, you could just tell me to suck it up and submit it to a month-long prediction.</p>
| [
{
"answer_id": 1812,
"pm_score": 4,
"text": "<p>Have you used <a href=\"http://toolkit.tuebingen.mpg.de/hhpred\">hhpred</a> to search for homologues? What was your criteria for defining there was no homologues? You could potentially go down to around 30% sequence identity to model. </p>\n\n<p>I would ... | [
{
"answer_id": 1804,
"pm_score": 2,
"text": "<p>Robetta's the best service I've found for a protein I'm working on that doesn't have a solved structure. It's down right now for the CASP10 competition, but I would submit it and wait. The wait time lately has been ~2 months.</p>\n"
}
] |
1,822 | <p>After I cut trees into logs and remove the branches in winter, they start growing. They sprout out and grow completely normal looking stems and leaves and maintain them all summer. The sprouts mostly appear around the cut branches. Sometimes they last all winter and grow for another year. How does it find the energy and water necessary to maintain and grow these stems without ground connection and a water source? </p>
<p><img src="https://i.stack.imgur.com/bUyEL.jpg" alt=""><img src="https://i.stack.imgur.com/O1IPT.jpg" alt=""></p>
| [
{
"answer_id": 1891,
"pm_score": 4,
"text": "<p>This is basically the same that happens after <a href=\"http://en.wikipedia.org/wiki/Pruning\">pruning</a> and involves a basic hormonal regulation mechanism in the plants.</p>\n\n<p>What happens is that the cut piece of the wood forms a new <a href=\"http... | [
{
"answer_id": 108534,
"pm_score": -1,
"text": "<p>I would guess that the nutrients and water they need to survive are still in the logs. This is Common with willow trees, and mulberry trees. I’ve cut many of these species, and it always happens. they are two very hardy trees. Do you know what kind ... |
1,827 | <p>When I checked it seemed trivial to answer: yes, all mammals can swim. But research on the internet provided different information. I found:</p>
<ul>
<li>people and primates cannot swim, but can be taught how to swim</li>
<li><a href="http://www.arkive.org/giraffe/giraffa-camelopardalis/video-ti06.html" rel="nofollow">giraffes can't swim</a></li>
<li>someone claimed elephants can't swim, but <a href="http://www.youtube.com/watch?v=-B7qlAeiXNE" rel="nofollow">this video ad shows the reverse</a></li>
<li><a href="http://answers.yahoo.com/question/index?qid=20080517194505AAbU1wf" rel="nofollow">porcupines nor rhinos</a> can't swim</li>
<li>at least some bats <a href="http://vimeo.com/2743336" rel="nofollow">can swim</a>, but according to <a href="http://www.si.edu/Encyclopedia_SI/nmnh/batfacts.htm" rel="nofollow">this source there's insufficient data</a>.</li>
</ul>
<p>Of each hit, I found other hits that claimed the reverse, sometimes with proof. Common sense tells me all mammals can swim, but is this true?</p>
| [
{
"answer_id": 1839,
"pm_score": 4,
"text": "<p>With respect to the giraffe claim, this article seems relevant:</p>\n\n<p>D. M. Henderson, D. Naish, <a href=\"http://dx.doi.org/10.1016/j.jtbi.2010.04.007\">Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational a... | [
{
"answer_id": 14699,
"pm_score": 2,
"text": "<p>I have found videos of porcupines, armadillos, anteaters.. all swimming.\nThe porcupine seemed to have no trouble at all.</p>\n\n<p>As for apes - quite well it seems. <a href=\"http://newswatch.nationalgeographic.com/2013/08/20/new-surprising-video-shows-... |
1,874 | <p>I am quite sure that there is this blood-placental barrier between the mother and the baby so that nothing (except a type of antibody) can pass through it.</p>
<p>But I remember reading somewhere that when a pregnant woman suffers an organ damage, fetus would send stem cells to the damage organ to help repair it.</p>
<p>Anything to support that?</p>
| [
{
"answer_id": 1875,
"pm_score": 5,
"text": "<p>Fetal RNA - mRNA and microRNA - has been detected in maternal blood as shown in <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/17885688\">this report</a>. Here's a second <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/22082491.1\">report</a> showing how fetus ... | [
{
"answer_id": 2315,
"pm_score": 2,
"text": "<p>I heard that as well and was skeptical at first, but apparently there IS science to support it- <a href=\"http://mblogs.discovermagazine.com/80beats/2011/11/21/helpful-mouse-fetuses-naturally-send-stem-cells-to-mom-to-fix-her-damaged-heart/\" rel=\"nofollo... |
1,894 | <p><strong>Hydroponics</strong> is a subset of hydroculture and is a method of growing plants using mineral nutrient solutions, in water, without soil.<a href="http://en.wikipedia.org/wiki/Hydroponics" rel="noreferrer"> [wikipedia]</a></p>
<p>My question is if <em>is it possible to grow any kind of plant soilless (hydroponics)?</em></p>
| [
{
"answer_id": 1895,
"pm_score": 1,
"text": "<p>Yes, There are a few i know of, a quick \"air plant\" google search will get you quiet a lot. \n<a href=\"http://en.wikipedia.org/wiki/Epiphyte\" rel=\"nofollow\">wiki 1</a>\n<a href=\"http://en.wikipedia.org/wiki/Tillandsia\" rel=\"nofollow\">wiki 2</a></... | [
{
"answer_id": 1916,
"pm_score": 3,
"text": "<p>Yes it is possible, and as far as I can see, there should not be any plant which would be impossible to grow in a such an environment, just more or less difficult, although this is just my speculation. </p>\n\n<p>I have myself grown tomatoes from only a li... |
1,901 | <p>CD47 aka the "don't eat me" signal has recently been claimed <a href="http://www.pnas.org/content/early/2012/03/20/1121623109.short">to be expressed on all tumor cells</a>. This doesn't seem to corroborate with other cell-biology experiments. On what other cells is CD47 expressed?</p>
| [
{
"answer_id": 1936,
"pm_score": 3,
"text": "<p>I don't know how extensive. Let's run a simple data query and find out: Go to <a href=\"http://www.ncbi.nlm.nih.gov/geo/\" rel=\"nofollow\">GEO</a> at NCBI. In the \"Gene profiles\" window, type CD47, and hit enter to launch the query. At the top of the re... | [
{
"answer_id": 1931,
"pm_score": 1,
"text": "<p>I can't give a comprehensive answer to this, but the <a href=\"http://en.wikipedia.org/wiki/Cluster_of_differentiation\" rel=\"nofollow\">CD</a> proteins are found on white blood cells of various types. If you think about it its impossible that a surface ... |
1,909 | <p>The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.</p>
<p>Chemical probes like diazirine and hydroxyl radicals show some bias regarding where they tend to bind. I'm realizing while I'm writing this question that NMR is a perfectly valid method to determine a solution based structure and then calculate the SASA. Similar strategies has also been used to examine structured RNAs. I'm curious about the variety of these methods and how accurate they are.</p>
| [
{
"answer_id": 2211,
"pm_score": 3,
"text": "<p>I only know of one method, but here it is. You create a sphere the diameter of the <a href=\"http://jmol.sourceforge.net/docs/surface/\" rel=\"nofollow noreferrer\">VdW radius of water, and then 'roll' it along the surface</a>. I know this as a Richards-... | [
{
"answer_id": 7764,
"pm_score": 0,
"text": "<p>I don't think SAS is a well-defined observable. (I like the work by <a href=\"http://www.cmps.lu.se/bpc/people/bertil_halle/\" rel=\"nofollow noreferrer\">Bertil Halle</a> on this and related problems.) You can measure <em>correlates</em> to SAS that have ... |
1,922 | <p>We recently found a nest in the back garden and a little bird inside. Can you help us identify it? The nest is quite small like the bird so we are wondering whether this is the parent or a baby chick. Is there anything we can do to help it or are we better off leaving it alone?</p>
<p>Update: I'm from the UK, currently in Oxfordshire to be more precise.</p>
<p><img src="https://i.stack.imgur.com/doFLY.jpg" alt="enter image description here"></p>
| [
{
"answer_id": 1924,
"pm_score": 4,
"text": "<p>It looks like a passerine bird, but I can't really tell the species without seeing the whole body. As for what to do with it, your best course of action is to leave it alone. Trust me. Once placed tissue paper over a pigeon's eggs to keep them warm, and th... | [
{
"answer_id": 1929,
"pm_score": 2,
"text": "<p>The bird needs to be left alone; that's the best help you can give it. Anything more than watching it is liable to lead to nesting failure (e.g. abandonment of the nest). The bird looks attentive and quiet, and so is most likely an adult keeping the eggs... |
1,927 | <p>Can someone provide me some information about the main method used to predict the <em>inferred electronic annotations</em> in Gene Ontology?</p>
| [
{
"answer_id": 1930,
"pm_score": 3,
"text": "<p>I believe the most common source of electronic annotations comes from analysis of peptide sequences. A collection of InterPro to GO mappings were created manually and can generate GO annotations. DNA binding domains of transcription factors would be give... | [
{
"answer_id": 1948,
"pm_score": 2,
"text": "<p>You can refer the <a href=\"http://www.geneontology.org/GO.evidence.shtml#iea\" rel=\"nofollow\">IEA documentation</a> maintained by GO consortium to get an idea about the automatically assigned evidence codes using IEA. Also please note that IEA is differ... |
1,944 | <p>Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables using the <em>E. coli</em> preferences, for example.</p>
| [
{
"answer_id": 1945,
"pm_score": 4,
"text": "<p>Try the <a href=\"http://www.kazusa.or.jp/codon/\">Codon Usage Database</a> at Kazusa. You can search by organism. The database contains 35,799 organisms and compiled from 3,027,973 complete protein coding genes (CDS's), but last updated in 2007.</p>\n"
... | [
{
"answer_id": 1961,
"pm_score": 2,
"text": "<p>Plenty of softwares doing that kind of functionality. A 2007 open access review lists >30 such softwares <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/17882154\" rel=\"nofollow\">http://www.ncbi.nlm.nih.gov/pubmed/17882154</a>. However, No correlation betwe... |
1,951 | <p>Are the dark marks aka "moles" on our skin a patch of dead cells? If so, why is it not cleared over time? In a (probably) similar vein, why do scar marks from injuries remain long after new cells replace the dead cells?</p>
<p>[Feel free to edit out the second question if the answers are unrelated]</p>
| [
{
"answer_id": 1956,
"pm_score": 4,
"text": "<p>A <a href=\"http://en.wikipedia.org/wiki/Melanocytic_nevus\">mole</a> is simply a benign tumour, i.e. a proliferated cell growth that hasn’t become cancerous. So moles are <em>not</em> dead cells, they are very much alive. The colour is caused by a high co... | [
{
"answer_id": 10204,
"pm_score": 0,
"text": "<p>A Mole may be a Hamartoma or a benign tumor. A congenital mole is usually a hamartoma, while acquired mole a benign tumor. In a few people mole very slowly grow in size. </p>\n"
}
] |
1,968 | <p>I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods.</p>
<p>1) Primer first partially hybridises to the gene, has a mis-match where the restriction site and extra bases are on the primer, then has a hybridised site following the restriction site, to DNA upstream of the gene.</p>
<p>or</p>
<p>2) Primer first partially hybridises to the gene, then completely dangling and non-hybridising has the restriction site and extra bases.</p>
| [
{
"answer_id": 1979,
"pm_score": 3,
"text": "<p>The option #2 is most common. Do not forget to add 3 or more additional terminal base pairs for optimal restriction enzyme cutting (source: <a href=\"http://www.biotechniques.com/multimedia/archive/00007/98244bm15_7837a.pdf\" rel=\"nofollow\">BioTechniques... | [
{
"answer_id": 1973,
"pm_score": 3,
"text": "<p>I think the best way is option #2:</p>\n\n<p>Suppose that your gene of interest is AAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGG</p>\n\n<p>and you want to insert EcoRI restriction site GAATCC</p>\n\n<p>Then your Fwd primer will be GAATCC AAAAAAAAAAAAAAA... |
1,982 | <p>I've noticed a peculiar phenomenon. A subject drinks 400 ml of water, then observes time until the urge to urinate is felt. The time is 15 minutes. The subject releases water. 14 minutes later another urge to urinate is felt. The subject releases water again.</p>
<p>I'm particularly interested in what kinds of biological systems are involved in <strong>timing of such events</strong>.
Does the time depend on how full the subject's stomach is? Does caffeine and other diuretics play a part?
Is it time of day (circadian rhythm) sensitive?
Does that predict anything about the suppression/release of diuretic hormones?</p>
<p>What I'm trying to understand is if the timing between human urges to urinate after water consumption can be used to make predictions about the human biological clock and the state of various systems within the body (for example the digestive system). </p>
<p>I will be conducting this experiment at different times of the day. <strong>My hypothesis is that at night, when diuretic hormones are suppressed, the timing would be longer for the same amount of water consumed.</strong> This is based on my limited research in the area.
Update: I did perform the same experiment at night, the time was 75 minutes for the same amount of water. The experiment was performed at the end of one of sleep cycles, which makes me think that 75 minutes was the duration of the subsequent sleep cycle. </p>
<p>I appreciate your input on the subject, along with any keywords that can help me advance my research in this area.
Thank you!</p>
| [
{
"answer_id": 1985,
"pm_score": 4,
"text": "<p>The fact that urine output (enuresis) and other kidney functions are circadian is well known, just search on pubmed 'circadian urine kidney'. This can be due both to the fact that liquid consumption is less during the night and to the fact that hormones re... | [
{
"answer_id": 2021,
"pm_score": 2,
"text": "<p>I would suggest a couple of papers</p>\n\n<p><a href=\"http://www.ncbi.nlm.nih.gov/pubmed/21811695\" rel=\"nofollow\">Circadian rhythms in urinary functions: possible roles of circadian clocks?</a> - Noh et al., Int Neurourol J., 2011</p>\n\n<p><a href=\"h... |
1,988 | <p>A while ago I picked up a book called "Eat right for your metabolic type". The book discussed the effects of the endocrine system on the overall shape and the speed of metabolism. </p>
<p>The book outlined few major metabolic types:</p>
<ul>
<li>Adrenal</li>
<li>Thyroid (hypo/hyper)</li>
<li>Muscular</li>
</ul>
<p>The book proceeded to discuss the overall shape of the body, including shape of fingers to help identify the metabolic type and give suggestions on which foods to avoid for a particular type. </p>
<p>The book then gave examples of effects of foods on metabolic types - for example an Adrenal type who eats too much sugar would crash and compensate for this by sleeping. </p>
<p>Since I can no longer find that book in print, <strong>I'm interested if there's really such a thing as a metabolic type that can be easily identified ? Are there indeed some foods that people should avoid eating?</strong> </p>
| [
{
"answer_id": 1993,
"pm_score": 4,
"text": "<p>In general the answer is yes. However, the degree in which this is true and the degree in which the human body can adjust and adapt to new food types is larger misjudged. I am of the opinion that metabolism is largely controlled by the microbiome. It is la... | [
{
"answer_id": 1991,
"pm_score": 3,
"text": "<p>That book was likely crap, but in short the answer is yes, probably there is a genetic basis in the metabolism, with human 'types' that could benefit from a personalized nutrition. The discipline studying these relationship is called nutrigenomics, and the... |
1,994 | <p>Is there any evolutionary advantage to finding melodies or harmonies pleasurable? Does the ear pick up these particular oscillating waves differently from other sounds, and if so, how does that affect our perception of pleasure? I'm looking for some sort of signalling pathway (most likely involving neurotransmitters I realize).</p>
| [
{
"answer_id": 1997,
"pm_score": 4,
"text": "<p>There are strong connections between the auditory cortex and the <a href=\"http://en.wikipedia.org/wiki/Limbic_system\">limbic system</a>, which includes such structures as the hippocampus and the amygdala.</p>\n\n<p>A recent paper [1] builds on earlier no... | [
{
"answer_id": 2003,
"pm_score": 1,
"text": "<p><strong>In music</strong>, <a href=\"http://en.wikipedia.org/wiki/Harmony\" rel=\"nofollow\">harmonies</a> are simultaneous combination of tones or chords that are concordant.</p>\n\n<p><strong>In physics</strong>, each note is actually a vibration with de... |
2,006 | <p>I may be embarking on a project involving a fairly extensive healthcare records data set, looking for the use of a particular type of drug (for example, "Proton Pump Inhibitors"). But these drugs are usually listed by their trade or generic names - is there a well maintained resource for looking up what drugs are members of a certain class (if class is indeed the right word)?</p>
| [
{
"answer_id": 2008,
"pm_score": 5,
"text": "<p>The <a href=\"http://www.who.int/en/\">WHO</a> has their own methodology, the Anatomical Therapeutic Chemical (ATC, thank you commenter) <a href=\"http://www.whocc.no/atc/structure_and_principles/\">classification system</a>, for organizing such data (its ... | [
{
"answer_id": 2007,
"pm_score": 3,
"text": "<p>Comprehensive, up-to-date drug information including trade names and categories are available from <a href=\"http://www.micromedex.com\">Micromedex®</a> (a division of Thomson Reuters) in the <a href=\"http://www.micromedex.com/products/redbook/\">RED ... |
2,022 | <p>I am currently reading 'The Selfish Gene' by Richard Dawkins, which I am sure many here have read. The topic are evolutionary stable strategies (ESS) regarding cooperation.</p>
<p>I apologise for the long question. If you are already familiar with the topic and Dawkins' model of Cheat, Sucker and Grudger: my question is, how can Grudger be an ESS if it could be invaded both by Suckers (because they have no disadvantage against Grudger) and Cheats (because a Cheat minority is unlikely to meet the same Grudger twice, turning Grudger into Sucker effectively)?</p>
<p>More detailed:</p>
<p><strong>The model</strong></p>
<p>Near the end of chapter 10 (p 185 in my version), Dawkins uses a model of birds who clean each other of parasites, therefore helping in survival (as cleaning themselves they cannot reach every spot of their body). He defines three different behaviours for the model:</p>
<ul>
<li>Sucker - birds who indiscriminately help and clean other birds</li>
<li>Cheat - birds who let others help them but never do so themselves</li>
<li>Grudger - birds who help others and remember who they helped. If the same bird does not help them later (reciprocate), they will not help that bird again.</li>
</ul>
<p><strong>Claim: Cheat and Grudger are ESS</strong></p>
<p>He claims that both Cheat and Grudger in themselves are ESS - that is, if all birds behave this way, none of the other behaviours can develop because they will be immediately penalised by lower chances of reproducing.</p>
<p><strong>The part that makes sense: Suckers is not an ESS, Cheat is</strong></p>
<p>Sucker is of course not an ESS. If all birds were Suckers, any Cheat that developed would have a huge reproductive advantage and Cheat genes would overtake the population.</p>
<p>Being an ESS makes sense for Cheat. If all birds cheat, nobody will ever be helping each other. A minority of Suckers would be spending all their time helping and not getting anything in return, Cheats have the advantage and Suckers die out again. Grudger would be unlikely to meet a Cheat who they helped before again, so they too will spend all their time helping and die out again.</p>
<p><strong>The part that confuses: Grudger is an ESS?</strong></p>
<p>But Dawkins also claims that Grudger is an ESS, and he seems very confident in that. Now I don't consider myself enough of a smartypants to claim that he's wrong, but I don't understand how Grudger can be an ESS. If all birds behave in this way, and for any reason some Sucker developed - the Sucker would have no disadvantage. All birds would still always be helping each other, so nothing would stop the Suckers from propagating equally well as the Grudgers, invading the gene pool. That's already the ESS broken, but even further, the presence of Suckers would mean that if Cheats came up, they would have a realistic chance of surviving - Grudgers would shun them after having helped once, but if the number of Suckers is large enough, Cheats will have an advantage.</p>
<p>Moreover, back to the initial setting of Grudgers only - if a Cheat developed, he would be unlikely to meet the same Grudger twice, receiving the benefit all the time but never paying the cost. He would have an advantage and spread Cheat genes.</p>
<p><strong>The problem</strong></p>
<p>I'm not familiar enough with how these kinds of models are calculated in order to state chances that Cheats will take over completely, but however I think of it Grudger does not seem to be an ESS to me.</p>
<p>Does anyone have an explanation why Dawkins is so sure that it is? Seeing as in nature we do see patterns like Sucker and Grudger all the time, I must be missing something important here. </p>
| [
{
"answer_id": 2023,
"pm_score": 5,
"text": "<p>Unfortunately it is not necessary to invoke group selection to answer this question. This is one of the reasons that Dawkins likes this discussion so much - he does not believe in group selection and so the discussion in SG does not invoke group selection... | [
{
"answer_id": 2035,
"pm_score": 3,
"text": "<p>In an infinite, well mixed population with single pairwise encounters, Grudger is indeed not an ESS. In fact, as you correctly note, in such a model the Grudger and Sucker strategies are indistiguishable, as the probability of anyone encountering the same... |
2,025 | <p>Basically, I want to know if it would be humanely possible to sleep one day, skip the next, sleep, skip, sleep, skip, etc, with a 8 hour sleep time.</p>
<p>If you need any extra information, let me know.</p>
| [
{
"answer_id": 2023,
"pm_score": 5,
"text": "<p>Unfortunately it is not necessary to invoke group selection to answer this question. This is one of the reasons that Dawkins likes this discussion so much - he does not believe in group selection and so the discussion in SG does not invoke group selection... | [
{
"answer_id": 2035,
"pm_score": 3,
"text": "<p>In an infinite, well mixed population with single pairwise encounters, Grudger is indeed not an ESS. In fact, as you correctly note, in such a model the Grudger and Sucker strategies are indistiguishable, as the probability of anyone encountering the same... |
2,056 | <p>I am totally confused whether ask this question to physics or biology stackexchange.</p>
<p>I downloaded a mobile application which claims to repel mosquitoes. This application basically produces sound from 16kHz to 22kHz (I doubt that it even produces more than 20kHz because we can't hear more than 20kHz naturally).</p>
<p>I totally doubt this application. Do mosquitoes go away in higher frequency of sound?</p>
| [
{
"answer_id": 2069,
"pm_score": 5,
"text": "<p>After seeing your question, I decided to do a bit of research on the topic.</p>\n\n<p><hr></p>\n\n<h1>First Source: <a href=\"http://www.eurekalert.org/pub_releases/2007-04/jws-mrt041607.php\" rel=\"nofollow noreferrer\">EurekAlert!</a></h1>\n\n<p><hr>\n<a... | [
{
"answer_id": 34241,
"pm_score": 2,
"text": "<blockquote>\n <p>Ultrasound emitting devices are used to repel mosquitoes. We tested\n the repelling properties of a commercially available ultrasound device\n in a domestic setting in Gabon. Devices emitting three different block\n frequencies ranging ... |
2,061 | <p>Why does looking at bright light trigger sneezing in some people?</p>
<p>Are there any recent studies that have found a cause for this <a href="http://en.wikipedia.org/wiki/Photic_sneeze_reflex">Photic sneeze reflex</a>? The Wikipedia article only references studies pertaining to the effect, stating that the cause is unknown. The article also states that "the condition affects 18–35% of the population", which seems to be quite a large percentage. </p>
<p>What could have lead to the development and persistence of such a genetic trait in humans? Are there any evolutionary advantages to this?</p>
| [
{
"answer_id": 2062,
"pm_score": 5,
"text": "<p>You are talking about the <a href=\"http://en.wikipedia.org/wiki/Photic_sneeze_reflex\">photic sneeze reflex</a>.</p>\n\n<p>The mechanisms are not entirely understood, but it affects <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/8108024\">18-35% of the popu... | [
{
"answer_id": 65446,
"pm_score": 2,
"text": "<p>In high school biology, we had to read a book called \"Survival of the Sickest\". In this book, the idea is presented that this reflex evolved during humankind's \"caveman\" days. The author presented the anthropological induction that after spending peri... |
2,079 | <p>For those who use Qiagen miniprep columns, they may be aware that the P3 buffer is the acetic acid step to neutralize cell lysis. They may also be aware that the Qiagen P3 buffer cannot be interchanged with the proprietary N3 buffer. It is also known that the N3 buffer is particularly unique since it primes the miniprep columns for binding. I was wondering about that priming step and what chemically primes the columns. Would it be appropriate to use QBT buffer to prime the miniprep columns?</p>
| [
{
"answer_id": 2082,
"pm_score": 4,
"text": "<p>The <a href=\"http://www.qiagen.com/literature/render.aspx?id=370\">Qiagen manual for the Miniprep Kit</a> states that buffer N3 contains guanidine hydrochloride and acetic acid. The <a href=\"http://www.qiagen.com/support/msds/de/buffer_n3_de5.pdf\">MSDS ... | [
{
"answer_id": 8335,
"pm_score": 2,
"text": "<p>N3 and P3 are different. N3 contain chaotropic agents. P3 does not.\nMainly there are two types of DNA purification kits on the market: silica membrane (glass fiber) based and DEAE anion exchange based. The silica membrane based method requires high concen... |
2,105 | <p>I'm sure the exact frequency varies, but does anyone know roughly how many revolutions per minute / second the rotating center part makes? </p>
| [
{
"answer_id": 2108,
"pm_score": 5,
"text": "<p>According to <a href=\"http://www.neuro.duke.edu/files/sites/yasuda/pub/0302207335.pdf\">\"Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase\"</a> (Yasuda <em>et al</em>., <em>Nature</em>, 2001), ATPase rotates at 1... | [
{
"answer_id": 89711,
"pm_score": 2,
"text": "<blockquote>\n<p>The rotation rates at various ATP concentrations obeyed the curve defined by a K m of ≈30 μM and a <strong>V max of ≈350 revolutions per second</strong> (21 000 revolutions per\nminute) at 37°C.</p>\n<p>Some reported values of very high ATPa... |
2,109 | <p>Thinking of behaviours an organism can adapt, at the very base an action can always be either selfish or altruistic (cooperative).</p>
<p>Usually, selfish behaviour is assumed to be the preferred choice and the question is how altruistic behaviour comes about.</p>
<p>But if reciprocal altruism can give both participants a higher benefit than their respective costs (which it usually does), why would selfish behaviour (in the sense of behaviour which reaps benefit at another entity's expense) be what we assume to happen? If evolution tends to optimise things, why does it not optimise this?</p>
| [
{
"answer_id": 2113,
"pm_score": 4,
"text": "<p>It basically comes down to a question of the <a href=\"http://en.wikipedia.org/wiki/Unit_of_selection\">unit of selection</a>.</p>\n\n<p>From the common viewpoint, in which natural selection is seen as acting on individual organisms, it's almost a tautolog... | [
{
"answer_id": 10969,
"pm_score": 2,
"text": "<p>Selfish behaviour is not necessarily preferred. It depends on the game (game theory). For example, in absence of relatedness and reciprocity, we would expect:</p>\n\n<ul>\n<li>All the population defect in the Prisoner's dilemna</li>\n<li>Some defect and s... |
2,132 | <p>When one exposes theirs body parts to cold environment (especially foot and hands), they may be numb, with temporarily blocked both muscles.</p>
<p>What is typical body temperature below which human muscles don't work properly?</p>
<p>Moreover, what is the mechanism behind it?</p>
<p>EDIT:</p>
<p>Interested in case when muscles almost cease to work (e.g one is not able to grasp a cup), not just in small perturbations to strength. </p>
| [
{
"answer_id": 7842,
"pm_score": 4,
"text": "<p>If you dissect striated muscle out of most-any organism, the actual contractile apparatus works over a wide range of temperatures. So that's at the single-muscle-fiber scale. The muscle itself continues to work at all (thawed) temperatures below body tempe... | [
{
"answer_id": 2390,
"pm_score": 2,
"text": "<p>This seems complicated, but I found <a href=\"http://jap.physiology.org/content/100/4/1361.full.pdf\" rel=\"nofollow\">a reference</a> that might answer these questions (if its right). </p>\n\n<p>Sports physiology common wisdom is that human muscles regula... |
2,134 | <p>The reaction in which dopamine beta-hydroxylase catalyses the conversion of dopamine to norepinephrine is shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves structural biology?</p>
<p>Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else. I'm really wondering <em>what</em> in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. In other words, what is the structural mechanism behind substrate specificity?</p>
<p><img src="https://i.stack.imgur.com/EuR7O.png" alt="Reaction pathway of tyrosine oxidation to epinephrine" /></p>
| [
{
"answer_id": 2563,
"pm_score": 4,
"text": "<p>There are various studies on the mechanism of action of dopamine beta-hydroxylase (DBH).</p>\n<p>This review (sorry, non-free article) by Kaufman and Friedman was written less than 10 years after the discovery of the reaction of conversion of tyrosine into... | [
{
"answer_id": 111124,
"pm_score": 2,
"text": "<p>The likely catalytic mechanism of dopamine β-hydroxylase, based on molecular modelling and the actual structure of peptidylglycine α-hydroxylating mono-oxygenase, was presented ten years ago in the extensive answer of @nico. The key point is that two cop... |
2,137 | <p>Looking at the swimming birds building nests just across my garden, I suddenly wondered how evolution came to swimming birds and whether flying birds started swimming or whether swimming bird like animals started flying.</p>
<p>What came first and when and why?</p>
| [
{
"answer_id": 2155,
"pm_score": 5,
"text": "<p>Flying came first, as far as we know. The earliest known bird (currently), <a href=\"http://www.ucmp.berkeley.edu/diapsids/birds/archaeopteryx.html\"><em>Archaeopteryx lithographica</em></a>, already had aerodynamic feathers (<a href=\"http://www.sciencema... | [
{
"answer_id": 2163,
"pm_score": 3,
"text": "<p>Another way to look at this is: <em>How do you evolve flight when you're aquatic?</em> There are <a href=\"http://en.wikipedia.org/wiki/Origin_of_avian_flight\">three proposed models</a> (or even <a href=\"http://www.ucmp.berkeley.edu/vertebrates/flight/or... |
2,157 | <p>Did animals evolve from plants? Did animals' ancestors have chloroplasts in their cells?</p>
| [
{
"answer_id": 2160,
"pm_score": 6,
"text": "<p>See this paper \"<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689654/pdf/10097391.pdf\">Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi</a>\" for information on the divergence estimates ... | [
{
"answer_id": 2159,
"pm_score": 3,
"text": "<p>No. Animals form the kingdom <a href=\"http://en.wikipedia.org/wiki/Animalia\">Animalia</a> (or Metazoa) which is distinct from the <a href=\"http://en.wikipedia.org/wiki/Plantae\">Plantae</a> kingdom.</p>\n\n<p>Both evolved independently from single-celle... |
2,172 | <p>I read <a href="http://www.nature.com/?file=/ijo/journal/v21/n9/abs/0800473a.html">here</a> and <a href="http://jas.fass.org/content/48/6/1530.full.pdf">here</a> that the function of lipoprotein lipase is to facilitate fat uptake and storage in adipose tissue. Could anyone provide a slightly more expanded explanation, without going into too much detail, and without the use of too much jargon (I am not a biologist). I have read the wikipedia page, but sadly I didn't understand it....Thanks !</p>
<p>Edit: One of the things that is confusing me is what "fat uptake" means in this context.</p>
| [
{
"answer_id": 2173,
"pm_score": 5,
"text": "<p>Fat uptake means cells eating fat.</p>\n\n<p>I'll try to keep it simple, so forget the many approximations. You need first to consider that most fat circulates in the blood under the form of <a href=\"http://en.wikipedia.org/wiki/Triglyceride\" rel=\"noref... | [
{
"answer_id": 53801,
"pm_score": 0,
"text": "<p>Adipocytes are fat cells. On their outer surface are enzymes called lipoprotein lipase abbreviated as 'LPL' . the major function of LPL is to break down triglycerides into soluble fats and facilitate their transportation into adipocytes. So as more trigly... |
2,213 | <p>Circulating Tumor Cells (CTCs) are linked with metastasis and their presence can be used to indicate the onset of metastatic cancer. Likewise, the Cancer Stem Cell (CSC) hypothesis suggests that tumorigenic stem cells are the source of cancer. However, <a href="http://www.ncbi.nlm.nih.gov/pubmed/21300848">microscopy experiments and cytometry</a> have suggested that the morphology of CTCs and CSCs are quite different. Essentially, we have not been able to find Circulating Cancer Stem Cells (asides Myeloma since they are circulating anyways).</p>
<p>My question is how similar are these cells? If they are different, is relapse caused by the CSCs from the primary tumor or CTCs in metasises that have become CSC-like?</p>
| [
{
"answer_id": 2226,
"pm_score": 4,
"text": "<p>There are several competing models of metastasis, and this question does go right to the differences between them.</p>\n\n<p>The primary thing to remember about CSCs is that all evidence suggests that they are a tiny, tiny subset of tumor cells.</p>\n\n<p>... | [
{
"answer_id": 55326,
"pm_score": 1,
"text": "<p>Actually people have been able to isolate circulating tumour cells that show the phenotypic hallmark of a CTC - the ability to give rise to an entire tumour and successfully implant in serial transplantation / dilution assays. </p>\n\n<p>See <a href=\"htt... |
2,223 | <p>I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid? </p>
<p>My problem with the assumption that RNA levels correlate with that of the active product (i.e. the protein) is that a <em>lot</em> of post translational regulation occurs, including co-factor binding and phosphorylation, to name but 2. Does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and <em>active</em> protein?</p>
<p>It makes sense to me that RNA would correlate with protein certainly, but whether this relates to the proteins active function is what I wonder - i.e. there could be a pool that is replenished as and when the protein levels drop, but the proteins are only actually active for short periods in response to specific stimuli. So, does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and active protein?</p>
<hr>
<h3>Update (04.07.12)</h3>
<p>I have not accepted any answers as yet because none address my question about levels of protein activation, but I concede to Daniel's excellent point that proteins are not all activated in the same way; some are constantly active, some require phosphorylation (multiple sites?), some binding partners... etc! So a study looking at 'global' activation is not yet possible. Yet I was hoping that someone may have read some specific examples.</p>
<p>I today found an <a href="http://www.kendricklabs.com/WP1_mRNAvsProtein.pdf" rel="nofollow">unpublished review by Nancy Kendrick</a> of 10 studies that have looked at the correlation between mRNA and protein <em>abundance</em> - still not relating to <em>activation</em>. However she finishes the paper as follows;</p>
<blockquote>
<p>The conclusion from the ten examples listed above seems inescapable: mRNA levels cannot be
used as surrogates for corresponding protein levels without verification.</p>
</blockquote>
<p>If this is her conclusion about protein levels, then any correlation between protein activation and mRNA abundance seems unlikely (as a rule. Some protein levels <em>do</em> correlate with the RNA - see the paper).</p>
<p>I am still interested in any answers that give any information about specific examples of protein activation and mRNA levels - it seems highly unlikely there are no such studies, but I have been as yet unable to find any!</p>
| [
{
"answer_id": 2224,
"pm_score": 5,
"text": "<p>It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. <a href=\"http://mcb.asm.org/content/19/3/1720.short\">This paper on yeast</a> and <a href=\"http://www.mcponline.org/content/1/4/304.short\">this ... | [
{
"answer_id": 2545,
"pm_score": 3,
"text": "<p><a href=\"http://www.ncbi.nlm.nih.gov/pubmed/20671182\">This study</a> in E.coli is useful in setting out some additional issues at play here, in a system where post-translational modifications are basically a non-issue. The authors see clearly a correlat... |
2,229 | <p>There are several companies (most notably <a href="http://23andme.com/">23andMe</a>) providing <a href="http://en.wikipedia.org/wiki/SNP_genotyping">SNP genotyping</a> for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it could be interpreted.</p>
<p>While this agrees with my understanding of the subject, I wonder whether there could be any use to perform full sequence of one's genome for means of personal health care?</p>
<p>The only effect I recall which affects individual's health and could not be caught by SNP genotyping is <a href="http://en.wikipedia.org/wiki/DNA_methylation">DNA methylation</a>, but complete sequencing procedure does not detect it either, as far as I know.</p>
| [
{
"answer_id": 2230,
"pm_score": 4,
"text": "<p>This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient.</p>\n\n<p>In terms of health risks based on SNP genot... | [
{
"answer_id": 5677,
"pm_score": 2,
"text": "<p>Genotyping only tests for SNPs in predetermined locations. If you have SNPs in other places in your genome, genotyping won't tell you that, but whole genome sequencing will (by comparing your genome to a reference genome available at NCBI). Also, there are... |
2,231 | <p>I know that there are companies that offer a kit+storage of your pet DNA for around $2k.
My question is if there is any other option for doing this yourself with a thought in mind that in 20+ years the technology will get so advanced that even this DIY sample can be utilized.</p>
<p>Any ideas? Maybe drying a blood drop or mixing blood with alcohol/acetone?</p>
<p>Also, I read somewhere that it is better if the pet is still very young, because if you take old pet DNA the clone will exhibit mature signs even as a youngster. Is this true? If yes then what is the top age that is safe?</p>
| [
{
"answer_id": 2257,
"pm_score": 5,
"text": "<p>For the impatient, I'm going to say that probably if you only have a regular home freezer, its unlikely that you will be able to do this. If you have access to a -80C or liquid nitrogen storage its possible, but also less likely. </p>\n\n<p><a href=\"http:... | [
{
"answer_id": 103023,
"pm_score": -1,
"text": "<p>To clone something you need a living cell, not just DNA. Although DNA could someday be used to make a clone, it would require technology that is a long way off. You can store DNA indefinitely by extracting it from a cell and storing it in alcohol.</p>\n... |
2,232 | <p>If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?</p>
| [
{
"answer_id": 11082,
"pm_score": 4,
"text": "<p>The easiest and most simplistic way to look at it is to assume that the amount of genetic material halves each generation. On average, humans are about 0.1% to 0.15% different from each other, so in order to get that you'd need around $1/2^{10}=0.0976\\%... | [
{
"answer_id": 2234,
"pm_score": 3,
"text": "<p>In \"The Selfish Gene\" Dawkins claims a relatedness factor of 1/128 to be pretty much the same as the baseline chance for the rest of the population to have the same gene, so that would be a third cousin. (Or your great great great great great grandparent... |
2,235 | <p>Inspired by the post about <a href="https://biology.stackexchange.com/questions/2231/how-to-diy-preserve-pet-dna-today-so-that-it-can-be-used-in-20-years">extracting pet DNA</a>, how long would genomic DNA be stable for in a -20°C freezer? It is common practice to store DNA (double-stranded, plasmid) in a -20°C freezer in the lab, but would genomic DNA last longer in a -80°C freezer? With either method, how long would it be stable for?</p>
| [
{
"answer_id": 2238,
"pm_score": 4,
"text": "<p>If the DNA is pure, it should last quite a long time. If there are enzymes and other biological molecules in there, -80C will work much better. </p>\n\n<p>I think you could keep pure DNA at -20C practically indefinitely. </p>\n\n<p>Purity is the main issu... | [
{
"answer_id": 10185,
"pm_score": -1,
"text": "<p>You can store your DNA for 1 week at -4C and for one month at -20C but with storing DNA over these period of time there is a deduction of 10-15% of yield from your DNA sample.</p>\n"
}
] |
2,240 | <p>Today I heard about a phenomenon called "translational coupling", where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. How does this work? Do they need to be in the same operon?</p>
| [
{
"answer_id": 2388,
"pm_score": 4,
"text": "<p>Translational coupling describes in how some cases an mRNA will code from more than one protein (i.e. will be polycistronic). Translational coupling is thought to be mostly used as a way to make a set of genes are translated at roughly the same amount in ... | [
{
"answer_id": 55888,
"pm_score": 2,
"text": "<p>The above answer isn't entirely accurate. It's true that polycistronic mRNAs (i.e. operons) are very common in bacteria. But this isn't what is meant by translationally coupled. </p>\n\n<p>Translational coupling happens when the second gene of two adjacen... |
2,262 | <p>My russian friend says that the USSR agents used/use the trick that they offered the victim first vodka and then last wine.</p>
<p>I have noted that this puts you faster to hangover: decreasing the alcohol proof.
Some people lose their motor function immediately and some their memory only. </p>
<p><strong>Why does a decrease in the alcohol proof cause you a) faster intoxication and b) faster hangover?</strong></p>
<p>Probably the change in the concentration of alcohol inside cells of brain tissue affects some parts of your brain like the cerebellum. I would like to have an explanation in Biochemistry.</p>
<p><strong>Is there any truth in my friend's argument?</strong></p>
| [
{
"answer_id": 2276,
"pm_score": 4,
"text": "<p>I would argue that your central point is intrinsically flawed. Your claim is that starting at a high alcohol percentage, then gradually decreasing alcohol content, gets you intoxicated faster. @nico is correct that you will get drunk faster this way (more ... | [
{
"answer_id": 86448,
"pm_score": 0,
"text": "<p>This has more to do with the person's tolerance to alcohol than the trick itself. People will be affected by different amount of alcohol differently. From personal experience in college, I have seen many people take several shots of vodka and still carry ... |
2,281 | <p>Is it a myth that modern whales have been found with hind legs sticking out of their sides and full formed tibias, fibias, and toe bones? I keep finding assertions, but no citations. For example, the wikipedia page has no citation for it.</p>
<p><a href="http://en.wikipedia.org/wiki/Whales#Appendages">http://en.wikipedia.org/wiki/Whales#Appendages</a></p>
| [
{
"answer_id": 2284,
"pm_score": 5,
"text": "<p>The link you give doesn't mention limbs sticking out of the body wall, but only vestigial hind limb elements. Many whales do retain pelves and femora, as <a href=\"http://bergenmuseum.uib.no/fagsider/osteologi/hvaler/e_bekken.htm\">this page at the Bergen ... | [
{
"answer_id": 13411,
"pm_score": 2,
"text": "<p>Yes there are several published sources (with photos) of whales born with protruding vestigial legs.</p>\n\n<p><a href=\"http://digitallibrary.amnh.org/dspace/bitstream/handle/2246/4849/N0009.pdf;jsessionid=55D6453968F5461B1B6BFF8D53C81F16?sequence=1\" re... |
2,286 | <p>A new study from MIT scientists <a href="http://www.sciencedaily.com/releases/2012/05/120515181256.htm" rel="nofollow">suggests that long-term exposure to low-radiation poses no risk of DNA damage</a> for mice (it is also important to note that mice are unusually susceptible to cancer). So apparently there may be a threshold for radiation damage to DNA.</p>
<p>But is this study conclusive? What are some other studies that show the biological effects of long-term low-dose radiation on DNA?</p>
<p>There are some studies that <a href="http://www.quora.com/Is-there-conclusive-medical-research-that-flying-in-airplanes-exposes-people-to-unsafe-amounts-of-radiation/answer/Alex-K-Chen" rel="nofollow">do show increased rates of cancer in frequent flyers</a>. So are are we going to reconcile this finding with the finding above?</p>
| [
{
"answer_id": 2284,
"pm_score": 5,
"text": "<p>The link you give doesn't mention limbs sticking out of the body wall, but only vestigial hind limb elements. Many whales do retain pelves and femora, as <a href=\"http://bergenmuseum.uib.no/fagsider/osteologi/hvaler/e_bekken.htm\">this page at the Bergen ... | [
{
"answer_id": 13411,
"pm_score": 2,
"text": "<p>Yes there are several published sources (with photos) of whales born with protruding vestigial legs.</p>\n\n<p><a href=\"http://digitallibrary.amnh.org/dspace/bitstream/handle/2246/4849/N0009.pdf;jsessionid=55D6453968F5461B1B6BFF8D53C81F16?sequence=1\" re... |
2,293 | <p>I've been wondering about head hair, facial hair in particular. Human males can grow very extensive beards should they choose to not shave - however you do not really see this in our chimpanzee cousins! Yes, they have little pseudo-beards, but the difference being that they do not shave, that is just the length they reach. Whereas in humans we can grow to our hearts content (*this may not be the case, see <a href="https://biology.stackexchange.com/questions/1267/why-can-hair-grow-without-limit-while-eyebrow-cannot">this question</a>). </p>
<p>I can't really see why this would have been selected, unless it's simply that (evolutionarily speaking) women like men with long beards?</p>
<p>So my question is: why can humans perpetually grow head hair, yet we have lost the majority of our body hair, in comparison to chimpanzees and other ape family members?</p>
| [
{
"answer_id": 2735,
"pm_score": 5,
"text": "<p>Wheeler (<a href=\"http://www.sciencedirect.com/science/article/pii/004724849290086O\">1992</a>; and <a href=\"http://scholar.google.com/scholar?hl=en&q=hominid%20loss%20of%20hair\">previous</a>) discusses the evolutionary loss of \"non-functional\" ha... | [
{
"answer_id": 66477,
"pm_score": 0,
"text": "<p>Hair on the head is an excellent built-in sun protection at minimal resource cost. If we didn't have hair on our heads then we would have to apply sunscreen on the scalp or take cover more often (often impossible for hunter-gatherers).</p>\n\n<p>No sun pr... |
2,299 | <p>Im an engineer by education and i program a lot, so the question sounds weird to people from other disciplines.</p>
<p>Im trying to better understand the human biological clock. Yet i do not really know what it is. I read about clock genes, endogenous cycles, and other observed phenomena that is time sensitive or cyclical in nature. But is there a centralized model of what the circadian rhythm is or how itis exhibited within the human body? </p>
<p>For example an electrical clock can be modelled with feedback loops or electrical flip flops that control the timing. Ive seen the heart modelled as Van Der Pol oscillator.</p>
<p>Does modern science have some notion of how the "master" clock within the human body work? Is there a feedback or an oscillator model of the master clock?</p>
<p>Thank you for any articles or keywords that ican use to research this question!</p>
| [
{
"answer_id": 2856,
"pm_score": 3,
"text": "<p>The situation is quite complex, and there are certain things that we do not fully understand, but I will try to give you an explanation.</p>\n\n<p>First of all, at the cellular level, you have the genetic components of the circadian clock, the clock genes ... | [
{
"answer_id": 5260,
"pm_score": 0,
"text": "<p>I've stumbled upon <a href=\"http://www.psycheducation.org/mechanism/Clock.htm\" rel=\"nofollow\">a detailed explanation of the Biological clock</a>. This one is broken into multiple steps and helped me better understand what PER and CRY are. I cannot vouc... |
2,324 | <p>I'm interested in horizontal gene transfer in bacteria, viruses, and organisms such as Bdelloid Rotifers. I've just read in Carl Zimmer's 'A Planet of Viruses' the following passage:</p>
<blockquote>
<p>As a host cell manufactures new viruses, it sometimes accidentally adds some of its own genes to them. The new viruses carry the genes of their hosts as they swim through the ocean, and they insert them, along with their own, into the genomes of their new hosts. By one estimate, viruses transfer a trillion trillion genes between host genomes in the ocean every year.</p>
</blockquote>
<p>It's interesting to consider the scale of DNA-swapping that has occurred given the frequency by which it happens and the evolutionary timescale.</p>
<p>Are there any examples of genes in the human genome that we know were deposited by viruses that would have given an evolving human a physical/mental advantage? Where did they come from? What benefit did they provide?</p>
<p>I'm interested in genetic additions from non-human-ancestor species, rather than the transfer of genes that occurred as mutations from other humans.</p>
| [
{
"answer_id": 2448,
"pm_score": 4,
"text": "<p>The processes that control the germline of metazoans (multicellular animals) are highly regulated compared to single cell bacteria and eukaryotes as well as plants.</p>\n<p>At this point there are no clear stories of gene transfer into a complex animal, th... | [
{
"answer_id": 2467,
"pm_score": 2,
"text": "<p>Human endogenous retroviruses (HERVs) have been an interesting (and expanding) topic of research in evolutionary biology and medicine. A retrovirus has an RNA genome in the virus particle, and integrates with the host cell's DNA upon infection to hijack th... |
2,328 | <p>To clarify, I think the answer should be able to explain:</p>
<ol>
<li>What are animals?</li>
<li>What are plants? </li>
<li>What's the difference between animals and plants (How do biologists differentiate them, if they differentiate them by moving ability of course it's simple, but we know they don't)?</li>
<li>How do those differences affect their evolutionary paths so that most animals can move around and most plants cannot? I know there are exceptions, but that's just the exceptions that show the rule.</li>
</ol>
| [
{
"answer_id": 2329,
"pm_score": 5,
"text": "<p>Animals and plants are both classified as Eukaryotes, and as such can form large, complex, multi-cellular organisms. There are several major differences at the cellular level that distinguish the 2 <a href=\"http://en.wikipedia.org/wiki/Kingdom_%28biology%... | [
{
"answer_id": 2389,
"pm_score": 3,
"text": "<p>Plants are multicellular organisms that utilize diffuse inorganic molecules (CO<sub>2</sub>, NO<sub>3</sub>, etc...) for energy and growth and thus they have evolved anatomical features that maximize the efficient concentration of these molecules (i. e., t... |
2,351 | <p>My understanding is that the possible mechanisms of evolution are: </p>
<ul>
<li>Environmental changes</li>
<li>Cultural/mating preferences</li>
<li>Population Immigration</li>
<li>Genetic Mutation</li>
</ul>
<p>Am I missing anything? I've heard that population shifts within a existing populaces will effect evolution, but imagining the most simplicity scenario, it's hard to see why the would make a difference. </p>
| [
{
"answer_id": 2359,
"pm_score": 5,
"text": "<p>Evolution is defined as a change in the allele frequency of population through time. The Hardy-Weinberg model predicts that the allele frequency of a population will not change (i.e., evolution will not occur) if the following conditions are met:</p>\n\n<... | [
{
"answer_id": 48033,
"pm_score": 3,
"text": "<p><strong>What is evolution?</strong></p>\n\n<p>The first step is to remind ourself of the definition of the term \"evolution\". <a href=\"https://biology.stackexchange.com/questions/11400/how-to-define-evolution\">Evolution</a> is most often defined as \"a... |
2,382 | <p>I'd like to know how antioxidants affect human metabolism and which ones are essential for metabolic processes.</p>
| [
{
"answer_id": 2412,
"pm_score": 4,
"text": "<p>This mainly depends on which kind of antioxidants you're talking about.</p>\n\n<ul>\n<li>Vitamin A and E are antioxidants acquired from the food</li>\n<li>Superoxide dismutase, Catalase and the Glutathione system are enzymes produced by the cell.</li>\n</u... | [
{
"answer_id": 21781,
"pm_score": 2,
"text": "<p>Anti-oxidants affect human metabolism by altering the redox states of the cell and redox-regulated functions and signaling mechanisms.</p>\n\n<p>The following quotes are from <a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267846/\" rel=\"nofollow\... |
2,396 | <p>I need to make a model of the digestive system. It would be really nice to actually show it in action, such as by breaking down bread into glucose or something similar. Is this feasible with a small budget and non-dangerous chemicals? If so, how? This should be as similar too the real digestive system as possible.</p>
| [
{
"answer_id": 2397,
"pm_score": 3,
"text": "<p>Amylase would be worth a try. The enzyme breaks down bread (starch), and you can buy it relatively cheaply online or probably at a chemist. Amylase is secreted in your saliva and in your stomach, so it would be most realistic if it was added in your model ... | [
{
"answer_id": 2403,
"pm_score": 2,
"text": "<p>Generally speaking and as suggested by Rory, mechanical force probably plays a role in most instances (crustless bread may be different):</p>\n\n<p><a href=\"http://www.modelgut.com/dmg.html\" rel=\"nofollow\">http://www.modelgut.com/dmg.html</a></p>\n\n<p... |
2,423 | <p>The human genome is about 770 MB, the <em>C. elegans</em> genome is about 100 MB, the yeast <em>S. cerevisiae</em> is about 12 MB. Different other genomes have been sequenced: how many GB of genomic DNA we have now?</p>
<p>Let say we would like to make a Noah hard-disk ark: how much space would it take to represent the genomes of all known species on earth? There is a way to provide an estimate?</p>
<p>I'm also interested in the total biodiversity: for instance, if two species each have 1 GB genomes and have half of their DNA in common this would count as 1.5 GB.</p>
| [
{
"answer_id": 2433,
"pm_score": 5,
"text": "<p>If you simply take one order of insects, Coleoptera, there are just under 400,000 described species with estimates from 850,000 to 4,000,000 species total in just this order. The number of primates is under 1,000. If your assumption of say 10MB for all o... | [
{
"answer_id": 77339,
"pm_score": 2,
"text": "<p>According to <a href=\"https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002168\" rel=\"nofollow noreferrer\">this paper</a> there is ~ $5.3 \\times 10^{34}$ base pairs of DNA on earth. One base pair contains approximately 2 bits wort... |
2,447 | <p>Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as "enrichment" associated to each gene in each species. It's <em>not</em> gene expression, it's enrichment of a certain marker n the gene. I would like to compare these lists, that are not fully overlapping, across the phylogeny of the species, to see significant changes in the trend of enrichment at the gene level, or at the branch level. What tools could I use for this?</p>
<pre><code>Species1 Z-score
Gene1 0.532
Gene2 0.531
...
Species2 Z-score
Gene1 0.51
Gene3 0.505
...
</code></pre>
| [
{
"answer_id": 2614,
"pm_score": 3,
"text": "<p>Phylogenetically analyzing genes that are not present in every species may present you with some problems, but it is completely feasible to simultaneously analyze the relatedness of the species (based on your enrichment score), and the relatedness of the s... | [
{
"answer_id": 2617,
"pm_score": 2,
"text": "<p>From your example</p>\n\n<pre><code>Species1 Z-score\nGene1 0.532\nGene2 0.531\n...\n\nSpecies2 Z-score\nGene1 0.51\nGene3 0.505\n</code></pre>\n\n<p>You need to get a matrix for all the Z-scores from your species, like this</p>\n\n<pre><code>G... |
2,455 | <p>In the past I have used <a href="http://www.springer.com/life+sciences/ecology/book/978-0-387-98928-0" rel="noreferrer">Limnological Analysis</a> by Wetzel and Likens and <a href="http://store.elsevier.com/Methods-in-Stream-Ecology/Richard-Hauer/isbn-9780123329073/" rel="noreferrer">Methods in Stream Ecology</a> edited by Hauer and Lamberti to develop labs and research methods for courses and projects with an aquatic focus. </p>
<p>These books detail the standard methods of lotic and lentic ecology with some emphasis on utilizing the methods in undergraduate or graduate level courses.</p>
<p>I am now developing a biogeochemistry course that is not limited to aquatic systems and I am looking for a summary of field methods for terrestrial systems.</p>
<p>Is there a book that summarizes terrestrial field ecology methods similar to Wetzel and Likens and Hauer and Lamberti?</p>
| [
{
"answer_id": 2470,
"pm_score": 3,
"text": "<p><a href=\"http://books.google.com/books/about/Methods_in_Ecosystem_Science.html?id=N_pGrSntap0C\" rel=\"nofollow\">Methods in Ecosystem Science</a> edited by Oswaldo Sala, Rob Jackson, Hal Mooney, and Robert Howarth is a classic standard reference used by ... | [
{
"answer_id": 3541,
"pm_score": 3,
"text": "<p>Take a look at <a href=\"http://books.google.com/books/about/Field_and_laboratory_methods_for_general.html?id=WFfwAAAAMAAJ\" rel=\"nofollow\">Field and Laboratory Methods for General Ecology</a> by James E. Brower, Jerrold H. Zar, and Carl N. von Ende.</p>... |
2,462 | <p>I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying that PAX6 can be considered as 3 TFs in one protein, acting independently in different situations: </p>
<p><a href="http://dx.doi.org/10.1186/1471-213X-10-39">Relative roles of the different Pax6 domains for pancreatic alpha cell development</a></p>
<p>Does anybody know of more examples like this?</p>
| [
{
"answer_id": 2466,
"pm_score": 5,
"text": "<p>The <a href=\"http://www.nf-kb.org\" rel=\"nofollow\">NF-κB</a> family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of <a href=\"http://en.... | [
{
"answer_id": 2475,
"pm_score": 2,
"text": "<p>There was a paper published in Cell last year that has shown that the binding motif of a Hox transcription factor will change depending on whether there's a co-factor bound to the Hox. </p>\n\n<blockquote>\n <p>Slattery <em>et al.</em> (2011) <a href=\"ht... |
2,473 | <p>Lately, I've started exercising in the gym and outside. I've also started to look at the details of food I eat.</p>
<p>Food usually has a label saying the amount of energy is inside it. For example, some chocolate says it has 400 kilocalorie for 100 grams.</p>
<p>I have some questions about that:</p>
<ol>
<li><p>Does the label say the amount of total chemical energy exists inside the food, which will be released if burned, or the energy available to the human body after digested, and because digesting requires energy, the food contains actually MORE energy then written?</p></li>
<li><p>When I'm riding on a static bike, it has a screen which counts the kcal I burn. It has a thing connected to my arm, measuring my heart beat. After about an hour of riding, it said I used about 700 kcal. Is it the amount of work I did, i.e if there was a battery connected to the bicycle, I'd generate 700 kcal of electricity, OR, the amount of energy my body LOST, because muscle efficiency is far from 100% (so, I lost 700 kcal, but generated only 150 kcal of electricity, for example)</p></li>
<li><p>When doing a physical activity, the heart beat and breathing rate increases. Lets say I'm riding a bicycle or running. Whats the ratio between energy consumed by the muscle to energy consumed by the lungs or heart?</p></li>
</ol>
| [
{
"answer_id": 2478,
"pm_score": 4,
"text": "<ol>\n<li><p>I speak only for the U.S. regulations: the calorie labels on wrappers refer to the energy released when burned. Sometimes these are inaccurate. Many dieticians recommend calculating the calories based on weights of protein, carbohydrates and fats... | [
{
"answer_id": 2474,
"pm_score": 1,
"text": "<p>1) It depends on each country and your minister. In Finland, the thing is done so that it says the energy stored in food, which will be released if burned.</p>\n\n<p>2) It is the energy pushed to the bike when the bike does not take into account your pulse... |
2,477 | <p>After following a course in Permaculture, I realised that if I want to get serious about it, I need to be able to distinguish plants. So I am looking for an online Video course on Plant Taxonomy and Physiology. My understanding is that it is a fairly standard course in basic Botany degrees, and since there are more and more school that put their material online it is quite possible that one of them might have placed this online too. Any suggestion?</p>
| [
{
"answer_id": 2478,
"pm_score": 4,
"text": "<ol>\n<li><p>I speak only for the U.S. regulations: the calorie labels on wrappers refer to the energy released when burned. Sometimes these are inaccurate. Many dieticians recommend calculating the calories based on weights of protein, carbohydrates and fats... | [
{
"answer_id": 2474,
"pm_score": 1,
"text": "<p>1) It depends on each country and your minister. In Finland, the thing is done so that it says the energy stored in food, which will be released if burned.</p>\n\n<p>2) It is the energy pushed to the bike when the bike does not take into account your pulse... |
2,489 | <p><a href="http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Active_Site#Models" rel="noreferrer">This Wikibook</a> shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is the proper one. However, my biochemistry professor mentioned that often times, enzymes behave as lock and key. I also noticed that the Wikibook doesn't mention which model is in fact true.</p>
<p><em>The Lock and Key Model</em>
<img src="https://i.stack.imgur.com/ekkPN.jpg" alt="The Lock and Key Model"></p>
<p><em>The Induced Fit Model</em>
<img src="https://i.stack.imgur.com/cBJ47.jpg" alt="The Induced Fit Model"></p>
<p><strong>Is there currently one accepted model? Which is it, and why?</strong></p>
| [
{
"answer_id": 2490,
"pm_score": 4,
"text": "<p>This is true of all protein binding as well as the special case of enzyme-substrate interaction:</p>\n\n<p>Various proteins are more dynamic than others: some have only one or two overall conformations and are relatively implastic otherwise. An example wou... | [
{
"answer_id": 2494,
"pm_score": 2,
"text": "<p>Both models are true depending on how you frame the mechanisms of catalysis. As mentioned by @Blues, proteins are highly dynamic. In that manner, a protein will adopt both the unbound active state shown in the induced fit model and the complementary shape ... |
2,498 | <p>A few friends of mine told me that salt provides zero nutritional value to us, and in fact can harm our bodies. Now, these guys are medical students, and being an engineering student myself, I decided not to argue with them. The rest of this question assumes that this fact is true, so if it's not, you can just go ahead and call me out now...</p>
<p>So here's my understanding of things: we 'like' doing things because of our instincts, which have slowly become refined over millions of years. For example, I 'like' eating foods with fat in it because my instinct compels me to do so. Fat is 'good' for my body, since it provides a lot of energy (obesity problems aside).</p>
<p>So are there certain things, such as eating salt, that are not in fact beneficial in any way, and we only do these things because we were trained to as children? This is the only thing I could come up with, but it's not a very satisfying explanation for a few reasons. First, I think humans have been eating salt for a long time. This would mean that most likely, it is actually our 'instinct' to eat salt. Also, salt is eaten in every culture today, which has the same implication.</p>
<p>So is there some better explanation?</p>
| [
{
"answer_id": 2502,
"pm_score": 6,
"text": "<p>In developed countries we usually consume enough salt (sodium to be exact) without actually adding table salt to food. Everything can become toxic when consumed in excess - even water - and when we frequently add more salt to foods, we tend to consume sodi... | [
{
"answer_id": 23282,
"pm_score": 1,
"text": "<p>I agree with Armatus, however I feel his answer incomplete.</p>\n\n<p>Sodium (along with chlorine) is the most important ion in the blood if we are talking about osmolarity and water transport. Water wants to move to the high osmolarity places so its tran... |
2,505 | <p>Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?</p>
<p>If you overexpress a gene for a protein involved in signal transduction (e.g., a kinase, scaffold, or receptor) by vector cell transfection, then you overdrive the cell using this signaling pathway, it's useful to isolate the pathway and study them.</p>
<p>Is there any way to modify the overall gene expression or cell differential expression pattern by gene transfection? I think this would work if you delivered a gene for overexpression in proteins involved for RNA processing (e.g., splicing, ribosomal proteins, etc.), RNA transcription (e.g., TFs) or protein translation.</p>
| [
{
"answer_id": 7805,
"pm_score": 3,
"text": "<blockquote>\n <p>Which are the factors that modify the overall gene differential\n expression by introducing a vector for single-gene overexpression</p>\n</blockquote>\n\n<p>This is a very relevant question and the field of experimental biology needs to re... | [
{
"answer_id": 7068,
"pm_score": 1,
"text": "<p>There are lots of different overexpression vectors (usually they're promoters/regulatory elements upstream of the transfected gene). Here's an example of an overexpression vector (overexpression vector pCAMBIA1300S) that was used to overexpress a transcrip... |
2,509 | <blockquote>
<p><strong>Possible Duplicate:</strong><br>
<a href="https://biology.stackexchange.com/questions/1981/how-many-genes-do-we-share-with-our-mother">How many genes do we share with our mother?</a> </p>
</blockquote>
<p>I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, workers were 3/4ths related to each other, so it was in their gene's interest to care for each other instead of having their own, half-related offspring.</p>
<p>However isn't it the case that members of the same species are much more related than 1/2 or 3/4s? I've read that we share anywhere from 95-99% of our genes with chimpanzees. Also I believe I've read (perhaps in Pinker) that we share some 60% of our genes with daffodils.</p>
<p>So when they talk about the relatedness of social insects, and they say it's 1/2 or 2/3 or 1/4, aren't they really talking about the 1% to 5% of genes that are in play in sexual reproduction within the species? In other words, aren't I 97% + 1/2 * 3% related to my sister, assuming human beings share 97% of our genes?</p>
| [
{
"answer_id": 2573,
"pm_score": 3,
"text": "<p>In evolutionary genetic comparison, you are talking about members within species. They will share almost <em>all</em> genes, because if they didn't they would belong to a different species.</p>\n\n<p>However, within species there exist different <em>versio... | [
{
"answer_id": 2572,
"pm_score": 0,
"text": "<p>The part that is probably specific to this question is that some species of insects divide their population in the reproducing individuals, that are usually diploid and the working individuals, that are sometimes haploids, meaning they only have one copy o... |
2,554 | <p>In genetics, does the word "polymorphism" properly refer to genes, to phenotypes, or both? For example, if there are two alleles that lead to differences in the structure of the D2 neuroreceptor, would I talk about "a polymorphism in the gene for the D2 neuroreceptor" or "a polymorphism in the D2 neuroreceptor"? I've seen both uses in the literature, but it's not my primary field, so I don't have a feel for whether one is more widely accepted.</p>
<p>Bonus question: is there a preference regarding "polymorphism of," "polymorphism in," and "polymorphism on"? </p>
| [
{
"answer_id": 2556,
"pm_score": 4,
"text": "<p>The term \"polymorphism\" itself is more generally defined as \"<em>the quality or state of existing in or assuming different forms</em>\" (<a href=\"http://www.merriam-webster.com/dictionary/polymorphism\">Merriam-Webster dictionary</a>). So I guess seman... | [
{
"answer_id": 2561,
"pm_score": 0,
"text": "<p>A difference in phenotypes might result from polymorphisms, but one doesn't refer to those differences as polymorphisms.</p>\n"
}
] |
2,555 | <p>I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides were <em>only</em> connected by one covalent disulfide bridge, would this be considered as quaternary structure, assuming that non-covalent interactions between the subunits are either negligible or even repulsive?</p>
<p>In other words, <strong>can a disulfide bridge, on its own, convey quaternary structure?</strong> </p>
<p>On a side note, are there any notable examples of this type of interaction?</p>
| [
{
"answer_id": 2557,
"pm_score": 3,
"text": "<p>I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within... | [
{
"answer_id": 2558,
"pm_score": 2,
"text": "<p>I've always just gone with the name hetereodimer but there isn't any technical reason why it isn't a quaternary structure. As for an example, I work with antibody fragments or FAbs and cys-diabodies which are exactly that, two distinct polypeptides that ar... |
2,583 | <p>All winged vertebrates have wings which are homologous to each other and to the forelimbs of the non-winged vertebrates. But what about insect wings? Are all insect wings homologous, and are there any homologies between insect wings and any vertebrate limbs?</p>
| [
{
"answer_id": 2587,
"pm_score": 4,
"text": "<p>Insects and vertebrates are extremely distantly related: they're on opposite sides of the oldest split among bilaterally symmetric animals. Their most recent common ancestor lived in the pre-cambrian and was almost certainly worm-shaped with no limbs at a... | [
{
"answer_id": 84958,
"pm_score": 0,
"text": "<p>Insect wings (and legs) and tetrapod limbs are analogous structures. Insects are protostomes, whereas vertebrates are deuterostomes; both lineages separated in the Precambrian from something resembling a worm (some Ediacaran organisms, such as Kimberella,... |
2,595 | <p>I am a computer scientist that studies biology and bioinformatics.
In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and behavior of genes and proteins in learning.</p>
<p>By <em>learning</em>, I mean the human process: the information <em>I</em> is absent at time <em>T</em>, and present at time <em>T+1</em>.</p>
<p>I would like to study more this problem, and I am wondering: how do proteins and genes behave during learning?
I have read that proteins that participate in learning are called marker proteins. Is it true? Which role do they have?</p>
<p><strong>Where could I find some resources to study this fascinating problem?</strong></p>
<p>Thank you very much!</p>
| [
{
"answer_id": 2598,
"pm_score": 4,
"text": "<p>The storage of memories in cells is rarely thought of on the protein level of the cell. Cells are usually given a developmental state, but no memory. A cell may become a liver cell, cancerous, or diabetic, but this is not memory, but a physiological chan... | [
{
"answer_id": 2601,
"pm_score": 2,
"text": "<p>If you're interested in understanding the maintenance of state, history, and information, I would look at <a href=\"http://en.wikipedia.org/wiki/Hysteresis\" rel=\"nofollow\">hysteresis</a>. The classic biophysics model for studying hysteresis has been the... |
2,609 | <p>I don't understand why darker skin is advantageous in hotter climates. Wouldn't it absorb more of the heat? I have heard that it reduces the incidence of cancer, but I would think absorbing more radiation would increase the risk?</p>
| [
{
"answer_id": 2636,
"pm_score": 5,
"text": "<p>One of the important pigments that the earlier answer hinted at is <a href=\"http://en.wikipedia.org/wiki/Melanin\" rel=\"noreferrer\">melanin</a>. Melanin is a brown pigment with photoprotectant properties. </p>\n\n<p>As you correctly identified in your... | [
{
"answer_id": 2610,
"pm_score": 2,
"text": "<p>I heard one proposition that has to do with cancer, and the other side of the coin is related to vitamin D and calcium. If I remember correctly, living in a sunnier climate can affect your skin and cause cancer. The trick is to produce pigments in the epid... |
2,618 | <p>Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?</p>
| [
{
"answer_id": 2620,
"pm_score": 4,
"text": "<p>Essentially, yes, \"proteins that we consume form new proteins that are different\".</p>\n\n<p>The processes are each of them topics for themselves. In short, consumed proteins are digested by <a href=\"http://en.wikipedia.org/wiki/Peptidase\">peptidases</... | [
{
"answer_id": 2619,
"pm_score": 2,
"text": "<p>You ingest daily dietary protein which your body <a href=\"http://en.wikipedia.org/wiki/Protein_hydrolysis\" rel=\"nofollow\">hydrolyzes</a> to get all the building blocks for other proteins (amino acids).</p>\n\n<p>Also, from diet you can get <a href=\"ht... |
2,622 | <p>Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (<em>S. cerevisiae</em>) and <em>S. pombe</em> genomes? Even if these are only <em>de novo</em> predictions, I would like to have access to them.</p>
| [
{
"answer_id": 2620,
"pm_score": 4,
"text": "<p>Essentially, yes, \"proteins that we consume form new proteins that are different\".</p>\n\n<p>The processes are each of them topics for themselves. In short, consumed proteins are digested by <a href=\"http://en.wikipedia.org/wiki/Peptidase\">peptidases</... | [
{
"answer_id": 2619,
"pm_score": 2,
"text": "<p>You ingest daily dietary protein which your body <a href=\"http://en.wikipedia.org/wiki/Protein_hydrolysis\" rel=\"nofollow\">hydrolyzes</a> to get all the building blocks for other proteins (amino acids).</p>\n\n<p>Also, from diet you can get <a href=\"ht... |
2,634 | <p>I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more powerful than in humans due to the extent of linkage disequilibrium and other population genetics considerations. Some claims say that many GWAS studies in dogs are 10-20x more powerful than many GWAS studies in humans. I have also heard from pigeons (pigeon-omics) to be a similar case. I would like to know if there are other comparisons for other species and the relative power of discovery for GWAS studies compared to human. For example, are there any numbers for yeast, <em>Drosophila sp.</em>, <em>C.elegans</em>, zebrafish and then also for plants like maize, rice, etc.?</p>
| [
{
"answer_id": 2637,
"pm_score": 4,
"text": "<p>Part of the increase in power to detect a genetic association via GWAS-genotyping comes from long haplotypes. Many dog breeds went through selective breeding bottlenecks 100-200 years ago. Many lab model organisms, such as flies, worms and plants, have rec... | [
{
"answer_id": 44768,
"pm_score": 1,
"text": "<p>question looks like it's been dormant for a while, but i think there's some discussion to be had here-</p>\n\n<p>I would argue that in many (most?) of the model organisms, power would be much greater than humans. Frequently (worms, mice, plants, yeast) yo... |
2,645 | <p>I've read that they all share some genes, internal structure, and behaviour with each other, but with different degrees of overlap depending of what the function is. E.g., archaea have some eukaryotic and some bacterial function, and eukaryotes have bacterial function in the form of mitochondria and plastids.</p>
<p>However I'm finding the nitty-gritty of all this rather confusing. Could anyone please explain some of the detail for me as I can't seem to make any sense of this from reading Wikipedia, etc.</p>
| [
{
"answer_id": 2648,
"pm_score": 4,
"text": "<p>The relationship between the three is so overly complicated because of horizontal gene transfer, i.e. cells sharing parts of their genome with others instead of the normal passing-down to the next generation. This works between eukaryotes, archaea and bact... | [
{
"answer_id": 2647,
"pm_score": 2,
"text": "<p>Indeed the situation is a bit complicated and not totally well understood. Archaea and bacteria are superficially very similar, they're both small, have circular chromosomes, and not a lot of internal complexity. However, there are some very important di... |
2,665 | <p>From what I read on wikipedia they are made of collagen. Collagen is just a protein. Right? How is this collagen structured (I imagine like fibers). Aren't there cells in this fibers as well?</p>
<p>From this picture:<br>
<img src="https://upload.wikimedia.org/wikipedia/commons/6/66/Tendon_-_very_high_mag.jpg" alt="Tendon H&E"> </p>
<p>Is the pink stuff the collagen? and the purple stuff the tenocytes?</p>
<p>If someone can expand on this with a picture preferably, it would be great.</p>
| [
{
"answer_id": 2666,
"pm_score": 4,
"text": "<p>As you correctly say, tendons are made up of collagen fibers. Collagen is one of the most important proteins (or, to be more specific, family of proteins, as there are many types of collagen) forming connective tissue in the body.</p>\n\n<p>Collagen molecu... | [
{
"answer_id": 85109,
"pm_score": 1,
"text": "<p>{4} has a similar micrograph as yours but with some labels:</p>\n\n<p><a href=\"https://i.stack.imgur.com/f68LX.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/f68LX.jpg\" alt=\"enter image description here\"></a></p>\n\n<p>with the... |
2,668 | <p>Single crossovers in circular pieces of DNA do not seem to be a big topic, because if they happened, they would lead to a kind of combined chromosome with two inner strands and one large outer strand. (A bit like an 8)</p>
<pre><code> ________
| ____ |
| | | |
| |____| |
| ____ |
| | | |
| |____| |
|________|
</code></pre>
<p>But do these single crossovers actually not <em>occur</em>, for example because the crossover machinery is physically not able to do it, or do we just not <em>observe</em> them because they will inevitably lead to cell death and/or the chromosome somehow breaking?</p>
| [
{
"answer_id": 6849,
"pm_score": 3,
"text": "<p>Although crossover events can be observed in mitosis (mitotic recombination), they most frequently occur in prophase I of meiosis (crossing over in bivalents). Circular chromosomes are common in prokaryotes, but eukaryotes have linear chromosomes. Remember... | [
{
"answer_id": 51104,
"pm_score": 0,
"text": "<p>Looking back at this question, I think this stems from a misconception in the first place. Crossovers are not events that affect single DNA strands but always both strands. The described double-ringed DNA molecule might exist as an intermediate in the pro... |
2,690 | <p>How do you calculate or predict the charge of a protein at pH 7 given a fasta sequence?</p>
<p>Any papers or online servers to do this is well appreciated.</p>
| [
{
"answer_id": 2691,
"pm_score": 3,
"text": "<p>ExPASy to the rescue! Although I didn't comb through all the tools, this nifty website provides quite the myriad of bioinformatics resources which most certainly contains the tool to calculate what you want.</p>\n\n<p>Bear in mind though, most tools will t... | [
{
"answer_id": 8276,
"pm_score": 1,
"text": "<p>To calculate the charge at different pH:</p>\n\n<p>At pH 3 K, R, H are + and D,E have no charge so add up all of the K,R,H in the sequence and that is your net charge at pH 3\nAt pH 6 K, R, H are + but now D,E are (-) so subtract one total from the other t... |
2,699 | <p>If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?</p>
| [
{
"answer_id": 4948,
"pm_score": 4,
"text": "<blockquote>\n <p>If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?</p>\n</blockquote>\n\n<p>As with <strong>everything</strong> in Evolutionary Biology, you... | [
{
"answer_id": 9598,
"pm_score": 0,
"text": "<p>Who says we are not streamlined? </p>\n\n<p>One could easily imagine body structures that would cause much greater drag in air and humans do not have them.</p>\n"
}
] |
2,700 | <p>I know from reading that a human in vacuum needs a space-suit to survive. </p>
<p>Is the body of any organism on Earth capable of living equally in vacuum, and on/below Earth's surface within the atmosphere?</p>
| [
{
"answer_id": 2703,
"pm_score": 4,
"text": "<p>Remarkably, <a href=\"http://en.wikipedia.org/wiki/Tardigrade\">Tardigrades</a> are multi-cellular animals which can <a href=\"http://www.newscientist.com/article/dn14690-water-bears-are-first-animal-to-survive-space-vacuum.html\">survive the vacuum of spa... | [
{
"answer_id": 2729,
"pm_score": 2,
"text": "<p>Adding to Noah's answer, some lichens can survive the vacuum of space too. In an experiment led by Leopoldo Sancho from the Complutense University of Madrid, two species of lichen - <em>Rhizocarpon geographicum</em> and <em>Xanthoria elegans</em> - were se... |
2,716 | <p>I'm having a conceptual nightmare trying to understand when a group of cells may become cancerous and the more resources I consult the more confused I seem to get.</p>
<p>In order for a cell to become cancerous, does it have to mutate to knock out tumour suppressor genes <strong>and</strong> have a proto-oncogene become an oncogene? </p>
<p>I'm currently working on the basis that that is the case, or at least that a mutated TSG on its own will not cause uncontrolled division. However wikipedia seems to suggest that an oncogene alone can cause uncontrolled division with a functional TSG in place. </p>
<p>It could be a flaw in the idea I have that tumour suppressor genes only trigger apoptosis once a cell has started to divide rapidly, are they actually carrying it out to a regular schedule independent of oncogene presence? </p>
| [
{
"answer_id": 2720,
"pm_score": 2,
"text": "<p>There is a nice <a href=\"http://www.nature.com/nature/journal/v458/n7239/full/nature07943.html\" rel=\"nofollow\">nature paper</a> by Dr. Micheal Stratton et al. that I think might be a good place to start.</p>\n\n<p>I think answering you question is comp... | [
{
"answer_id": 2717,
"pm_score": 2,
"text": "<p>The typical idea is that several \"hits\" are required. The difference between proto-oncogene and TSG is mainly in their heritability - TSG mutations are usually recessive (because a heterozygote will still express sufficient suppressor, e.g. p53) whereas ... |
2,719 | <p>It is my understanding that the hair on the head is there to protect us from sunburn. I've never seen a bald animal, so isn't evolution in charge of addressing these type of things? </p>
<p>How is it that evolution gave us a thumb, but hasn't found a way to keep the hair on our heads?</p>
| [
{
"answer_id": 2726,
"pm_score": 4,
"text": "<p>As is typical for questions about fitness, this question has more than one valid answer. </p>\n\n<p>The essential question @AndrewSalmon is answering is the right one:</p>\n\n<p>\"If evolution eliminates disadvantages, why can xyz trait still be seen the ... | [
{
"answer_id": 2725,
"pm_score": 1,
"text": "<p>The closest research I can find with a little poking is <a href=\"https://doi.org/10.1007/s00439-009-0668-z\" rel=\"nofollow noreferrer\" title=\"Hillmer, A.M., Freudenberg, J., Myles, S. et al. Recent positive selection of a human androgen receptor/ectody... |
2,721 | <p>Do genes that occupy a similar locus on the genome have correlated function, specifically in human beings? It is my understanding that adjacent genes are inherited together, and so location plays a role there. However it terms of function, I don't know to what extent location plays a role. Furthermore, if say two adjacent genes have the same expression, does this necessarily mean that their function is correlated, or is that interpretation stretch?</p>
| [
{
"answer_id": 2731,
"pm_score": 4,
"text": "<p>In bacteria, this is often true. This is because more than one gene is often transcribed onto a single RNA. This grouping of genes is called an operon. It is usually true that these have a related function because they are being translated to protein in... | [
{
"answer_id": 27763,
"pm_score": 3,
"text": "<p>A group of tightly linked genes that are involved in similar molecular pathway is called a <a href=\"http://en.wikipedia.org/wiki/Supergene\" rel=\"nofollow noreferrer\">supergene</a>.</p>\n\n<p>For the pleasure to formulate a slight opposition to @shiget... |
2,724 | <p>What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have a) a strong sense of smell, b) the ability to fly and c) a comfortable couch shaped saddle on its back. What's the sequence of steps you need to take so that you can create this life-form in the lab?</p>
<p>I realize that we are probably far away from solving this very general problem. But perhaps there are some smaller subproblems that we do know how to solve.</p>
<p>For example, as far as I gather, you can probably make any living being fluorescent green in color by inserting into its genome the gene responsible for expressing the Green Fluorescent Protein. So may be if we limit the set of features one is allowed to choose from, the above problem can be solved. So my first question of the set of questions is:</p>
<p>1) What features can be easily inserted into almost any organism easily?</p>
<p>Next, I imagine that to design and create an artificial life-form will consist of three steps: </p>
<ol>
<li>Figure out which proteins will give rise to those feaures, </li>
<li>Design a genome that will express those proteins in the right quantities and </li>
<li>Implant that genome into a cell and actually let the being grow.</li>
</ol>
<p>2) Is the above sequence of steps correct, or am I missing something?</p>
<p>3) What is the state of the art for each of these steps?</p>
<p>Finally, in light of the recent spur in the open source biology groups and DIYbio enthusiasts, I feel that there might be some very simple but really cool things related to my question that you can already do in your garage. For example, may be there is some very simple single-cell life-form that's so well understood that you can add or subtract tons of features from it with a budget of a few hundred dollars. So my final question is:</p>
<p>4) What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)</p>
| [
{
"answer_id": 2727,
"pm_score": 4,
"text": "<p>The problem is of course very complex so take my answers as simplifications.</p>\n<p>Most transgenesis so far has been done on unicellular beings (bacteria, yeast), which we can change as much as we want fairly "easily", plants, insects and some ... | [
{
"answer_id": 74532,
"pm_score": 1,
"text": "<p>This answer is mostly meant to be an addition to nico's answer, which while correct and on the point, does not completely cover what we can do nowadays.</p>\n\n<blockquote>\n <p>1) What features can be easily inserted into almost any organism\n easily?... |
2,732 | <p>I know there's a similar question <a href="https://skeptics.stackexchange.com/questions/734/do-men-have-a-monthly-cycle">here</a>. But that discussion dissolved into lunar cycle and a correlation with it. I want to find more towards the original question of is there a periodic hormone cycle in men.
The <a href="http://answers.google.com/answers/threadview?id=431376" rel="nofollow noreferrer">links</a> i have read suggest that there's probably a daily one for sure. But few hint at monthly ones <a href="http://www.theirritablemale.com/" rel="nofollow noreferrer">too</a>.
That link seems to have very shaky science, but my biology is too weak for me to find the actual studies. Anyone else with more informed opinions? Any studies tracking purely hormone levels in men over a period of couple of months/years?</p>
<p>[EDIT]
I understand it's clear there are cycles within the day or around the 24-hr mark now. I still am looking for studies focusing on longer term cycles like week,months etc.</p>
| [
{
"answer_id": 3480,
"pm_score": 4,
"text": "<p>I found this -</p>\n<blockquote>\n<p>Celec et al. (2003) Circatrigintan cycle of salivary testosterone in human male. Biological Rhythm Research 34: 305-315</p>\n<p>Conclusion. We believe that this is the first study demonstrating the existence of circatri... | [
{
"answer_id": 2740,
"pm_score": 3,
"text": "<p>Short answer: yes.</p>\n\n<p>Although clearly the infradian changes in steroid hormones in females are quite \"obvious\", other changes are less evident, but happen nonetheless in males as well as in females.</p>\n\n<p>Most of the hormones produced by endo... |
2,778 | <p>We are planning to send an ecoli strain to another lab. What is the appropriate way to do so. No MTA is required but the options seem to be using filter paper or sending a glycerol stock on dry ice.</p>
| [
{
"answer_id": 2782,
"pm_score": 4,
"text": "<p>I believe Addgene send strains as bacterial stabs.</p>\n\n<p>This is the protocol from Qiagen.</p>\n\n<blockquote>\n <p>E. coli strains can also be stored for up to 1 year as stabs in soft\n agar. Stab cultures are used to transport or send bacterial str... | [
{
"answer_id": 2781,
"pm_score": 2,
"text": "<p>I think the best way is to use <a href=\"http://en.wikipedia.org/wiki/Freeze-drying\" rel=\"nofollow\">lyophilization</a>. The American Type Culture Collection send the strains that way.</p>\n"
}
] |
2,783 | <p>To check a protein expression I pelleted a small amount of <em>E. coli</em> before and after induction and lysed them by redissolving them in SDS-PAGE loading buffer and heating them to 95 °C for 1 minute.</p>
<p>This lead to a solution with some very sticky and viscous parts in it, that make pipetting the sample into the gel wells extremely annoying. As far as I heard, this is probably genomic DNA, and my usual way to deal with this is to centrifuge the samples and only pipet a small part out from the top. This does seem to help sometimes, but not always.</p>
<p>How can I avoid the formation of that sticky and viscious stuff or how can I avoid pipetting that stuff into my wells?</p>
| [
{
"answer_id": 2784,
"pm_score": 4,
"text": "<p>Yes, it is the genomic DNA that is causing you trouble. Although a brief 1000g spin should bring it all down, the pellet is never tight and you almost always are going to pull up some gunk with the clear supernatant. A better solution is to include a quick... | [
{
"answer_id": 2791,
"pm_score": 0,
"text": "<p>In addition to gkadam's suggestion, for my protein gels, I heat my samples at 95C for 10 minutes. I would also look into different lysing conditions. Rather than using SDS loading buffer, look into more vigorous lysing steps either with a kit like bug-bust... |
2,804 | <p>As far as I understand it, PCR can be used to make many copies of one gene. My question is, is it possible to sequence DNA after PCR and is it easier than sequencing it via other methods. If it is possible, how would you do it?</p>
| [
{
"answer_id": 2819,
"pm_score": 4,
"text": "<p>All sequencing methods, be it classical Sanger sequencing or next-generation sequencing (or even third generation) need a certain amount of DNA to work with.</p>\n\n<p>You either need to extract DNA from a large-ish tissue sample or you need to amplify DNA... | [
{
"answer_id": 2805,
"pm_score": 2,
"text": "<p>We do it all the time. You can use one of your end/flanking primers and use that as a primer for sequencing. Companies will typically have a setup where they can take a \"premixed\" sample.</p>\n\n<p>Since we tend to use sequetech, here are their details: ... |
2,839 | <p>Why do we sweat after running?
Also we sweat sometime after drinking lots of water. Why it is so?
Can someone please enlighten me in this regard? </p>
| [
{
"answer_id": 2842,
"pm_score": 4,
"text": "<p>Exercise, such as running, increases muscle activity. This increases the energy demand of these tissues, which increases the rate of cellular respiration. Respiration releases heat as a by-product, therefore the body is hotter during and after exercise. ... | [
{
"answer_id": 21206,
"pm_score": 2,
"text": "<ol>\n<li><p>If the meal you eat is hot, you will get some heat and if your body will consider it as excessive heat, it will try to get rid of some by making you sweat.</p></li>\n<li><p>Drinking water and sweating after a meal may be coincidentally related a... |
2,846 | <p>A family member suffers from migraines so I have been reading a little around the subject. </p>
<p>There seem to be any number of "triggers", but I have seen mention several times of the role of histamine in migraine activation as an active area of research. The suggestion is that high histamine levels in the body can cause migraines.</p>
<p>Is there solid evidence that histamine can trigger migraines? How does this mechanism operate?</p>
| [
{
"answer_id": 2847,
"pm_score": 4,
"text": "<p>Yes, this is true.</p>\n<p>Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase. NO is then available to act locally on the vasculature as a vasodilator.</p>\n<p>NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to ... | [
{
"answer_id": 7061,
"pm_score": 0,
"text": "<p>I've experienced migraines for 10 years, and now for the last 14 months that I've taken anti histamine medicine to see if there would be a benifit I've had good results. The frequency has dropped from approx 3 times a month to a migraine approx every 6-8 w... |
2,870 | <p>I am looking to purchase Pyruvate Kinase from the <a href="http://www.sigmaaldrich.com/catalog/search?interface=All&term=P9136&lang=en&region=GB&focus=product&N=0%20220003048%20219853121%20219853286&mode=match%20partialmax" rel="nofollow">Sigma Website</a>, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein.</p>
<p>Does this mean one unit is one protein? so 1KU is 1000 units of protein?
What is the relationship between the KU and mg? and how can I use this relationship to calculate my concentration in um or mg.</p>
<hr>
<p>EDIT</p>
<p>In this <a href="http://pubs.acs.org/doi/abs/10.1021/jp906242m" rel="nofollow">paper</a> (look at the methods section) they calculated the concentration of 25,000 units of calmodulin in 0.5 ml to be approximately 75um which is 40,000 units/mg. How did they calculate this? </p>
| [
{
"answer_id": 2847,
"pm_score": 4,
"text": "<p>Yes, this is true.</p>\n<p>Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase. NO is then available to act locally on the vasculature as a vasodilator.</p>\n<p>NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to ... | [
{
"answer_id": 7061,
"pm_score": 0,
"text": "<p>I've experienced migraines for 10 years, and now for the last 14 months that I've taken anti histamine medicine to see if there would be a benifit I've had good results. The frequency has dropped from approx 3 times a month to a migraine approx every 6-8 w... |
2,883 | <p>From my reading on <em>M. tuberculosis</em>, I know that this organism has a pretty high mutation rate due to uncorrected sloppy replication, which leads to a high rate of development of spontaneous resistance to treatment.</p>
<p>Are there species that can beat <em>M. tuberculosis</em> in this degree of mutation, due to polymerase sloppiness or other mechanism?</p>
| [
{
"answer_id": 3630,
"pm_score": 3,
"text": "<p>You seem to be assuming that mutation rates are somehow constant over evolutionary time. They are not. Mutation rates will change according to the stresses a species is subjected to. If you take a bacterial population and place it in a stressful environmen... | [
{
"answer_id": 3631,
"pm_score": 2,
"text": "<blockquote>\n <p>From my reading on M. tuberculosis, I know that this organism has a pretty high mutation rate</p>\n</blockquote>\n\n<p>Huh, that's news to me. In fact, Mtb has a rather low mutation rate and rather low genetic variance. See the paper by <a ... |
2,884 | <p>What is the possible health issue the women would face in this record?</p>
<blockquote>
<p>The record for most children born to a single couple belongs to the
first wife of Feodor Vassilyev of Russia. In 27 pregnancies between
1725 and 1765 she gave birth to 16 pairs of twins, 7 sets of triplets,
and 4 sets of quadruplets for a grand total of 69 children.</p>
</blockquote>
| [
{
"answer_id": 2890,
"pm_score": 4,
"text": "<p>A common problem for any woman who has experienced pregnancy and childbirth is damage to the <em>levator ani</em> muscle, which comprises a portion of the \"pelvic floor.\"</p>\n\n<p><img src=\"https://i.stack.imgur.com/5jZmr.png\" alt=\"enter image descri... | [
{
"answer_id": 41710,
"pm_score": 1,
"text": "<p>One health risk from going through multiple pregnancies is the risk of a <em><a href=\"http://www.m.webmd.com/women/guide/prolapsed-uterus\" rel=\"nofollow\">uterine prolapse</a></em>, also called a <em>prolapsed uterus</em>. The weakening of ligaments ba... |
2,885 | <p>Cockroaches are known to live in very dirty places like sewers. Does this cause them to evolve to be stronger against parasites and bacteria? Recently I read online that cockroaches can sustain radioactive harm 6-15 more than humans, so does that mean that cockroaches are less likely to get cancer?</p>
<p>refernece for the radioactive exposure:</p>
<p><a href="http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience" rel="nofollow">http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience</a></p>
| [
{
"answer_id": 8077,
"pm_score": 2,
"text": "<p>AndroidPenguin, where did you read that our immune systems are far better than those of 'a cockroach'? This seems pretty strange to me, but I'd be interested in reading a study that compared human and cockroach immune systems if you can provide a reference... | [
{
"answer_id": 8075,
"pm_score": 0,
"text": "<p>Different pathogens affect different organisms. We live longer because we have an advanced immune system far better than that of a cockroach and because of a hundred other reasons. A cockroach that were to keep itself well fed and clean would live longer, ... |
2,891 | <p>Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor.
E.g. Caves, Undersea</p>
<p>For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1" spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?</p>
| [
{
"answer_id": 8077,
"pm_score": 2,
"text": "<p>AndroidPenguin, where did you read that our immune systems are far better than those of 'a cockroach'? This seems pretty strange to me, but I'd be interested in reading a study that compared human and cockroach immune systems if you can provide a reference... | [
{
"answer_id": 8075,
"pm_score": 0,
"text": "<p>Different pathogens affect different organisms. We live longer because we have an advanced immune system far better than that of a cockroach and because of a hundred other reasons. A cockroach that were to keep itself well fed and clean would live longer, ... |
2,892 | <p>(after some deliberation in the comments, I've decided to make the question more general)</p>
<p>An <a href="http://en.wikipedia.org/wiki/Eschar" rel="nofollow">eschar</a> or "dry scab" often forms at a site of injury over a large cut or sore.</p>
<p>It seems as though the healing scab portion binds more strongly to the other scab cells than to those of the surrounding healthy tissue initially, as evidenced by the ability to remove the scab <em>en masse</em> without disturbing the edges of the actual wound (in surgical debridement or when the area is "picked" at). Then, the eschar bonds then bonds more strongly with the edges of the wounds (so it's more difficult to remove), and then finally, the underlying newly formed skin seems to push it off completely.</p>
<p>Does this accurately describe the "lifecycle" of a common dry scab, or are there other well defined stages in the process? What types of cells (platelets in the beginning? epithelials at the end?) are involved with each stage of the process?</p>
| [
{
"answer_id": 3011,
"pm_score": 3,
"text": "<p>Response to cutaneous tissue damage occurs is several distinct but overlapping phases. First an scab is formed as the blood is 'allowed' to clot. A matrix is formed as the platelets adhere to one another, which contracts and 'dries' (forces out the serum) ... | [
{
"answer_id": 74593,
"pm_score": 0,
"text": "<p>First, eschar (\"es-CAR\") is NOT a scab. They are entirely different, both physically and biochemically. A scab is made up mostly of blood products and fibrin, and sits on top of the wound or skin. Eschar is the skin itself (or other tissue), which ha... |
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