qid int64 2 112k | question stringlengths 61 6.7k | positives listlengths 1 1 | negatives listlengths 1 10 |
|---|---|---|---|
46,034 | <p>I get that in a single gene locus, an individual can have <code>RR</code>, <code>Rr</code>, or <code>rr</code> as the two alleles for that gene. <code>R</code> is "wild type" because it is the allele occurring most frequently. <code>r</code> is the allele that is not WT.</p>
<p><code>RR</code> and <code>Rr</code> show dominant phenotypes, whereas <code>rr</code> shows the recessive phenotype.</p>
<p>But what's the difference between <code>r</code> and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where <code>_</code> is a null allele, my questions are below:</p>
<ul>
<li><code>R _</code> would produce the same as <code>Rr</code>, correct or not? <br></li>
<li><code>r _</code> would produce the same as <code>rr</code>, correct or not? <br></li>
<li><code>_ _</code> would produce the same as <code>rr</code>, correct or not?</li>
</ul>
| [
{
"answer_id": 46036,
"pm_score": 3,
"text": "<p>Good question +1. Unfortunately, the mechanisms by which dominance work is relatively poorly understood and it is likely that the mechanism differs from one locus to another.</p>\n\n<p>You might want to have a look at the posts</p>\n\n<ul>\n<li><a href=\"... | [
{
"answer_id": 46045,
"pm_score": 0,
"text": "<p>Basically, a recessive allele leads to formation of a product that has a low activity or no activity, which is complemented in the presence of the dominant allele (there can be effects related to dosage, in some cases). This can be easily understood in te... |
46,180 | <p>I'm more than 100% sure that the kilograms I eat don't get directly converted to feces and urine.</p>
<p>I'm sure some of it goes to regenerating tissue that is constantly being disposed as well, and maybe some of it is also being exhaled. </p>
<p>But I have a feeling that $E=mc^2$ might have something to do with the disposal of ingested kilograms.</p>
<p>We are constantly radiating electromagnetic waves in the nonvisible spectrum, we generate heat, we generate chemical bonds, all of these processes can convert mass to energy.</p>
<p>So I was wondering if $E=mc^2$ is relevant to biology?</p>
<p>Thanks.</p>
| [
{
"answer_id": 46182,
"pm_score": 4,
"text": "<p><strong>Short answer</strong></p>\n\n<p>Any law of physics will of course be applicable to living beings. However, in the absence of mass gain and mass loss, the <code>input = output</code> equation for matter holds true and does not require any spontaneo... | [
{
"answer_id": 46183,
"pm_score": 3,
"text": "<p>No, it is not. There are no nuclear fission or fusion reactions being performed in a biological context, for reasons that should be immediately obvious. Mass is not being converted to energy, or vice versa, when we generate heat or create or break chemica... |
46,416 | <p>All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system.
Thank you.</p>
| [
{
"answer_id": 46417,
"pm_score": 3,
"text": "<p>RNA and proteins are not electrical systems, but the idea of translating a signal between incompatible systems can be applied here. </p>\n\n<p>Proteins are made through a process called <a href=\"https://en.wikipedia.org/wiki/Protein_biosynthesis\" rel=\"... | [
{
"answer_id": 70273,
"pm_score": 1,
"text": "<p>Francis Crick published the <em>The adaptor hypothesis</em> in a privately circulated article (<a href=\"https://profiles.nlm.nih.gov/ps/retrieve/ResourceMetadata/SCBBZY\" rel=\"nofollow noreferrer\">now available online</a>) “On Protein Synthesis” in 195... |
46,617 | <p>So cell wall is an organelle?
Whereas, it is not a membrane-closed organelle?</p>
<p>Cytoplasm is an organelle?
Whereas, it is not a membrane-closed organelle?</p>
| [
{
"answer_id": 46619,
"pm_score": 2,
"text": "<p>The cell wall isn't an organelle (according to VCE biology textbook) and the cytoplasm is not.\nMy guess is that the wall regulates movement (ie, active function), whereas cytoplasm is just a fluid in which the other cells are surrounded (ie, passive).</p... | [
{
"answer_id": 46659,
"pm_score": 2,
"text": "<p><a href=\"https://en.wikipedia.org/wiki/Organelle#Types_of_organelles\" rel=\"nofollow noreferrer\">Wikipedia</a> gives quite clear and sourced answers in this case:</p>\n<blockquote>\n<p>an organelle is a specialized subunit within a cell that has a spec... |
46,712 | <p>I can assume that the hands used to be the same as legs. And they got weaken, and changed direction when human started to walk on two?
Also why do the hand palms facing the body and not facing down like the feet?</p>
| [
{
"answer_id": 46763,
"pm_score": 4,
"text": "<p>I am no expert on comparative anatomy, but I will give this a shot. Please edit if you know more about this subject!</p>\n\n<p>The configuration of opposing elbow and knee joints is a feature we humans share with large group of mammals. For example, below... | [
{
"answer_id": 46721,
"pm_score": -1,
"text": "<p>It's an amazing question, really. And you might be right about your assumption. In the womb, our legs and arms bent in the same direction. But as the foetus continued to develop, the legs and arms rotated to bend in opposite direction (to each other). As... |
46,736 | <p>Which databases you know that store data on tracking of marine animals?</p>
<p>I am interested particularly on mammals (for which I know meop storing data on sea lions) but also on fish schools (not sure they exist though).</p>
| [
{
"answer_id": 46763,
"pm_score": 4,
"text": "<p>I am no expert on comparative anatomy, but I will give this a shot. Please edit if you know more about this subject!</p>\n\n<p>The configuration of opposing elbow and knee joints is a feature we humans share with large group of mammals. For example, below... | [
{
"answer_id": 46721,
"pm_score": -1,
"text": "<p>It's an amazing question, really. And you might be right about your assumption. In the womb, our legs and arms bent in the same direction. But as the foetus continued to develop, the legs and arms rotated to bend in opposite direction (to each other). As... |
47,797 | <p>My thoughts are that maybe the TB antigens necessary to produce an immune response are proteins; therefore they can be digested in the stomach and small intestine. But I may be wrong though. I am confused why I can't say the same for polio vaccine.</p>
| [
{
"answer_id": 47799,
"pm_score": 6,
"text": "<p>There are different polio vaccines - one live (attenuated) vaccine which is given orally and one inactivated, which is injected. The main reason for using the live orally vaccine is that it provides excellent immunity (better than the inactivated) since i... | [
{
"answer_id": 47813,
"pm_score": 3,
"text": "<p>The reason why the oral polio vaccine is not digested in the stomach is that the poliovirus itself has adapted such that <a href=\"https://en.wikipedia.org/wiki/Poliovirus#Immune_system_avoidance\" rel=\"nofollow\">it can survive the acidic conditions of ... |
47,806 | <p>Today, my classmate and I stained a slide of cheek cells. After we put on a coverslip, our teacher said that we are supposed to remove excess solution using a tissue.</p>
<p>Why should we do this? I am so confused</p>
| [
{
"answer_id": 47811,
"pm_score": 2,
"text": "<p>Well, from personal experience, whenever there was excess solution on the glass slide, our teacher always commented that our slides were messy. So I guess the entire idea is to keep the slide neat, clean and to make it look presentable for observation. Al... | [
{
"answer_id": 47821,
"pm_score": 2,
"text": "<p>Neither of the current answers fully answer the question. </p>\n\n<p>The amount of liquid underneath a coverslip should be just sufficient to hold the coverslip and sample onto the slide. If there is too much water, the surface tension would become reduce... |
47,874 | <p>I remember reading a while ago that there is a "general rule" in biology between an animals lifespan and when they reach reproductive age. </p>
<p>In other words, an organism that reaches sexual maturity after a short amount of time (for example, less than a year) will have a short lifespan (for example, 2-3 years) and an animal that reaches sexual maturity after a long time (elephant, 10-12 years) will have a much longer lifespan (40-60 years in case of elephant).</p>
<p><strong>Is there a special name for this "law" or "rule"?</strong> Are there any major papers/theories supporting it that also attempt to propose why (perhaps from an evolutionary perspective) this trend exists?</p>
<p>Some quick supplemental questions:</p>
<p>1.) Is there also a trend between lifespan and animal size?</p>
<p>2.) Is there also a trend between lifespan and base metabolic rate? </p>
<p>3.) Do the two aforementioned "trends" or "rules" have technical names that I could look up as well?</p>
| [
{
"answer_id": 52092,
"pm_score": 3,
"text": "<p>The sort of thing you're talking about would be called a <em>Life History Invariant</em>: a dimensionless ratio between two life history traits $A$ and $B$, such that although the traits themselves vary widely between species, the ratio $\\frac{A}{B}$ is ... | [
{
"answer_id": 47887,
"pm_score": -1,
"text": "<p>I can't find a very fine writings/documents to support this or satisfy your question.</p>\n\n<p>I think, it's related somehow. Let's take a sample: (It's not super accurate but you can make a search)</p>\n\n<pre><code> -----------------------------------... |
47,896 | <p>I am doing an experiment where I have to do both Immunohistochemistry and SDS-PAGE. I am assuming that the native conformation of the protein is maintained in the IHC. But during the blot, we heat the protein (at least in our lab) at 95<sup>o</sup>C in mercaptoethanol to denature the protein by breaking the disulphide bonds thereby destroying the tertiary structure.</p>
<p>My question is when we are using the same antibody against the protein in the tissue (intact for IHC) and isolated (denatured for SDS-PAGE) protein, <em>how can it bind both</em>? So, the antibodies bind to the epitope based on the AA sequence or the 3D conformation? Wouldn't there be a lot if cross reactivity if it binds just based on sequence (since you could have the same sequence in many proteins, having the same conformation is much less likely)?</p>
| [
{
"answer_id": 52092,
"pm_score": 3,
"text": "<p>The sort of thing you're talking about would be called a <em>Life History Invariant</em>: a dimensionless ratio between two life history traits $A$ and $B$, such that although the traits themselves vary widely between species, the ratio $\\frac{A}{B}$ is ... | [
{
"answer_id": 47887,
"pm_score": -1,
"text": "<p>I can't find a very fine writings/documents to support this or satisfy your question.</p>\n\n<p>I think, it's related somehow. Let's take a sample: (It's not super accurate but you can make a search)</p>\n\n<pre><code> -----------------------------------... |
47,957 | <p>I understand that turtles are reptiles because like all reptiles, they have scales on their body. But turtles (specifically sea turtles) live on both land and water, very much like amphibians. Also, don't sea turtles have more of a moist skin unlike reptiles? So is there any anatomical difference which makes turtles different from amphibians?</p>
| [
{
"answer_id": 47961,
"pm_score": 6,
"text": "<p>Amphibians are not defined for having a moist skin, neither are reptiles defined for having scales on their body.</p>\n\n<p>In biology, organisms (elements) are grouped according to their evolutive history in <strong>monophyletic</strong> groups, also kno... | [
{
"answer_id": 47962,
"pm_score": 3,
"text": "<p>In addition to @Gerardo's answer:</p>\n\n<p><strong>Reptiles</strong></p>\n\n<p>The term <em>Reptiles</em> as used in popular language does not represent a monophyletic group. When using the term <em>Reptiles</em>, one is typically thinking of turtles, sn... |
48,110 | <p>Is there an agreed definition as to how many nucleic acid bases constitute a gene? </p>
<p>If not, why not? I'm not sure I understand how the exact sizes of genes are defined. </p>
| [
{
"answer_id": 48119,
"pm_score": 4,
"text": "<blockquote>\n<h2>Is there an agreed-upon definition as to how many nucleobases constitute a gene?</h2>\n<h3>If not, why not?</h3>\n</blockquote>\n<p>There is no such definition. A gene is a region of the DNA that is transcribed. Typically a gene should have... | [
{
"answer_id": 48117,
"pm_score": 3,
"text": "<p><strong>How are gene size defined?</strong></p>\n\n<p>DNA is made of 4 nucleotides <code>A</code>,<code>T</code>,<code>C</code> and <code>G</code>. A series of such nucleotide make up any section of the genome including the genes. The number of nucleotide... |
48,200 | <p>I have been following documentaries about crocodiles and amazingly, crocodiles and hippos apparently seem to live happily in the same pond together without attacking each other. </p>
<p>Why is it so? Like no matter how strong hippo is, its soft skin is no match to the brutal jaws of a crocodile?</p>
| [
{
"answer_id": 48208,
"pm_score": 6,
"text": "<p><strong>Skin</strong></p>\n\n<p>First, you are being misled by your wrong assumption that hippos have soft skin. Hippos have a 5 cm thick skin! For fun, here is a picture of a hippo skin.</p>\n\n<p><a href=\"https://i.stack.imgur.com/TSt6j.jpg\" rel=\"nof... | [
{
"answer_id": 76232,
"pm_score": 2,
"text": "<p>As Remi.b explained above, the average hippo is just too big and dangerous for the average croc to handle. That said, there were cases that very large crocodiles (such as the <a href=\"https://en.wikipedia.org/wiki/Gustave_(crocodile)\" rel=\"nofollow nor... |
48,207 | <p>I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly appreciated.</p>
| [
{
"answer_id": 48208,
"pm_score": 6,
"text": "<p><strong>Skin</strong></p>\n\n<p>First, you are being misled by your wrong assumption that hippos have soft skin. Hippos have a 5 cm thick skin! For fun, here is a picture of a hippo skin.</p>\n\n<p><a href=\"https://i.stack.imgur.com/TSt6j.jpg\" rel=\"nof... | [
{
"answer_id": 76232,
"pm_score": 2,
"text": "<p>As Remi.b explained above, the average hippo is just too big and dangerous for the average croc to handle. That said, there were cases that very large crocodiles (such as the <a href=\"https://en.wikipedia.org/wiki/Gustave_(crocodile)\" rel=\"nofollow nor... |
48,610 | <p>Beadle and Tatum proposed the <a href="https://en.wikipedia.org/wiki/One_gene%E2%80%93one_enzyme_hypothesis" rel="nofollow noreferrer">“one gene, one enzyme” hypothesis</a> in the 1940s, and this was later modified to “one gene, one protein”, i.e. that one gene codes for one protein. </p>
<p>Have any exceptions to this emerged subsequently? Are there single proteins, parts of which are encoded by separate genes?</p>
| [
{
"answer_id": 73322,
"pm_score": 3,
"text": "<p>There <em>are</em> proteins encoded by more than one gene. </p>\n\n<p>It would be a <strong>heterodimer</strong> protein of <strong>quaternary</strong> structure. One famous example would be haemaglobin, which is assembled from alpha and beta sub-units.</... | [
{
"answer_id": 48612,
"pm_score": 0,
"text": "<p>There are protein complexes which are made up of multiple subunits. Whether you call that one protein or a multi-protein complex might depend on whether you have a gene-centric or protein-centric point of view.</p>\n"
},
{
"answer_id": 73346,
... |
48,613 | <p>Can somebody identify this damselfly? Found near a stream about 15 miles west of Boston.<a href="https://i.stack.imgur.com/Vx8Ky.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Vx8Ky.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 73322,
"pm_score": 3,
"text": "<p>There <em>are</em> proteins encoded by more than one gene. </p>\n\n<p>It would be a <strong>heterodimer</strong> protein of <strong>quaternary</strong> structure. One famous example would be haemaglobin, which is assembled from alpha and beta sub-units.</... | [
{
"answer_id": 48612,
"pm_score": 0,
"text": "<p>There are protein complexes which are made up of multiple subunits. Whether you call that one protein or a multi-protein complex might depend on whether you have a gene-centric or protein-centric point of view.</p>\n"
},
{
"answer_id": 73346,
... |
48,672 | <p>Just a basic question on alleles, I am just trying to learn the basic concepts.</p>
<p>So if we are to screen two parents, both with one dominant and one recessive allele for a given characteristic e.g. eye colour, does this mean that we can say for certain (given a correct screen) that the child has a 3/4 chance of having the dominant characteristic (expressed) and a 1/4 chance of having the recess characteristic?</p>
<p>Similarly, if both parents had 2 dominant alleles, does this mean it is certain for the child to exhibit said quality given that the screen was effective?</p>
<p>Also, are there only these two types of alleles? I heard something about gene driving creating 'super dominant' alleles and would appreciate if someone could explain this to me.</p>
<p>Finally, is it the case that all alleles have a 50% chance of being passed on? </p>
<p>(assume in this question there aren't any relevant mutations going on)</p>
| [
{
"answer_id": 48715,
"pm_score": 2,
"text": "<p>It can be a little confusing. A genetic allele is just a portion of the genome responsible for an observable trait or phenotype. Examples of phenotypes consist of your example (eye color) and millions of others. As @swbarnes alluded to, most phenotypes ar... | [
{
"answer_id": 48675,
"pm_score": 0,
"text": "<blockquote>\n <p>does this mean that we can say for certain (given a correct screen)\n that the child has a 3/4 chance of having the dominant characteristic\n (expressed) and a 1/4 chance of having the recess characteristic?</p>\n</blockquote>\n\n<p>If y... |
48,806 | <p>Assume that the epidermis has been scraped off by a fall (not just scratched). Also assume that the dermis is completely untouched. Does this allow pathogens to enter the body more easily, or does the dermis still provide adequate protection?</p>
| [
{
"answer_id": 48829,
"pm_score": 4,
"text": "<p>Our epidermis is the first line defence against natural infections; it is also a part of the innate immune system. This is due to </p>\n\n<ol>\n<li><p>it contains a layer of dead cells that separates the living cells of the deeper layers of epidermis and ... | [
{
"answer_id": 48811,
"pm_score": 0,
"text": "<p>The dermis provides some protection, and if it is removed the danger of deep tissue infection becomes extremely high. However, the epidermis provides an additional and important layer of antimicrobial protection. That is why first and second degree burns,... |
49,105 | <p>My friend got stung by a stingray yesterday and the lifeguard quickly stuck her foot into hot water (she said the water burned slightly on contact) and remarkably, she was walking without pain in a hour. I have heard that rattlesnake's bites can be helped by applying heat to denature the proteins. I am assuming this is what happened here, please correct if wrong. Because I am often in areas where immediate help in cases of animal bites/stings is not available, this is important to me as a first response as I get the person to help.</p>
<ol>
<li>What kinds of venom are susceptible to denaturing by heat? How do I know which the previous categories a given venom falls into?</li>
<li>Is there a rough temperature I should aim for to denature the venom?</li>
<li>How likely is it that I would end up doing more harm by applying heat out of ignorance than doing nothing till I get to help (could be a day or more depending on the location)?</li>
</ol>
| [
{
"answer_id": 54330,
"pm_score": 3,
"text": "<p>Regarding snake venoms, they tested 28 snake venoms at 100'C: 19/28 of the venoms were still very dangerous after 5 minutes at 100'C.</p>\n\n<p>\"Heating all venoms led to the denaturation and loss of some proteins; however, most of the venoms retained a ... | [
{
"answer_id": 54326,
"pm_score": 0,
"text": "<p>All venoms are proteins and proteins are chemicals whose shape is determined by the amino acids with the sequence of the protein coding gene. Applying UV radiation or heat can denature it by breaking the chemical interactions amongst the side chains inevi... |
49,138 | <p>I live in Belgium, and I've just witnessed a weird looking wasp/fly flying around in my room. Here's a picture:</p>
<p><a href="https://i.stack.imgur.com/ircDd.png" rel="noreferrer"><img src="https://i.stack.imgur.com/ircDd.png" alt="enter image description here"></a></p>
<p>So, what's this? It's still in my room, just chilling there. It zooms like a wasp, and flies VERY FAST. You can see white vertical stripes on his upper body, and then golden vertical patches. I couldn't get the camera to focus, so it's not really full-hd.</p>
<p>[Edit (better picture)]</p>
| [
{
"answer_id": 49161,
"pm_score": 4,
"text": "<p>This is a hoverfly! Specifically in the genus <a href=\"http://bugguide.net/node/view/7310\" rel=\"noreferrer\"><em>Helophilus</em></a>. A lot of species of hoverflies exhibit Batesian mimicry of wasps/bees, as we see here, while they mainly feed on poll... | [
{
"answer_id": 49141,
"pm_score": 2,
"text": "<p>It looks like a <a href=\"https://en.wikipedia.org/wiki/Horse-fly\" rel=\"nofollow noreferrer\">horse-fly</a></p>\n\n<p><a href=\"https://i.stack.imgur.com/Ow57U.jpg\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/Ow57U.jpg\" alt=\"ente... |
49,201 | <p>I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks!</p>
<p><strong>UPDATE - Reference of lncRNAs violating Central Dogma:</strong></p>
<blockquote>
<p><em>Although the central dogma remains a core tenet of cellular and
molecular biology, the appreciation of lncRNAs as functional genomic
elements that defy the central dogma may be essential for fully under-
standing biology and disease.</em> [<em><a href="http://www.nature.com/ng/journal/v47/n3/full/ng.3192.html" rel="noreferrer">Iyer et al. Nature, 2015</a></em>]</p>
</blockquote>
| [
{
"answer_id": 49210,
"pm_score": 5,
"text": "<p><a href=\"https://profiles.nlm.nih.gov/ps/access/SCBBZY.pdf\" rel=\"noreferrer\">Crick’s Central Dogma</a> was actually:</p>\n\n<blockquote>\n <p><em>The Central Dogma</em><br> \n This states that once ‘information’ has passed into protein it cannot get... | [
{
"answer_id": 49212,
"pm_score": 1,
"text": "<p>The \"Central Dogma\" is an obsolete concept. It has no biological significance today. It's been outdated for decades since the discovery of reverse transcriptase, but it was never intended to be taken particularly seriously anyway; Crick deliberately ga... |
49,226 | <p>Due to the dynamism of protein expression, a genome can give rise to different proteomes, but could we say that a proteome comes from different genomes? </p>
| [
{
"answer_id": 49228,
"pm_score": 2,
"text": "<p>Yes, different genomes can produce the same proteome.</p>\n\n<p>Imagine a genome that only has a single protein-coding sequence (without splicing isoforms), the rest of the genome is simply regulatory sequences. Whatever those regulatory sequences may be,... | [
{
"answer_id": 49238,
"pm_score": 2,
"text": "<p><strong>No</strong>, if you want to have a generally valid statement. You can not say: <em>\"that a proteome comes form different genomes\"</em>.</p>\n\n<p>The official (MeSH) definition of the term \"proteome\" is:</p>\n\n<p>The protein complement of an ... |
49,227 | <p>I have been working on western blots for about a month now using actin and fetuin-b primary antibodies to no avail. My background is always high and I only had one good result. I want to know if there is a certain blocking buffer I should use instead of 5% milk with my membranes to get a better result.</p>
| [
{
"answer_id": 49228,
"pm_score": 2,
"text": "<p>Yes, different genomes can produce the same proteome.</p>\n\n<p>Imagine a genome that only has a single protein-coding sequence (without splicing isoforms), the rest of the genome is simply regulatory sequences. Whatever those regulatory sequences may be,... | [
{
"answer_id": 49238,
"pm_score": 2,
"text": "<p><strong>No</strong>, if you want to have a generally valid statement. You can not say: <em>\"that a proteome comes form different genomes\"</em>.</p>\n\n<p>The official (MeSH) definition of the term \"proteome\" is:</p>\n\n<p>The protein complement of an ... |
49,327 | <p>Please apologies if this has been answered somewhere else, but I couldn't find an answer to this problem.</p>
<p>I would like to retrieve all the predicted coding sequences on the NCBI ftp for <strong>a given species</strong>. Let's say my interest species today is <em>Stegastes partitus</em> and that I go <a href="ftp://ftp.ncbi.nih.gov/genomes/Stegastes_partitus/" rel="nofollow">here</a>. I know how to get all the predicted <strong>mRNAs</strong> (./RNA/Gnomon_mRNA.fsa) or all the predicted <strong>proteins</strong> (./protein/protein.fa) but I cannot find how to get the CDS... if ever it's possible? This can be done on the <a href="http://metazoa.ensembl.org/info/website/ftp/index.html" rel="nofollow">Ensembl FTP.</a></p>
<p>Thanks for any insight!</p>
<hr>
<p>EDIT: The output would ideally be a multifasta file like this:</p>
<pre><code>>Stegastes_partitus_gene1_cds
ATG(.................................)TAA
>Stegastes_partitus_gene2_cds
ATG(.............................)TGA
>Stegastes_partitus_gene3_cds
...
</code></pre>
| [
{
"answer_id": 50607,
"pm_score": 3,
"text": "<p>The GNOMON and GFF folder contains the files you want, the GNOMON if you check the README relates to the GNOMON gene predictor and the GFF I think links back to the same file. I think the file you want is <code>ref_Stegastes_partitus-1.0.2_scaffolds.gff3.... | [
{
"answer_id": 49345,
"pm_score": 0,
"text": "<p>The RNA folder of your link provides several annotated file formats. These include reference to the CDS for every transcript.</p>\n\n<p><a href=\"ftp://ftp.ncbi.nih.gov/genomes/Stegastes_partitus/RNA/\" rel=\"nofollow\">Stegastes_partitus/RNA/</a></p>\n\n... |
50,470 | <p>I was reading Cellular and Molecular Immunology
By Abul K. Abbas, Andrew H. H. Lichtman, Shiv Pillai and stumbled upon the following excerpt $-$</p>
<blockquote>
<p>In every individual there are millions of different clones of B-cells,each producing antibody molecules with the same antigen binding site and different in this site from the antibodies produced by other clones.</p>
</blockquote>
<p>What are these clones of B-cells, one producing monoclonal antibodies and the other polyclonal antibodies?</p>
| [
{
"answer_id": 50471,
"pm_score": 4,
"text": "<p>When you read further you'll get it. Basically, when the antibody expressed on a B-cell recognizes an antigen, then the B-cell divides and expands its population to produce more antibodies (through plasma cells). This process is called clonal expansion.</... | [
{
"answer_id": 50558,
"pm_score": 1,
"text": "<p>B cells are a type of cells that produce antibodies. Each B cell produces a different type of antibody. For example, consider the following B cells: C1, C2, and C3, which produce antibodies A1, A2, and A3, respectively. We are dealing with 3 B cell <stron... |
50,595 | <p>Most people are familiar with the following diagram. Some genomic DNA with a promoter region, exons and introns. This is transcribed into RNA that is then translated into a polypeptide.</p>
<p><a href="https://i.stack.imgur.com/5ltHV.gif" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/5ltHV.gif" alt="Central Dogma"></a></p>
<p>When we look closer at the strand that is being transcribed we can distinguish between the two as the sense and anti-sense strands.</p>
<p><a href="https://i.stack.imgur.com/2FkWW.gif" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/2FkWW.gif" alt="transcription"></a></p>
<p>So the transcription factors and RNA polymerase bind and begins transcribing mRNA in the 5' to 3' direction and thus reading the anti-sense strand in the 3' to 5' direction and have the same sequence as the sense DNA strand, substituting U for T in the mRNA.</p>
<p><a href="https://i.stack.imgur.com/1HKAa.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/1HKAa.jpg" alt="enter image description here"></a></p>
<p>My question would be, shouldn't the exons be numbered in the reverse order as shown in the first picture I provided. So instead of Promoter -> Exon1 -> Intron -> Exon 2, should it be, Promoter -> Exon N -> Intron -> Exon N-1?</p>
<p>Also, in bioinformatic sites are the gene sequences listed in the sense or anti-sense strand? I have noticed in some <a href="http://www.attotron.com/cybertory/analysis/trans.htm" rel="nofollow noreferrer">bioinformatic tools</a>, to determine what polypeptide will result from a DNA sequence, one must input the sense strand in 5'to 3' orientation and not the anti-sense strand.</p>
| [
{
"answer_id": 50604,
"pm_score": 2,
"text": "<p>All visual representations and nearly all coordinate systems are based on the sense strand. The polymerase machinery has no clue about what is sense and what is antisense, because each is the antisense of the other. </p>\n\n<p>For visual representation th... | [
{
"answer_id": 50596,
"pm_score": 2,
"text": "<p>Gene sequences are annotated in the sense strand. So, these diagrams are correct.</p>\n"
},
{
"answer_id": 50597,
"pm_score": 2,
"text": "<p>In the top diagram, the ATG start is on the left, and the stop codon is on the right. Exon one is... |
50,598 | <p>In glycolysis, 2 ATP molecules are produced from each triose phosphate molecule (to give a total of 4 ATP produced; 2 net produced as 2 were initially used up in the reaction).</p>
<p>I don't understand how this would be the case, as each triose phosphate only has one phosphate group available to form ATP from ADP, meaning that one ATP is produced per triose phosphate. I know this cannot be the case as this would mean a 0 net production of ATP defeating the purpose of glycolysis, but i can't get my head around why.</p>
<p><strong>out of curiosity, would the other remaining two phosphates that are required come from other sources, i.e. 2 phosphates + the 2 phosphates already from the two trios phosphate molecules to give us the 4 ATP molecules (2 net ATP)</strong></p>
<p>Many thanks in advance.</p>
| [
{
"answer_id": 50604,
"pm_score": 2,
"text": "<p>All visual representations and nearly all coordinate systems are based on the sense strand. The polymerase machinery has no clue about what is sense and what is antisense, because each is the antisense of the other. </p>\n\n<p>For visual representation th... | [
{
"answer_id": 50596,
"pm_score": 2,
"text": "<p>Gene sequences are annotated in the sense strand. So, these diagrams are correct.</p>\n"
},
{
"answer_id": 50597,
"pm_score": 2,
"text": "<p>In the top diagram, the ATG start is on the left, and the stop codon is on the right. Exon one is... |
51,304 | <p>I read online that they have found around 10 million single nucleotide polymorphisms (SNPs) across individuals in the human genome <a href="https://ghr.nlm.nih.gov/primer/genomicresearch/snp" rel="nofollow noreferrer">[1]</a>. However, this number includes all SNPs found in all people who have been sampled and does not tell us much about SNPs in any single person.</p>
<p>I was wondering instead how many SNPs there are in a single person on average. I had trouble finding trustworthy evidence about this question.</p>
| [
{
"answer_id": 51316,
"pm_score": 3,
"text": "<blockquote>\n <p>I was wondering how many SNPs there are in a single person on average</p>\n</blockquote>\n\n<p>A SNP is a polymorphism in the population, it is not a thing a haplotype can carry. Each individual has a given variant for any given of the SNP... | [
{
"answer_id": 51308,
"pm_score": 0,
"text": "<p>There was only one source I was able to find, It stated that each genome contains 1 SNP every 1000bp. (Take a look <a href=\"http://massgenomics.org/2009/06/whole-genome-sequencing-how-many-snps-remain.html\" rel=\"nofollow\">here</a>). However I have no ... |
51,468 | <p><strong>5'... ATGCC|CCGTA ...3'</strong></p>
<p><strong>3'... TACGG|GGCAT ...5'</strong> </p>
<p>or say </p>
<p><strong>5'... AAGT|TGAA ...3'</strong></p>
<p><strong>3'... TTCA|ACTT ...5'</strong></p>
<p>or in generalised way; on each strand;</p>
<p><strong>ABCDEF|FEDCBA</strong></p>
<p>Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat? Does they really exist in nature?
(I could not yet found any helpful answer in web, including wikipedia.)</p>
<h2>UPDATE</h2>
<p>I asked this question because the term <a href="https://en.wikipedia.org/wiki/Palindromic_sequence" rel="nofollow noreferrer">"palindromic sequence"</a> is not like the situation in OP <a href="https://biology.stackexchange.com/questions/51516/how-to-write-a-palindrome-sequence-as-wish-create-theoretically-self-answe">but "palindromic sequence" is like this</a>:</p>
<p>5'... <strong><em>A</em>TGCTTTC</strong>|GAAAGCAT ...3' </p>
<p>3'... TACGAAAG|<strong>CTTTCGT<em>A</em></strong> ...5' </p>
<p>or in general;</p>
<p>5'... <em>A B C D E F</em> | M N P Q R S ...3'</p>
<p>3'... S R Q P N M | <em>F E D C B A</em> ...5'</p>
<p>Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3'). </p>
<p>BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each <strong>single strand</strong> when read (3'---> 5') or (5' ---> 3'). </p>
<p>like </p>
<p><strong>5'... <em>A B C</em> D E F | F E D <em>C B A</em> ...3'</strong></p>
<p><strong>3'... S R Q P N M | M N P Q R S ...5'</strong> </p>
<p><strong>From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.</strong></p>
<p>This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like </p>
<p>I EAT CAKE</p>
<p>EKAC TAE I</p>
<p>So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.</p>
<hr>
<blockquote>
<p><a href="http://www.answers.com/Q/Mirror_repeats_in_DNA" rel="nofollow noreferrer">One other Q/A site</a> mentions about a term "mirror repeat", with exact same situation as OP, but gave no reference and further biological importance.</p>
<blockquote>
<p><a href="https://i.stack.imgur.com/qnigj.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/qnigj.png" alt="enter image description here"></a>
<a href="http://www.answers.com/Q/Mirror_repeats_in_DNA" rel="nofollow noreferrer">http://www.answers.com/Q/Mirror_repeats_in_DNA</a></p>
</blockquote>
<p>Latest revision of <a href="https://en.wikipedia.org/w/index.php?title=Repeated_sequence_(DNA)&oldid=716148908#Other_types" rel="nofollow noreferrer">Wikipedia</a> also mentions a term <em>mirror repeat</em> and <em>everted repeat</em>, but no further explanation and hyperlink is given.</p>
<p>Another result from google search.</p>
<blockquote>
<p><a href="https://i.stack.imgur.com/nl5x1.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/nl5x1.jpg" alt="https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg"></a>
URL: <a href="https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg" rel="nofollow noreferrer">https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg</a></p>
</blockquote>
</blockquote>
| [
{
"answer_id": 51503,
"pm_score": 3,
"text": "<p>I think the situation you showed should be called <em>mirror-everted repeats</em>: to my knowledge they occur very rarely, and I only found references in <a href=\"http://www.microbiologyresearch.org/docserver/fulltext/micro/150/11/3519.pdf?expires=147371... | [
{
"answer_id": 51536,
"pm_score": 2,
"text": "<p>As an example of biological symmetry, with my tongue in my cheek, I would call this a <a href=\"http://dictionary.cambridge.org/dictionary/english/mirage\" rel=\"nofollow\"><strong>mirage</strong></a>.</p>\n\n<p>My reason is that from a structural point o... |
51,476 | <p>This question is similar to a previous question, but is not the same. </p>
<p>I was told, you are born with a bacteria in your digestive track that are made by the body. Can a body in development create it's own bacteria from nothing? Also said by the teacher the first time you take an antibiotic it is gone forever? Can a body in development create it own bacteria from stem cells? Is there such a bacteria, can it be cultured and re-introduced into the body?</p>
| [
{
"answer_id": 51481,
"pm_score": 3,
"text": "<p>No, no human (or any other eukaryote lineage) are able to \"create bacteria\". The story you were told is wrong.</p>\n\n<p>However and interestingly, female parasitoid wasps seem to \"create viruses\" (<a href=\"http://rstb.royalsocietypublishing.org/cont... | [
{
"answer_id": 51512,
"pm_score": 1,
"text": "<p>Pasteur and Redi disproved spontaneous generation a century ago. So no, babies are not magically making bacteria in their guts.</p>\n"
},
{
"answer_id": 51593,
"pm_score": 2,
"text": "<p>Whoever told you this story is wrong. Bacteria are ... |
52,088 | <p>I understand that:</p>
<ul>
<li><a href="http://www.scientificamerican.com/article/latest-theory-human-body-hair/" rel="noreferrer">Chimpanzees are the closest species to humans genetically</a>. Only <a href="http://www.scientificamerican.com/article/human-chimp-gene-gap-wide/" rel="noreferrer">1%-6%</a> of their genes are different.</li>
<li>Within any species there is <a href="https://en.wikipedia.org/wiki/Genetic_diversity" rel="noreferrer">genetic diversity</a>, i.e. no two individuals have the same exact DNA sequence.</li>
<li>This variability applies to <a href="https://en.wikipedia.org/wiki/Human_genetic_variation" rel="noreferrer">humans</a> and <a href="https://www.upf.edu/cexs/news/genetica.html" rel="noreferrer">chimps</a>. </li>
<li>Thus, there exists a pair consisting of a human and a chimp that will have the smallest number of different (edit: <s>genes</s>) DNA base-pairs within the two populations. One can say that the pair forms an "inter-species genetic gap".</li>
</ul>
<p><strong>Question: What is the smallest estimated inter-species genetic gap between humans and chimpanzees?</strong></p>
<p>Edit: I changed the last point to base-pairs instead of genes. Most of the comments seem to suggest the population genetic variabilities are much, much smaller than the genetic distance between the populations. Visually, that looks something like this:</p>
<p><a href="https://i.stack.imgur.com/fzfg8.png" rel="noreferrer"><img src="https://i.stack.imgur.com/fzfg8.png" alt="Human chimpanzee genetic differences"></a></p>
<p>Is this a fairly accurate picture of the human-chimp genetic distance?</p>
| [
{
"answer_id": 52936,
"pm_score": 4,
"text": "<p>You may be interested in this 2005 Nature paper from the Chimpanzee Sequencing and Analysis Consortium: <a href=\"http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html\">Initial sequence of the chimpanzee genome and comparison with the hum... | [
{
"answer_id": 52973,
"pm_score": 3,
"text": "<p>The answer given by leekaiinthesky and partially in the comments on the question give a good general picture. I also think that the <strong>variation within the respective species is way less than between the species</strong>. Keep in mind that also archa... |
52,290 | <p>So in my book I have the reaction</p>
<p>$$ATP \rightarrow ADP +P_i$$</p>
<p>and hence $$\Delta G^0 = G^0_{ADP} + G^0_{P_i} - G^0_{ATP}$$</p>
<p>This is easily understood, but I have not been given any actual concentrations of values to use to calculate the result, which is given as</p>
<p>$$\Delta G^0 = -31.0kJ\text{mol}^{-1}$$</p>
<blockquote>
<p>Where do I find the values of $G^0_{ADP}, G^0_{P_i} \text{ and } G^0_{ATP}$? </p>
</blockquote>
<p>I have the formula $$\Delta G = \Delta G^0 + RT\ln \bigg( \frac{AB}{CD} \bigg)$$</p>
<p>where $A,B$ are the concentrations of the products and $CD$ are the concentrations of the reactants.</p>
| [
{
"answer_id": 52322,
"pm_score": 1,
"text": "<p>You can't measure the energy of ATP itself, but you can measure the amount of energy that is released every time a P group is removed from the molecule, that is about 30 kj/mol.</p>\n<p><a href=\"http://book.bionumbers.org/how-much-energy-is-released-in-a... | [
{
"answer_id": 52318,
"pm_score": 0,
"text": "<p>I <em>think</em> the answer to your question of where you find standard free energy values is <strong>‘nowhere’</strong>. Free energy is a concept that you can expres in equations but that you cannot measure. You can only measure the <strong>change</stron... |
52,412 | <p>I know that the mitochondria is basically the power house of the body,
it consumes amino acids, fatty acids, glucose, etc and oxygen.</p>
<p>When these molecules meet up in a enzyme, a series of reactions happen (Krebs
cicle) which end up in CO2, H20 and energy.</p>
<p>Then the enzyme and later mitochondria will release its energy which will be stored in ATP molecules.</p>
<p>My question is what is this <strong>energy</strong>?</p>
| [
{
"answer_id": 52413,
"pm_score": 2,
"text": "<p><a href=\"https://en.wikipedia.org/wiki/Adenosine_triphosphate\" rel=\"nofollow\">ATP</a> is a form of chemical energy. Hydrolysis of the third phosphate group produces quite a bit of energy: </p>\n\n<pre><code>ΔG° = −30.5 kJ/mol (−7.3 kcal/mol)\n</code><... | [
{
"answer_id": 52417,
"pm_score": 2,
"text": "<p>The use of the energy in ATP is quite complex. Since my college days our knowledge of how ATP is used has broadened considerably.</p>\n\n<p>Let's look first at the role of ATP in the sodium-potassium pump. This pump uses roughly 20% of the ATP your body p... |
52,610 | <p>The effects of coffee as a stimulant are quite well-known. What are the mechanisms by which coffee helps prevent sleepiness? I have heard of the presence of caffeine, but what does it actually do inside our body?</p>
| [
{
"answer_id": 52611,
"pm_score": 4,
"text": "<p>Drowsiness is caused by the chemical adenosine binding to a nerve cell's adenosine receptor. A compound that binds and elicits a response, in this case a slow down of nerve activity, is called an agonist.</p>\n\n<p>Caffeine is also capable of binding to t... | [
{
"answer_id": 52612,
"pm_score": 2,
"text": "<p>Adenosine is a naturally produced hormone. It inhibits neurons and makes you tired. The longer you stay awake, more adenosine is produced.</p>\n\n<p>Caffeine is a competitive inhibitor. It will bind to the adenosine receptors and prevent adenosine from bi... |
52,642 | <p>A trait is defined as an inherited characteristic, like eye color and height.
A phenotype is defined as the specific physical manifestation of a trait, like blue eyes and 6 feet, respectively.</p>
<p>Now, genes code for traits. And because alleles are different versions of the SAME gene, they must code for the same trait. Let's say gene A codes for hair color (trait). Gene A(1) (allele) codes for brown hair (phenotype) while gene A(2) codes for blonde hair. Therefore, alleles code for the same TRAIT, but differing PHENOTYPES.</p>
<p>Here is the problem. When I google: "heterozygous", I get a bunch of websites defining it as "referring to a gene pair in which the two alleles do not code for the same trait"</p>
<p>This is not correct because a gene-pair refers to genes located at the same locus on a chromosome. In other words, they are alleles of the SAME gene and code for the SAME trait. They only code for different phenotypes associated with that trait.</p>
<p>So. Either my definition of traits is wrong. My definition of alleles is wrong. My understanding of alleles being different versions of the same gene is wrong. OR. The internet loves to be imprecise with their language and interchangeably use terms that mean different things.</p>
<p><strong>Which is it?</strong></p>
| [
{
"answer_id": 52645,
"pm_score": 2,
"text": "<p>I fear you won't get a definitive answer on this. A survey indicates both usages of trait all over the Internet. As a teacher, I generally used trait to apply to the gene. This made teaching the \"central dogma\" clear: DNA -> RNA -> protein -> trait. Of ... | [
{
"answer_id": 52646,
"pm_score": 0,
"text": "<p>The way I see it, the semantics in this area of genetics are somewhat loose and you are correct about all your definitions.</p>\n\n<p>I think the word 'trait' is not currently used as much as it used to e.g. in early 20th-century genetics, or earlier. The... |
52,648 | <p>I was wondering if it's an evolutionary advantage to have many sensory systems in a small place of the body, the head. This applies to mammals, reptiles, synapsid, dinosaurs... and many more.</p>
<p><strong>My theories:</strong></p>
<ul>
<li>The distance to the brain is short and thus smaller time delay to
respond faster to the outside world,have more reflexes, hunt faster
prey and fight more accurately.</li>
<li>The short distance makes the "wire" (signal carrying) shorter and
thus less vulnerable to be cut from a injury, because for a organism
losing an eye reduces possibilities of survival dramatically.</li>
<li>In humans at least the head is the upper part, then vision organs
<em>see more</em> with less obstacles such as vegetation or terrain irregularities, or anything that obstacles vision, normally higher
means seeing more things. This I'm not sure applies so strongly to
smell. To taste, certainly not. To hearing, possibly a little,
thought nor much as vision.</li>
</ul>
<p>We evolved from a common ancestor that was like that but that doesn't explain why it's not common to get out of that coincidence.</p>
| [
{
"answer_id": 52645,
"pm_score": 2,
"text": "<p>I fear you won't get a definitive answer on this. A survey indicates both usages of trait all over the Internet. As a teacher, I generally used trait to apply to the gene. This made teaching the \"central dogma\" clear: DNA -> RNA -> protein -> trait. Of ... | [
{
"answer_id": 52646,
"pm_score": 0,
"text": "<p>The way I see it, the semantics in this area of genetics are somewhat loose and you are correct about all your definitions.</p>\n\n<p>I think the word 'trait' is not currently used as much as it used to e.g. in early 20th-century genetics, or earlier. The... |
52,698 | <p>My question is whether mutations which lead to evolution occur by any environmental force or it occur spontaneously? I have read in genetics that x-rays, ultraviolet rays and chemical mutagens are the causes of mutation but how are they responsible for evolutionary mutations?</p>
| [
{
"answer_id": 52699,
"pm_score": 4,
"text": "<p>Mutations occur spontaneously because all molecular processes are stochastic in nature: DNA replication is an imperfect process. However, certain external factors can increase the probability of a mutation to occur or even cause specific types of mutation... | [
{
"answer_id": 52710,
"pm_score": 2,
"text": "<p>In a sense all mutations \"lead to evolution\". The genetic make up of the population has changed. Some mutations become \"fixed\", are persistent in the gene pool. You are thinking of evolution as progressive, it isn't; it is statistically adaptive.</p>\... |
52,815 | <p>According to this <a href="https://genographic.nationalgeographic.com/neanderthal/" rel="nofollow">article</a>, a small amount of Neanderthal DNA was introduced into the modern human gene pool. How do biologists even know what the Neanderthals' DNA look like?</p>
<p>The article doesn't mention how the science recognize what the Neanderthals' DNA actually is at the first place. So how do we know what the Neanderthals' DNA is if I'm guessing we never tested Neanderthals body cell samples? </p>
<p>If you say "From their bones/skull" but how do you know they are actually Neanderthals and not modern humans with some rare gene mutation or something else?</p>
| [
{
"answer_id": 52817,
"pm_score": 5,
"text": "<p>Neandertal DNA has been completely sequenced multiple times now, using DNA from bone and tooth samples found in cool or cold environments. The first Neanderthal genome sequence was described in 2010:</p>\n\n<p><a href=\"http://science.sciencemag.org/cont... | [
{
"answer_id": 52816,
"pm_score": 2,
"text": "<p>The sequence of the neanderthal genome is known because it has been sequenced and could then be compared to the human reference genome. The DNA was extracted from a toe bone found in Siberia, as described in reference 1.</p>\n\n<p>The sequencing was done ... |
52,875 | <p>How does one choose PCR conditions? Does it depend on the taxon, on the DNA concentration, on the primers or anything else? </p>
| [
{
"answer_id": 52883,
"pm_score": 3,
"text": "<p>You need to first build an initial protocol and then optimize it.</p>\n\n<p>The most important to determine the conditions is the polymerase used. Some polymerases work at higher or lower temperatures and will work faster or slower. Find the default proto... | [
{
"answer_id": 52895,
"pm_score": 0,
"text": "<p>Use primer3 to design your primers, then just use whatever protocol your lab usually used for PCR.</p>\n\n<p>A high annealing temp solves many problems, and a good enough taq won't mind.</p>\n\n<p>I successfully sanger sequenced thousands and thousands of... |
52,882 | <p>I've been farming freshwater fishes. After some time, i found some green algae grows there. When the algae dried, it looks like nori (which commonly used for sushi wrapping).</p>
<p>So, i wonder if those algae edible for human. Are the algae safe to eat?</p>
<p>Here's the picture:</p>
<p><a href="https://i.stack.imgur.com/24wgV.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/24wgV.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 52883,
"pm_score": 3,
"text": "<p>You need to first build an initial protocol and then optimize it.</p>\n\n<p>The most important to determine the conditions is the polymerase used. Some polymerases work at higher or lower temperatures and will work faster or slower. Find the default proto... | [
{
"answer_id": 52895,
"pm_score": 0,
"text": "<p>Use primer3 to design your primers, then just use whatever protocol your lab usually used for PCR.</p>\n\n<p>A high annealing temp solves many problems, and a good enough taq won't mind.</p>\n\n<p>I successfully sanger sequenced thousands and thousands of... |
53,185 | <p>Trees in a forest, alongside the fungi, animals and plants that live there in, capture atmospheric carbon dioxide and store it inside their tissues and in the soil as humus.</p>
<p>It is possible to estimate the amount of carbon stored in some portion (say 100 square meters) of a <a href="https://en.wikipedia.org/wiki/Climax_community" rel="nofollow">climax</a> forest?</p>
<p>This should depend on the specific <a href="https://en.wikipedia.org/wiki/Biome" rel="nofollow">biome</a>, for example Eucaliptus and Pine forests seem to contain less organic matter than broad-leaved tree forests in temperate regions.</p>
<p>PS: A slightly more speculative aspect of this topic is to evaluate weather reforestation can contribute to lower the amount of carbon dioxide in the atmosphere.</p>
| [
{
"answer_id": 53843,
"pm_score": 3,
"text": "<p>There are some well established methods for this. For example, estimating forest C stocks and fluxes is done for national C accounts which are used by the Intergovernmental Panel on Climate Change (IPCC) for global reporting.</p>\n\n<p>The usual method is... | [
{
"answer_id": 53191,
"pm_score": 2,
"text": "<p>This question is very broad and this would require a lot of calculations, I will focus on the carbon dioxide in the trees, hopefully some other users can add details in respect to the organism and their carbon dioxide storage.</p>\n\n<p>I found an article... |
53,207 | <p>It is quite simple to understand the concept of <a href="https://en.wikipedia.org/wiki/Sound_localization" rel="nofollow noreferrer">lateral localization of sound</a>. It depends upon the loudness and time (and wave phase) difference between 2 ears. </p>
<p>But how can we detect <strong>front-back</strong> localization (<em>if someone is calling me from my front/back direction</em>) and <strong>up-down</strong> localization (<em>such as an aeroplane's sound is coming from upper place</em> and a <em>car's whistle is coming from lower-direction of the balcony I'm standing</em>). How does that happen? Or doesn't localization happen at all under these conditions? Is it just an illusion just because we are already aware about the possible source (such as since it is aeroplane's sound then it might coming from upward place, or I can see my friend is talking by standing my front so the sound must coming from front... etc.)</p>
<p>I've searched wikipedia and other sites, but I found nothing that explained the matter sufficiently.</p>
| [
{
"answer_id": 53685,
"pm_score": 3,
"text": "<ul>\n<li><p><strong>Localization along the <a href=\"https://en.wikipedia.org/wiki/Azimuth\" rel=\"nofollow noreferrer\">azimuth</a></strong> (horizontal left-right axis) is mediated by various processes: 1) First, there is the <strong>head shadow</strong> ... | [
{
"answer_id": 53208,
"pm_score": 2,
"text": "<p>The <a href=\"https://en.wikipedia.org/wiki/Sound_localization#Sound_localization_in_the_median_plane_.28front.2C_above.2C_back.2C_below.29\" rel=\"nofollow noreferrer\">Wikipedia article</a> is quite good.</p>\n\n<p>In brief, as you state, the wave phase... |
53,221 | <p>This is a question that's been bugging me, and I haven't been able to find a definite answer anywhere.</p>
<p>We know there are thousands of enzymes (proteins, let's ignore catalytic RNA for now) that catalyze many different reactions, and they do this because they have the correct shape to fit the substrates.</p>
<p>Theoretically, given some reaction, can an enzyme be created to catalyze that reaction? Or is there some reaction that it's not possible to catalyze with an enzyme? Can any given shape be created out of polypeptide chains? If not, what determines the shapes that it's possible to create?</p>
| [
{
"answer_id": 53223,
"pm_score": 4,
"text": "<p>This will probably be a difficult question to answer definitively without some hand-waving or redefining the question; I can't imagine proving the negative result that no enzyme is possible for a given reaction, except for some cases where the reaction is... | [
{
"answer_id": 53226,
"pm_score": 3,
"text": "<p><em>Are there enzymes for every reaction?</em> The short answer is, \"<strong>No</strong>\" - there are reactions that occur within the human biology that do not require enzymes. One example of this is the formation of <a href=\"https://en.wikipedia.org/w... |
53,380 | <p>Chlorophyll and hemoglobin are very similar molecules, as far as I understand. The important difference being one using an iron atom and the other a magnesium atom. Do any organisms use <strong>both</strong> to get energy from both oxygen and solar rays? If not, is there any good explanation of why?</p>
<p>And do organisms that use chemosynthesis also use macro molecules similar to chlorophyll and hemoglobin?</p>
| [
{
"answer_id": 53395,
"pm_score": 5,
"text": "<p>Besides the unicellular organisms cited by other answers (and the fact that plants actually do respiration), there are <a href=\"http://umich.uloop.com/news/view.php/77109/4-incredible-photosynthetic-animals\" rel=\"noreferrer\">some animals</a> who are a... | [
{
"answer_id": 53385,
"pm_score": 2,
"text": "<p>Indeed several organisms can do both. </p>\n\n<p>Another good example following the answer from Prince of an organism that can do both photosynthesis and respiration would be cyanobacteria. </p>\n\n<p>Source: \n<a href=\"http://www.synechocystis.asu.edu/p... |
53,399 | <p>I thought that massive changes among organisms are over long periods of time. This is caused by, to my knowledge:</p>
<ul>
<li>Evolutionary pressure</li>
<li>Natural/artificial selection</li>
<li>Mutations</li>
<li>Genetic drift</li>
</ul>
<p>Will mutations be the only factor in human change? Will humans change at all over a long time?<br><br></p>
| [
{
"answer_id": 53400,
"pm_score": 5,
"text": "<p><strong>Issue in your introduction</strong></p>\n<blockquote>\n<p>I thought that massive changes among organisms are over long periods of time.</p>\n</blockquote>\n<p>Actually, some evolutionary events can happen on a very short time scale. A single mutat... | [
{
"answer_id": 53467,
"pm_score": -1,
"text": "<p>In sexed organisms, evolution is largely due to errors during chromosome duplication, cutting/copying/pasting/swapping/shortening/duplicating full genes sections. It is a way more efficient and fast way to evolve, since mixing sentences have more chances... |
53,571 | <p>My job is to <a href="https://biology.stackexchange.com/questions/53570/how-to-prevent-blobs-under-the-microscope">photograph mushroom spores</a> at x100 using immersion oil. </p>
<p>What is the best practice for cleaning the oil from the lens?</p>
<p>Right now I am just wiping it with a cotton swab.</p>
| [
{
"answer_id": 53589,
"pm_score": 3,
"text": "<p>In my experience, any microscope worth using has a minder. I would strongly suggest finding that minder, their opinions about cleaning practice should be respected. Objective lenses can be very pricey so they should be handled with care.</p>\n\n<p>Deterge... | [
{
"answer_id": 58518,
"pm_score": 0,
"text": "<p>The least possible amount of cleaning naphtha, pharmaceutical quality (in German: \"wundbenzin\") and high grade lens cleaning paper. In the ol' days microscopists used some saliva on a piece of cloth, but that was in the pre-coated optics era.</p>\n"
}... |
54,093 | <p>I have thawed Hl-60 cells from liquid nitrogen chamber two times in RPMI 1640 media (containing 10% FBS, L glutamin, penicillin/streptomycin). In the first day the cells remain okay. But when subcultured from the first flask to new flasks (cell solution : media= 1:3) all the flasks became contaminated on the 2nd day of culture. Cloud was found in both time. It can be mentioned that I used sterile one-time usable pipettes and uncoated flask for growth. All the transfers to other flasks and media addition were done very carefully and done inside clean bench. Before using clean bench, it was sprayed by 70% EtOH. </p>
<p>Has anyone experienced like this problem? Please share and if have, please give some valuable suggestions or references.</p>
<p>Thanks </p>
| [
{
"answer_id": 54104,
"pm_score": 3,
"text": "<p>The single most likely reason for the contamination is that your frozen stock is contaminated. Assuming you've been properly trained in cell culture, you're working in a correctly-maintained biosafety cabinet, your reagents are all sterile (has your media... | [
{
"answer_id": 54094,
"pm_score": 1,
"text": "<p>Avoid passing your hands through the openings of the flasks/tubes since skin originated bacteria are the major source of contamination. It's safe to briefly burn the caps and the opening of the tubes before opening or capping. If you maintained good asept... |
54,143 | <p><em>With the acceptance of being a little overweight</em></p>
<p>I hear of people saying they were born morbidly obese and it was genetically passed on. I'm aware being so obese leads to countless health issues, yet we have people defending fat shaming and the likes. Is the excuse of having 'obese' genetics scientifically justified? Do people have genetics that make them ridiculously fat? Alongside, would this simply be down to the diet of the person from a young age?</p>
<p>Thanks.</p>
| [
{
"answer_id": 54161,
"pm_score": -1,
"text": "<p>It's a <a href=\"http://www.livescience.com/1116-myth-fat-gene.html\" rel=\"nofollow noreferrer\">myth</a> that obesity is mostly caused by genes. Yes, there are many genes that predetermine your <a href=\"https://en.wikipedia.org/wiki/Genetics_of_obesit... | [
{
"answer_id": 59600,
"pm_score": 2,
"text": "<p>It is certainly a very difficult question to answer.</p>\n\n<p>There are some genetic disorders that can predispose individuals for becoming obese: <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/18230893\" rel=\"nofollow noreferrer\">https://www.ncbi.nlm.n... |
54,147 | <p>I am aware the Human brain has many functionally distinct components, but let us specifically consider the <strong>Human visual cortex</strong>: could <strong>Artificial Neural Networks</strong> (ANNs) be "trained" (through, e.g. backpropagation) in an analogous way to how the visual cortex "learns"?</p>
<p>Is the concept of backpropagation in ANNs a phenomena actually observed in the Human brain?</p>
<p><strong>Related</strong></p>
<ul>
<li><a href="https://biology.stackexchange.com/questions/54918/books-on-machine-learning-applications-in-biology">Books on machine learning applications in Biology</a></li>
</ul>
| [
{
"answer_id": 57222,
"pm_score": 4,
"text": "<p>I recommend Yoshua Bengio's recent works. E.g.: <a href=\"https://arxiv.org/abs/1502.04156\" rel=\"noreferrer\">https://arxiv.org/abs/1502.04156</a> and <a href=\"http://www.iro.umontreal.ca/~bengioy/talks/Brains+Bits-NIPS2016Workshop.pptx.pdf\" rel=\"nor... | [
{
"answer_id": 54148,
"pm_score": 2,
"text": "<p>Not in the same sense as in artificial neural networks. Importantly, there is no biological mechanism for errors to be back-propagated further than a single cell/synapse.</p>\n\n<p>You can look into <a href=\"https://en.wikipedia.org/wiki/Spike-timing-dep... |
54,152 | <p>In most societies marriages between cousin are viewed negatively, due to a fear of "bad genes".
But lets say I am a girl and I marry the son of my mother's brother (i.e. my uncle), than there is no gene similarity.
Then I have two X-chromosomes, where one came from my father and the other one from my mother. My cousin (the son of my uncle) will have one Y-chromosome from his father and one X-chromosome from his mother (wh o is unrelated to me). My mother will also not be a carrier of my cousins Y-chromosome (since she is a female).</p>
<p>Does this all mean that this particular cousin marriage is unproblematic, and no different than a marriage between completely unrelated people?</p>
| [
{
"answer_id": 54162,
"pm_score": 4,
"text": "<p>The problem is that humans have 22 other pairs of chromosomes than just the sex chromosomes X and Y. Reproducing with your cousin (the son of your mother's brother is the son of your uncle which means your cousin) is generally looked down upon because of ... | [
{
"answer_id": 54153,
"pm_score": 2,
"text": "<p>Welcome to Biology.SE!</p>\n\n<blockquote>\n <p>In most of society cousins marriage [..]</p>\n</blockquote>\n\n<p>Who cares about marriage in biology? We only care about reproduction. Marriage is a social construct that is mainly irrelevant here.</p>\n\n... |
54,215 | <p>The figure shows the relationship between the water depth and net primary production (=P-R). I want to know why the production (P) initially increases with water depth near the surface? I have seen similar relationships from other sources but never seen a clear explanation.</p>
<p><a href="https://i.stack.imgur.com/1tyKI.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/1tyKI.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 54291,
"pm_score": 3,
"text": "<p>After a quick glance at the book \"<a href=\"http://www.cambridge.org/se/academic/subjects/life-sciences/ecology-and-conservation/light-and-photosynthesis-aquatic-ecosystems-3rd-edition?format=PB&isbn=9780521151757\" rel=\"nofollow noreferrer\"><em>Li... | [
{
"answer_id": 54225,
"pm_score": 1,
"text": "<p>I think it has to do with what wavelength of light is absorbed by photosynthetic organisms at what depth.</p>\n\n<p>Ultraviolet light with short wavelength is absorbed closest to the surface. Red light (which is responsible for photosynthesis) is absorbed... |
54,277 | <p>The upper limit of hearing is approximately 15 kHz, dependent on age and other factors. According to the principles of digital signal-processing, such an upper limit would mean that the auditory system samples at least at 30 kHz or more. </p>
<p>Now suppose an ultrasonic signal, say a 40-kHz acoustic frequency - why would I hear nothing, instead of that signal aliased at a 30 kHz sampling rate?</p>
| [
{
"answer_id": 54354,
"pm_score": 3,
"text": "<p><strong>Short answer</strong><br>\nThe cochlea is a tonotopic map with certain physically determined boundaries that determine the range of frequencies perceived. Ultrasonic soundwaves simply do not have a correlate on this map. </p>\n\n<p><strong>Backgro... | [
{
"answer_id": 54339,
"pm_score": 2,
"text": "<p>I think that you are misquoting Aliasing.</p>\n\n<p>Digital acoustics is explained in a mathematical sense, Aliasing is a maths concept. Real life acoustics is explained in a physical sense, which talks about reflection, absorption, phase change, harmonic... |
54,294 | <p>So we were studying this amino acid called cysteine. Specifically we were studying it's effect on melanin genesis.
Our teacher told us how excess of cysteine affects the melanin synthesis by generating more pheomelanin. Low amount of cysteine promotes formation of eumelanin.
He told us that if the concentration of cysteine is increased in cells then the above reaction starts producing pheomelanin in brown/black skinned people. I searched it on net and it seems to be true.
The question is that if someone who has fair skin (produces more pheomelanin) is forced to live in low cysteine condition, then what happens? Eumelanin production should increase. His complexion must change. But it doesn't occur anywhere. Fair skinned people affected by malnutrition remain fairskinned. How is this possible? The pheomelanin production must stop since they aren't getting enough cysteine. Then how...?</p>
<p>He also told us that onions contain large amount of cysteine yet it can't be used since it is destroyed by stomach acids.</p>
| [
{
"answer_id": 54296,
"pm_score": 3,
"text": "<p>First: Your teacher is right with the statement that a low cysteine concentration affects the synthesis of pheomelanin. To understand this, you need to take a look at the biosynthesis pathway of melanin (from <a href=\"https://www.adapaproject.org/doggene... | [
{
"answer_id": 77983,
"pm_score": -1,
"text": "<p><a href=\"https://i.stack.imgur.com/L2f7J.png\" rel=\"nofollow noreferrer\"><img src=\"https://i.stack.imgur.com/L2f7J.png\" alt=\"enter image description here\"></a></p>\n\n<p>\"Pheomelanogenesis may have evolved as an excretory mechanism to remove exce... |
54,617 | <p>I am currently studying the chapter called macromolecule. I get that a nucleic acid consists of repeating units of nucleotides, and I personally think <strong><em>"the repeating units"</em></strong> does not mean the nucleotdes are all the same, as nitrogen bases have four types either in DNA or RNA. How about the protein molecule. A protein molecule is made up of amino acids. However, I am sure about whether a protein molecule are made up of <strong>same and repeating units</strong> of amino acids. Theoretically, the R group in each protein is differed from one another. Therefore, <strong>does that mean we cannot state that a protein molecule is made up of repeating units of amino acids?</strong></p>
| [
{
"answer_id": 54618,
"pm_score": 3,
"text": "<p>They are repeating units in the sense that all of the units are amino acids. The R group is different in different amino acids (it is not just different theoretically). The different R groups contribute to the different shape, structure, function of prote... | [
{
"answer_id": 54623,
"pm_score": 0,
"text": "<p>Proteins are heteropolymers of amino acids. Many Amino acids are joined together by peptide bond. During peptide bond formation C terminal of former amino acid & N terminal of successive amino acid join , that's why proteins always start with the N t... |
54,630 | <p>Wings serve most birds for flying, or (as in penguins) for swimming. But ostriches, which exclusively use only their legs for locomotion, still have wings. Why?</p>
| [
{
"answer_id": 54634,
"pm_score": 4,
"text": "<p>There is a common misconception that a selective process is needed to <em>remove</em> a feature from a population. However, the correct approach is quite the opposite: selective processes normally <em>maintain</em> a feature in a population: if a given fe... | [
{
"answer_id": 54631,
"pm_score": 2,
"text": "<p>Why not? \nSince the wing on a ostrich does not harm the animal, there is no selection pressure to remove it from the population. And male ostriches do use their wings for mating displays. So it isn't completely without use. </p>\n"
},
{
"answer_... |
54,644 | <p>After I googled 'sigma TF' I stumbled upon two papers(only).</p>
<p>From a <a href="https://www.ncbi.nlm.nih.gov/pubmed/17055433" rel="nofollow noreferrer">paper</a>:</p>
<blockquote>
<p>Sigma factors (sigmas) are bacterial transcription factors that bind core RNA polymerase (RNAP) and direct transcription initiation at cognate promoter sites.</p>
</blockquote>
<p>and another <a href="http://www.nature.com/nature/journal/v358/n6385/abs/358422a0.html" rel="nofollow noreferrer">paper</a> had the title -</p>
<blockquote>
<p>Specific binding of the transcription factor sigma-54 to promoter DNA.</p>
</blockquote>
<p>However this contradicts with my book- Principle of Genetics Snustard and Simmons:</p>
<blockquote>
<p>Unlike their prokaryotic counterparts, eukaryotic RNAPs cannot initiate transcription by themselves .... require the assistance of protein transcription factors to start synthesis.</p>
</blockquote>
<p>Is it a TF?</p>
<p>Note: From what TFs are, sigma factor seems to be a TF to me.</p>
| [
{
"answer_id": 54634,
"pm_score": 4,
"text": "<p>There is a common misconception that a selective process is needed to <em>remove</em> a feature from a population. However, the correct approach is quite the opposite: selective processes normally <em>maintain</em> a feature in a population: if a given fe... | [
{
"answer_id": 54631,
"pm_score": 2,
"text": "<p>Why not? \nSince the wing on a ostrich does not harm the animal, there is no selection pressure to remove it from the population. And male ostriches do use their wings for mating displays. So it isn't completely without use. </p>\n"
},
{
"answer_... |
54,796 | <p>What are some of the standard books to study :</p>
<ul>
<li>Biological Interactions: Symbiosis, Mutualism...etc</li>
<li>Concept of Limiting factors</li>
<li>Niche concept </li>
<li>Resource partitioning</li>
<li>Concepts of community change</li>
<li>Theories of climax</li>
<li>Models of Succession</li>
</ul>
<p>P.S. I am looking for a book for beginners for studying ecology at UG level.</p>
| [
{
"answer_id": 54800,
"pm_score": 4,
"text": "<p>A classic standard textbook that I've used a lot myself (earlier editions) is <a href=\"http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1405111178.html\" rel=\"nofollow noreferrer\">Begon, Harper & Townsend</a>. This book is very broad and comprehen... | [
{
"answer_id": 56746,
"pm_score": 2,
"text": "<h3> Ecology Textbooks: </h3>\n<p>Molles, M.C. 2010. <strong>Ecology: Concepts and Applications</strong>. Fifth edition. McGraw-Hill. New York, NY. p. 572.</p>\n<ul>\n<li><p>I'd say this is the "standard" undergraduate textbook. Those planning on c... |
54,798 | <p>Using a new microscope with my son, we cannot see images beyond a certain magnification:</p>
<pre><code>Eyepiece: 25x - Objective lens: 4x --> OK
Eyepiece: 25x - Objective lens: 10x --> OK
Eyepiece: 25x - Objective lens: 40x --> not focused
Eyepiece: 25x - Objective lens: 100x --> not focused
</code></pre>
<p>In the last two cases, we try moving the stage along all its range, without getting anything.</p>
<p>Same issue using a 10x eyepiece.</p>
<p>On the 100x objective lens "OIL" is written; does it mean the observation needs to be done through oil instead of air? Or just that oil is used inside the objective?</p>
<p>We did not prepare the leaf; we just put a small piece of it between two slides.</p>
<p>Are we doing anything wrong?</p>
<p>Observing a leaf at 250x, we can see tiny round structures (I think barely bigger than what can be possibly seen by our eye): are those the cells?</p>
| [
{
"answer_id": 58742,
"pm_score": 4,
"text": "<p>This is probably the problem: \"We did not prepare the leaf; we just put a small piece of it <strong>between two slides</strong>.\".</p>\n\n<p>I suppose you mean you put a leaf fragment between two regular microscope slides, those measuring 26mm * 76mm (1... | [
{
"answer_id": 54807,
"pm_score": 2,
"text": "<p>25X is a mighty strong ocular (eyepiece) lens, certainly for home use. This means with the 40X objective you are already at 1000X overall. It would take a seriously thin, well mounted and well lit specimen for you to see a good image. This assumes the opt... |
54,850 | <p>In a strand of DNA, why does identifying the 3' side and the 5'side matter? Or the 3' --> 5' strand and the 5' --> 3' strand? Also, what is a single strand of DNA called, is it just a helix, or is the helix just the backbone?</p>
| [
{
"answer_id": 54859,
"pm_score": 3,
"text": "<p>A double strand is a helix, as the basepairs move with a horizontal angle with each step to the next basepair. Identifying the sides is important for DNA-replication and RNA synthesis as the way DNA is read is from 3' to 5' so that the complementary bases... | [
{
"answer_id": 54853,
"pm_score": 0,
"text": "<p>A single strand is a helix, as the basepairs move with a horizontal angle with each step to the next basepair. Identifying the sides is important for DNA-replication and RNA synthesis as the way DNA is read is from 3' to 5' so that the complementary bases... |
55,094 | <p>Does the brain always think of an appropriate response when reacting to a stimulus? </p>
<p>For example, when seeing things, does the brain have to think of an appropriate response to the eyes?</p>
| [
{
"answer_id": 55097,
"pm_score": 4,
"text": "<p>Well, not always but most of the time; reacting to stimuli is what defines the nervous system and the part of the nervous system that includes the brain is called the 'central nervous system' or CNS. Reactions to stimuli (nerve impulses) don't always have... | [
{
"answer_id": 55101,
"pm_score": 2,
"text": "<p><strong>No:</strong></p>\n\n<p><a href=\"https://en.wikipedia.org/wiki/File:Caf%C3%A9_wall.svg\" rel=\"nofollow noreferrer\"><img src=\"https://upload.wikimedia.org/wikipedia/commons/thumb/d/d2/Caf%C3%A9_wall.svg/800px-Caf%C3%A9_wall.svg.png\" alt=\"\"></... |
55,247 | <blockquote>
<p>And as a B cell matures, it develops the ability to determine friend from foe, developing both
immunocompetence -- or how to recognize and bind to a particular antigen -- as well as
self-tolerance, or knowing how to NOT attack your body’s own cells.
Once it’s fully mature, a B lymphocyte displays at least 10,000 special protein receptors
on its surface -- these are its membrane-bound antibodies.
All B lymphocytes have them, but the cool thing is, every individual lymphocyte has
its own unique antibodies, each of which is ready to identify and bind to a particular kind of antigen.
That means that, with all of your B lymphocytes together, it’s like having 2 billion keys
on your immune system’s keychain, each of which can only open one door.</p>
</blockquote>
<p>This is what Hank said in <a href="https://youtu.be/2DFN4IBZ3rI?t=179" rel="noreferrer">Crash course</a>. So the b cells, each are having several unique antibodies and I also saw that this is true for T cells too and the dendritic cells look for a helper T cell that can bind the parts of the intruders which the dendritic cell has presented on its membrane.</p>
<p>my question is </p>
<p>What if there is no antibody in any cell against an antigen?</p>
<p>Does the immune system has antibodies against all antigens in the world?</p>
<p>What happens if an antigen came into our body which has no antibody matching for it? </p>
| [
{
"answer_id": 55265,
"pm_score": 2,
"text": "<p>The same thing that happens to the native american when they were first exposed to smallpox. Extermination of 90%-95% of the population. <a href=\"https://en.wikipedia.org/wiki/History_of_smallpox\" rel=\"nofollow noreferrer\">https://en.wikipedia.org/wik... | [
{
"answer_id": 55262,
"pm_score": 0,
"text": "<p>If you have no antibody to a particular antigen, you have no immunity to that molecular pattern (and the organism it belongs to).</p>\n\n<p>That's the basis of immunity.</p>\n\n<p>This is why you have vaccinations. You are artificially exposed to an antig... |
55,286 | <p>Millions of colors in the visible spectrum can be generated by mixing red, green and blue - the RGB color system. Is there a basic set of smells that, when mixed, can yield all, or nearly all detectable smells ?</p>
| [
{
"answer_id": 55287,
"pm_score": 7,
"text": "<p>There are about 100 <a href=\"https://www.ncbi.nlm.nih.gov/books/NBK10824/\">(Purves, 2001)</a> to 400 <a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC33394/\">(Zozulya <em>et al</em>., 2001)</a> functional <strong><a href=\"https://senselab.med.ya... | [
{
"answer_id": 55300,
"pm_score": 3,
"text": "<p>There are many, many more parameters than 200! As an example, look at the nomenclature system for olfactory receptors (ORnXm). </p>\n\n<ul>\n<li>\"OR\" is the root name (Olfactory Receptor superfamily)</li>\n<li>n = an integer representing a family (e.g.,... |
55,358 | <p>Let's imagine a family composed of Mr A and Mrs B, who have a son named John.</p>
<p>Now, if for whatever twisted reason, John had a child with Mrs B, could a paternity test yield positive result for Mr A ?</p>
<p>Since John's genes all come from Mr A and Mrs B, the child's genes would all come originally from Mr A and Mrs B as well. Thus it seems to me like the test could suggest Mr A is the father of the child.</p>
<p>Or would there definetly be some "red flags" that suggest something wrong happened ?
Like, for example, if the child is a girl, that would mean both of her X chromosomes originally came from Mrs A (since John's X chromosome comes from his mother, as for all males), possibly even the same chromosome twice.</p>
<p>Let's consider that only Mr. A is tested, and not John. Would the child be considered genetically close enough to Mr. A that a test could attest that he is probably the child's father, granting there is no other test showing someone else as a much more likely candidate ?</p>
| [
{
"answer_id": 55361,
"pm_score": 4,
"text": "<p>Let's approach some different methods of distinguishing parents:</p>\n\n<p>1: The Y chromosome. These are passed down from father to son. Therefore, if the baby is male, its Y chromosome will be the same as John's and his father's - it will be indistingui... | [
{
"answer_id": 55359,
"pm_score": -1,
"text": "<p>No, Mr. A would not be flagged the father. \nThis is becasue when a parental test is done they look to what genes have the mother, the father and the baby. First they look at what genes has the mother and the baby. The one missing should be from the fath... |
55,505 | <p>Are humans capable of both anaerobic respiration, and lactic acid fermentation?</p>
<p>And if so, when do they do each?</p>
<p>I understand that the difference between respiration and fermentation is that respiration takes place in the electron transport chain. I understand that aerobic respiration uses oxygen in the electron transport chain, and anaerobic respiration uses some other molecule in the electron transport chain instead of oxygen, like nitrate. Whereas fermentation doesn't use the electron transport chain at all.</p>
<p>I know humans have an anaerobic metabolic process that produces lactic acid, but I'm not clear whether it's respiration or fermentation, or whether it could be either, in which case when it is which? </p>
<p>added<br>
some further discussion w roland at <a href="http://chat.stackexchange.com/rooms/56615/discussion-on-answer-by-roland-are-humans-capable-of-both-anaerobic-respiration">the chat link</a> / <a href="https://pastebin.com/raw/mkxckeqA" rel="nofollow noreferrer">https://pastebin.com/raw/mkxckeqA</a> / <a href="http://archive.is/CwCRL" rel="nofollow noreferrer">http://archive.is/CwCRL</a> and <a href="http://chat.stackexchange.com/rooms/56614/discussion-on-question-by-barlop-are-humans-capable-of-both-anaerobic-respiratio">on this q at chat link here</a> / <a href="https://pastebin.com/raw/9sV38LnQ" rel="nofollow noreferrer">https://pastebin.com/raw/9sV38LnQ</a> / <a href="http://archive.is/HJVVe" rel="nofollow noreferrer">http://archive.is/HJVVe</a> and example of conflicting definitions available <a href="https://pastebin.com/raw/3EKGmEb6" rel="nofollow noreferrer">https://pastebin.com/raw/3EKGmEb6</a> / <a href="http://archive.is/9sAlY" rel="nofollow noreferrer">http://archive.is/9sAlY</a> </p>
| [
{
"answer_id": 55510,
"pm_score": 5,
"text": "<p>Humans have no anaerobic respiration, if we define this as oxidation of a substrate with an external electron acceptor other than oxygen. In humans, the terminal electron acceptor in respiration is always oxygen, which is reduced at <a href=\"https://en.w... | [
{
"answer_id": 55511,
"pm_score": 2,
"text": "<p>Muscle tissue is a good example of anaerobic fermentation. Lactic Acid is fermented and builds up in this tissue when we do large amounts of exercise. We use the Pyruvate molecule and LDH to produce Lactate when required but it is only for short bursts of... |
55,512 | <p>Is glycolysis the beginning part of fermentation, or does fermentation follow glycolysis?</p>
<p>I see conflicting information from different sources</p>
<p><a href="https://honchemistry.wikispaces.com/Lactic+Acid+and+Alcohol+Fermentation+in+Humans" rel="nofollow noreferrer">https://honchemistry.wikispaces.com/Lactic+Acid+and+Alcohol+Fermentation+in+Humans</a></p>
<blockquote>
<p>"..Alcohol fermentation follows glycolysis, just like lactic acid
fermentation..." <-- So glycolysis is preceding fermentation, not part of fermentation</p>
</blockquote>
<p>and</p>
<blockquote>
<p>" The Actual Fermentation Part</p>
<p>Glycolysis and fermentation are two separate processes. Glycolysis was
explained briefly to give the reader an idea of the events leading up
to fermentation and the starting conditions in terms of molecules
available for reaction.....Going into the fermentation, the molecules NADH and pyruvic acid are present. " <--- so glycolysis is preceding fermentation, not part of fermentation.</p>
</blockquote>
<p>Whereas these two links put glycolysis as part of fermentation, not a preceding stage before fermentation.</p>
<p><a href="https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/variations-on-cellular-respiration/a/fermentation-and-anaerobic-respiration" rel="nofollow noreferrer">https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/variations-on-cellular-respiration/a/fermentation-and-anaerobic-respiration</a></p>
<blockquote>
<p>"Fermentation and cellular respiration begin the same way, with
glycolysis" <-- glycolysis is part of fermentation, not preceding it.</p>
</blockquote>
<p>and</p>
<p><a href="http://study.com/academy/lesson/anaerobic-respiration-lactic-acid-alcoholic-fermentation.html" rel="nofollow noreferrer">http://study.com/academy/lesson/anaerobic-respiration-lactic-acid-alcoholic-fermentation.html</a> </p>
<blockquote>
<p>"fermentation, which is a process that anaerobically generates ATP by
performing glycolysis..." <-- fermentation includes glycolysis, so glycolysis is part of fermentation, not preceding it.</p>
</blockquote>
<p>So, which is it?</p>
<p>Is it a)like khanacademy and study.com, or b)like honchemistry.wikispaces.com</p>
<p>I have heard the idea that glycolysis is independent, in that it can produce some (not much, but some), energy on its own, and it can happen without fermentation or cellular respiration following. Though when would glycolysis occur without fermentation or respiration following? And even if glycolysis is that independent, it may still be at the beginning of respiration and fermentation and not preceding it.</p>
<p>Wikipedia speaks in a contrary way..</p>
<p><a href="https://en.wikipedia.org/wiki/Fermentation" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Fermentation</a></p>
<blockquote>
<p>"Before fermentation takes place, one glucose molecule is broken down
into two pyruvate molecules. This is known as glycolysis." <-- so glycolysis is preceding fermentation, not part of it.</p>
</blockquote>
<p>so the above quote from wikipedia suggests that glycolysis is not the beginning part of fermentation, but a step preceding it</p>
<p>whereas still on the fermentation wikipedia page, it says </p>
<blockquote>
<p>"Fermentation is a metabolic process that converts sugar to acids,
gases, or alcohol....The first step, glycolysis" <-- so glycolysis is part of fermentation.</p>
</blockquote>
<p>Links on respiration are more unambiguous that glycolysis is part of respiration.. the links on fermentation vary a bit on whether glycolysis precedes fermentation or is part of it.</p>
| [
{
"answer_id": 55545,
"pm_score": 4,
"text": "<p>As @bpedit indicates in his comment, this is a semantic question — i.e. one regarding the meaning and usage of words. I will explain how I and others use these words and why. If you are convinced by my logic you will wish to use them in the same way, if n... | [
{
"answer_id": 56098,
"pm_score": 1,
"text": "<p>Glycolysis is the beginning portion of BOTH types of respiration; aerobic and anaerobic. It makes a couple of ATP. If aerobic respiration occurs, it recharges more ATP. If anaerobic respiration occurs, the organism can make other compounds (like Lactic Ac... |
55,517 | <p>I have read in an article on the internet that cancer is caused due to deficiency of vitamin B17 which has been removed from our diets long ago in the western food. But some people say that vitamin B17 does not work. So, is it deficiency of vitamin B17 which causes cancer i.e. can this vitamin really be used to cure cancer?</p>
| [
{
"answer_id": 58285,
"pm_score": 5,
"text": "<p><strong>Short Answer:</strong> No.</p>\n\n<p><strong>Background:</strong> First of all, there is no such thing as vitamin B17. The compound, amygdalin or laetrile, which is referred to by this term, is not a vitamin<sup><a href=\"https://dx.doi.org/10.332... | [
{
"answer_id": 55521,
"pm_score": 4,
"text": "<p>Short version: This is nonsense, cancer does not arise from nutritional deficiencies.</p>\n\n<p>Long version: The substance is called <a href=\"https://en.wikipedia.org/wiki/Amygdalin\" rel=\"noreferrer\">Amygdalin</a>, a poisonous cyanogenic glycoside. I... |
55,620 | <p>In the introduction to a review article entitled <a href="http://www.nature.com/nrm/journal/v7/n6/abs/nrm1939.html" rel="nofollow noreferrer">“Interpreting the protein language using proteomics”</a> the author uses the term ‘cognate genes’ in a manner which I do not understand:</p>
<blockquote>
<p>Whereas <strong>cognate genes</strong> encode the basic biological functions of
proteins, the real-time dynamics and regulation of protein structure
and function are generally carried out by specific post-translational
modifications (PTMs) of proteins such as phosphorylation,
glycosylation and acylation.</p>
</blockquote>
<p>What does it mean?</p>
| [
{
"answer_id": 55662,
"pm_score": 3,
"text": "<p>The sentence quoted accidentally misuses the word ‘cognate’ because in attempting to appear profound it has become overweight and off-balance. Notice the sentence also contains the meaningless nonsense of “real-time dynamics”, and in the rest of the paper... | [
{
"answer_id": 55626,
"pm_score": 0,
"text": "<p>I think it may be referring to constitutive expression of those \"cognate genes\". So, cognate genes are those who codify for essential proteins which are constantly produced in the cell, and their function is regulated by said PTMs (Post Translational Mo... |
55,796 | <p><a href="https://www.ncbi.nlm.nih.gov/pubmed/15228837" rel="noreferrer">The appendix has a role in the immune response</a>.</p>
<p>So is it therefore recently removed from the list of vestigial organs?</p>
| [
{
"answer_id": 56553,
"pm_score": 5,
"text": "<p><strong>Short Answer:</strong> No, the appendix is still considered a vestigial organ.</p>\n\n<p><strong>Long Answer:</strong> The idea that that vermiform appendix is vestigial originated when <a href=\"https://en.wikipedia.org/wiki/Special:BookSources/0... | [
{
"answer_id": 56552,
"pm_score": 3,
"text": "<p><strong>Short answer</strong><br>\nThe appendix is a vestigial organ.</p>\n\n<p><strong>Background</strong><br>\nAccording to the <a href=\"https://en.oxforddictionaries.com/definition/vestigial\" rel=\"noreferrer\">Oxford Dictionaries</a> <em>vestigial</... |
56,004 | <p>Somewhere I read following paragraphs giving one counter-example to Darwin's theory of evolution. </p>
<p>(By the way, I am a physicist and not a biologist, but I am interested in this field.)</p>
<p>Do these paragraphs point to the reality? What is the current status of "theory of evolution of species" ? </p>
<blockquote>
<p>"Darwin cited the giraffe as an outstanding example of natural
selection. Supposedly, as a result of extended droughts, the supply
of green leaves could be obtained only at the top of the trees, and
therefore the shorter necked giraffe died off. The giraffes which
grew longer necks survived. However, there is no evidence whatever in
the fossil record or elsewhere that giraffes with short necks have
ever existed. And what would have happened to young giraffes with
relatively short necks?</p>
<p>Darwin failed to realize that body characteristics in offsprings are
determined and programmed by DNA factors of the Genes or the Genetic
material of the parents, and not by the stretching of the neck or any
other bodily exercise."</p>
</blockquote>
| [
{
"answer_id": 56006,
"pm_score": 4,
"text": "<p>Giraffe necks being long because of 'reaching' is false. The neck size is due <a href=\"https://www.jstor.org/stable/2463405\">sexual selection</a>.</p>\n\n<p>The writer of the paragraph fundamentally misunderstood Darwin, he never argued that the act of ... | [
{
"answer_id": 56012,
"pm_score": 3,
"text": "<blockquote>\n <p>Darwin cited the giraffe as an outstanding example of natural selection. Supposedly, as a result of extended droughts, the supply of green leaves could be obtained only at the top of the trees, and therefore the shorter necked giraffe died... |
56,092 | <p>I have found a large, wild patch, some 200m long, of mainly Datura Stramonium, in our street. I have always been keenly interested and well read on the shamanic, and - very rare - medicinal uses of this species, but scattered amongst them, like family, are two other plants I don't know, but am convinced are also some kind of Datura. I would please like some help on identifying the other two based on the two photos I have of all three.</p>
<p><a href="https://i.stack.imgur.com/SVj43.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/SVj43.jpg" alt="What I know as the Stramonium Flower"></a></p>
<p>This is the well known - to me - Stramonium flower, the plant characterized by jagged leaves and the well known spiked seed pod of Jimson Weed seeds.</p>
<p><a href="https://i.stack.imgur.com/gkbpT.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/gkbpT.png" alt="Morning Flory - Flowers, leaf, and other foliage"></a></p>
<p>It looks like user29734's answer is correct, and the above is Morning Glory, but of course subject to confirmation. I now do recognize at least the purple flower as Morning Glory, but from some 30 odd years ago. And it now looks like what I confused with Datura Alba is really just another colour flower of the Morning Glory.</p>
<p>If anyone could please confirm my ID of the Stramonium, and confirm the identification of the second image as morning glory, and suggest what species.</p>
<p>These plants are all around my neighbourhood, with is the northern part of Randburg, South Africa. This city borders on the Northern side of Johannesburg. <a href="https://i.stack.imgur.com/SVj43.jpg" rel="nofollow noreferrer">1</a> It's a temperate climate, with very hot and rainy summers, and bitterly cold and dry winters. The soil is reddish and lacks much humus. </p>
<p>It is a semi-rural area, having been rapidly urbanised over the last ten or so years, when it was still just farms and small holdings. Farming is mainly vegetables or lucerne; and lots of maize further out from the city. We are a few km south of the <a href="https://en.wikipedia.org/wiki/Cradle_of_Humankind" rel="nofollow noreferrer">Cradle of Humankind</a>.</p>
<p><a href="https://i.stack.imgur.com/SVj43.jpg" rel="nofollow noreferrer">1</a> Strangely enough, there are two cities in the US with the same names, both in California, I believe. I know Johannesburg is.</p>
| [
{
"answer_id": 56118,
"pm_score": 3,
"text": "<p>Okay, so as far as the blue and white flower goes I'm pretty sure it's a cultivar of ipomoea called Flying Saucer which is a hybrid of heavenly blue (I. tricolor) and Pearly gates (also I. tricolor) meaning it's a hybrid and no seed output. \nAs far as th... | [
{
"answer_id": 56103,
"pm_score": 2,
"text": "<p>The second flower is, I'm guessing by the valentine shaped leaf and violet tubular flowers, a morning glory vine (ipomoea violacea or ipomea tricolor). These plants both are closely related cultivars of ololioqui and tlitlitzen which had a history of sham... |
56,108 | <p>We all know there are three pathways to activate complement: classical pathway, lectin pathway and alternative pathway. What is the advantage of having multiple pathways?</p>
| [
{
"answer_id": 56118,
"pm_score": 3,
"text": "<p>Okay, so as far as the blue and white flower goes I'm pretty sure it's a cultivar of ipomoea called Flying Saucer which is a hybrid of heavenly blue (I. tricolor) and Pearly gates (also I. tricolor) meaning it's a hybrid and no seed output. \nAs far as th... | [
{
"answer_id": 56103,
"pm_score": 2,
"text": "<p>The second flower is, I'm guessing by the valentine shaped leaf and violet tubular flowers, a morning glory vine (ipomoea violacea or ipomea tricolor). These plants both are closely related cultivars of ololioqui and tlitlitzen which had a history of sham... |
56,283 | <p>If a person has a specific mutation in a gene (2281 del/ins in a single copy of the Bloom BLM gene), is he more likely than the general population to have other types of mutations in the same gene?</p>
| [
{
"answer_id": 56286,
"pm_score": 4,
"text": "<p>A priori, no! Why would it? Do you have any specific hypothesis in mind you would like to discuss?</p>\n\n<p>Below are some expectations from a simple model and possible reasons for why this expectation may break down under more complicated models.</p>\n\... | [
{
"answer_id": 56353,
"pm_score": 0,
"text": "<p>Bear in mind that the average mutation rate of DNA polymerase is about 1 error for every 1 x 10^6 bases. So the probability of mutation is independent at each base pair, but low - there's nothing that would prevent another mutation, but there also is not... |
56,523 | <p>The Wikipedia entry for <a href="https://en.wikipedia.org/wiki/Gene" rel="nofollow noreferrer">Gene</a> contains the statement:</p>
<blockquote>
<p>The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons.</p>
</blockquote>
<p>But the page on the <a href="https://en.wikipedia.org/wiki/Start_codon" rel="nofollow noreferrer">Start codon</a> says:</p>
<blockquote>
<p>The start codon is often preceded by a 5' untranslated region (5' UTR)</p>
</blockquote>
<p>So is the start codon a part of the UTR?</p>
| [
{
"answer_id": 56526,
"pm_score": 4,
"text": "<p>Because the <em>start codon</em> is translated into methionine, it clearly can <em>not</em> be part of the 5'-untranslated region, as @Johnny writes in his answer. </p>\n\n<p>The more contentious question would be for the <em>stop codons</em> and the <em>... | [
{
"answer_id": 56524,
"pm_score": 2,
"text": "<p>The start codon both in prokaryotes and eukaryotes isn't a part of the 5'UTRs, it is present downstream the UTRs.</p>\n\n<p>In prokaryotes the Ribosome binds to the Shine-Dalgarno sequence (AGGAGGU) of 5'UTR. This sequence is found 3-10 base pairs upstrea... |
56,531 | <p>I have come across two set of definitions which are not contradictory but different.</p>
<p>From <a href="https://en.wikipedia.org/wiki/Gene_expression#Regulation_of_gene_expression" rel="nofollow noreferrer">wikipedia</a>:</p>
<blockquote>
<p>A constitutive gene is a gene that is transcribed <strong>continually</strong> as opposed to a facultative gene, which is only transcribed when needed.</p>
<p>A housekeeping gene is typically a constitutive gene that is transcribed at a <strong>relatively constant level</strong>. The housekeeping gene's products are typically needed for maintenance of the cell. It is generally assumed that their expression is unaffected by experimental conditions. Examples include actin, GAPDH and ubiquitin.</p>
</blockquote>
<p>My question from these definitions: What does 'transcribed at a relatively constant level' mean? Does it mean that a constant level of gene product is maintained in a cell? I can't understand there meanings atal.</p>
<p>Again,according to Oxford dictionaries</p>
<blockquote>
<p>Constitutive Genes are genes that are expressed following interaction between a promoter and RNA polymerase without additional regulation.
<sub>(Oxford Dictionary of Biochemistry and Molecular Biology)</sub></p>
<p>Housekeeping genes - Constitutive loci that are theoretically expressed in all cells in order to provide the maintenance activities required by all cells: e.g., genes coding for enzymes of glycolysis and the and the citric acid cycle.<sub>(Dictionary of Genetics)</sub></p>
</blockquote>
<p>These definitions do not tell whether they are continually transcribed or the synthesised products are present in constant amount.</p>
<p>Which one best define them?</p>
| [
{
"answer_id": 56526,
"pm_score": 4,
"text": "<p>Because the <em>start codon</em> is translated into methionine, it clearly can <em>not</em> be part of the 5'-untranslated region, as @Johnny writes in his answer. </p>\n\n<p>The more contentious question would be for the <em>stop codons</em> and the <em>... | [
{
"answer_id": 56524,
"pm_score": 2,
"text": "<p>The start codon both in prokaryotes and eukaryotes isn't a part of the 5'UTRs, it is present downstream the UTRs.</p>\n\n<p>In prokaryotes the Ribosome binds to the Shine-Dalgarno sequence (AGGAGGU) of 5'UTR. This sequence is found 3-10 base pairs upstrea... |
56,689 | <p>In non-cyclic photophosphorylation 1 ATP and 2 $NADPH_2$ molecules are produced.</p>
<p>In cyclic photophosphorylation 2 ATP molecules are produced.</p>
<p>For production of one molecule of Glucose 18 ATP and 12 $NADPH_2$ molecules are reqiured.</p>
<p>According to my understanding,6 turns of cyclic and non-cyclic photophosphorylation is required to produce one molecule of glucose.</p>
<p>Because 6 turns of non cyclic photophosphorylation will produce 12 $NADPH_2$ and 6 ATP molecules.</p>
<p>And cyclic photophosphorylation will produce 12 ATP molecules. </p>
<p>Total=12 $NADPH_2$ and 18 ATP.</p>
<p>I think Iam missing something , Please answer me if I am correct or not.</p>
| [
{
"answer_id": 56913,
"pm_score": 3,
"text": "<p>In non-cyclic photophosphorylation the stoichiometry of ATP:NADPH is predicted as 3:2, i.e, for every two NADPH formed, a total of three ATP are produced.</p>\n<p><a href=\"http://jfallen.org/%7Ejohn/webstar/john/pdf/32775.pdf\" rel=\"nofollow noreferrer\... | [
{
"answer_id": 77508,
"pm_score": 0,
"text": "<p>The numbering of 1ATP from noncyclic photophosphorylation and 2ATP from cyclic is little too much to be right. However, the formation of 2NADPH + H+ out of noncyclic photophosphorylation is correct.</p>\n\n<p>Because according to the Chemiosmotic Hypothes... |
56,775 | <blockquote>
<p>For this reason "insulin insensitivity", or a decrease in insulin receptor signaling, leads to diabetes mellitus type 2 – the cells are unable to take up glucose, and the result is hyperglycemia (an increase in circulating glucose), and all the sequelae that result from diabetes <a href="https://en.wikipedia.org/wiki/Insulin_receptor" rel="nofollow noreferrer"><span class="math-container">$^{(1)}$</span></a></p>
</blockquote>
<p>Also</p>
<blockquote>
<p>Type 2 diabetes is due to insufficient insulin production from beta cells in the setting of insulin resistance. <a href="https://en.wikipedia.org/wiki/Type_2_diabetes" rel="nofollow noreferrer"><span class="math-container">$^{(2)}$</span></a></p>
</blockquote>
<p>So why don't we give people a medicine which just increases the number of receptors or increases the sensitivity of receptors? Isn't it illogical to give more of insulin for a deficit amount of receptors? So, what is the logic behind giving insulin?</p>
| [
{
"answer_id": 56778,
"pm_score": 5,
"text": "<p><code>Isn't it illogical to give more of insulin for a deficit amount of receptors?</code></p>\n\n<p>Seems like there is some confusion in the definition of type-2 DM itself. According to the <a href=\"http://www.diabetes.org/diabetes-basics/type-2/\" rel... | [
{
"answer_id": 56776,
"pm_score": 3,
"text": "<p>This is true for the beginning of the disease. As a reaction to the reduced sensitivity of the cells in the body to insulin (and thus less uptake of glucose from the blood and a resulting hyperglycemia) the body produces more and more insulin to cope with... |
56,798 | <p>I fell asleep while listening to a podcast, and I am sure I was dreaming but I could also still hear the podcast. </p>
<p>The podcast played an important role in the dream, I was searching for the source of the voice, wondering if others in the dream could hear the same voice. I started to feel a bit panicky and woke up as the podcast also happened to end. I rewound the show and confirmed that it was all there, exactly as I had heard in my dream!</p>
<p>I would like to read more about this type of experience, but I am having trouble finding the right words to search. Is there a name for this phenomenon? Is there anything that contributes to experiences like these? I know it wasn't lucid dreaming, because I wasn't aware of being asleep.</p>
| [
{
"answer_id": 56870,
"pm_score": 3,
"text": "<p>I think I found a good expression : \"sensory incorporation in dreams\"</p>\n\n<p><a href=\"https://www.psychologytoday.com/blog/dream-factory/201409/sensory-incorporation-in-dreams\" rel=\"nofollow noreferrer\">https://www.psychologytoday.com/blog/dream-... | [
{
"answer_id": 56861,
"pm_score": -1,
"text": "<p>My answer is going to be verily based on my experience and thinking, so don't take it for absolute.</p>\n\n<p>When we are dreaming, at the level of the brain, sensual (meaning from senses) experience is being created by projection in the sensitive cortic... |
56,837 | <p>For a homework assignment I received the following question: </p>
<p><strong>Which statement best explains the evolution of fins in whales and fish?</strong></p>
<p>a. The common ancestor of whales and fish possessed genes for fins.</p>
<p>b. Whales and fish possess the same mutations in their genomes.</p>
<p>c. Fins evolved in whales and fish because they both use them to swim in water.</p>
<p>d. Fins evolved in whales and fish because of different mutations that occurred
in their genomes.</p>
<p>e. Fins evolved in whales and fish because their most recent common ancestor swam in water.</p>
<p>My answer is (c). Of the given options, it seems most accurate. I feel that the language is unclear as many organisms who do not have fins swim in water. That can be a logic against the option. But, the given answer is (d). That seems too bizarre as even humans and fishes have different mutations in their genomes. (c) seems more appropriate as it can exemplify convergent evolution.</p>
| [
{
"answer_id": 56839,
"pm_score": 4,
"text": "<p><strong>Short answer</strong><br>\nd) is definitely correct.</p>\n\n<p><strong>Background</strong><br>\nThe crucial element is that whales returned from land to the sea and re-evolved fins.</p>\n\n<ul>\n<li>a) is incorrect, as the common ancestor may not ... | [
{
"answer_id": 56854,
"pm_score": 4,
"text": "<p>I agree with you that the question is ambiguous, and also that the most sensible answer would be C. However, one <em>could</em> make a more or less reasonable argument in favor of several other answers, too.</p>\n\n<blockquote>\n <p>a. The common ancest... |
57,626 | <p>According to <a href="https://www.ncbi.nlm.nih.gov/books/NBK21129/#A5997" rel="nofollow noreferrer">Genomes</a></p>
<p>PCR is </p>
<blockquote>
<p>A technique that results in exponential amplification of a selected region of a DNA molecule [in test tube].</p>
</blockquote>
<p>DNA cloning is</p>
<blockquote>
<p>Insertion of a fragment of DNA into a cloning vector, and subsequent propagation of the recombinant DNA molecule <strong>in a host organism</strong>.</p>
</blockquote>
<p>While, <a href="https://books.google.co.in/books?id=jK6UBQAAQBAJ&printsec=frontcover&dq=Molecular%20Biology%20of%20the%20Cell&hl=en&sa=X&redir_esc=y#v=onepage&q&f=false" rel="nofollow noreferrer">Molecular Biology of the Cell</a>, Sixth Edition says in a summary:</p>
<blockquote>
<p><strong>DNA cloning</strong> (through the use of either cloning vectors or the <strong>polymerase chain reaction</strong>) in which portion of a genome (often an individual gene) is purified away from the remainder of the genome by repeatedly copying to generate many billions of identical molecules.</p>
</blockquote>
<p>Here DNA cloning has been used to mean DNA replication in general.</p>
<p><strong>Question:</strong> Which author's view is correct, or at least provides the most accepted definitions?</p>
| [
{
"answer_id": 59298,
"pm_score": 3,
"text": "<h3>Short answer</h3>\n\n<p>The Oxford English Dictionary is quite clear on this. For the verb <em>clone</em> there are two meanings:</p>\n\n<p><strong>Biology</strong> To propagate (an organism or cell) as a clone.</p>\n\n<p><strong>Molecular Biology</stron... | [
{
"answer_id": 57628,
"pm_score": 3,
"text": "<p><strong>Short answer</strong><br>\nAll of your sources are correct as they are not mutually exclusive. PCR is used to isolate and amplify DNA to yield small quantities of pure target product. Gene cloning can subsequently be applied to scale the productio... |
57,849 | <p>I will be moving across the country in the coming weeks, and I have realised that I will likely have leftover perishable food in my apartment before I leave and I was thinking of trying to prepare some of it the night before I leave to bring with me. The trip will take me four days, and I was going to cook (extra thoroughly) hardboiled eggs, pork, bacon and sausages. I might even add some salt or something. And keep all of my packaging as sanitary as possible, <em>eg.</em> straight from pan/pot to sterile ziplock.</p>
<p>The eggs I'm unsure of because of the protective outer layer that is chemically removed during processing. The pork and bacon, I feel like they will be alright if they're eaten first. And I'm not too worried about the sausages because they've been processed and cooked.</p>
<p>I think a visual and olfactory test of the foods before I eat them would be wise - especially if nearing day 4. But, realistically, if I keep the food out of the sun covered up it will probably stay safe to eat, right? Or is this a bad idea?</p>
<p>I think that the food would definitely be safe to eat up until the end of the second day. But, what about any longer than that? How did people back in the old days travel with food?</p>
<p>Edit:
Just to clarify my question. I am not asking about whether or not my apartment is sterile. And I'm not asking about whether or not bacteria can multiply. I'm very well aware of these answers.</p>
<p>I'm looking for a realistic estimate on food longevity - not the food-standards enforced onto food manufacturers or restaurants by the FDA/Health Canada.</p>
| [
{
"answer_id": 57877,
"pm_score": 3,
"text": "<p>The biggest factor in whether bacteria can grow in food is water bio-availability. Most non-sterile methods of preserving food (note that canning IS sterile) utilize this fact. Over salting while curing, adding lots of sugar, and dehydrating (or freeze-dr... | [
{
"answer_id": 57850,
"pm_score": 0,
"text": "<p>Your apartment isn't sterile, and cooking kills many but not all bacteria - cooked food isn't sterile either, no matter how thoroughly cooked. No matter how well you pack things, they will have bacteria on them. Without refrigeration, that bacteria will m... |
58,005 | <p>I asked a question earlier today about birds with infrared vision but this time I am asking about animals in general. I know that many snakes have receptors between their eyes and their snout that allows them to sense infrared radiation but I am looking for an animal that actually uses its eyes.</p>
<p>Googling and searching around found me this statement:</p>
<blockquote>
<p>It's worth noting that, though there are numerous animals that sense
infrared light, relatively few of them sense it with their eyes</p>
</blockquote>
<p>The article didn't list any specific animal that used its eyes to sense infrared light, it just says 'very few'. However, I haven't been able to find any species that can sense infrared light with their eyes. </p>
| [
{
"answer_id": 58046,
"pm_score": 4,
"text": "<p><strong>Short answer</strong><br>\nAs far as I can see, there are no animalia with high-sensitivity infrared photoreceptors in their retinae. Instead, infrared is detected at low thresholds with a dedicated sensory system in some species - the pit organ. ... | [
{
"answer_id": 58051,
"pm_score": 3,
"text": "<p>Yes, <a href=\"https://en.wikipedia.org/wiki/Mantis_shrimp\" rel=\"noreferrer\">Mantis shrimp</a> have 12 photo-receptors and can detect the low-end of IR.</p>\n\n<p>In <em>H. trispinosa</em> one of the photoreceptors, R3P, detects right at the edge of 'd... |
58,058 | <p>TCGA provide CNV data for each cases like <a href="https://portal.gdc.cancer.gov/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.case_id%22,%22value%22:%5B%22001ad307-4ad3-4f1d-b2fc-efc032871c7e%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%5B%22Copy%20Number%20Variation%22%5D%7D%7D%5D%7D&facetTab=cases" rel="nofollow noreferrer">this</a>.</p>
<p>I want to know, how can I calculate CNVs from this data? What are standard algorithms and methods used? </p>
| [
{
"answer_id": 58189,
"pm_score": 3,
"text": "<p>The files you're referencing are completely processed files in the SEG format. The basic files are calculated using both germline and somatic CNV, whereas files denoted nocnv are only somatic (the numbers <strong>will</strong> differ because they are calc... | [
{
"answer_id": 58139,
"pm_score": 2,
"text": "<p>Copy number variation (CNV) has traditionally been detected in the wet lab via FISH, fluorescent in-situ hybridization. By combining targeted DNA oligos to fluorescent reporter proteins, a region with high CNV will \"glow more brightly\" than a region tha... |
58,127 | <p>When you type <strong>Trypophobia Trigger Images</strong> in google, you see a variety of images with irregular lumps and bumps among some more gory images.</p>
<p>Many people report that these images induce phobia like symptoms of anxiety.</p>
<p>Why do we get anxious when exposed to these images? What advantage is there to be had from this response? </p>
<p>I find the reasons like this <a href="http://bodyodd.nbcnews.com/_news/2011/09/13/7561543-spiders-ants-did-that-make-you-itchy-heres-why?lite" rel="noreferrer">ABC news report on ants and spiders</a>. But still didn't get it any info from it.</p>
| [
{
"answer_id": 58129,
"pm_score": 5,
"text": "<p><a href=\"https://en.wikipedia.org/wiki/Trypophobia\" rel=\"nofollow noreferrer\">Trypophobia</a> is not a recognised specific anxiety disorder (<a href=\"https://www.washingtonpost.com/national/health-science/phobia-about-holes-is-not-officially-recogniz... | [
{
"answer_id": 58137,
"pm_score": 2,
"text": "<p>The \"That's Odd\" feeling is real. And now I understand the term \"trypophobia\" as a specific example of a more general aversion response which seems common in nature, and might even be hard-wired in the neural-circuits of many animals. The brightly co... |
58,169 | <p>I recently read in my Ecology course notes that a mosquito feeding on human blood is not considered as a parasite. However, since it sucks blood from the human body, shouldn't it be regarded as a parasite, just like lice and ticks?</p>
| [
{
"answer_id": 58173,
"pm_score": 6,
"text": "<p><strong>A mosquito is a biological parasite, it is not a medical parasite.</strong> </p>\n\n<p>There are two definitions of parasite. A biological/ecological definition and a medical/physiological interaction definition.</p>\n\n<ul>\n<li><p>A <strong>para... | [
{
"answer_id": 58171,
"pm_score": 3,
"text": "<p>To be a parasite, an organism needs to fulfill two criteria</p>\n\n<p>1) It needs to have a non-mutual relationship between itself and its host. \nThe organism derives benefit and the host suffers harm. </p>\n\n<p>2)The organism also needs to live in or o... |
58,176 | <h1>1.</h1>
<p>Some sources (including the current <a href="https://biology.stackexchange.com/tags/biophysics/info">Tag-info</a> at biology SE) state; biophysics is the adoption of <em>techniques</em> / <em>methodologies</em> from physics to study biological systems.</p>
<blockquote>
<p>The <em>use of method</em>s from the physical sciences to aid in the study of biological systems…</p>
</blockquote>
<p>Bio-SE- Tag <a href="/questions/tagged/biophysics" class="post-tag" title="show questions tagged 'biophysics'" rel="tag">biophysics</a>.</p>
<blockquote>
<p>Biophysics or biological physics is an interdisciplinary science that applies the approaches and methods of physics to study biological systems…</p>
</blockquote>
<p><a href="https://en.wikipedia.org/wiki/Biophysics" rel="nofollow noreferrer">Wikipedia</a> (<a href="https://en.wikipedia.org/w/index.php?title=Biophysics&oldid=770680639" rel="nofollow noreferrer">permalink</a>).</p>
<blockquote>
<p>Biophysics — the branch of biology that applies the methods of physics to the study of biological structures and processes…</p>
</blockquote>
<p><a href="http://www.dictionary.com/browse/biophysics" rel="nofollow noreferrer">Dictionary.com</a></p>
<hr />
<h1>2.</h1>
<p>According to other sources, biophysics is the subject concerned with how the laws or phenomena of physics work in living systems.</p>
<blockquote>
<p>“The subject of biophysics are the physical <em>principles</em> underlying all process of living systems.”</p>
</blockquote>
<p>Google Book: <a href="https://books.google.co.in/books?id=xxsYe6z_IA4C&lpg=PP1&pg=PR19#v=onepage&q&f=false" rel="nofollow noreferrer">Biophysics, An introduction</a>, By Ronald Glaser (<a href="https://books.google.co.in/books?id=xxsYe6z_IA4C&lpg=PA1&ots=torX9QfguC&dq=what%20is%20the%20term%20for%20interdiscipline%20between%20biology%20and%20physics%3F&pg=PA1#v=onepage&q=what%20is%20the%20term%20for%20interdiscipline%20between%20biology%20and%20physics?&f=false" rel="nofollow noreferrer">permalink</a>).</p>
<blockquote>
<p>Biophysics is a bridge between biology and physics. ... Biophysics looks for principles that describe patterns. If the principles are powerful, they make detailed <em>predictions</em> that can be tested. ---</p>
</blockquote>
<p><a href="http://www.biophysics.org/Education/WhatisBiophysics/tabid/2287/Default.aspx" rel="nofollow noreferrer">Biophysical society</a></p>
<hr />
<p>These two, although apparently quite similar (and I agree, have overlapping areas) basically indicate completely different things.</p>
<p>The first group of definitions refer to <strong>techniques and methodologies</strong>; such as “how does an electron microscope work?”, or “what could be the best strategy to separate membrane-lipids?”, or “how could you identify cells with the expression of certain RNA”; etc.</p>
<p>The second group refers to the physical principles applicable to living systems. Such as “why do phospholipids form a bilayer?” or “how do brain waves reach the scalp?” or “how does a humming bird move its wings when it hovers in a stationary manner?” or “what are the mechanisms working in the path of transport through phloem?”.</p>
<p>Now my question is: Is there a dual and different meaning, or use of the term ‘biophysics’?</p>
| [
{
"answer_id": 58173,
"pm_score": 6,
"text": "<p><strong>A mosquito is a biological parasite, it is not a medical parasite.</strong> </p>\n\n<p>There are two definitions of parasite. A biological/ecological definition and a medical/physiological interaction definition.</p>\n\n<ul>\n<li><p>A <strong>para... | [
{
"answer_id": 58171,
"pm_score": 3,
"text": "<p>To be a parasite, an organism needs to fulfill two criteria</p>\n\n<p>1) It needs to have a non-mutual relationship between itself and its host. \nThe organism derives benefit and the host suffers harm. </p>\n\n<p>2)The organism also needs to live in or o... |
58,212 | <p>Vena cava is valve less. So, during atrial systole what prevents backflow of blood to them? </p>
| [
{
"answer_id": 58222,
"pm_score": 1,
"text": "<p>Besides @Bryan Krause answer, there's another very important factor that prevents the blood from flowing back from the right atrium to the vena cava during systole. </p>\n\n<p>Part of the muscle that constitutes the atrial walls also wraps around the site... | [
{
"answer_id": 58218,
"pm_score": 2,
"text": "<p>Pressure differences. Atrial contractions are much more gentle than ventricular ones, and in normal circulation the venous pressure in the vena cava often stays higher than the right atrium, even during atrial systole. If the pressure in the atrium does r... |
58,221 | <p><strong>My understanding of null and alternate hypotheses :</strong></p>
<p>The <em>null hypothesis</em> is a hypothesis whose plausibility is being tested by a test statstic and is denoted by H0. It assumes that observed data follows a standard scientific theory (and the variation/deviation is due to
chance).<sup>1</sup> <em>Alternative hypothesis</em> is a hypothesis that contradicts null hypothesis. It assumes that the variation in the observed data is real, not due to chance.It is usually the hypothesis that a scientist is trying to establish.
<sub>(Source: Biostatistics by Lee & Forthofer & Statistics by David Freedman)</sub></p>
<p>This<sup>1</sup> holds good for Goodness-of-fit test but not <em>chi-square test for independence</em> as there is no theoretical data to compare the observed data with. </p>
<p><em>So my question is in a given problem of chi-square test for independence how to determine what the null should be?</em></p>
<ul>
<li><p><strong>When what the scientist is trying to establish is mentioned:</strong></p>
<p><strong>Q :</strong> In a study of effectiveness of an antipsychotic drug, patients are treated with the drug and were compared to those receiving a placebo. 698 of 1068 patients were released after taking the placebo while 639 out of 2,127 relapsed after taking the antipsychotic drug.
Test the prediction that the antipsychotic drug is significantly more effective in preventing relapse than placebo.</p>
<p><strong>A:</strong> Ho : E<sub>drug</sub> = E<sub>placebo</sub> Ha : E<sub>drug</sub> > E<sub>placebo</sub></p>
<p>(Reasoning: Ha is the hypothesis the scientist is trying to establish and so Ho should be something that opposes the Ha that he has to disprove.)</p></li>
<li><p><strong>When what the scientist is trying to establish is not mentioned (at least not clearly):</strong></p>
<p><strong>Q:</strong> Among 60 males and 50 females, 25 males and 20 females were with attached ear lobes. Statistically prove whether or not the attached pinna has any relation with sex.</p>
<p>Not sure what the scientist wants to establish so unable to assume a null.</p></li>
</ul>
| [
{
"answer_id": 58222,
"pm_score": 1,
"text": "<p>Besides @Bryan Krause answer, there's another very important factor that prevents the blood from flowing back from the right atrium to the vena cava during systole. </p>\n\n<p>Part of the muscle that constitutes the atrial walls also wraps around the site... | [
{
"answer_id": 58218,
"pm_score": 2,
"text": "<p>Pressure differences. Atrial contractions are much more gentle than ventricular ones, and in normal circulation the venous pressure in the vena cava often stays higher than the right atrium, even during atrial systole. If the pressure in the atrium does r... |
58,247 | <p>Say I have a disease that is autosomal recessive. If one was heterozygous for this trait, could the recessive gene still be expressed?</p>
<p>I know sickle cell anemia has a heterozygous advantage so it must be possible but what are the conditions for this to happen and also to what degree?</p>
<p>EDIT: This isn't asking how a gene is recessive or dominant in a molecular level.</p>
| [
{
"answer_id": 58249,
"pm_score": 4,
"text": "<p><strong>Short answer</strong></p>\n\n<p>The concepts dominance, additivity, epistasis, recessivity and others are all specific to a given phenotype. Here you are getting confused because you are considering two different phenotypes at once.</p>\n\n<p><str... | [
{
"answer_id": 58260,
"pm_score": 2,
"text": "<p>There are a couple of distinctions to make here. You can have an allele which is 'Phenotypically Expressed', that is it's visible at the organism level by some feature. In that case, no, recessive alleles by definition do not express that particular pheno... |
58,283 | <p>Why honey bees built hive in perfect hexagonal shape ? </p>
<p>Due to Hexagonal shape, I can go near without any anxious or fear.( Apart from Honey bee's stings)</p>
<p>From this <a href="https://biology.stackexchange.com/questions/58127/why-do-humans-suffer-anxiety-when-they-view-trypophobia-trigger-images">Question</a>, Most creatures look like or tries to look like irregular to fear the other creatures to attack. </p>
| [
{
"answer_id": 58287,
"pm_score": 4,
"text": "<blockquote>\n <p>Why honey bees built hive in perfect hexagonal shape ?</p>\n</blockquote>\n\n<p>Honeycomb cells (not the hive or the honeycomb itself) are hexagonal, in some species of bees but not all. The regularity of this shape has puzzled people for... | [
{
"answer_id": 74756,
"pm_score": -1,
"text": "<p>in \"the origin of species\" pages 178 and 179, Darwin has stated that if a bee could build a cell slightly more hexagonal than the other bees then this bee would have a survival benefit since a perfect hexagon is the most economical structure in storing... |
58,297 | <p>Usually, people are interested in expressing human proteins in fast-growing organisms like bacteria to yield a maximum of protein within a short time lapse. Codon usage harmonization/optimization have been used to increase the protein production. The role of codon usage have been studied in the context of viral protein expression, but outside this viral context, is there any example of using human cell lines for heterologous expression?</p>
| [
{
"answer_id": 58287,
"pm_score": 4,
"text": "<blockquote>\n <p>Why honey bees built hive in perfect hexagonal shape ?</p>\n</blockquote>\n\n<p>Honeycomb cells (not the hive or the honeycomb itself) are hexagonal, in some species of bees but not all. The regularity of this shape has puzzled people for... | [
{
"answer_id": 74756,
"pm_score": -1,
"text": "<p>in \"the origin of species\" pages 178 and 179, Darwin has stated that if a bee could build a cell slightly more hexagonal than the other bees then this bee would have a survival benefit since a perfect hexagon is the most economical structure in storing... |
58,569 | <p>I have come across <a href="https://www.youtube.com/watch?v=RuzLXxbGc4c" rel="noreferrer">this</a> video which put forth the hypothesis that bramble actually qualifies as a carnivorous plant. The observations that have led to the hypothesis are:<br>
1. Sheep getting caught frequently in bramble<br>
2. Sheep will die without human intervention.<br>
3. The rotting corpse of the sheep will nourish the plant for many days.<br>
4. The thorns angle inward -- supposedly evidence for adaptation that helps trap prey animal. </p>
<p>I agree , on the surface it looks plain silly but that is a reflexive reaction, not an argument. Is this a plausible hypothesis? If not , please give reasons. </p>
| [
{
"answer_id": 58671,
"pm_score": 4,
"text": "<p><strong>Even if the adaptations to tangle were well supported, brambles would still not be carnivorous.</strong></p>\n\n<p>Carnivorous plants release digestive enzymes to digest their prey or have other adaptations specifically to pull nutrients from the ... | [
{
"answer_id": 58617,
"pm_score": 3,
"text": "<p>This is really more of a comment than an answer, but I'd challenge most of those premises.</p>\n\n<p>1) Sheep getting caught. But (AFAIK) wooly sheep are the (recent, in evolutionary terms) product of human breeding. Blackberries &c wouldn't have ha... |
58,669 | <p>I've come across a spruce tree that is growing 15ft up in the crotch of a sugar maple tree:</p>
<p><a href="https://i.stack.imgur.com/Y2DFI.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Y2DFIm.jpg" alt="enter image description here"></a>
<a href="https://i.stack.imgur.com/kV4VU.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/kV4VUm.jpg" alt="enter image description here"></a></p>
<p>According to Google StreetView, the spruce has been there since before 2007 (over 10 years ago!).</p>
<p>I've seen other trees growing out of rotted stumps or in trunks near ground level before, but I've always just assumed that the roots of those trees reached down to soil -- in one way or another -- to get the nutrients they need for survival.</p>
<p>But with the subject tree, it's so high up that I would assume that that the roots do not have access to any soil. It's my guess that the spruce is getting all of its nutrients from decomposed wood in some rotten portion of the trunk.</p>
<p>I didn't know biology worked like this. I <strong>wouldn't</strong> have guessed that a live, partially decomposed trunk could contain 100% of the nutrients that a tree needs to survive for 10+ years. I know soil is made, in part, from decomposed wood, but it's my understanding that there are a lot more ingredients too.</p>
<p>Can the decomposed wood in a partially rotted trunk completely sustain a tree?</p>
| [
{
"answer_id": 58901,
"pm_score": 3,
"text": "<p><strong>Note</strong> This answer makes the presumption that the crotch in the maple's trunk is indeed a breach through its bark, and does reach the inner woody tissues.</p>\n\n<hr>\n\n<p>The heartwood of most trees consists of the dead connective tissue... | [
{
"answer_id": 58678,
"pm_score": 2,
"text": "<p>In the Hoh Rainforest in Olympic National park, there are many \"nurse trees\" and <a href=\"https://en.wikipedia.org/wiki/Nurse_log\" rel=\"nofollow noreferrer\">\"nurse logs\"</a>; the latter are trees that have fallen and now act as a nutrient source f... |
58,684 | <p>I'll first provide lots of background information. My actual question is at the very end.</p>
<h1>Background</h1>
<h3>The spread of athlete's foot</h3>
<p>Athlete's foot is a fungal infection which is mildly contagious. The infection can be spread by skin particles left on towels. <a href="http://www.webmd.com/skin-problems-and-treatments/guide/understanding-athletes-foot-basics" rel="nofollow noreferrer">(Source.)</a></p>
<p>If one person in a family has a fungal infection (e.g. athlete's foot or jock itch), their laundry may also contain fungi. I suspect that towels and laundry machines might make it easier for these fungi to spread: e.g. from the patient's feet to their groin. See, for example, <a href="http://www.mayoclinic.org/diseases-conditions/athletes-foot/symptoms-causes/dxc-20235876" rel="nofollow noreferrer">here</a>.</p>
<h3>Water at 140 °F</h3>
<p>You can kill fungi using water at 140 °F (60 °C). Unfortunately, your water heater probably doesn't produce such hot water, because such hot water is dangerous and can kill unsuspecting individuals. <a href="https://health.stackexchange.com/questions/3618/how-to-do-laundry-to-kill-and-prevent-athletes-foot-fungus#11743">(Sources.)</a> Still, you can make such hot water in other ways. <a href="https://health.stackexchange.com/questions/3618/how-to-do-laundry-to-kill-and-prevent-athletes-foot-fungus#11743">(Source.)</a></p>
<h3>Antifungal rinses</h3>
<p>Another option is to use a suitable antifungal rinse.</p>
<p>The most common cause of athlete's foot is <em>T. rubrum</em>. <a href="https://en.wikipedia.org/wiki/Trichophyton_rubrum" rel="nofollow noreferrer">(Source.)</a></p>
<p><em>T. rubrum</em> is a dermatophyte-type fungus. Dermatophytes spread through spores. These spores can sometimes live for up to 20 months. <a href="http://www.cfsph.iastate.edu/Factsheets/pdfs/dermatophytosis.pdf#page=3" rel="nofollow noreferrer">(Source.)</a></p>
<p>Canesten Laundry Hygiene Rinse is 7% benzalkonium chloride. <a href="http://www.catalog.md/drugs/canesten-hygiene-laundry-rinse.html" rel="nofollow noreferrer">(Source.)</a> A competing product is Bluo Laundry Sanitiser, which is also 7% benzalkonium chloride. <a href="https://go.lupinsys.com/pascoes/harms/pm/0f6658df30a31950dd0ef9698828e3ad-published/attachment/sds.pdf" rel="nofollow noreferrer">(Source.)</a> These products are sold in Australia but not in North America. (How safe are they? I dunno; I'm not a toxicologist.)</p>
<p>The Canesten rinse label makes an impressive claim: "eliminates ... fungi from your washing". Still, it looks like these rinses' fungistatic effects are stronger than their fungicidal effects. In reality, they're not perfect at killing <em>T. rubrum</em>, but they're still better than nothing. An Australian lab found that, in 20 minutes, these types of rinses reduced <em>T. rubrum</em> by between 90% and 99%. <a href="http://old.asa.co.nz/decision_file.php?ascbnumber=00140" rel="nofollow noreferrer">(Source.)</a></p>
<p>(Each rinse is marketed as both antifungal and antibacterial, though there's <a href="http://www.which.co.uk/news/2014/05/revealed-antibacterial-products-you-dont-need-364826/" rel="nofollow noreferrer">limited evidence</a> that people can catch bacterial infections from clothing. I'm not convinced that their antibacterial effects are really necessary.)</p>
<h3>Use during the rinse cycle, not the wash cycle</h3>
<p>Each manufacturer says that its benzalkonium chloride rinse should be added during your washing machine's final rinse cycle, not its initial wash cycle.</p>
<p>You can do this using your clothes washer's fabric-softener dispenser, if present. On a top-loader, this is usually a cup-like device on top of the machine's central agitator post. <a href="http://downy.com/en-us/fabric-conditioner-tips/how-to-use-downy/how-to-use-liquid-fabric-softener" rel="nofollow noreferrer">(Source.)</a> Or you can buy a softener dispenser ball, though they're not always 100% reliable. Or you can add the rinse manually at the correct moment.</p>
<h3>A sample washer program</h3>
<p>Washing machines can vary. Here's a description of the normal program of certain inexpensive top-loading Whirlpool agitator-type washing machines:</p>
<ul>
<li>Fill - agitate: 16 minutes.</li>
<li>Drain: 2 minutes.</li>
<li>Spin: 2 minutes.</li>
<li>Rinse, fill, & agitate: 4 minutes.</li>
<li>Drain: 2 minutes.</li>
<li>Spray & spin: 2 minutes.</li>
<li>Spin only: 4 minutes.</li>
</ul>
<p>Total: 32 minutes.</p>
<p>(Based on: wiring diagram W10118358, rev. A.)</p>
<p>The wash cycle is longer than the rinse cycle.</p>
<h1>My question</h1>
<p>To summarize the above background information: Canesten laundry rinse (7% benzalkonium chloride) has both antifungal and antibacterial effects.</p>
<p>And so I wonder: Why does the manufacturer recommend that it be used during your laundry machine's rinse cycle instead of its (longer) wash cycle?</p>
<p>Any answers or guesses are welcome.</p>
| [
{
"answer_id": 65616,
"pm_score": 3,
"text": "<p>The label of the veterinary product Fung-A-Way, which is Benzalkonium Chloride 0.15%, states that \"Efficiency is neutralized by <strong>soap or detergent</strong> residues.\"</p>\n\n<p>The website <a href=\"http://www.mpbio.com\" rel=\"nofollow noreferre... | [
{
"answer_id": 58686,
"pm_score": 2,
"text": "<p>Benzalkonium chloride is what's known as a quaternary ammonium cation, or quat. These are disinfectants commonly used in medical settings, for example. The mechanism of action is thought to be due to the long alkyl chains, causing membrane leakage (<a hre... |
58,732 | <p>Place: South India,</p>
<p>Metropolitan, Year: 2017; Night Time.</p>
<p>Size: 1-2 cm (Very Tiny)</p>
<p><a href="https://i.imgur.com/FvuN9xL.jpg" rel="noreferrer"><img src="https://i.imgur.com/FvuN9xL.jpg" alt="enter image description here"></a> </p>
| [
{
"answer_id": 58735,
"pm_score": -1,
"text": "<p>It's 'Indian skipper'. Family :Hesperiidae.\nSource: <a href=\"http://abeautiful-butterflys.blogspot.in/2010/04/hesperiidae-butterflies-of-india.html\" rel=\"nofollow noreferrer\">http://abeautiful-butterflys.blogspot.in/2010/04/hesperiidae-butterflies-o... | [
{
"answer_id": 58994,
"pm_score": 0,
"text": "<p>From the posture, it looks like it can belong to Geometridae (Larentiinae). But I haven't been able to find a species that has that particular color. </p>\n"
},
{
"answer_id": 59735,
"pm_score": -1,
"text": "<p>Definitely a moth; possible ... |
58,758 | <p>Why do fruits have such a low protein content (with a few exceptions) ? Don't seeds need protein while growing up? In comparison, the egg of a hen contains lots of protein, used to make a chick. </p>
| [
{
"answer_id": 58761,
"pm_score": 4,
"text": "<p>I don't have time to document this enough to make it a good answer but it's too long for a comment so I'll post it anyway.</p>\n\n<p>A big difference between plants and animals is how they get their food, that implies they have different elements to work ... | [
{
"answer_id": 58766,
"pm_score": 3,
"text": "<p>In brief the lower protein content of a seed compared to an egg is caused by two reasons.</p>\n\n<p>(1) The structural components of a plant versus that of an animal.\nThe structural components of plant is made by cellulose which is made of glucose subuni... |
59,227 | <p>I am getting slightly confused about how the above relate to each other. My current understanding is that P680 and P700 refer to the primary pigment reaction centres in Photosystems 2 and 1 respectively, with the numbers giving the peak wavelength of absorption. Now I initially thought that one of these primary pigment reaction centres must be composed of chlorophyll a and the other of chlorophyll b, hence the slightly differning absorption wavelengths. Instead, <a href="http://www.encyclopedia.com/science/dictionaries-thesauruses-pictures-and-press-releases/reaction-centre" rel="noreferrer">here</a> it seems to suggest that the primary pigment reaction centre is always chlorophyll a. Most sources I have looked at do not specify what forms the primary pigment reaction centre (the Wikipedia article on photosynthetic reaction centre, for example, does not state for the general case of for photosystem 2; however it does mention that photosystem 1 has a special pair of chlorophyll a molecules at the centre).</p>
<p>So my specific questions are:</p>
<ul>
<li>Is the primary pigment reaction centre in both photosystem 1 and 2 (i.e. P700 and P680) a pair of chlorophyll a molecules?</li>
<li>If so, what is chlorophyll b? Is it simply an accessory pigment?</li>
<li>Finally, if it is the case that the primary pigment reaction centre is chlorophyll a in both cases, how can it be that it absorbs at a different wavelength in the two photosystems if it is the same molecule?</li>
</ul>
| [
{
"answer_id": 59283,
"pm_score": 4,
"text": "<p>Regarding your questions #1 (<em>\"Is the primary pigment reaction centre in both photosystems a pair of chlorophyll a molecules?\"</em>) and #3 (<em>\"How can it be that it absorbs at a different wavelength in the two photosystems if it is the same molec... | [
{
"answer_id": 59232,
"pm_score": 1,
"text": "<blockquote>\n <p>The antenna pigments are predominantly chlorophyll b, xanthophylls, and carotenes. Chlorophyll a is known as the core pigment. Their absorption spectra are non-overlapping and broaden the range of light that can be absorbed in photosynthes... |
59,355 | <p>Green fluorescent protein (GFP) is a small protein that emits bright green fluorescence in blue light. It was first isolated from the jellyfish. </p>
<p>The gene coding for GFP can be expressed in bacteria, and so it is often used as a marker to show successful uptake of a gene by the bacterium.</p>
<p>What is the <strong>advantage</strong> of using the gene for GFP to produce easily detectable fluorescence, rather than using a gene for an enzyme that produces a fluorescent substance?</p>
<p>Ps. The original question I got was to explain about the <strong>disadvantage</strong>, which is that GFP may not fluoresce very brightly and so may be difficult to detect.</p>
<p>Thank you for your help.</p>
| [
{
"answer_id": 59358,
"pm_score": 4,
"text": "<p>GFP has a lot of advantages:</p>\n\n<ul>\n<li>The detection of the fluorescence works directly and doesn't need a lysis step or the uptake of a reagent.</li>\n<li>Fluorescence can be detected directly using a fluorescence or confokal microscope with the c... | [
{
"answer_id": 59359,
"pm_score": 2,
"text": "<p>There are no genes that I know of that encode proteins, more specifically enzymes, that will catalysed the production of a fluorescent compound from intermediates present in the average cell. Presumably one would need a whole pathway. </p>\n\n<p>So I susp... |
59,523 | <p>I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation. </p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795131/" rel="nofollow noreferrer" title="paper">This paper</a> mentions that</p>
<blockquote>
<p>It is important that each type of methionyl tRNA be restricted to its separate function, as competition for tRNA by the initiation and elongation machinery could lead to serious problems for the cell</p>
</blockquote>
<p>I don't understand what these problems may be. </p>
| [
{
"answer_id": 59658,
"pm_score": 3,
"text": "<p><strong>Interaction with tRNA-binding factors is why separate tRNA<sup>Met</sup> species are employed</strong></p>\n\n<blockquote>\n <p>A specific tRNA<sup>Met</sup> is required for initiation as the initiating\n met-tRNA must interact with a specific t... | [
{
"answer_id": 59526,
"pm_score": 2,
"text": "<p>The same paper states the following just before the part you have quoted:</p>\n\n<blockquote>\n <p>The cell acquires an additional degree of control by having a separate tRNA for initiation, and thus regulates the levels of\n initiator and elongator met... |
59,565 | <p>I understand that when the human body loses weight, the vast majority of that weight is lost as $CO_2$ (and a small bit is lost as water). I expect the predominant way $CO_2$ exits the body is through exhaling. </p>
<p>So, let's take a human with no influx of carbon (they are not eating); I expect such a person is slowly losing weight, a near infinitesimal amount with each breath (correct me if I'm wrong). </p>
<p>If the person breathes faster (more breaths per minute), that causes an increase in the rate at which $CO_2$ is expelled, correct (more mass per minute)? Is this rate expected to decrease, i.e., as one breathes faster, less $CO_2$ is contained in each subsequent breath? Or, does perhaps the body mobilize and oxidize carbon fuels (carbohydrates first and eventually lipids) to generate $CO_2$ in an attempt to restore homeostatic equilibrium? </p>
<p>Could breathing quickly and heavily possibly cause an increase in the $CO_2$ content of exhaled breaths? That is, would voluntary hyperventilation cause an increase in heart rate (and thus increase in carbon catabolism)? How much $CO_2$ is in a typical exhalation during exercise?</p>
<p>I realize that without exercise, the amount of $CO_2$ being lost during normal breathing is nearly negligible. But perhaps laying down and breathing quickly could cause a measurable increase in the net rate at which mass leaves the body. What do you think?</p>
<p>Thank you for your time.</p>
| [
{
"answer_id": 59568,
"pm_score": 4,
"text": "<p>The rate of CO<sub>2</sub> production is normally set by the rate of metabolism and breathing rate is determined by the level of CO<sub>2</sub> in the blood. What you are suggesting is known as <a href=\"https://en.wikipedia.org/wiki/Hyperventilation?wpr... | [
{
"answer_id": 59597,
"pm_score": 2,
"text": "<p>There are two organs which govern pH: the lung and the kidney. If one is having some problem the other steps in to correct it. The body does not like pH to drift far from 7.4. </p>\n\n<p>CO<sub>2</sub> gas is blown off or retained by the lungs. More C... |
59,617 | <p>I came across this plant yesterday (14th May) and was wondering what it might be? Would anybody know the scientific name and if it's indigenous to the UK (personally I doubt it is)? The plant grows in an Asian style garden near <a href="https://www.google.co.uk/maps/place/The+Great+Steward+of+Scotland's+Dumfries+House+Trust/@55.455564,-4.310152,17z/data=!3m1!4b1!4m5!3m4!1s0x4888285c7c0209a5:0xbb95a95acaee65a!8m2!3d55.455561!4d-4.307958" rel="noreferrer">Cumnock, Scotland</a>.</p>
<p><a href="https://i.stack.imgur.com/2csxk.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/2csxk.jpg" alt="enter image description here"></a></p>
<p>Close up of leaves:</p>
<p><a href="https://i.stack.imgur.com/VtCsB.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/VtCsB.jpg" alt="enter image description here"></a></p>
| [
{
"answer_id": 59618,
"pm_score": 6,
"text": "<p>This is the \"<a href=\"https://en.wikipedia.org/wiki/Acer_palmatum\" rel=\"noreferrer\">Acer palmatum</a>\" or Japanese maple, which shows a wide variety of different leaf forms (from <a href=\"https://en.wikipedia.org/wiki/Acer_palmatum\" rel=\"noreferr... | [
{
"answer_id": 59619,
"pm_score": 4,
"text": "<p>Looks like a cultivar of the <a href=\"https://en.wikipedia.org/wiki/Acer_palmatum\" rel=\"noreferrer\">Japanse maple</a> (<em>Acer palmatum</em>). I assume that is why you have found it in an Asian stlye garden. There are various cultivars that differ by... |
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